• The Zoonomia project aligned the genome sequences of 240 mammalian species and determined that only 10.7% of the human genome is conserved. (blogspot.com)
  • There are a million potential transcription regulatory sites in the human genome. (blogspot.com)
  • One of the important questions about the human genome concerns how gene expression is regulated. (blogspot.com)
  • Understanding the regulatory landscape of the human genome is a long-standing objective of modern biology. (blogspot.com)
  • Our annotations illuminate the regulatory functions of the human genome. (blogspot.com)
  • STRs make up about 5% of the human genome. (stanford.edu)
  • An integrated encyclopedia of DNA elements in the human genome. (nature.com)
  • The papers published in Nature describe maps of promoters and enhancers - short regions of DNA that influence the activity of genes - encoded in the human genome, and their activity across the vast wealth of human cell types and tissues of the human body. (riken.jp)
  • The Nuclear Receptor family is a large group of ligand-activated transcription factors with 48 members presently identified in the human genome. (jnu.ac.in)
  • Approximately 3% of the human genome codes for miRNA sequences, which can suppress gene expression by mediating translational repression [ 5 ]. (hindawi.com)
  • The glossary features nearly 250 terms explained in an easy-to-understand way by leading scientists and professionals at the National Human Genome Research Institute. (genome.gov)
  • As of August 10, 2000, draft sequence was available for 87% of the human genome (https://www.ncbi.nlm.nih.gov/genome/seq/), and at least 39 prokaryotic genomes, including those of more than a dozen human pathogens, had been completely sequenced https://www.tigr.org/tdb/mdb/mdbcomplete.html). (medscape.com)
  • Epigenetic components (for example, Polycomb PRC1/2 and Trithorax group proteins) maintain the 'off' states of certain genes and the 'on' states of others, in a cell-type- and time-specific manner (the bottom panels show three genes, depicted schematically as chromatinized templates, in which transcription is triggered by specific transcription factors and silent or active states are maintained by PRC1/2 or Trithorax proteins, respectively). (nature.com)
  • We have learned that genes in mammalian cells are transcribed into messenger RNAs (mRNAs), which are to be translated into polypeptides (proteins). (intechopen.com)
  • For decades, scientists have known that, despite its name, "junk DNA" in fact plays a critical role: While the coding genes provide blueprints for building proteins, which direct most of the body's functions, some of the noncoding sections of the genome, including regions previously dismissed as "junk," seem to turn up or down the expression of those genes. (stanford.edu)
  • But it's been unclear how certain noncoding regions influence gene-expression levels - that is, the number of times a gene is copied into RNA and used to make proteins. (stanford.edu)
  • For the study, the researchers looked at how STRs interact with proteins called transcription factors. (stanford.edu)
  • The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. (mdpi.com)
  • In eukaryotic cells, chromatin comprises a complex consisting of DNA, RNA, and proteins where covalent modifications correlate with regulation of gene expression [ 1 ]. (biomedcentral.com)
  • GRFs are a large gene family with highly conserved proteins. (biomedcentral.com)
  • Light effects on the expression of nuclear genes for plastid proteins and for the 18S, 5.8S and 25S ribosomal RNAs are discussed, together with some recent information concerning the expression of chloroplast genes in developing plastids. (ncsu.edu)
  • Gene expression is regulated in part by the interactions of genomic DNA with the packaging histone proteins. (wayne.edu)
  • Intriguingly, a remarkable number of the differentially expressed genes encode proteins engaged in histone modification and remodeling of nucleosome structure, emphasizing that extensive changes in chromatin structure are required for regulated gene transcription in the transition from proliferating myoblasts to terminally differentiated myotubes. (au.dk)
  • Informatics analyses and functional assays revealed that transcriptional bursting kinetics was regulated by a combination of promoter- and gene body-binding proteins, including the polycomb repressive complex 2 and transcription elongation factors. (janelia.org)
  • In addition, over expression of the histone variant H2A.Z as well as deregulated expression of Polycomb group proteins including EZH2 have been well-documented. (oncotarget.com)
  • DNA methyltransferases are not limited to catalyzing DNA methylation, but also take part in the regulation of gene expression through interactions with other proteins that repress transcription and modify chromatin structure. (caister.com)
  • Finally, higher-order 3D chromosome folding is also thought to modulate gene expression and might contribute to inheritance 15 . (nature.com)
  • Title: Sequencing of candidate chromosome instability genes in endometrial cancers reveals somatic mutations in ESCO1, CHTF18, and MRE11A. (genscript.com)
  • This gene is one of several homeobox HOXC genes located in a cluster on chromosome 12. (nih.gov)
  • In HPV-induced tumours, misappropriate random integration of the viral genome into the host chromosome often leads to disruption of the E2 gene and the loss of E2 expression. (bris.ac.uk)
  • Even in wild-type “Chinese Spring”, the NOR on chromosome 1B is partially dominant to that on chromosome 6B, since the 1B locus is more active in spite of having fewer genes. (ncsu.edu)
  • Position effect is the effect on the expression of a gene when its location in a chromosome is changed, often by translocation. (definitions.net)
  • Position effect refers to the phenomenon in genetics where the physical position of a gene on a chromosome or within the genome influences its expression or mutation rate. (definitions.net)
  • The chromosome distribution and analysis for WGD-derived duplicated blocks revealed that the legume bZIP genes have expanded mainly by segmental duplication rather than tandem duplication. (datadryad.org)
  • Using a combination of miRNA hairpin predictions and co-mapping with miRBase entries, we identified a highly conserved cluster of miRNA genes on the X chromosome in the tammar and a total of 94 other predicted miRNA producing genes. (biomedcentral.com)
  • The characterization of new miRNA target genes and a unique profile for crasiRNAs has allowed for insight into multiple RNA mediated processes in the tammar, including gene regulation, species incompatibilities, centromere and chromosome function. (biomedcentral.com)
  • Small RNAs play important roles in many aspects of pre- and post-transcriptional gene regulation, epigenetic modifications, chromosome segregation and genome structure. (biomedcentral.com)
  • The epigenetic modification of DNA with 5-methylcytosine is an important regulatory event involved in chromatin structure, genomic imprinting, inactivation of the X chromosome, transcription, and retrotransposon silencing. (caister.com)
  • Twenty-two of the pairs, chromosome numbers 1 to 22, the autosomes, are normally homologous (identical in size, shape, and position and number of genes). (msdmanuals.com)
  • the smaller Y chromosome carries genes that initiate male sex differentiation, as well as a few other genes. (msdmanuals.com)
  • The genes that occupy the same locus on each chromosome of a pair (one inherited from the mother and one from the father) are called alleles. (msdmanuals.com)
  • A chromosome contains many genes. (msdmanuals.com)
  • TCF7L2 was discovered as a type 2 diabetes susceptibility gene after a strong linkage signal was mapped to chromosome 10q in a Mexican-American population. (medscape.com)
  • They identified 180,000 promoters and 44000 enhancers on the genome and find that the activity of the large majority of these transcriptional regulation regions is highly specific to cell type. (riken.jp)
  • This study indicates that chloroplast genes are often grouped into multigene transcriptional units which can be cotranscribed, and that light-stimulated plastid development involves changes in the relative abundance of the overlapping RNAs of different length that result from transcription of these genes or gene clusters. (ncsu.edu)
  • Emphasis is given to the diversity of different responses observed with different genes and evidence for light effects at both transcriptional and post‐transcriptional levels. (ncsu.edu)
  • Different mRNAs are characterized by different nuclear-cytoplasmic `partitioning coefficients', indicating that post-transcriptional events play a significant role in regulating the accumulation of these mRNAs during light induction. (ncsu.edu)
  • Mitra A, Vo L, Soukar I, Chaubal A, Greenberg ML, Pile LA. Isoforms of the transcriptional cofactor SIN3 differentially regulate genes necessary for energy metabolism and cell survival. (wayne.edu)
  • These cellular processes are strictly regulated in a spatiotemporally manner through a coordinated patterns of gene expression governed by specific transcriptional activators and networks of signal transduction. (au.dk)
  • Combining transcriptional data and in silico modeling along with in vitro validation, we identified CAD gene ZEB2 as a target through which these lncRNAs exert their function in SMC phenotypic transition.Expression of a large and diverse set of lncRNAs in human coronary artery SMC are highly dynamic in response to CAD-related stimuli. (stanford.edu)
  • The dynamic changes in expression of these lncRNAs correspond to alterations in transcriptional programs that are relevant to CAD, suggesting a critical role for lncRNAs in SMC phenotypic transition and human atherosclerotic disease. (stanford.edu)
  • To better understand the epigenetic and transcriptional mechanisms that mediate these cell state changes, and how they relate to risk for coronary artery disease (CAD), we have investigated the causality and function of transcription factors (TFs) at genome wide associated loci. (stanford.edu)
  • Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells. (janelia.org)
  • Transcriptional bursting is the stochastic activation and inactivation of promoters, contributing to cell-to-cell heterogeneity in gene expression. (janelia.org)
  • These results uncovered the key molecular mechanisms underlying transcriptional bursting and cell-to-cell gene expression noise in mammalian cells. (janelia.org)
  • Kacme is associated with marks of active chromatin, increased transcriptional initiation and is regulated in response to biological signals. (bvsalud.org)
  • HBV-X protein: This acts as a transcriptional transactivator for many viral and host genes through interaction with various transcription factors. (medscape.com)
  • Their mutagenic potential and gene regulatory effect have shaped the evolution of transcriptional networks involved in development, pluripotency, and inflammation. (lu.se)
  • We found that the regulation of TE transcription during brain development is essential for the establishment of long-term transcriptional repression carried to adulthood (Paper I and IV). (lu.se)
  • PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast. (slackbuilds.org)
  • Transcription factors attach to noncoding DNA, regulating the expression of protein-coding genes. (stanford.edu)
  • Consistent with previous long noncoding RNA studies, these lncRNAs overall have fewer exons, are shorter in length than protein-coding genes (pcGenes), and have relatively low expression level. (stanford.edu)
  • The Genome Structure Function section of the Institute of Cancer and Genomic Sciences investigates the fundamentals of the active information database that is our genome, in normal and disease states. (birmingham.ac.uk)
  • Genomic location of these long noncoding RNA is disproportionately enriched near CAD-related TFs (transcription factors), genetic loci, and gene regulators of SMC identity, suggesting the importance of their function in disease. (stanford.edu)
  • During my graduate studies, I used a systems biology approach to demonstrate that chromatin environments at different genomic loci decouple transcription factor mediated initiation of gene expression from subsequent gene activation 6 . (confex.com)
  • Thus, DNA methylation influences the functional integrity of mammalian genome by shaping its overall structure and leaving its marks in the genomic DNA sequence during evolution. (caister.com)
  • 2002). Expression and genomic organization of the zebrafish chaperonin gene complex . (sgu.edu)
  • Whole genome sequencing of HRSV offers enhanced resolution of strain variability for epidemiological surveillance and provides genomic information essential for antiviral and vaccine development. (cdc.gov)
  • The pluripotency of the initial cell and the establishment of cell types depend to a large extent on the coordinated deployment of hundreds of transcription factors that bind to specific DNA sequences to activate or repress the transcription of cell lineage genes 1 . (nature.com)
  • The following ESCO1 gene cDNA ORF clone sequences were retrieved from the NCBI Reference Sequence Database (RefSeq). (genscript.com)
  • ORF sequences can be delivered in our standard vector, pcDNA3.1 + /C-(K)DYK or the vector of your choice as an expression/transfection-ready ORF clone. (genscript.com)
  • Changes to short, repetitive sequences in the genome have been linked to diseases like autism and schizophrenia. (stanford.edu)
  • Starting in the 1980s, researchers noticed that changes to these repetitive sequences can affect gene expression," said the study's lead author, Connor Horton, who was a technician in Fordyce's lab. (stanford.edu)
  • Researchers have spent a lot of time characterizing these transcription factors and figuring out which sequences - called motifs - they like to bind to the most," Fordyce said. (stanford.edu)
  • In this study, we're showing that the STR sequence around the motif can have a really big effect on transcription factor binding, providing clues as to what these repeated sequences might be doing. (stanford.edu)
  • The experiments compared how tightly transcription factors attached to thousands of DNA sequences - those with a preferred motif, those without one, and those surrounded by random sequences or by a wide variety of STRs. (stanford.edu)
  • This file includes the bZIPs protein sequences from Arabidopsis thaliana and six legume genomes (Glycine max,Medicago truncatula,Cajanus cajan,Cicer arietinum,Phaseolus vulgaris and Lotus japonicus). (datadryad.org)
  • We examined each of these small RNA classes with respect to the newly assembled tammar wallaby genome for gene and repeat features, salient features that define their canonical sequences, and the constitution of both highly conserved and species-specific members. (biomedcentral.com)
  • Phylogenetic analysis of the genome sequences obtained from the 130 clinical specimens revealed a wide diversity of HRSV genotypes demonstrating methodologic robustness. (cdc.gov)
  • infection of these two bacteria in strikingly different types of As additional genome sequences become available for other ticks provide examples of possible adaptations for their trans- pathogenic and free-living spirochetes, comparisons of their mission. (cdc.gov)
  • Here we analyzed the genome-wide changes in gene transcription occurring during growth and differentiation of porcine primary myoblast cells. (au.dk)
  • Small RNAs have proven to be essential regulatory molecules encoded within eukaryotic genomes. (biomedcentral.com)
  • The organisation and evolution of the eukaryotic genomes. (lu.se)
  • For many regions of the genome, we have detected multiple overlapping transcripts including both small, gene-sized RNAs and large transcripts covering entire gene clusters. (ncsu.edu)
  • Whereas most regions of the genome are constantly methylated these elements are mainly kept free of methylation thereby facilitating the establishment of an open chromatin structure and of initiation of transcription. (caister.com)
  • The PEP enzyme recognizes the -10 and -35 cis -elements, similar to those found in bacterial promoters whereas the NEP enzyme recognizes the YRTA-motif, which can also be found upstream of several genes with PEP promoters indicating that these genes can be transcribed by both polymerases ( Pfannschmidt and Liere, 2005 ). (frontiersin.org)
  • Most PgGRF and PgGIF gene promoters contain some hormone- and stress- related cis-regulatory elements. (biomedcentral.com)
  • Using a highly sensitive technique called Cap Analysis of Gene Expression (CAGE), developed at RIKEN (ref. 4, 5), the researchers monitored the activity of promoters and enhancers across over 180 human primary cells. (riken.jp)
  • The cis- component is caused by differences in regulatory elements such as promoters or enhancers that only affect the expression of a nearby gene or genes on the same DNA molecule. (biomedcentral.com)
  • CpG island elements are associated with most mammalian gene promoters, yet how they contribute to gene regulation remains poorly understood. (nih.gov)
  • First, there's the ENCODE view, which maps the binding sites of 1600 transcription factors and the associated methylation and histone modification patterns. (blogspot.com)
  • DNA methylation is the most commonly studied epigenetic mark in humans, as it is well recognised as a stable, heritable mark that can affect genome function and influence gene expression. (frontiersin.org)
  • Retrospective studies of the survivors of famines, such as those exposed to the Dutch Hunger Winter of 1944-45, have linked exposures around conception to later disease outcomes, some of which correlate with DNA methylation changes at certain genes. (frontiersin.org)
  • Placenta-associated pregnancy complications, such as preeclampsia and intrauterine growth restriction, are all associated with aberrant patterns of DNA methylation and expression which are only now being linked to disease risk later in life. (frontiersin.org)
  • Cytosine methylation in ribosomal DNA and nucleolus organiser expression in wheat. (ncsu.edu)
  • Cytosine methylation has been studied in wheat rRNA genes at nucleolar organizers displaying different activities. (ncsu.edu)
  • The methylation pattern within a specific multigene locus is influenced by the number and type of rRNA genes in other rDNA loci in the cell. (ncsu.edu)
  • It is concluded that cytosine methylation in rDNA is regulated and that the methylation pattern correlates with the transcription potential of an rRNA gene. (ncsu.edu)
  • In mammals, cytosine methylation at CpG positions of the DNA sequence is one of the hallmarks of epigenetic gene silencing. (caister.com)
  • Besides its role in the regulation of genes, DNA methylation silences repetitive elements and appears to be important for the stability of the mammalian genome. (caister.com)
  • Dr. Martin's research expertise includes the use molecular biology techniques such as PCR, mRNA differential display, in situ hybridization, and DNA chip microarrays to identify, clone and characterize genes that are expressed during zebrafish development and whose transcription is regulated by DNA methylation. (sgu.edu)
  • Lysine acetylation and methylation are especially important for regulating chromatin and gene expression2-4. (bvsalud.org)
  • The investigators first began the research by utilizing a genome-wide RNAi screening tool. (healthjockey.com)
  • CCGs consist of a significant portion of the genome and are involved in diverse biological pathways. (nih.gov)
  • Current objectives of the lab are to understand regulatory pathways that affect SIN3 activity and to understand the consequences of SIN3 recruitment at target genes. (wayne.edu)
  • Two-component pathways thus often enable cells to sense and respond to stimuli by inducing changes in transcription. (genome.jp)
  • These analyses expand our knowledge of the temporal expression patterns and provide an insight into known and unknown genes and pathways that are transcriptionally regulated and, therefore, likely to be critically implicated in myogenesis. (au.dk)
  • While the resulting list of AS-DEGs from hybrids is likely more accurate and isolates the cis- regulatory component, there are often thousands of AS-DEGs which make it difficult to prioritize candidate genes and pathways that may have played a major role in evolution. (biomedcentral.com)
  • The overall response of the smallest chromatin fragment to compressive stress leaves the nucleosome assembly with a substantial plastic deformation and localised defects, which can have a potential impact on DNA transcription, downstream signaling pathways, the regulation of gene expression, and DNA repair. (bvsalud.org)
  • The prin2.2 and csp41b-2 single mutants displayed pale phenotypes, abnormal chloroplasts with reduced transcript levels of photosynthesis genes and defects in embryo development. (frontiersin.org)
  • These phenotypes are often due to a chromosomal translocation such that the color gene is now close to a region of heterochromatin. (definitions.net)
  • From an engineering perspective, gene expression regulation can be viewed as the output of a network of complex chemical and physical processes, and understanding how these processes interact and integrate to govern cellular phenotypes has been a major focus of my graduate and postdoctoral research. (confex.com)
  • If this gene also varies by two-fold within each species individual members of the same species, it is unlikely to account for any species-specific phenotypes. (biomedcentral.com)
  • These genes were selected based on their role in asthmatic inflammatory processes and History previously reported associations with asthma phenotypes. (cdc.gov)
  • Of these mediators, cytokines play a single nucleotide polymorphisms (SNP) in pro-inflammatory cytokine genes and asthma phenotypes (Che et al. (cdc.gov)
  • To overcome this limitation, recent advances in molecular biology have enabled genome-wide single-cell measurements of the transcriptome, genome or certain epigenetic marks that capture this cell-to-cell heterogeneity. (confex.com)
  • This microbiota-diet interaction leads to changes in histone modification at active enhancers that are enriched for binding sites for signal responsive transcription factors. (biomedcentral.com)
  • The diet/microbiome-dependent changes are reflected in both the composition of the recipient animals' microbiome as well as in the set of transcription factor motifs identified at diet-influenced enhancers. (biomedcentral.com)
  • Fig. 4: The role of eRNAs in regulating condensate assembly on enhancers. (nature.com)
  • A key discovery on the way was that by employing CAGE, the technology used to find active genes, the team could identify the additional DNA regions that regulate the activity of genes in every cell type, called enhancers. (riken.jp)
  • In this case the difference in expression is often due to enhancers that regulate neighboring genes. (definitions.net)
  • These local enhancers can also affect the expression pattern of the transgene. (definitions.net)
  • Diet-induced obesity led to altered acetylation of lysine 27 on histone H3 (H3K27ac) and to altered monomethylation of lysine 4 on histone H3 (H3K4me1) at numerous loci, with concomitant changes in the expression of genes that were functionally relevant to intestinal cancers. (biomedcentral.com)
  • Dominant, very active loci have a higher proportion of rRNA genes with unmethylated cytosine residues in comparison with recessive and inactive loci. (ncsu.edu)
  • Ribosomal RNA genes at different nucleolar organizer (NOR) loci in hexaploid wheat are expressed at different levels. (ncsu.edu)
  • The degree of expression of a particular organizer depends on the genetic background, especially on the presence of other NOR loci. (ncsu.edu)
  • Here, we show that rRNA genes at dominant loci are organized in a chromatin conformation that renders them more sensitive to DNase I digestion than other rRNA genes. (ncsu.edu)
  • We show that nuclear targeting is regulated by environmental signals and that KGDH is enriched at thousands of loci in Arabidopsis thaliana. (bvsalud.org)
  • Cohesin recruits the Esco1 acetyltransferase genome wide to repress transcription and promote cohesion in somatic cells. (genscript.com)
  • We are currently investigating how the SIN3 histone deacetylase complex functions to repress transcription at the epigenetic level. (wayne.edu)
  • The recently acquired genome sequence of globe artichoke (Cynara cardunculus var. (researchgate.net)
  • The same search parameters were applied to reveal the SSR content of 14 other plant species for which genome sequence is available. (researchgate.net)
  • Upon phosphorylation by the receptors, Smad complexes translocate into the nucleus, where they cooperate with sequence-specific transcription factors to regulate gene expression. (nih.gov)
  • The maintenance phase often involves a plethora of non-DNA sequence specific chromatin cofactors that set up and maintain chromatin states through cell division and for extended periods of time-sometimes in the absence of the initial transcription factors 3 . (nature.com)
  • ChIRP-seq of candidate lncRNAs revealed that lncRNA occupancy sites within the parasite genome are focal and sequence-specific with a particular enrichment for several parasite-specific gene families, including those involved in pathogenesis, erythrocyte remodeling, and regulation of sexual differentiation. (biorxiv.org)
  • Epigenetic marks are heritable DNA modifications that can influence gene expression without changing the DNA sequence. (frontiersin.org)
  • The proper copying and repair of DNA to maintain the correct sequence and structure of genomes is critical to the proper function of cells, and repair and replication is frequently disrupted in cancers and targeted by cancer treatments. (birmingham.ac.uk)
  • Although, the sequence of Chinese white pear genome (cv. (biomedcentral.com)
  • A protein consists of one or more chains of amino acids (called polypeptides) whose sequence is encoded in a gene. (genome.gov)
  • To understand the molecular basis of observed regional shifts in the genome types of adenovirus type 7 (Ad7) isolated in Korea during nationwide outbreaks from 1995 to 2000, the genetic variabilities of Ad7d and Ad7l were studied by sequence analysis of hexon, fiber, E3, and E4 open reading frame (ORF) 6/7 peptides. (cdc.gov)
  • Our data also provide evidence that the rapid divergence of Ad7d to a novel genome type Ad7l could have been due to viral strategies involving multiple sequence changes in E4. (cdc.gov)
  • Previously, sequence variations among the different genome types of Ad7 strains have been observed at 2 variable regions of the hexon gene and in a 14.9-kDa protein encoded by an ORF in the E3 region ( 6 , 14 ). (cdc.gov)
  • DNA microarrays exploit primary sequence data to measure transcript levels and detect sequence polymorphisms, for every gene, simultaneously. (medscape.com)
  • Gene expression must be appropriately maintained to regulate development, differentiation, and proliferation of cells. (intechopen.com)
  • However, the full promise of regenerative medicine has been difficult to achieve so far, partly due to our incomplete understanding of the genetic and epigenetic mechanisms regulating differentiation of stem cells to specific lineages and tissues. (confex.com)
  • Thus, my research interests are to develop novel single-cell genomics methods to better understand how changes in the epigenetic landscape during normal development regulates cellular differentiation, information that is critical towards realizing the full potential of regenerative medicine. (confex.com)
  • It possesses a unique forkhead domain combined with a fragment of the target gene to initiate transcription [ 10 ] and regulates various biological processes such as tumor cell differentiation, cell proliferation, and migration [ 11 ]. (hindawi.com)
  • Increasing evidence now suggests a major role for epigenetic mechanisms in gene expression in the parasite. (biorxiv.org)
  • Smooth muscle cell (SMC) phenotypic transition, which leads to the formation of various cell types in atherosclerotic plaques, is regulated by a network of genetic and epigenetic mechanisms and governs the risk of disease. (stanford.edu)
  • Further, while cell-to-cell heterogeneity in gene expression has been shown to drive dramatic phenotypic variations, the upstream epigenetic mechanisms regulating this heterogeneity remain largely unknown 8 . (confex.com)
  • Epigenetic mechanisms involved in prostate cancer include hypermethylation of tumor suppressor genes, general hypomethylation of the genome, and alterations in histone posttranslational modifications (PTMs). (oncotarget.com)
  • Molecular mechanisms of the initiation of transcription from TATA box have been well known as the most essential nuclear events in mammalian cells. (intechopen.com)
  • To better understand the role of short tandem repeats in gene expression, the researchers stripped the mechanisms down to their basics: transcription factors and naked DNA. (stanford.edu)
  • Here, we review recent insights into the biogenesis of eRNAs and the mechanisms underlying their multifaceted functions and consider how these findings could inform future investigations into enhancer transcription and eRNA function. (nature.com)
  • Molecular mechanisms for regulation of gene expression at different levels: remodeling of chromatin, initiation of transcription, nuclear transport and signalling, and RNA interference. (lu.se)
  • Mechanisms that regulate development from single cell to multicellular organisms. (lu.se)
  • By understanding the molecular details of this interaction, we can identify virulence-associated microbial genes and host-defense strategies and characterize the cues to which they respond and mechanisms by which they are regulated. (medscape.com)
  • Expression can be controlled by reversible post-translational modifications on histone amino acid tails, with complex cross-talk between modifications ( Kouzarides, 2007 ). (frontiersin.org)
  • We provide data showing that metformin epigenetically targets PCa by altering the levels and gene binding dynamics of histone variant H2A.Z. Moreover, we show that the increase in H2A.Z upon metformin treatment occurs preferentially due to H2A.Z.1 isoform. (oncotarget.com)
  • We found that the tricarboxylic acid cycle-associated enzyme α-ketoglutarate (α-KG) dehydrogenase (KGDH) entered the nucleus, where it interacted with various JMJs to regulate α-KG-dependent histone demethylations by JMJs, and thus controlled genome-wide gene expression in plants. (bvsalud.org)
  • Unexpectedly, we also find that CpG islands are occupied by low levels of PRC1 throughout the genome, suggesting that the KDM2B-PRC1 complex may sample CpG island associated genes for susceptibility to polycomb mediated silencing. (nih.gov)
  • These results suggest that genetic variations in TNF, TGFB1, PTGS1 and PTGS2 genes contribute to DA susceptibility. (cdc.gov)
  • In addition, using ASE to identify differentially expressed genes (referred to as AS-DEGs) enables the elimination of many confounding factors (including the environmental, batch, compositional, and developmental timing effects mentioned above). (biomedcentral.com)
  • Conclusions: In summary, this genome-wide identification, characterization and expression analysis of legume bZIP genes provides valuable information for understanding the molecular functions and evolution of the legume bZIP transcription factor family, and highlights potential legume bZIP genes involved in regulating tissue development and abiotic stress responses. (datadryad.org)
  • These rhythmic processes are believed to be driven by endogenous molecular clocks that regulate rhythmic expression of clock-controlled genes (CCGs). (nih.gov)
  • We utilize a combination of biochemical, molecular and genetic techniques to understand the mechanism of SIN3 gene regulation. (wayne.edu)
  • As a result, comparing gene expression between species can enable the identification of molecular changes underlying phenotypic divergence. (biomedcentral.com)
  • Both epidemiologic and molecular evidence strongly suggest that unique patterns of genome type shifts are restricted to geographic areas. (cdc.gov)
  • This study was undertaken to determine genetic differences and to understand the molecular basis of regional shifts observed in the genome types of Ad7 isolated in Korea. (cdc.gov)
  • Gene technology: basic and applied molecular genetic methods. (lu.se)
  • Similarly, by using host gene microarrays, one can explore host response at the level of gene expression and provide a molecular description of the events that follow infection. (medscape.com)
  • The pace of gene discovery rapidly accelerates, but its potential for explaining life at the molecular level remains largely unrealized because our understanding of gene function lags increasingly far behind. (medscape.com)
  • His interests include Bordetella molecular pathogenesis and gene expression bioinformatics. (medscape.com)
  • KaiA was discovered while studying the clock mutations in Synechococcus by using bacteria luciferase as a reporter on clock controlled gene expression. (wikipedia.org)
  • We are investigating the impact of specific classes of gene mutations, such as ATM, BRCA1, and MYBL2 on genome integrity. (birmingham.ac.uk)
  • Similarly, in specific cases, such as cancers, viral infections and in certain cell-types during normal development, mutations and other structural variations within the genome also influences cellular functions. (confex.com)
  • To investigate the biological role of these RSV G gene mutations, recombinant RSV strains harboring either a wild type A2 strain G gene (one stop codon preceding a wild type gene end signal), an A4G gene end signal preceded by one stop codon, or the 2stop+A4G virulence-associated combination were generated and characterized. (cdc.gov)
  • The researchers concluded that the transcription factors directly interact with the repetitive genetic code, attaching to it and the motif with the DNA binding domain. (stanford.edu)
  • The authors aim to reveal at least one novel genetic pathway, which possibly regulates the key transcription factor. (healthjockey.com)
  • Because tissues are composed of several cell-types and even cells within the same cell-type have been shown to display dramatic cell-to-cell variability in gene expression, bulk measurements obscure quantification of how genetic or epigenetic features directly influence the function of individual cells. (confex.com)
  • 90% of Your Genome Is Junk, by Laurence A. Moran, 2023. (blogspot.com)
  • The April 28, 2023 issue of science contains eleven papers reporting the results of a massive study comparing the genomes of 240 mammalian species. (blogspot.com)
  • The homeobox transcription factor HOXC13 upregulates human papillomavirus E1 gene expression and contributes to viral genome maintenance. (nih.gov)
  • The vertebrate genome encodes many ligands, fewer type II and type I receptors, and only a few Smads. (nih.gov)
  • Transcription of the wheat chloroplast gene that encodes the 32 kd polypeptide. (ncsu.edu)
  • The AR1 gene, which encodes the TGMV coat protein, was transcribed transiently in leaf discs after agroinoculation of TGMV A DNA. (ncsu.edu)
  • While each DNA blueprint, or gene, encodes for a different machine or structure, the genome, the collection of DNA wrapped up inside the nucleus, is much more active than a quiet library of neatly stacked blue-prints. (birmingham.ac.uk)
  • Dr. Cong's group is developing novel genome technology for genome engineering and single-cell genomics, leveraging scalable computational methods. (stanford.edu)
  • Genome type Ad7l was described as a novel genome type and was found to be closely related to Ad7d based on unique Bam HI restriction patterns ( 9 ). (cdc.gov)
  • In Korea, genome type Ad7d was predominantly observed at the beginning of the 1995-1997 epidemic, but it was rapidly replaced by a novel genome type Ad7l from 1998 to 2000 ( 9 ). (cdc.gov)
  • Schoenfelder, S. & Fraser, P. Long-range enhancer-promoter contacts in gene expression control. (nature.com)
  • A promoter level mammalian expression atlas. (riken.jp)
  • The bacterial genes encoding chloramphenicol acetyltransferase (CAT) and beta-glucuronidase (GUS) were transiently expressed in leaf discs from the AR1 promoter in TGMV A. The levels of AR1 and GUS RNAs were similar in leaf discs after adjusting for viral DNA copy number, while CAT RNA was less abundant. (ncsu.edu)
  • During evolution, CpG rich regions, so-called CpG islands, have been established as prominent features of promoter regions of genes. (caister.com)
  • Methods for analysis of gene expression: microarray, hybridisation, promoter analyses. (lu.se)
  • Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, which are located on different chromosomes and consist of 9 to 11 genes arranged in tandem. (nih.gov)
  • In this study, 20 GRF gene members of ginseng were systematically identified and found to be distributed on 13 chromosomes. (biomedcentral.com)
  • The ginseng GIF gene family has only ten members, which are distributed on ten chromosomes. (biomedcentral.com)
  • Autosomal" means that the gene in question is located on one of the numbered, or non-sex, chromosomes. (genome.gov)
  • Genes are contained in chromosomes in the cell nucleus and mitochondria. (msdmanuals.com)
  • The 23rd pair, the sex chromosomes (X and Y), determines a person's sex as well as containing other functional genes. (msdmanuals.com)
  • Genes are arranged linearly along the DNA of chromosomes. (msdmanuals.com)
  • Each gene has a specific location (locus), which is typically the same on each of the 2 homologous chromosomes. (msdmanuals.com)
  • Some genes occur in multiple copies that may be next to each other or in different locations in the same or different chromosomes. (msdmanuals.com)
  • Cellular identity is now accepted to be the result of the expression of specific combinations of genes (Fig. 1 ). (nature.com)
  • Genes near constrained elements perform fundamental cellular processes, whereas genes near primate-specific elements are involved in environmental interaction, including odor perception and immune response. (blogspot.com)
  • The activated RR can then effect changes in cellular physiology, often by regulating gene expression. (genome.jp)
  • Nuclear Receptors (NRs), that include steroid hormone receptors, are intra-cellular transcription factors that regulate gene expression in response to their cognate ligands. (jnu.ac.in)
  • These short RNAs participate in a diverse array of cellular processes including gene regulation, chromatin dynamics and genome defense. (biomedcentral.com)
  • To understand how the genome and epigenome regulates cellular function, development of high-throughput sequencing methods, known as next-generation sequencing, are beginning to unravel genome-wide correlations between the genome, epigenome and transcriptome within a large population of cells or tissues. (confex.com)
  • For the adaptation of cyanobacteria, circadian clock genes exhibit forms of significant importance since they regulate fundamental physical processes such as regulation of nitrogen fixation, cell division, and photosynthesis. (wikipedia.org)
  • This expression pattern must be established and maintained-two distinct, but connected, processes. (nature.com)
  • Genome condensation and packaging are essential processes in the life cycle of viruses. (mdpi.com)
  • Within the genome, many processes occur almost simultaneously so that the regulation of possibly chaotic access is tightly controlled. (birmingham.ac.uk)
  • We examine the impact that processes such as transcription and replication have on genome stability. (birmingham.ac.uk)
  • The basic helix-loop-helix (bHLH) transcription factors play important roles in many processes in plant growth, metabolism and responses to abiotic stresses. (biomedcentral.com)
  • Using the reference-free alignment across 241 mammalian genomes produced by the Zoonomia Consortium, we charted evolutionary trajectories for 0.92 million human candidate cis-regulatory elements (cCREs) and 15.6 million human transcription factor binding sites (TFBSs). (blogspot.com)
  • Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis -regulatory evolution. (nature.com)
  • The change in expression can occur due to the gene being moved to a new location (as in chromosomal translocation), or due to changes in nearby genes or regulatory regions. (definitions.net)
  • Measuring allele-specific expression in interspecies hybrids is a powerful way to detect cis- regulatory changes underlying adaptation. (biomedcentral.com)
  • As a result, allele-specific differences in gene expression can only be explained by cis- regulatory differences. (biomedcentral.com)
  • Therefore, investigating the expression and regulation of miRNAs may elucidate the mechanism of gastric cancer. (hindawi.com)
  • genomes may elucidate genes that are unique to those species of spirochetes associated with ticks. (cdc.gov)
  • We further validated the function of one specific lncRNA (lncRNA-ch14) using the CRISPR-Cas9 genome editing tool. (biorxiv.org)
  • His work has led to one of the first CRISPR/Cas9 gene-editing tools for in vivo gene therapy. (stanford.edu)
  • Furthermore, large-scale CRISPR-Cas9-based screening identified that the Akt/MAPK signaling pathway regulated bursting kinetics by modulating transcription elongation efficiency. (janelia.org)
  • Dvornyk performed phylogenetic analysis of kai genes and found that the kai genes have different evolutionary histories the feedback loop that kaiA is in evolved about 1,000 Mya. (wikipedia.org)
  • PCC7942 has kaiA whereas P.marinus does not, even though they are closely related unicellular organisms, further demonstrating the evolutionary youth of the kaiA gene. (wikipedia.org)
  • Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. (nature.com)
  • Dangshansuli') has already been reported, there is still a lack of clarity regarding the bHLH family genes and their evolutionary history. (biomedcentral.com)
  • However, genes with large and significant fold changes may often have low evolutionary constraint on expression level. (biomedcentral.com)
  • Bacteria often can't support over-expression needed to get workable quantities of protein for an assay, and in vitro expression often can't synthesize a fully functional transcription factor. (genomeweb.com)
  • The FANTOM project (for Functional Annotation of the Mammalian genome) is a RIKEN initiative launched in 2000 to build a complete library of human genes using the capabilities offered by new, state-of-the-art cDNA technologies. (riken.jp)
  • In this work, a genome-wide identification of the bHLH genes in Chinese white pear was performed, and we characterized the functional roles of these PbrbHLH genes in response to abiotic stresses. (biomedcentral.com)
  • A gene, the basic unit of heredity, is a segment of DNA containing all the information necessary to synthesize a polypeptide (protein) or a functional RNA molecule. (msdmanuals.com)
  • The eukaryotic epigenome is postulated to respond to environmental stimuli through alterations in chromatin features and, ultimately, gene expression. (biomedcentral.com)
  • My graduate and postdoctoral research has focused on investigating how the genome and epigenome regulates the dynamics of gene expression in viral and mammalian systems 8 . (confex.com)
  • In this study, the researchers combined a novel in vitro protocol adapted for studying estrogen deprivation and re-stimulation with the latest epigenomics and bioinformatics tools, which enabled a genome-wide interrogation of the epigenome and transcriptome changes. (who.int)
  • A putative function has been assigned, using the gene ontology approach, to the set of genes harboring at least one SSR. (researchgate.net)
  • Deplancke himself wondered whether this was a scalable technology, or whether it would only be useful to labs interested in transcription factor function. (genomeweb.com)
  • Plank, J. L. & Dean, A. Enhancer function: mechanistic and genome-wide insights come together. (nature.com)
  • The results of this study may be helpful for further study of the function of PgGRF and PgGIF genes and lay a foundation for further study of their role in the growth and development of Panax ginseng . (biomedcentral.com)
  • The genome of the geminivirus tomato golden mosaic virus (TGMV) consists of two circular DNA molecules designated as components A and B. The A component contains the only virally-encoded function required for autonomous replication in infected plant cells. (ncsu.edu)
  • This tool helped then to analyze a dozen genes that affect the function of a protein, vital for glioma cells to grow. (healthjockey.com)
  • For example, even in the heavily studied Escherichia coli, no function has been assigned to more than one third of its genes [ 1 ] . (medscape.com)
  • Global profiling of gene expression is one attractive approach to assessing function. (medscape.com)
  • Because a gene is usually transcribed only when and where its function is required, determining the locations and conditions under which a gene is expressed allows inferences about its function. (medscape.com)
  • Several independent high-throughput methods for differential gene expression (including SAGE and differential display) may enable function annotation of sequenced genomes [ 2 ] . (medscape.com)
  • The WRC domain can be combined with the cis-acting regions of downstream genes to regulate their expression. (biomedcentral.com)
  • KaiA genes are also found in the genomes of the species of the kaiC subtree, in younger clades than Prochlorococcus. (wikipedia.org)
  • Tapryal N., Mukhopadhyay C., Das D., Fox P.L., and Mukhopadhyay C.K. Reactive oxygen species regulate ceruloplasmin by a novel mRNA decay mechanism involving its 3'-untranslated region: Implications in neurodegenerative diseases. (jnu.ac.in)
  • However, it remains difficult to identify genes most likely to explain species-specific traits. (biomedcentral.com)
  • Here, we outline a simple strategy that leverages population-scale allele-specific RNA-seq data to identify genes that show constrained cis- regulation within species yet show divergence between species. (biomedcentral.com)
  • In hybrids, the genomes of both species share the same nucleus and are exposed to identical environments, so there are no confounding environmental, batch, compositional, or developmental effects. (biomedcentral.com)
  • Therefore, a large and significant fold change alone is not sufficient to determine the importance of the gene in the evolution of the parental species. (biomedcentral.com)
  • For example, consider a gene whose expression varies by two-fold between species. (biomedcentral.com)
  • In contrast, a gene that is under strong stabilizing selection-with little variation in expression within species but with a two-fold change between species-is more likely to have contributed to phenotypic divergence between species. (biomedcentral.com)
  • We've known for a while that short tandem repeats, or STRs, aren't junk because their presence or absence correlates with changes in gene expression," Fordyce said. (stanford.edu)
  • Here, we profile the gut microbiome and chromatin characteristics in colon epithelium from mice fed either an obesogenic or control diet, followed by an analysis of the resultant changes in gene expression. (biomedcentral.com)
  • Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. (nature.com)
  • Many of these changes occur within so-called enhancer regions of DNA that are known to regulate gene transcription and are associated with specific chromatin configuration. (who.int)
  • it was induced by GA3 (gibberellin) [ 3 ] and played an essential role in regulating stem elongation. (biomedcentral.com)
  • The results illustrate a complex set of interactions regulating expression of the nuclear and chloroplast genomes. (ncsu.edu)
  • The gradual conversion from endosymbiont to organelle during the course of evolution has clearly been accompanied by a dramatic reduction in genome size as the chloroplasts lost most of their genes to the nucleus. (frontiersin.org)
  • Nuclear and cytoplasmic mRNAs for several phytochrome-regulated genes were examined in Pisum seedlings in order to investigate possible light effects on mRNA partitioning between the nucleus and cytoplasm. (ncsu.edu)
  • Based on the available public RNA-Seq data, the expression patterns of PgGRF and PgGIF genes were analysed from 14 different tissues. (biomedcentral.com)
  • Patterns of phytochrome-induced gene expression in etiolated pea buds. (ncsu.edu)
  • Particularly interesting were the distinctive patterns of circulating genome types during the Ad7 epidemic in Korea and in 3 neighboring countries, China, Taiwan, and Japan. (cdc.gov)
  • Mobile DNA elements and the dynamics of genomes. (lu.se)
  • GRF genes are usually expressed at higher levels in young tissues but at lower levels in mature tissues [ 6 ]. (biomedcentral.com)
  • After many years of concerted effort to systematically analyze the expression of genes in all human cells and tissues, RIKEN and the FANTOM consortium publish the findings today in two landmark Nature reports, and 16 related articles in ten other scholarly journals (ref.1,2,3). (riken.jp)
  • Expression data further revealed that the legume bZIP genes were expressed constitutively or in an organ-specific, development-dependent manner playing roles in multiple seed developmental stages and tissues. (datadryad.org)
  • qRT-PCR was used to detect the expression of miRNA-149 and FOXC1 in gastric cancer tissues and cells. (hindawi.com)
  • One CCGG site 164 base-pairs upstream from the start of transcription is preferentially unmethylated in some genes. (ncsu.edu)
  • The difference between all these cells is what parts of the genome they use - for instance, brain cells use different genes than liver cells, and therefore they work very differently. (riken.jp)
  • In silico analysis of available array data showed that a large number of genes traditionally classified as PEP dependent genes are transcribed during early embryo development from the pre-globular stage to the mature-green-stage. (frontiersin.org)
  • The product of this gene may play a role in the development of hair, nail, and filiform papilla. (nih.gov)
  • Noncoding RNAs (ncRNAs) direct a remarkable number of diverse functions in development and disease through their regulation of transcription, RNA processing and translation. (nature.com)
  • These findings will help in the identification of genes involved in disease and the development of personalized and regenerative medicine. (riken.jp)
  • We recently discovered new ways the BRCA1 gene functions which could help expand our understanding of the development of ovarian and breast cancers. (birmingham.ac.uk)
  • Several studies have confirmed that miRNA can be used as an oncogene or tumor suppressor gene to regulate the occurrence and development of gastric cancer [ 6 ]. (hindawi.com)
  • Dr. Martin has also conducted research on the effect of environmental perturbations and their effects on gene expression and embryonic development. (sgu.edu)
  • Dr. Martin's journal review activities include peer reviewed journals Genome, Genes & Development, Transgenic Research, and GENE. (sgu.edu)
  • 2001). Expression of the chaperonin 10 gene during zebrafish development . (sgu.edu)
  • Transient expression of heterologous RNAs using tomato golden mosaic virus. (ncsu.edu)
  • The geminivirus transient expression system allows rapid analysis of RNAs transcribed from foreign genes and can serve as a preliminary screen in the construction of transgenic plants. (ncsu.edu)
  • Discovery of Transacting Long Noncoding RNAs That Regulate Smooth Muscle Cell Phenotype. (stanford.edu)
  • As part of the genome sequencing initiative for the tammar, we have explored the evolution of each of the major classes of mammalian small RNAs in an Australian marsupial for the first time, including the first genome-scale analysis of the newest class of small RNAs, centromere repeat associated short interacting RNAs (crasiRNAs). (biomedcentral.com)
  • This study encompasses the first analyses of the major classes of small RNAs for the newly completed tammar genome, validates preliminary annotations using deep sequencing and computational approaches, and provides a foundation for future work on tammar-specific as well as conserved, but previously unknown small RNA progenitors and targets identified herein. (biomedcentral.com)
  • The first class of small RNAs identified were the micro RNAs (miRNAs), which are small (~22 nt) non-coding RNAs that regulate gene expression by base pairing to mRNAs where they direct either mRNA cleavage or repress translation [ 8 ]. (biomedcentral.com)
  • MicroRNAs (miRNAs) are noncoding RNAs of approximately 22 nucleotides, which are key regulators of gene expression [ 4 ]. (hindawi.com)
  • Together, the findings reveal that Smad3 expression in SMC inhibits the emergence of specific SMC phenotypic transition cells that mediate adverse plaque features, including outward remodelling, monocyte recruitment, and vascular calcification. (stanford.edu)
  • These large fold changes in unconstrained genes (e.g., pseudogenes) could result in no or very limited phenotypic changes, since a lack of constraint implies a lack of phenotypic consequence of changes in expression. (biomedcentral.com)
  • We used agroinoculation of petunia leaf discs with the A component to develop a transient expression system which permits direct examination of viral transcripts by S1 nuclease protection. (ncsu.edu)
  • We have found that at least 85 kb of the 120 by pea chloroplast genome is represented as detectable transcripts. (ncsu.edu)
  • Nuclear-Cytoplasmic Partitioning of Phytochrome-Regulated Transcripts in Pisum sativum. (ncsu.edu)
  • Transcripts from each of five light-regulated genes exhibited different responses to a variety of light treatments, but for each transcript we observed a characteristic linear relationship between nuclear and cytoplasmic levels over a wide range of total transcript abundance. (ncsu.edu)
  • Analysis for differential expression revealed 1656 gene transcripts with significant changes in expression levels during myogenesis. (au.dk)
  • Based on the phylogenetic analysis and structural characteristics, 197 identified bHLH genes could be well classified into 21 groups. (biomedcentral.com)
  • The first high-quality genome assembly of the globe artichoke has been produced within the Compositae Genome Project and the resequencing analyses of four globe artichoke genotypes, representative of the core varietal types, as well as a genotype of the related taxa cultivated cardoon was, later on, carried out. (researchgate.net)