• We generated 931 whole-genome sequences for Korean simplex families to detect DNMs and identified target genes dysregulated by noncoding DNMs via long-range chromatin interactions between regulatory elements. (biorxiv.org)
  • Correspondingly, target genes were significantly involved in histone modification, prenatal brain development, and pregnancy. (biorxiv.org)
  • By binding to specific DNA sequences known as regulatory elements, regulatory proteins stimulate the transcription of target genes. (keydifference.in)
  • Through interactions with transcriptional machinery, regulatory proteins facilitate gene transcription initiation and progression for target genes thereby shaping cell processes and development. (keydifference.in)
  • By binding with these regulatory elements, regulatory proteins can either activate or suppress the transcription of target genes. (keydifference.in)
  • The binding of regulatory proteins to DNA occurs through specific protein-DNA interactions in which a specific motif recognizes and binds with specific regulatory proteins, leading to molecular events that ultimately modulate the transcriptional activity of target genes. (keydifference.in)
  • This includes detailed investigations of noncoding gene regulatory element function, transcriptional regulation and gene/protein function with the aim of connecting pancreatic cancer risk variants to target genes and molecular phenotypes to explain the underlying biology of the risk at each locus. (nih.gov)
  • Three-dimensional chromosomal conformations regulate transcription by moving enhancers and regulatory elements into spatial proximity with target genes. (mssm.edu)
  • In contrast to 4Tran-PCR, Capture-4Tran can uniquely identify both ends of an interaction that involve retroviral repeat sequences, providing a powerful tool for uncovering the individual transposable element insertions that interact with and potentially regulate target genes. (biomedcentral.com)
  • 4Tran provides new insight into the manner in which transposons contribute to chromosome architecture and identifies target genes that transposable elements can potentially control. (biomedcentral.com)
  • It has been demonstrated that COUP-TFs repress the hormonal induction of target genes by PPAR, VDR, TR, and RAR in transient transfection assays through direct competition with VDR, TR, and RAR for the available binding sites. (guidetopharmacology.org)
  • The loss of RXR indirectly decreases the DNA-binding affinity of TR, VDR, RAR, and PPAR and thereby interferes with the potential of this subgroup of receptors to transactivate their target genes. (guidetopharmacology.org)
  • RNA polymerase pausing was initially described at the promoters of a handful of genes where RNA polymerase synthesized a short segment of RNA before pausing downstream of the promoter. (nih.gov)
  • The promoter regions of human CBS and murine CSE genes have been cloned and have revealed a few regulatory elements responsible for the transcriptional activity of CBS and CSE promoters. (medscape.com)
  • [ 55 , 56 ] It was found that myeloid zinc finger protein-1, specificity protein-1 and upstream stimulatory factor-1 consensus sequences are important for the transcriptional activity of both CBS and CSE promoters. (medscape.com)
  • Transcriptional enhancers have been proposed to activate transcription independent of their location, distance or orientation with respect to gene promoters. (nih.gov)
  • Studies have largely focused on coding sequences and promoters, even though distal regulatory elements play a central role in controlling transcription patterns. (nih.gov)
  • In transgenic Arabidopsis with the expression of the GUS reporter gene under the control of one of these promoters, the activities of GUS were strong in almost all tissues except the seeds, and the activities were induced after abiotic stress. (biomedcentral.com)
  • The yeast one-hybrid system and EMSA demonstrated that TaMYB bound TaGAPCp2 P /3 P. By analyzing different 5′ deletion mutants of these promoters, it was determined that TaGAPCp2 P (− 1312~ − 528) and TaGAPCp3 P (− 2049~ − 610), including the MYB binding site, contained enhancer elements that increased gene expression levels under drought stress. (biomedcentral.com)
  • However, most analyses have focused on the effects of genomic variation at cis-regulatory elements such as promoters and enhancers that control transcriptional activity, and little is understood about the influence of post-transcriptional processes on transcript evolution. (nih.gov)
  • The major mechanism of differential gene expression is transcriptional regulation [ 1 ] which is controlled by transcription factors that bind to DNA cis -elements located in gene promoters and/or introns. (biomedcentral.com)
  • The first author of the study, Tim Donlon, further discovered that the interaction of FOXO3 with its neighboring genes involved CCCTC-binding factor zinc finger protein (CTCF), a transcription factor that binds promoters, so attracting tissue-specific transcriptional activators, repressors, cohesion, and RNA polymerase II. (databasefootball.com)
  • TEs contain their own regulatory sequences, including specific signals that lead to the termination of transcripts initiated from element promoters. (biomedcentral.com)
  • Here, using a reporter gene assay in imaginal discs, we show that a PRE from the Drosophila Hox gene Ultrabithorax potently silences different heterologous enhancers and promoters that are normally not subject to Polycomb repression. (silverchair.com)
  • From a teleological standpoint, this arrangement [of focused promoters] is consistent with the notion that it would be easier to regulate the transcription of a gene with a single transcription start site than one with multiple start sites. (wikiversity.org)
  • RNA polymerase II is recruited to the promoters of protein-coding genes in living cells. (wikiversity.org)
  • Initiation marks the beginning of transcription, where RNA polymerase, the enzyme responsible for transcription, recognizes specific DNA sequences known as promoters and binds to them. (microbiologynote.com)
  • Promoters are typically found just ahead of the gene on the DNA strand. (medlineplus.gov)
  • In order to understand the mechanisms by which toxicants impact gene expression, it is necessary to better understand how exposure affects the proteins and processes upstream of DNA methylation and other epigenetic marks. (nih.gov)
  • The purpose of this FOA is to encourage research applications that will potentially move the field from descriptive and correlative studies to an enhanced mechanistic understanding of how environmental exposures affect the proteins and functional genomic elements involved in establishing and maintaining gene expression patterns and chromatin states. (nih.gov)
  • DNA methylation is thought to be one of the last steps of epigenetic gene regulation - a read-out of chromatin states established by other proteins. (nih.gov)
  • In order to understand the mechanism by which toxicants impact gene expression, we must examine how exposures perturb the proteins and processes upstream of DNA methylation and other epigenetic marks. (nih.gov)
  • The purpose of this FOA is to better define the biology of how environmental exposures affect the proteins and other elements involved in establishing and maintaining gene expression patterns and chromatin state. (nih.gov)
  • UPF1 is a highly nonspecific RNA binding protein, raising the question of how sequence-specific RNA-binding proteins such as PTBP1 and hnRNP L can effectively suppress UPF1 binding to long 3'UTRs. (nih.gov)
  • This mechanism relies on a short regulatory loop in the helicase core of UPF1, and we have shown that a naturally occurring alternative UPF1 isoform containing an extension of this loop (termed long-loop UPF1 or UPF1 LL ) is able to overcome the protective proteins. (nih.gov)
  • These elements mostly regulate either the stability or translation rate of mRNAs via interaction with different trans -acting proteins, many of which are unknown. (biomedcentral.com)
  • At the molecular level, transcriptomic profiling revealed extensive changes in the expression of genes encoding proteins important in the endoplasmic reticulum stress response and in protein folding as well as involved in the formation of primary germ layer, mesendoderm and endoderm development, heart morphogenesis and cell migration. (bvsalud.org)
  • Within this intricate mechanism of gene regulation are two classes of proteins with separate roles in this complex machinery: regulatory proteins and repressor proteins. (keydifference.in)
  • Regulatory proteins are an array of biomolecules that activate or enhance gene expression. (keydifference.in)
  • Repressor proteins exert an inhibitory effect on gene expression by binding to operator sites in DNA and blocking access for RNA polymerase to transcription. (keydifference.in)
  • Regulatory proteins are an essential class of biomolecules in controlling gene expression. (keydifference.in)
  • Regulatory proteins exert their effects by binding to specific DNA sequences known as regulatory elements or enhancer sequences located near genes they regulate, known as regulatory elements or enhancer sequences. (keydifference.in)
  • Gene expression regulation by regulatory proteins is a complex and subtle process, enabling organisms to respond and adapt to changing environmental conditions, developmental stages, and cell requirements. (keydifference.in)
  • together these regulatory proteins form complex regulatory networks for precise control over gene expression in cells and organisms. (keydifference.in)
  • Repressor proteins are a class of biomolecules that play an essential role in gene regulation by inhibiting or suppressing transcription. (keydifference.in)
  • Repressor proteins bind to certain DNA sequences known as operator sites near genes they regulate in order to do their work. (keydifference.in)
  • Repressor proteins bind to DNA through specific protein-DNA interactions in which they recognize and bind to specific DNA sequence motifs in an operator site. (keydifference.in)
  • Repressor proteins play an integral part in maintaining proper gene regulation and ensuring appropriate expression levels in response to internal and external cues. (keydifference.in)
  • 6. Transactivation of GATA-1 promoter with ETS1, ETS2 and ERGB/Hu-FLI-1 proteins: stabilization of the ETS1 protein binding on GATA-1 promoter sequences by monoclonal antibody. (nih.gov)
  • Probe Set ID Ref Seq Protein ID Signal Strength Name Gene Symbol Species Function Swiss-Prot ID Amino Acid Sequence 1367452_at NP_598278 16.52 small ubiquitin-related modifier 2 precursor Sumo2 Rattus norvegicus " Ubiquitin-like protein that can be covalently attached to proteins as a monomer or as a lysine-linked polymer. (nih.gov)
  • 1986) Persistence of DNA synthesis arrest sites in the presence of T4 DNA polymerase and T4 gene 32, 44, 45 and 62 DNA polymerase accessory proteins, Nucl. (nih.gov)
  • This study highlights a potentially hitherto unrecognized host genome surveillance mechanism that exploits the targeting of a specific class of transposable elements by proteins of another class to rein in transposable element activities. (nature.com)
  • Expression of genes occurs through transcription - the assembly of continuous, single stranded, messenger ribonucleic acid (mRNA) copies of exons, which are translated into proteins. (ddw-online.com)
  • The Gronostajski Lab has established this database as a centralized source of information to examine the structure of the control elements of genes known to be regulated by NFI proteins. (buffalo.edu)
  • It makes contact with tens of thousands of sites across the genome by using different combinations of its 11 zinc finger domains to bind different DNA target sequences and proteins. (databasefootball.com)
  • Together, these results suggest that PREs function as general silencer elements through which PcG proteins mediate transcriptional repression. (silverchair.com)
  • After the decay of segmentation gene products, transcriptional ON and OFF states of Hox genes are heritably maintained by Polycomb group (PcG) and trithorax group (trxG)proteins which, however, are present in all cells. (silverchair.com)
  • Thus,it appears that both PcG and trxG proteins regulate gene expression by modifying the structure of chromatin. (silverchair.com)
  • Nevertheless, silencing by Polycomb group proteins requires specific cis-acting sequences, called Polycomb response elements (PREs). (silverchair.com)
  • [7] In humans RNAP II consists of seventeen protein molecules (gene products encoded by POLR2A-L, where the proteins synthesized from 2C-, E-, and F-form homodimers). (wikiversity.org)
  • The gene orf7 encodes a 140-amino-acid (aa) protein exhibiting limited homology with sigmaF of Bacillus subtilis, whereas orf8 encodes a 76-aa peptide that does not share any sequence homology with any cognate proteins. (pasteur.fr)
  • For example , Saccharomyces cerevisiae OLE1 expression is regulated at transcriptional and post-transcriptional (mRNA or protein stability) levels: the transcription is activated by unsaturated fatty acids through ubiquitin-mediated proteolytic processing of two membrane proteins, Mga2p and Spt23p, triggering their nuclear targeting to become transcriptional co-activators. (biomedcentral.com)
  • Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. (embl.de)
  • Such elements provide sites for specialized proteins (called transcription factors) to attach (bind) and either activate or repress the process by which the information from genes is turned into proteins (transcription). (medlineplus.gov)
  • Advances in sequencing have enabled large-scale sequencing studies across many tumor types, emphasizing the discovery of alterations in protein-coding genes. (nih.gov)
  • The zebrafish ( Danio rerio ) has been widely used in the study of human disease and development, and about 70% of the protein-coding genes are conserved between the two species 1 . (nature.com)
  • Approximately 25,000 protein-coding genes are interspersed throughout the genome as discontinuous sets of exons. (ddw-online.com)
  • These findings are interesting in that genotype-phenotype correlations common in the study of complex traits often focus on single protein-coding genes but ignore gene neighborhoods. (databasefootball.com)
  • Bioinformatics programs usually allow for alternate start codons when searching for protein coding genes. (wikiversity.org)
  • RNA polymerase II is responsible for transcribing protein-coding genes, producing messenger RNAs (mRNAs) that carry the genetic information to the site of protein synthesis . (microbiologynote.com)
  • It transcribes protein-coding genes to produce precursor messenger RNA (pre-mRNA). (microbiologynote.com)
  • Some noncoding DNA regions, called introns, are located within protein-coding genes but are removed before a protein is made. (medlineplus.gov)
  • TOSPEAK emerged de novo in an ancestor of extant primates across a 540 kb region of the genome with a pre-existing highly conserved long-range laryngeal enhancer for a neighbouring bone morphogenetic protein gene GDF6 . (nih.gov)
  • At the level of the DNA, depolarization- induced activation is conferred on the proenkephalin gene by a previously characterized cAMP-inducible enhancer. (jneurosci.org)
  • Multiple copies of a single component element of that enhancer, containing the CGTCA sequence motif characteristic of cAMP regulatory elements, can reconstitute the entire repertoire of responses to both cAMP and depolarization. (jneurosci.org)
  • The Eµ intronic enhancer of the mouse immunoglobulin heavy-chain (IgH) locus located on chromosome 12 has been shown to be DNase I hypersensitive and have a significant role in epigenetic modifications, transcriptional regulation, and VDJ recombination. (nih.gov)
  • Whereas the Eµ enhancer is critical for activation of IgH transcription in cis, it remains unknown whether it is also involved in trans regulation of other pro-B cell specific genes. (nih.gov)
  • We used genome-wide DHS sequencing to probe the open chromatin structure at the single nucleotide level to determine whether the Eµ enhancer in mouse pro-B cells has trans activity on other transcriptional regulatory elements in the murine genome. (nih.gov)
  • We propose that reproducible changes in the epigenome at enhancer elements drive a specific transcriptional program to promote colon carcinogenesis. (nih.gov)
  • 1. Transactivation of an intronic hematopoietic-specific enhancer of the human Wilms' tumor 1 gene by GATA-1 and c-Myb. (nih.gov)
  • 4. Identification and characterization of the hematopoietic cell-specific enhancer-like element of the mouse hex gene. (nih.gov)
  • 11. A GATA box in the GATA-1 gene hematopoietic enhancer is a critical element in the network of GATA factors and sites that regulate this gene. (nih.gov)
  • 16. GATA-1 and GATA-2 binding to 3' enhancer of WT1 gene is essential for its transcription in acute leukemia and solid tumor cell lines. (nih.gov)
  • Genes acting in a redundant manner can be identified in a complementary gain-of-function approach using EP (enhancer/promoter) elements. (sdbonline.org)
  • Vertebrate insulin gene enhancer binding protein isl-1. (embl.de)
  • a beta-cell-specific transcriptional enhancer found in the insulin gene. (embl.de)
  • Here, we identify a CCAAT/Enhancer Binding Protein beta (C/EBPbeta) binding site in the RIG-I promoter as a repressor element, and show that NS1 promotes C/EBPbeta phosphorylation and its recruitment to the RIG-I promoter as a C/EBPbeta/NS1 complex. (cdc.gov)
  • In addition, other factors such as non-coding RNAs, chromatin remodeling complexes, inter- and intra-chromosomal interactions and functional genomic elements play important roles in this process. (nih.gov)
  • One powerful assay to analyze chromatin structure and identify genomic regulatory elements involved in tissue specific and developmentally regulated gene expression is DNase I hypersensitivity (DHS) coupled with high-throughput sequencing. (nih.gov)
  • To further characterize the mechanisms controlling acetyl LDL receptor transcription , genomic sequences encoding the promoter and upstream regulatory elements have been cloned. (grantome.com)
  • Functional characterization of cis active elements will be performed by transfection analysis of wild type and mutant genomic sequences linked to suitable reporter genes. (grantome.com)
  • Dr. Amundadottir's laboratory conducts fine-mapping of risk loci identified in PanScan and collaborative gene mapping efforts, as well as genomic, molecular and cell biology wet-lab based studies to uncover functional variants at each locus and unravel the mechanism by which they influence risk of pancreatic cancer. (nih.gov)
  • As an extension to their extensive genetic and genomic studies in pancreatic tissue samples, Dr. Amundadottir and her team have recently started investigating noncoding somatic mutations as drivers of pancreatic cancer, using large WGS datasets from pancreatic tumors and their well annotated epigenetic datasets mapping noncoding gene regulatory elements in normal and tumor derived pancreatic tissues. (nih.gov)
  • In the latest version of the method, part of the reporter vector containing the cis -element of interest upstream of the reporter gene is introduced into the yeast genomic DNA via homologous recombination with a non-essential gene [ 9 ]. (biomedcentral.com)
  • Collaborative Bioinformatics research projects in my lab involve large scale genomic studies, particularly focusing on the regulation of human genes involved in cancer, apoptosis, and neurological abnormalities, including autism, dementia and Parkinson's disease. (ramapo.edu)
  • The non-exonic component of the genome accomplishes control primarily by transcription into a plethora of regulatory RNA types (including smRNA, ncRNA, tRNA, rRNA and antisense transcription) or by containing structural genomic DNA features that influence transcription and replication (both control elements and DNA methylation). (ddw-online.com)
  • Recently, the Willcox team reported in Aging Cell that FOXO3 operates by interacting directly with 46 genes either side of its genomic location on chromosome 6q21. (databasefootball.com)
  • the MS1 protein was shown to bind to the second exon of its genomic locus and to repress its own expression. (nottingham.ac.uk)
  • The Transcriptional Responses in Disease Group focuses on mechanisms of RNA polymerase pausing and its role in human disease. (nih.gov)
  • Thus to understand the mechanisms involved in the environmental control of gene regulation and the central role of epigenetics in the process, it is critical to understand all the interacting pathways. (nih.gov)
  • Understanding the regulatory mechanisms for H 2 S synthesis pathways may help develop new therapeutic strategies. (medscape.com)
  • The resources of the Intramural Research Program allow us to be flexible in our approach to understanding NMD and other post-transcriptional regulatory mechanisms. (nih.gov)
  • Understanding their differences is vital to comprehending how gene expression control mechanisms operate. (keydifference.in)
  • The emphasis of the studies proposed in this Unit will be to examine the molecular mechanisms that function to regulate the expression of the acetyl LDL receptor and 15 lipoxygenase genes in macrophages. (grantome.com)
  • Activators of protein kinase C have recently been demonstrated to stimulate acetyl LDL receptor expression, and the mechanisms responsible for this effect will be examined in model macrophage cell lines. (grantome.com)
  • Intense studies of globin gene expression over the past two decades have enhanced our understanding considerably of the molecular mechanisms that together ensure a highly specialized, tissue- and stage-specific transcription pattern of the β-like genes during development. (ku.edu)
  • Much of the current research on the human β-globin locus has been focused on further elucidating the mechanisms involved in the regulation of the fetal γ-globin genes in an effort to develop potential therapies that will enhance fetal hemoglobin expression in individuals with sickle cell disease or β-thalassemia. (ku.edu)
  • Identification of cis-acting elements bound by specific transcription factors can reveal transcriptional regulatory mechanisms and gene expression patterns involved in environmental adaptation processes [ 11 ]. (biomedcentral.com)
  • It serves as a riboswitch [ 12410317 , 12464185 ] that binds directly to thiamine pyrophosphate (TPP) to regulate gene expression through a variety of mechanisms [ 12756322 , 12376536 ]. (lbl.gov)
  • Nevertheless, these data fail to reveal the transcriptional regulatory mechanisms because of the complexity of the promoter sequences, the relatively small number of cis -regulatory elements and transcription factors that have been characterised, and lack of data about cooperative regulation of gene expression in plants by several transcription factors simultaneously. (biomedcentral.com)
  • To understand transcriptional mechanisms that lead to differential gene expression, genes have to be experimentally coordinated with the corresponding TFs that regulate their expression. (biomedcentral.com)
  • Dynamic regulation of chromosomal conformations emerges as a novel layer for transcriptional mechanisms impacting neuronal signaling and cognition. (mssm.edu)
  • Host genomes have evolved defence mechanisms, including chromatin modifications and RNA interference, to regulate transposable elements. (nature.com)
  • Therefore, additional RNAi-independent mechanisms probably exist to recognize and silence transposable elements. (nature.com)
  • Global regulatory mechanisms involving chromatin assembly and remodelling in the promoter regions of genes is implicated in eukaryotic transcription control especially for genes subjected to spatial and temporal regulation. (biomedcentral.com)
  • The potential to utilise global regulatory mechanisms for controlling gene expression might depend upon the architecture of the chromatin in and around the gene. (biomedcentral.com)
  • The presence of global regulatory mechanisms mediated through chromatin organisation can decrease the burden of invoking gene specific regulators for maintenance of the active/silenced state of gene expression. (biomedcentral.com)
  • In this study, we examined whether the potential to utilise global regulatory mechanisms to control gene expression through chromatin organisation varies between housekeeping and tissue specific genes (Hkg and Tsg respectively) by virtue of their organisation. (biomedcentral.com)
  • The identification of specific candidate genes and variants in sporadic PD is an important stepping stone to understanding the molecular mechanisms in underlying PD and discovering potential therapeutics. (nih.gov)
  • In these studies, we will ultimately address the molecular mechanisms responsible for the regulation of adipose glucose transporter gene expression. (elsevierpure.com)
  • These regulatory mechanisms appear to be quite conserved among different fungi [ 9 ]. (biomedcentral.com)
  • 8. The leukemia associated ETO nuclear repressor gene is regulated by the GATA-1 transcription factor in erythroid/megakaryocytic cells. (nih.gov)
  • Distal intronic and 3' intergenic loop formations competed with repressor elements to access promoter-proximal sequences, and facilitated expression via a "cargo" of AP-1 and NRF-1 transcription factors and TALE-based transcriptional activators. (mssm.edu)
  • MS1 may therefore be a unique plant-specific histone reader family protein that participates in gene repression as a co-repressor. (nottingham.ac.uk)
  • It is thought that the main function of TADs is to restrict the influence of enhancers to genes found in the same domain. (biomedcentral.com)
  • The SCP is the strongest core promoter observed in vitro and in cultured cells and yields high levels of transcription in conjunction with transcriptional enhancers. (wikiversity.org)
  • Enhancers can be found on the DNA strand before or after the gene they control, sometimes far away. (medlineplus.gov)
  • Regulatory elements, such as enhancers, can be located in introns. (medlineplus.gov)
  • In the second analysis, we identified a number of function-specific regulatory motifs, based on which we devised a classifier that can be used for homology-independent function prediction in T. brucei . (biomedcentral.com)
  • We find that m6A evolution occurs in parallel with evolution of consensus RNA sequence motifs known to be associated with the enzymatic complexes that regulate m6A dynamics, and expression evolution of m6A-modified genes occurs in a parallel evolutionary pattern with m6A evolution. (nih.gov)
  • Using the alignment of 170 THI elements, additional conserved helices and sequence motifs were revealed [ 12376536 ]. (lbl.gov)
  • Menendez, C., Frees, S., and Bagga, P. (2012) QGRS-H Predictor: A Web Server for Predicting Homologous Quadruplex forming G-Rich Sequence Motifs in Nucleotide Sequences. (ramapo.edu)
  • Understanding the common candidate motifs, transcriptional factors binding sites, and regulatory elements of the mer operon gene cluster using a machine learning approach could help us better understand gene expression patterns in heavy metal bioremediation. (researchsquare.com)
  • There are many superfamilies of Znf motifs, varying in both sequence and structure. (embl.de)
  • Three evolutionarily conserved non-coding sequences (CNS), enriched with unusually long consensus motifs, and binding site combinations of MS1 upstream transcription factors (TFs) were found within the −2 kb MS1 upstream sequence. (nottingham.ac.uk)
  • [ 56-59 ] There are several other potential regulatory elements that appear to be of particular importance for hormone regulation of CBS or CSE gene expression, such as the negative insulin response sequence and phosphoenolpyruvate carboxykinase motif within the CBS core promoter, [ 55 ] and the signal transducers and activators of transcription x and heat-shock factor 2 consensus sequences within the CSE core promoter. (medscape.com)
  • Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. (ugent.be)
  • Eukaryotic gene transcription is largely known to be orchestrated by protein factors like activators, co-activators and co-repressors [ 1 ]. (biomedcentral.com)
  • Recent developments in computational tools for prediction of fRNAs have shown a widespread set of RNA elements that are specifically involved in post-transcriptional regulatory processes [ 5 ]. (biomedcentral.com)
  • The sensor of choice was qacR, a member of the TetR family of transcriptional repressors , which controls the expression of an efflux pump (qacA) in Staphylococcus aureus bacteria to remove antibiotics. (epigenie.com)
  • PcG repressors keep Hox genes inactive in cells in which these genes must remain inactive whereas trxG regulators are needed to maintain the active state of Hox genes in appropriate cells. (silverchair.com)
  • Data revealed that transcriptional gene regulation in terms of activation and repression was observed at 36.4% and 54.56% respectively. (researchsquare.com)
  • This shows that the vast majority of TFs are involved in the transcription gene repression rather than activation. (researchsquare.com)
  • However, once the effector arrives, it causes a conformational change in qacR that releases it from the DNA and relieves repression of downstream genes. (epigenie.com)
  • Polycomb response elements (PREs) are cis-regulatory sequences required for Polycomb repression of Hox genes in Drosophila . (silverchair.com)
  • During this project, three regulation levels of MS1 were studied: (i) transcriptional activation, (ii) auto-repression and (iii) post-translational proteolysis. (nottingham.ac.uk)
  • RNA polymerase pausing regulates stress-responsive genes whose expression levels need to be titrated carefully to maintain homeostasis. (nih.gov)
  • In turn, the group seeks to uncover how RNA polymerase pausing regulates gene expression in health and disease. (nih.gov)
  • The promoter is a DNA sequence upstream of the 5′-flanking region of the structural gene and is capable of specifically recognizing and binding RNA polymerase, which regulates the expression of downstream genes by binding to specific recognition sites of transcription factors [ 10 ]. (biomedcentral.com)
  • Molecular imaging of transcription factor activity is done in animal models and mostly in transgenic reporter mice, where the transgene essentially consists of a promoter that regulates a reporter gene. (biomedcentral.com)
  • Foxo3, by binding to the promoter of various genes across the genome, regulates a wide array of processes that confer cell resilience and healthy aging. (databasefootball.com)
  • Here we performed RNA sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) experiments in up to eleven adult and two embryonic tissues to generate a comprehensive map of transcriptomes, cis -regulatory elements, heterochromatin, methylomes and 3D genome organization in the zebrafish Tübingen reference strain. (nature.com)
  • Genome-wide association studies (GWAS) in large case-control and cohort studies, as well as targeted and whole-genome sequencing (WGS) studies in individuals and families at increased risk of disease, have provided new insights into the inherited factors that contribute to risk of developing cancer. (nih.gov)
  • However, studies in zebrafish remain constrained by the sparse annotation of functional control elements in the zebrafish genome. (nature.com)
  • Overall, our work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionarily conserved elements of 3D genome organization. (nature.com)
  • Functional RNAs, including non-coding RNAs (ncRNAs) and cis -acting RNA elements involved in post-transcriptional gene regulation, were predicted based on two independent computational analyses of the genome of Trypanosoma brucei . (biomedcentral.com)
  • Experimental identification of cis -acting fRNA elements is an exhausting task that requires extensive functional assays with several strains carrying deletion/substitution mutants of a likely regulatory sequence. (biomedcentral.com)
  • Expressed Structurally Stable Inverted Duplicates in Mammalian Genomes as Functional Noncoding Elements. (nih.gov)
  • The locus consists of five functional β-like globin genes, ϵ- Gγ-Aγ-δ-β and a powerful upstream regulatory element, the locus control region (LCR) that is physically composed of five DNase-I hypersensitive sites. (ku.edu)
  • B efore discussing specific areas of drug discovery and development that we anticipate will be profoundly impacted by Generation II (or NextGen) sequencing, we first review current knowledge of nucleic acid variation, its functional correlates, and the current technical capabilities of Generation II sequencers. (ddw-online.com)
  • These studies are very complex since GWAS identifies variants that are often in large LD blocks and the functional human genome is folded in three-dimensional space so sequences that are far apart can still interact with one another. (nih.gov)
  • The complexity of the inflammatory response requires that its many functional elements are controlled coordinately in some situations and independently in others. (biomedcentral.com)
  • It is suggested that various sets of genes encode the different functional elements and that these genes are coordinately regulated by dedicated transcription factors [ 2 ]. (biomedcentral.com)
  • The structural organization of the genome is regulated at different levels to establish a functional framework that facilitates cellular processes such as gene expression and programmed somatic recombination. (biomedcentral.com)
  • In future studies, the functional DNA sequences determined in specific aims 3 and 4 will be used in mobility shift and DNase 1 footprint assays to identify trans-factors in nuclear extracts which affect adipocyte-specific GLUT4 expression. (elsevierpure.com)
  • The identity of regulatory elements and other functional regions in noncoding DNA is not completely understood. (medlineplus.gov)
  • In addition, this resource would provide bioinformatics links to existing NIH-supported genomics databases and make pancreatic cDNA libraries available as microarrays to be used by researchers for gene discovery and functional investigations in both normal and diabetic pancreas. (nih.gov)
  • Here we analyze the complete genome sequences of 863 human tumors from The Cancer Genome Atlas and other sources to systematically identify noncoding regions that are recurrently mutated in cancer. (nih.gov)
  • One of the first applications of Generation II sequencing has been maturation of reference genome sequences and variation catalogues, with compilation variant frequencies by sequencing of many human genomes (resequencing) (116-119). (ddw-online.com)
  • Our classifier for function prediction based on cis -acting regulatory elements can also, in combination with other methods, provide the means for homology-independent annotation of trypanosomatid genomes. (biomedcentral.com)
  • Analysis of sequenced genomes revealed that transcription factors compose up to 10% of metazoan genomes [ 2 ] and more than 5% of the genes in Arabidopsis were identified as transcription factors [ 3 ]. (biomedcentral.com)
  • Transposable elements and their remnants constitute a substantial fraction of eukaryotic genomes. (nature.com)
  • Our results reveal a probable ancient retrotransposon surveillance pathway important for host genome integrity, and highlight potential conflicts between DNA transposons and retrotransposons, major transposable elements believed to have greatly moulded the evolution of genomes. (nature.com)
  • The emerging, primary function of the remaining 98% of the genome is to control gene transcription precisely and ensure faithful copying of genomes during cell replication. (ddw-online.com)
  • The option of sequenced primate genomes [23-26] and the capability to transform bloodstream B cells into immortal lymphoblastoid cell lines (LCLs) using the Epstein-Barr pathogen (EBV) [27] facilitates useful genomics evaluations across different primate types. (biopaqc.com)
  • This enables the identification of transposable element interaction profiles for individual ERV families and integration events specific to particular genomes. (biomedcentral.com)
  • These mobile elements, which have been propagated in the genomes of all eukaryotic species, can be classified as either DNA transposons or retrotransposons, depending on their mode of transposition. (biomedcentral.com)
  • Fig. 3: Analysis of heterochromatin and repetitive elements and de novo assembly of zebrafish chromosome 4. (nature.com)
  • However, due to very high levels of repetitive DNA and reliance on short-read sequencing, AaloF1 remains highly fragmented with more than 150,000 scaffolds, limiting its utility. (biomedcentral.com)
  • In the present study, we carried out a comparative analysis of chromatin characteristics in terms of the scaffold/matrix attachment regions, nucleosome formation potential and the occurrence of repetitive sequences, in the upstream regulatory regions of housekeeping and tissue specific genes. (biomedcentral.com)
  • Given their repetitive nature, reads associated with these elements are generally discarded or randomly distributed among elements of the same type in genome-wide analyses. (biomedcentral.com)
  • A large portion of a typical mammalian genome is comprised of transposable elements (TEs) however they are typically ignored in high-throughput sequencing-based studies due to their repetitive nature [ 17 , 18 ]. (biomedcentral.com)
  • Repetitive noncoding DNA sequences also form satellite DNA, which is a part of other structural elements. (medlineplus.gov)
  • Embryonic development of the mammalian face relies on a sequence of complex and interdependent molecular, cellular, and tissue interactions. (nih.gov)
  • Methods in Molecular Biology Series: Post-Transcriptional Gene Regulation. (ramapo.edu)
  • Although these highly conserved, transcriptionally active CTCF-YY1 co-bound regions are often promoter-proximal, gene-distal regions show comparable molecular features. (biopaqc.com)
  • We here present a brief introduction to experimental use and design of transgenic reporter mice and a more extensive review of the various studies where molecular imaging of transcriptional regulation has been applied during inflammation. (biomedcentral.com)
  • The most common molecular genetic change in prostate cancer involves silencing of expression of GSTP13, a critical enzyme of carcinogen defense, through methylation of deoxycytidine residues in "CG islands" in the 5 regulatory region of the GSTP1 gene (4, 5). (brocon.co)
  • We present the molecular characterization of four fatty acid desaturase (FAD) genes in R. toruloides . (biomedcentral.com)
  • Phylogenetic footprinting analysis and molecular promoter dissection was used to investigate the transcriptional control of expression and a distal upstream sequence (−2900 to −2066 bp) was found to be essential for the activation of MS1. (nottingham.ac.uk)
  • These findings provide an important insight into the molecular mechanism by which influenza NS1 commandeers RIG-I transcriptional regulation and suppresses host antiviral responses. (cdc.gov)
  • The human β-globin locus is a highly complex genetic system that has become a classical model for studying the regulation of eukaryotic gene expression. (ku.edu)
  • Alternative polyadenylation (APA), which is regulated by both cis-elements and trans-factors, plays an important role in post-transcriptional regulation of eukaryotic gene expression. (mdc-berlin.de)
  • Indeed, noncoding DNMs resulted in alterations, via chromatin interactions, in target gene expression in primitive neural stem cells derived from human induced pluripotent stem cells from an ASD subject. (biorxiv.org)
  • When mapping the sequenced region to the nucleotide record indicated (which includes 5000 base pairs upstream from the transcriptional start site), a 25 base pair deletion upstream and including the transcriptional start site was found. (nih.gov)
  • We hypothesized that if the O and P regions do in fact function to silence the γ-globin genes during development, then the deletion of these regions from the human β-globin locus would result in the persistence of γ-globin in the adult erythroid cells To test this hypothesis, the O and P regions were deleted from a 213 kb human β-globin locus yeast artificial chromosome (β-YAC). (ku.edu)
  • Transgenic mice were produced with the modified β-YAC and the effects of this OP deletion on expression of the human β-like globin genes were analyzed. (ku.edu)
  • Deletion of these regions resulted in the abolishment of ϵ-globin gene expression during embryonic erythropoiesis and a substantial decrease in β-globin globin gene expression during definitive erythropoiesis. (ku.edu)
  • Neuronal deletion or overexpression of Kmt2a/Mll1 H3K4- and Kmt1e/Setdb1 H3K9-methyltransferase was associated with higher-order chromatin changes at distal regulatory Grin2b sequences and impairments in working memory. (mssm.edu)
  • The conserved THI element discovered by comparative genomics [ 12376536 ] is an extension of a previously detected thiamin-regulatory element, the thi box [ 11470904 ]. (lbl.gov)
  • Therefore, two regions, O and P, located upstream of the δ-globin gene, that had previously been shown to function as silencers of the γ-globin genes in transient transfection assays were investigated. (ku.edu)
  • 3) To identify sequences important for the adipocyte-specific and hormonal/metabolic-dependent transcriptional regulation of this gene, fusions between the GLUT4 promoter region and a CAT reporter gene will be used in transient transfection assays. (elsevierpure.com)
  • Our data show that putative scaffold/matrix attachment regions are more abundant and nucleosome formation potential is higher in the 5' regions of tissue specific genes as compared to the housekeeping genes. (biomedcentral.com)
  • An in-silico comparison of chromatin related organisational differences in the 5' and 3' regulatory regions of housekeeping and tissue specific genes was carried out to shed light in this direction. (biomedcentral.com)
  • RNA Pol I primarily operates within the nucleolus, where it transcribes specific genes responsible for producing three essential ribosomal RNA (rRNA) molecules. (microbiologynote.com)
  • Post-transcriptional regulation of gene expression is the dominant regulatory mechanism in trypanosomatids as their mRNAs are transcribed from polycistronic units. (biomedcentral.com)
  • Although crucial in many different species, post-transcriptional regulation is especially the major mechanism for regulation of gene expression in a group of unicellular parasites called trypanosomatids. (biomedcentral.com)
  • Regulation of gene expression which occurs mostly during or after splicing involves several cis -acting fRNA elements, such as U-rich elements (UREs), short interspersed degenerated retroposons (SIDERs), etc. [ 3 , 4 ]. (biomedcentral.com)
  • Regulation of gene expression is a core biological function, which allows cells and organisms to respond to internal and external stimuli, maintain homeostasis in cells, and perform various biological functions. (keydifference.in)
  • However, nucleosomal organisation, non-passive structural scaffolds and global structure of chromatin are increasingly being recognised as major players in the regulation of gene expression. (biomedcentral.com)
  • Transcriptional regulation of gene expression is known to involve formation of dynamic chromatin loops mediated by S/MAR attachment to the nuclear matrix [ 3 ]. (biomedcentral.com)
  • We have investigated the intracellular pathways and DNA regulatory elements through which membrane depolarization activates expression of the neural gene encoding human proenkephalin. (jneurosci.org)
  • Further, genes modified by evolved m6A in humans are significantly enriched in transcriptional regulatory processes and disease related pathways, suggesting an important role in human biology for the evolution of m6A modification. (nih.gov)
  • This regulation occurs through the specificity of recruited immune cells and their differentiation, signaling pathways and gene expression. (biomedcentral.com)
  • NF-κB is attractive for inflammation studies due to the early activation, and the involvement in the large numbers of signaling pathways and the many genes related to immune functions that it controls [ 4 , 5 ]. (biomedcentral.com)
  • What pathways are this gene/protein implicaed in? (cancerindex.org)
  • The sequencing method also will not detect gross genetic alterations including most duplications, inversions, or deletions (in females). (nih.gov)
  • As a quality control pathway, NMD degrades mRNAs that contain premature termination codons, a class of gene alteration responsible for ~15% of human genetic disease alleles. (nih.gov)
  • Although complete genome sequence exists for sweet orange ( Citrus sinensis ) and clementine ( Citrus clementina ), olive tree ( Olea europaea ) and grapevine ( Vitis vinifera ), the development of biotechnological tools to improve stress tolerance still relies on the study of the available genetic resources including interspecific hybrids, naturally occurring (or induced) polyploids and wild relatives under field conditions. (frontiersin.org)
  • Cas9 is a member of a class of RNA-guided DNA nucleases which are part of a natural prokaryotic immune system that confers resistance to foreign genetic elements such as plasmids and bacteriophage. (vectorbuilder.cn)
  • Genetic polymorphisms and isogenic deletions of loop-bound sequences conferred liability for cognitive performance and decreased GRIN2B expression. (mssm.edu)
  • To image activation of transcription factors, most commonly genetic constructs with a promoter coupled to reporter gene are used. (biomedcentral.com)
  • The Notch signaling pathway is an evolutionarily conserved suppressor of proneural bHLH factor expression. (nih.gov)
  • The laboratory primarily studies these questions in the context of nonsense-mediated mRNA decay (NMD), an evolutionarily conserved pathway that performs important quality control and regulatory functions. (nih.gov)
  • A comparison of zebrafish, human and mouse regulatory elements enabled the identification of both evolutionarily conserved and species-specific regulatory sequences and networks. (nature.com)
  • DNA binding assays will be performed using nuclear extracts prepared from cells that express the scavenger receptor to identify putative transcription factors that direct its expression. (grantome.com)
  • The process of gene expression regulation depends on timely synthesis and degradation of messenger RNAs (mRNAs). (nih.gov)
  • A few cis -acting RNA elements in 3'-untranslated regions of mRNAs have been identified in trypanosomatids, which affect the mRNA stability or translation rate in different life stages of these parasites. (biomedcentral.com)
  • GRSDB2 and GRS_UTRdb: Databases of Quadruplex Forming G-rich Sequences in pre-mRNAs and mRNAs. (ramapo.edu)
  • There are several known examples whereby TE sequences located within, or nearby, human genes have been shown to terminate transcription of genic mRNAs. (biomedcentral.com)
  • An early study of HERVs provided the first direct evidence that TE-derived sequences can terminate the transcription of non-TE human mRNAs and further suggested that different subfamilies of these elements may serve to terminate transcription in a cell type-specific manner[ 7 ]. (biomedcentral.com)
  • 2018). Stomata regulation by tissue-specific expression of the Citrus sinensis MYB61 transcription factor improves water-use efficiency in Arabidopsis. (uai.cl)
  • In Arabidopsis, pCsMYB15 directs the expression of the reporter gene GUS in stomata in the presence of light. (uai.cl)
  • TE sequences within the introns of human genes show an antisense orientation bias, which has been proposed to reflect selection against TE sequences in the sense orientation owing to their ability to terminate the transcription of host gene transcripts. (biomedcentral.com)
  • However, those TE-TTS located within the introns of human genes were found to be far more cell type-specific than the canonical TTS. (biomedcentral.com)
  • Differences in the binding of transcriptional regulators have been inferred from the presence of several hundred species-specific DNase I hypersensitive sites near genes differentially expressed between humans and chimpanzees [37]. (biopaqc.com)
  • Here we describe activity-regulated long-range loopings bypassing up to 0.5 Mb of linear genome to modulate NMDA glutamate receptor GRIN2B expression in human and mouse prefrontal cortex. (mssm.edu)
  • Regulatory T cells (Tregs) are specialized immune cells that modulate tissue homeostasis. (pharmaceuticalintelligence.com)
  • Further systematic sequence analysis of the regions in proximity to cis-divergent pAs revealed that the local RNA secondary structure and a poly(U) tract in the upstream region could negatively modulate the pAs usage. (mdc-berlin.de)
  • Inactivation results, in part, from high levels of DNA modification (methylation) that prevent gene activity, along with the production of an inhibitory molecule called long non-coding RNA(named Xist) that binds to the X chromosome. (nih.gov)
  • When the effector isn't present, qacR binds to regulatory elements to prevent the expression of qacA. (epigenie.com)
  • Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. (embl.de)
  • The MYB binding sites (AACTAAA/C) in TaGAPCp2 P/ 3 P were identified as the key cis-elements for responding to drought stress and were bound by the transcription factor TaMYB. (biomedcentral.com)
  • FOXO3 encodes the transcription factor forkhead/winged helix box gene, group O, type 3 (Foxo3). (databasefootball.com)
  • Sequences of the CsMYB61 coding region, a transcription factor implicated in the closure of stomata, together with a putative stomata-specific promoter from CsMYB.1.5, were identified and cloned. (uai.cl)
  • Fig. 2: Characterization of tissue-specific cis -regulatory elements. (nature.com)
  • This level of regulation may be distinctly different for genes whose expression is constitutive in comparison to genes that exhibit tissue specific expression. (biomedcentral.com)
  • In the present study, we have taken 2 distinct sets of genes differing predominantly in their spatial expression aspect, namely, housekeeping and tissue specific, to understand the various attributes of the regulatory role played by chromatin organisation in the 5' region. (biomedcentral.com)
  • In addition, we propose to characterize adipocyte-specific DNA binding factors responsible for the hormonal/metabolic and tissue-specific regulation of this gene. (elsevierpure.com)
  • By combining long-read DNA sequencing and Hi-C, we assembled the sex-determining chromosome 4 de novo. (nature.com)
  • The X chromosome contains hundreds of genes that are associated with diseases. (nih.gov)
  • Most of these diseases are more common in males because they only have one X chromosome, so inheriting just one faulty copy of an X-linked gene can result in the disease. (nih.gov)
  • EXPLANATION near F8 (Xq28) NG_011403.1: This result is reported due to a request for reporting all variants in gene gene region g.4980_5005del regions known to be associated with those associated with Hemophilia. (nih.gov)
  • Certain sequence variants of the α-synuclein gene are linked to the risk of Parkinson's disease. (natureasia.com)
  • An analysis of these variants using gene-editing technology provides a possible explanation for this increased risk. (natureasia.com)
  • The advantage of using separate vectors over an all-in-one vector for expressing Cas9 and gRNA is that it offers the flexibility of combinatorial usage of different gRNA expression vectors in conjunction with a variety of Cas9 variants (wild type nuclease, nickase, nuclease-dead) depending upon the user's experimental goal. (vectorbuilder.cn)
  • Recently, Boyle and co-workers at Stanford proposed an "omnigenic" model, which suggests that complex polygenic traits are caused by minuscule contributions from a vast number of sufficiently interconnected peripheral DNA variants that affect core disease-related genes in relevant tissues . (databasefootball.com)
  • Jason Watts M.D., Ph.D., leads the Transcriptional Responses in Disease Group and holds a secondary appointment in the NIEHS Genome Integrity and Structural Biology Laboratory . (nih.gov)
  • Group members use renal, and other human cell types, to study how RNA polymerase pausing mediates transcriptional responses to physiologic and environmental stresses. (nih.gov)
  • RNA polymerase pausing mediates the transcriptional responses to physiologic and environmental stress. (nih.gov)
  • These data suggest a model in which membrane depolarization activates gene expression through a calcium-dependent pathway, potentially involving calmodulin, and in which the transcriptional responses to both cAMP and calcium are transduced by the same DNA element. (jneurosci.org)
  • Of these, NF-κB was regarded as the activator and thus illustrates how NF-κB, which is required for most types of inflammatory responses, can engage in regulation of a specific set of inflammatory genes. (biomedcentral.com)
  • Influenza virus non-structural protein 1 (NS1) counteracts host antiviral innate immune responses by inhibiting Retinoic acid inducible gene-I (RIG-I) activation. (cdc.gov)
  • The promoter activities were significantly improved under abiotic stress via regulation of Rluc reporter gene expression, while promoter sequence analysis indicated that these fragments were not almost identical. (biomedcentral.com)
  • A part of the promoter or tandem copies of putative transcription regulatory DNA elements are cloned upstream of a reporter gene in a reporter vector. (biomedcentral.com)
  • The Y1H reporter strain is transformed with a cDNA library vector, and interaction between target DNA and hybrid protein is detected by reporter gene expression [ 10 ]. (biomedcentral.com)
  • e.g., sulforaphane will increase expression of a reporter gene downstream of promoter constructs containing the ARE consensus sequence and a minimal promoter. (brocon.co)
  • PREs function as potent silencers in the context of Hox reporter genes and they have been shown to partially repress a linked miniwhite reporter gene. (silverchair.com)
  • Silencing of these reporter genes is abolished in PcG mutants and excision of the PRE from the reporter gene during development results in loss of silencing within one cell generation. (silverchair.com)
  • Genome-wide approaches have led to the understanding that RNA polymerase pausing is a general feature of metazoan gene transcription, where the movement of RNA polymerase during chain elongation is highly regulated leading to punctuated pauses that are coupled to RNA processing and fine-tuning of transcriptional output. (nih.gov)
  • Transposable elements (TEs) encode sequences necessary for their own transposition, including signals required for the termination of transcription. (biomedcentral.com)
  • For instance, RNA polymerase I transcribes genes that encode structural components of the ribosome . (microbiologynote.com)
  • Additionally, RNA Pol II is involved in transcribing genes that encode small nucleolar RNAs (snoRNAs) involved in rRNA processing and small nuclear RNAs (snRNAs) involved in mRNA processing, with the exception of U6 snRNA. (microbiologynote.com)
  • Located within the nucleoplasm, RNA Pol III transcribes genes that encode diverse RNA molecules. (microbiologynote.com)
  • Further, the NMD pathway plays a major role in gene expression regulation, impacting as many as 10% of all human genes. (nih.gov)
  • The zebrafish reference genome sequence and its relationship to the human genome. (nature.com)
  • Allan Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) - An atlas describing the transcriptional mechanism of human brain development, which includes RNA sequencing and exon microarray data profiling up to 16 cortical and subcortical structures across the full course of human brain development. (nih.gov)
  • This could partially explain the lower number of genes estimated in the human genome. (biomedcentral.com)
  • Inter-primate evaluations of regulatory advancement have already been performed for histone adjustments, which can explain 7% of gene expression differences among human, chimpanzee, and rhesus macaque cell lines [34]. (biopaqc.com)
  • While there is evidence in support of this model for some elements, the extent to which TE sequences actually terminate transcription of human gene across the genome remains an open question. (biomedcentral.com)
  • Using high-throughput sequencing data, we have characterized over 9,000 distinct TE-derived sequences that provide transcription termination sites for 5,747 human genes across eight different cell types. (biomedcentral.com)
  • TE sequences provide numerous termination sites to human genes, and TE-derived TTS are particularly cell type-specific. (biomedcentral.com)
  • For any individual human, different kinds of somatic cells contain the same genome sequence, but are obviously functionally distinct. (biomedcentral.com)
  • Human endogenous retroviral elements (HERVs), for example, have polyadenylation signals in their long terminal repeat (LTR) regions that terminate transcription[ 6 ]. (biomedcentral.com)
  • Thus, numerous TE sequences located within, or nearby, human gene sequences may contribute substantially to the termination of gene transcription via the provisioning of termination signals. (biomedcentral.com)
  • Later, the same family of ERVs was demonstrated to terminate transcription of a novel alternatively spliced version of the human NAAA gene[ 8 ]. (biomedcentral.com)
  • There is also experimental evidence showing that L1 (LINE) retrotransposon sequences can terminate the transcription of human genes, and in this same study the intronic content of L1 sequences in human genes was found to be negatively correlated with their expression levels[ 9 ]. (biomedcentral.com)
  • Sulforaphane induces phase 2 enzyme expression and activity significantly in human prostatic cells. (brocon.co)
  • Each human gene is made up of deoxyribonucleic acid (DNA) in a double helix. (wikiversity.org)
  • There are "nearly 50,000 acetylated sites [punctate sites of modified histones] in the human genome that correlate with active transcription start sites and CpG islands and tend to cluster within gene-rich loci. (wikiversity.org)
  • C/EBPbeta overexpression and siRNA knockdown in human lung epithelial cells resulted in suppression and activation of RIG-I expression respectively, implying a negative regulatory role of C/EBPbeta. (cdc.gov)
  • Maston GA, Evans SK, Green MR. Transcriptional regulatory elements in the human genome. (medlineplus.gov)
  • An integrated encyclopedia of DNA elements in the human genome. (medlineplus.gov)
  • The group studies how nucleic acid structure and chromatin environment influence gene transcription. (nih.gov)
  • The local chromatin environment for these TE-TTS is similar to that seen for 3 ′ UTR canonical TTS and distinct from the chromatin environment of other intragenic TE sequences. (biomedcentral.com)
  • These changes can affect gene expression patterns and likely contribute to disease or other phenotypes associated with exposure. (nih.gov)
  • They include the cis-acting regulatory elements, such as the LCR and gene-proximal regulatory sequences, involved in establishing and maintaining specific chromatin conformations and histone modification patterns throughout the locus, and transcriptional activation, as well as trans-acting factors, both erythroid-specific and general. (ku.edu)
  • This is further supported by their mostly nonoverlapping mRNA expression patterns. (sdbonline.org)
  • It aids in grouping genes by common regulatory elements and finding patterns of structure and function of transcription factors in control elements. (buffalo.edu)
  • REDfly includes all experimentally verified fly regulatory elements along with their DNA sequence, their associated genes and the expression patterns they direct. (buffalo.edu)
  • 15. Nitric oxide-releasing agents and cGMP analogues inhibit murine erythroleukemia cell differentiation and suppress erythroid-specific gene expression: correlation with decreased DNA binding of NF-E2 and altered c-myb mRNA expression. (nih.gov)
  • Here we identify four CSL binding sites within the Atoh7 proximal regulatory region and demonstrate Rbpj protein interaction at these sequences by in vitro electromobility shift, calorimetry and luciferase assays and, in vivo via colocalization and chromatin immunoprecipitation. (nih.gov)
  • Then, the Y1H system and EMSA assay demonstrated that these MYB binding sites in TaGAPCp2 P (− 1135 and − 985) and TaGAPCp3 P (− 1414 and − 665) were the target cis-elements of TaMYB. (biomedcentral.com)
  • We used MAR Finder (new version) and ChrClass programs for predicting S/MAR binding sites in the sequences (Table 1 ). (biomedcentral.com)
  • We use experimental systems ranging from in vitro biochemistry to whole-transcriptome studies of RNA expression and RNA-protein interactions. (nih.gov)
  • Complementary experiments will be performed in transgenic mice to verify the physiologic importance of cis elements defined In vitro. (grantome.com)
  • 1984) The Role of Palindromic and Nonpalindromic Sequences in Arresting DNA Synthesis In Vitro and In Vivo ,J. Mol. (nih.gov)
  • They are a specialized subset of T lymphocytes that function as suppressive immune cells and inhibit various elements of immune response in vitro and in vivo. (pharmaceuticalintelligence.com)
  • The workflow of sequence selection aided by computational screens, screening with a cell-free TX-TL system, and then validating in vitro and in vivo is a valuable addition to the synthetic biologist's toolkit. (epigenie.com)
  • 1) In comparison to in vivo regulation of adipose tissue GLUT4, we will examine the effect of in vitro insulin and glucose treatments in isolated primary adipocytes from control, STZ-diabetic and insulin-treated STZ- diabetic rats in terms of altered basal and insulin-stimulated glucose transport activity and relative expression of glucose transporter protein and mRNA levels. (elsevierpure.com)
  • In addition, transgenic lines expressing the CsMYB61 coding region under transcriptional control of pCsMYB15 have a normal phenotype under in vitro and greenhouse conditions. (uai.cl)
  • In addition, a 1.2 kb promoter region of the gene CsMYB15 (pCsMYB15) containing regulatory elements for expression in guard cells and in response to Abscisic Acid (ABA) and light was isolated. (uai.cl)
  • Notably, noncoding DNMs that affect chromatin interactions exhibited transcriptional dysregulation implicated in ASD risks. (biorxiv.org)
  • The ability of sequences to position nucleosomes and to be anchored to the nuclear matrix to provide a spatial context for regulation of expression are measurable parameters that may influence the interactions with transcription machinery [ 2 , 3 ]. (biomedcentral.com)
  • Brian Morris, the author for correspondence on the FOXO3 article, has suggested that physical interactions between genes themselves might be an additional contributory factor in the omnigenic model . (databasefootball.com)
  • Exposure to environmental toxicants can be associated with changes in gene expression and DNA methylation profiles, which together likely contribute to disease or other phenotypes associated with exposure. (nih.gov)
  • Further, DNA methylation studies revealed that promoter methylation differences underlie 12 to 18% of gene expression differences between humans and chimpanzees and that approximately 10% of CpG islands are significantly differentially methylated between the two species [35,36]. (biopaqc.com)
  • Although it is harder to regulate the transcription of genes with multiple transcription start sites, "variations in the expression of a constitutive gene would be minimized by the use of multiple start sites. (wikiversity.org)
  • observed that, in the streptozotocin-diabetic rats, insulin treatment significantly reduced the elevated H 2 S biosynthesis in the pancreas and liver, accompanying the decreased mRNA expression of CBS and CSE. (medscape.com)
  • Altogether, our results demonstrate that the expression of zc3h12a must be tightly controlled during the first cell divisions of zebrafish embryos and that a rapid decrease in its mRNA expression is an important factor promoting proper embryo development. (bvsalud.org)
  • Activation of the gene by KCl-induced depolarization or the calcium ionophore A23187 was dependent upon and synergistic with cAMP in PC12 and C6-glioma cells, but neither depolarization nor treatment with A23187 affected cAMP levels. (jneurosci.org)
  • The use of microarray data and clustering algorithms enables identification of genes with similar expression profiles that may be involved in similar biological processes [ 4 ]. (biomedcentral.com)
  • Importantly, like FOXO3 , its 46 neighboring genes are also involved in various processes that contribute to cell resilience, such as autophagy, stress response, energy/nutrient sensing, cell proliferation, apoptosis and stem cell maintenance. (databasefootball.com)
  • Additionally, non-coding RNAs, which make up the majority of the transcriptional output in cells, play crucial roles in various cellular processes. (microbiologynote.com)