• The PGC Network and Pathway Analysis Subgroup analyzed genome-wide data from more than 60,000 people. (nih.gov)
  • Researchers of the Psychiatric Genomics Consortium (PGC) reported the findings of the first large genome-wide study focusing on biological pathways, January 19, 2015 in the journal Nature Neuroscience . (nih.gov)
  • The "teach the teachers" approach, adds Nakonechny, is an efficient way to bring greater understanding of the basics of genomics-molecular biology techniques, use of genome databases, and social, ethical and legal issues-to public schools. (jax.org)
  • With genomics techniques, it's possible to survey the entire genome at a very high molecular resolution, but most of the time you can only measure things in bulk, averaged over thousands or millions of cells. (embl.org)
  • Over the next five years, as microscopes reach higher resolution and genomics moves to single-cell methods for studying genome regulation, these two views will merge. (embl.org)
  • This project combines the use of state-of-the-art functional genomics, genome editing, and biochemistry. (ircm.qc.ca)
  • We will cover the challenges of genome annotation, comparative genomics, and informatic approaches to understanding evolution and function. (manchester.ac.uk)
  • Lectures begin with an introduction to the post genome world, then briefly covering recent advances in genome sequencing technology, followed by genome annotation and comparative genomics. (manchester.ac.uk)
  • These chips are frequently used in the analysis of gene expression profiles to detect diseases, biomarkers, and therapeutic responses in the fields of molecular biology, biomedical research, and genomics. (grandviewresearch.com)
  • Our lab uses a combination of high-throughput, functional genomics, bioinformatics and molecular approaches to study the co-transcriptional gene regulation of mammalian expression programs. (bu.edu)
  • Understanding how alternative RNA-processing events influence gene expression is of particular importance in cancer genomics, as their aberrant regulation contributes to the ~10 million cancer-related deaths each year. (bu.edu)
  • Comparative genomics of plants, organelles, and plant gene families. (psu.edu)
  • In genomics specifically, the completion of the Human Genome Project, the HapMap project, and hundreds of genome-wide association studies have not directly resulted in new FDA-approved tests or therapies. (genengnews.com)
  • The Myers lab focuses on using genomics tools and genetics to understand how changes in gene expression contribute to human health and disease, as well as to basic biological processes. (hudsonalpha.org)
  • Research in the past two decades has shown that the nuclear envelope is a complex cellular compartment, which harbors tissue-specific resident proteins, extensively interacts with chromatin and contributes to spatial genome organization and regulation of gene expression. (nih.gov)
  • They recruit chromatin that has been modified with specific epigenetic marks, provide silencing factors that add new epigenetic modifications to genes located at the nuclear periphery, and sequester transcription factors away from the nuclear interior. (nih.gov)
  • On the other hand, proteins of the nuclear pores anchor as well as help generate active chromatin, promote transcription, and coordinate gene expression with mRNA export. (nih.gov)
  • The importance of these functions is underscored by aberrant distribution of peripheral chromatin and changes in gene expression that occur in cancer and heritable human diseases linked to mutations in nuclear envelope proteins. (nih.gov)
  • Chromatin domains, insulators, and the regulation of gene expression. (nih.gov)
  • In a more practical sense, epigenetics includes the study of the protein constituents of chromatin, the interaction of microRNAs with the genome, and the protein and DNA modifications that appear to define biologic states in local regions of chromosomes. (nih.gov)
  • In a sense, the chromosome contains two intertwined types of information: the linear sequence of nucleotide bases in DNA codes for biologic macromolecules, and the regulatory information embedded in the nucleoprotein architecture of chromatin specifies which regions of the genome are active in any given cell. (nih.gov)
  • The genome is enclosed within the nucleus by the nuclear envelope membrane, which contains a set of proteins that actively participate in chromatin organization and gene regulation. (nih.gov)
  • In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. (nih.gov)
  • Also available to Connecticut-area researchers are a symposium on the new field of immunogenomics and a course on new, 3-D genome mapping technology (charmingly known as ChIA-PET, for Chromatin Interaction Analysis by Paired-End Tag Sequencing). (jax.org)
  • Yon utilizes cell biology assays, CRISPR genome editing and next-generation sequencing (NGS) techniques to gain insights into the regulation of 3D chromatin. (nih.gov)
  • A new technique called immunoGAM, which combines genome architecture mapping (GAM) with immunoselection, enabled the discovery of specialized chromatin conformations linked to gene expression in specific cell populations from mouse brain tissues. (nature.com)
  • The organization of chromatin in the nucleus plays an essential role in gene regulation. (biomedcentral.com)
  • As a result, we only have a partial understanding of how transposons contribute to chromatin folding and how they impact gene regulation. (biomedcentral.com)
  • We are doing genome-wide analyses of receptor and other transcription factor cistromes (chromatin binding sites by ChIP-Seq) and transcriptomes (gene expression, miRNAs, other RNAs by RNA-Seq) and are examining the bidirectional cross-talk between nuclear hormone receptors and cell signaling pathways. (illinois.edu)
  • Biological processes are regulated at multiple levels ranging from chromatin remodeling for gene expression regulation, to specific localization of enzymes for metabolic regulation. (imsc.res.in)
  • This includes showing that spindle positioning is controlled by heterotrimeric G protein signalling, discovering a connection between chromatin marking and mRNA splicing, and most recently revealing mechanisms and principles of genome organisation and gene expression regulation. (cam.ac.uk)
  • Scholars@Duke publication: A compendium of promoter-centered long-range chromatin interactions in the human genome. (duke.edu)
  • To bridge this gap, we generate maps of long-range chromatin interactions centered on 18,943 well-annotated promoters for protein-coding genes in 27 human cell/tissue types. (duke.edu)
  • The candidate will integrate our group 'Physical Biology of Chromatin' that mainly focuses on understanding the fundamental bases of chromatin and gene regulation using physical modeling and computational approaches within a strong interdisciplinary environment. (ens-lyon.fr)
  • 10. Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2. (nih.gov)
  • 14. Unfolding SARS-CoV-2 viral genome to understand its gene expression regulation. (nih.gov)
  • This region of the viral genome encodes a series of related proteins with multifunctional capabilities. (bdbiosciences.com)
  • Two viral oncogenes, E6 and E7, are responsible for papillomaviral carcinogenesis and are highly expressed from the integrated viral genome. (cancer.gov)
  • Insulin promoter in human pancreatic β cells contacts diabetes susceptibility loci and regulates genes affecting insulin metabolism. (nih.gov)
  • Since there are nearly 5 million RE loci across the mammalian genome, the group is currently working to determine how many genes have patterns of expression that are influenced by adjacent REs. (nih.gov)
  • We identified 11 203 potential cis-acting CpG loci whose degree of methylation was associated with gene expression (eMS) at a false discovery rate threshold of 0.001. (cdc.gov)
  • Whereas DNA methylation patterns are generally inherited during replication, both embryonic and somatic differentiation processes require the removal of cytosine methylation at specific gene loci to activate lineage-restricted elements. (biomedcentral.com)
  • After being produced, the stability and distribution of the different transcripts is regulated (post-transcriptional regulation) by means of RNA binding protein (RBP) that control the various steps and rates controlling events such as alternative splicing, nuclear degradation (exosome), processing, nuclear export (three alternative pathways), sequestration in P-bodies for storage or degradation and ultimately translation. (wikipedia.org)
  • Risk genes for different mental disorders affect the same biological pathways, a new and powerful analysis of genome-wide data has found. (nih.gov)
  • People with schizophrenia, bipolar disorder and depression shared genetic risk affecting pathways for a key gene expression regulation mechanism, the immune system, and neuronal communication. (nih.gov)
  • It turned out that disorders that share a typical age-of-onset, with symptoms first appearing in young adulthood , also shared the same risk gene pathways. (nih.gov)
  • Genes that confer risk for schizophrenia, bipolar disorder, and depression most strongly work through pathways involved in the process of histone methylation, an epigenetic mechanism that regulates the switching on-or-off of genes in response to environment and experience. (nih.gov)
  • Risk genes also were found to work via pathways involved in the communication between brain cells, and through effects on the immune system - which other lines of evidence have recently implicated in susceptibility to psychological stress and mood disorders. (nih.gov)
  • Moving beyond identification of individual risk genes to understanding of the pathways through which they work to cause illness moves the field closer to pinpointing new biological targets for future treatments, say the researchers. (nih.gov)
  • Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways. (nih.gov)
  • A total of eight main Kyoto Encyclopedia of Genes and Genomes pathways were identified, the top three of which were hematopoietic cell lineage, focal adhesion, and regulation of actin cytoskeleton. (cancerindex.org)
  • Similarly, DHT exerted a significant, but primarily cell-specific, influence on many gene ontologies and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. (molvis.org)
  • to this end, we investigate the effects of DNA repair pathways on the formation of episomal HIV-1 vector forms and the mechanisms, which down regulate transgene expression from non-integrated vectors. (unc.edu)
  • Integrative analysis of these promoter-centered interactome maps reveals widespread enhancer-like promoters involved in gene regulation and common molecular pathways underlying distinct groups of human traits and diseases. (duke.edu)
  • What pathways are this gene/protein implicaed in? (cancerindex.org)
  • These genes were enriched in RNA processing pathways and encoded ~100 SFs, e.g. hnRNPA1. (iscb.org)
  • Using purified primary monocytes from subjects in a large community-based cohort (n = 1264), we characterized methylation (>485 000 CpG sites) and mRNA expression (>48K transcripts) and carried out genome-wide association analyses of 8370 expression phenotypes. (cdc.gov)
  • Our findings can be used to augment gene expression profiling analyses in the distantly related yeast Schizosaccharomyces pombe and a human cancer cell model. (biorxiv.org)
  • 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)
  • Our studies involve detailed biochemical and structure-function analyses of the receptors (and of mutant receptor forms) and coregulators and their gene interactions, and examination of their biological activities in normal and cancer, in particular breast cancer, cells and tumors. (illinois.edu)
  • Analyses for target genes of the identified miRNAs will follow. (usda.gov)
  • In short, the dsRNA sequences, which will be broken down into siRNA inside of the organism, will match up with the RNA to inhibit the gene expression in the cell. (wikipedia.org)
  • Although much effort has focused on the gene-environment axis, there is a growing body of information that suggests that environmental influences may extend beyond the DNA sequences of our genes. (nih.gov)
  • We have previously shown that human virus genomes are enriched in G-rich sequences that fold in four-stranded nucleic acid secondary structures, the G-quadruplexes.Here, by extensive bioinformatics analysis on all available genomes, we showed that human viruses are enriched in highly conserved multiple A (and T or U) tracts, with such an array that they could in principle form quadruplex structures. (frontiersin.org)
  • We argue that, while in E. coli the gradient of DNA thermodynamic stability and gene order along the origin-to-terminus axis represent major organizational features orchestrating temporal gene expression, the genomic sequence organization of Dickeya is more complex, demonstrating extended chromosomal domains of thermodynamically distinct DNA sequences eliciting specific transcriptional responses to various kinds of stress encountered during pathogenic growth. (mdpi.com)
  • Yet, as more and more individuals learn about their genomes, the information these sequences contain cannot be understood or explained without reference to the basic ideas of genetics. (cshlpress.com)
  • Genome sequences allow us to peer back into our ancestry and assist doctors in tailoring treatments for whatever ails us. (cshlpress.com)
  • 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)
  • To improve transgene expression we use MLV/HIV-1 chimera vectors to identify and to remove cis sequences that down-regulate transgene expression from HIV-1 vectors. (unc.edu)
  • describe modern approaches to genome sequencing and annotation, and how genome sequences can be compared to gain biological understanding. (manchester.ac.uk)
  • We aim to build new computational tools to predict gene regulatory programs from genome sequences and gene architecture and design new strategies to manipulate gene expression with therapeutical purposes. (bu.edu)
  • We currently seek to understand three key aspects of gene regulation: (i) how promoter sequences drive RNA processing decisions, (ii) how transcription interferes with expression from nearby promoters, and (iii) how transcript starts and transcript ends are connected. (bu.edu)
  • A large number of putative cis-regulatory sequences have been annotated in the human genome, but the genes they control remain poorly defined. (duke.edu)
  • MicroRNAs (miRNAs) directly regulate gene expression post-transcriptionally through base-pairing with regions in the 3'-untranslated sequences of the target gene mRNAs. (usda.gov)
  • Slight modifications in their genome sequences play a crucial role in the conversion of pluripotent stem cells into various differentiated cell types. (uni-muenchen.de)
  • Which genes are activated and which are turned off is in part determined by a second tier of information which is superimposed on the nucleotide sequences that provide the blueprints for protein synthesis. (uni-muenchen.de)
  • Steady-state gene expression is a coordination of synthesis and decay of RNA through epigenetic regulation, transcription factors, micro RNAs (miRNAs), and RNA-binding proteins. (nih.gov)
  • These genome regulatory roles of proteins of the nuclear periphery have important influences on development, disease and ageing. (nih.gov)
  • A growing mouse oocyte, arrested at diplotene of its first meiotic prophase, transcribes and translates many of its own genes, thereby producing a store of proteins sufficient to support development to the 8-cell stage. (nih.gov)
  • Elena studies the involvement of two paralogous proteins, CTCF and BORIS/CTCFL in 3D genome organization, transcriptional regulation of gene expression, transgenerational epigenetic inheritance, and epigenetic resetting in normal and cancer cells. (nih.gov)
  • Like HPV E7 and SV40 large T antigen, E1A proteins can form a specific complex with the retinoblastoma tumor suppressor gene product (Rb protein). (bdbiosciences.com)
  • Proteomics follows this, explaining how the proteins encoded in the genome can be studied, and how they may be quantified and networks of interactions characterised. (manchester.ac.uk)
  • We are interested in understanding the biochemistry, physiology, and molecular biology of nuclear hormone (estrogen, progesterone) receptors, intracellular proteins that mediate the biological actions of these hormones in target cells, and the mechanisms by which these proteins regulate gene expression and the growth and functioning of target cells, especially cells of the reproductive system and mammary gland, and of tumors that develop in these tissues. (illinois.edu)
  • For instance, cancer involves altered gene expression, with the activation or silencing of several proteins significantly affecting cellular activity.In particular, the activation or silencing of genes can drastically alter the overall cellular activity. (grandviewresearch.com)
  • However, using an innovative method for the identification of factors capable of binding to and "reading" the chemical tags that characterize unconventional DNA bases, Carell and colleagues have shown that stem cells contain specific proteins that recognize hydroxymethyluracil, and could therefore contribute to the regulation of gene activity in these cells. (uni-muenchen.de)
  • Oncogenic HPV E6 and E7 destabilize cellular tumor suppressor proteins and induce aberrant expression of a subset of oncogenic and tumor-suppressive microRNAs (miRNAs) and long noncoding RNAs (lncRNAs). (cancer.gov)
  • Together, the HPV infection-induced degradation of host tumor suppressive proteins, aberrant expression of oncogenic and tumor-suppressive miRNAs and lncRNAs, and enhancement of SRp20 expression could be the major distinguishable mechanisms leading to the development of cervical cancer. (cancer.gov)
  • Gene regulation occurs at transcriptional, but particularly post-transcriptional levels, including RNA processing, nuclear export, mRNA stability and translation. (medscape.com)
  • The group is broadly interested in understanding the role of epigenomic transcriptional regulation in an organism's response to environmental exposures. (nih.gov)
  • Many of these elements have powerful regulatory elements and exhibit complex patterns of transcriptional expression throughout mammalian development. (nih.gov)
  • The inflammatory response in human cells involves rapid and dramatic changes in gene expression, and the Bru-Seq and BruChase-Seq techniques revealed a coordinated and complex regulation of gene expression both at the transcriptional and posttranscriptional levels. (nih.gov)
  • Post-transcriptional regulation is the control of gene expression at the RNA level. (wikipedia.org)
  • E1A regulates the transcriptional regulation of a wide variety of viral and cellular promoters. (bdbiosciences.com)
  • 2) Kaposi's sarcoma-associated herpesvirus (KSHV) gene expression and post-transcriptional regulation. (cancer.gov)
  • In KSHV lytic infection, the viral lytic gene ORF57 encodes a multifunctional, caspase-7-sensitive protein to regulate the expression of a subset of viral lytic genes at the post-transcriptional level. (cancer.gov)
  • The group is also examining the role of mitochondrial metabolism in the epigenetic regulation of genes, including REs, within the nuclear genome. (nih.gov)
  • Epigenetic regulation is a primary driving force behind the creation of different cell types, each with the DNA sequence, during development of multicellular organisms. (nih.gov)
  • Given the importance of epigenetic regulation to normal nuclear function, it is pertinent to ask whether alterations in this form of regulation might impact disease. (nih.gov)
  • Epigenetic regulation and allele specific patterns. (psu.edu)
  • These REs are distributed across the entire genome and are highly abundant. (nih.gov)
  • Many of these procedures simultaneously measure the entire genome, or all the genes in a particular cell.Expression profiling experiments often involve measuring the relative amount of mRNA expressed in two or more experimental conditions. (grandviewresearch.com)
  • This Focus issue includes Review articles and comments that discuss how mechanical forces are transduced into the cell, including into the nucleus, to control gene expression and to regulate morphogenesis, tissue regeneration and tumorigenesis. (nature.com)
  • As an interesting fact, there are some mechanisms that attack this nuclear export process to regulate gene expression. (wikipedia.org)
  • Our findings support our hypothesis that androgens regulate gene expression in human meibomian gland and conjunctival epithelial cells. (molvis.org)
  • MicroRNAs also indirectly regulate gene expression through regulation of other epigenetic factors. (usda.gov)
  • This study aims to understand how RNA splicing and small regulatory RNAs regulate the expression of viral and host genes in viral carcinogenesis. (cancer.gov)
  • Moving from a small to whole genome metabolic modeling, I will present our work focusing on analyzing gut microbial metabolic models for post-biotic production abilities. (imsc.res.in)
  • But how are those not trained in genetics supposed to understand how genomes work? (cshlpress.com)
  • Completion of DNA sequencing of each genome presents opportunities for novel insights into genomic function, the regulation of gene expression, and evolutionary processes. (nih.gov)
  • The workshop title, " Teaching the Genome Generation ™," sums up much of Tom Litwin's grand plan for JAX Genomic Medicine's educational programs. (jax.org)
  • Recent studies strongly suggest that in bacteria, both the genomic pattern of DNA thermodynamic stability and the order of genes along the chromosomal origin-to-terminus axis are highly conserved and that this spatial organization plays a crucial role in coordinating genomic transcription. (mdpi.com)
  • Use bioinformatics webtools and software to investigate example genomic datasets in the context of genomes. (manchester.ac.uk)
  • Genomic products capture a large share of these funds thanks to a steady stream of high-profile projects such as the 1000 Genomes Project, the Cancer Genome Project, the Human Microbiome Project, an anticipated wave of genome-wide association studies, and the potential for large-scale de novo sequencing projects. (genengnews.com)
  • Genome centers and genomic service providers across the globe were first to jettison fleets of traditional sequencing instruments in favor of NGS' low cost per data point. (genengnews.com)
  • Greg Cooper, PhD, researches the structures, functions and evolutionary histories of human genomes, with an emphasis on applying genomic approaches to study human disease. (hudsonalpha.org)
  • Jane Grimwood, PhD, co-directs the Genome Sequencing Center at HudsonAlpha, managing one of the few centers in the world that produces, analyzes, and interprets genomic data on economically important plant species to improve crop breeding and other agricultural practices. (hudsonalpha.org)
  • In fact, it has been estimated that REs comprise more than 50 percent of a typical mammalian genome. (nih.gov)
  • 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)
  • Recent genome-wide studies revealing overlap in genetic risk that cuts across mental disorders hinted at shared biological processes, such as the workings of certain ion channels, but didn't systematically focus on these. (nih.gov)
  • Using a new statistical technique called "genetic pathway analysis," they pinpointed processes through which risk genes cause illness across diagnostic categories. (nih.gov)
  • Using light microscopy you can look at a single cell and observe the dynamics of these processes, but you can only study a few regions of the genome at a time and only ones that are spaced far enough apart in the nucleus. (embl.org)
  • 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)
  • Her research has illuminated our understanding of the processes underlying cell polarity and gene expression. (cam.ac.uk)
  • Gene expression regulation is critical for all cellular processes since dysregulation of it often results in elevated disease risk and compromised cellular immunity. (usda.gov)
  • Richard Woychik, Ph.D., is Director of NIEHS & NTP and head of the Mammalian Genome Group. (nih.gov)
  • All mammalian genomes are comprised of a large assortment of different classes repetitive elements (REs) that include LINE's, intracisternal A particles (IAPs), VL30 elements, endogenous retroviral elements (ERVs), SINEs, transposons, and various other types of repetitive elements. (nih.gov)
  • About half of the mammalian genome comprises transposable elements. (biomedcentral.com)
  • The architecture of mammalian genes enables the production of multiple transcripts by using alternative promoters, alternative termination sites, and differentially spliced exons, which greatly expand the coding capacity of our genomes. (bu.edu)
  • Indeed, alternative structures have been identified in the genome of several microorganisms ( Saranathan and Vivekanandan, 2019 ), including viruses ( Ruggiero and Richter, 2020 ). (frontiersin.org)
  • Berardino BG, Chertoff M, Gianatiempo O, Alberca CD, Priegue R, Fiszbein A, Long P, Corfas G, Cánepa ET (2019) Exposure to enriched environment rescues anxiety-like behavior and miRNA deregulated expression induced by perinatal malnutrition while altering oligodendrocyte morphology. (bu.edu)
  • Zalcman G, Federman N, Fiszbein A, de la Fuente V, Ameneiro L, Schor IE, Romano A (2019) Sustained CaMKII delta gene expression is specifically required for long-lasting memories in mice. (bu.edu)
  • Formally, epigenetics constitutes the study of changes in gene expression not accompanied by alterations in DNA sequence. (nih.gov)
  • Changes in gene expression and regulation in the brain may help drive the development of psychiatric disorders. (nih.gov)
  • The recent completion of sequencing projects for the genomes of humans and several model organisms has provided, for the first time, a glimpse of the information required for the diversity of eukaryotic life. (nih.gov)
  • Genes in central carbon metabolism, however, are regulated independently of these global physiological cues. (biorxiv.org)
  • B. Experimental design to orthogonally probe the effects of growth rate and amino acid metabolism on gene expression. (biorxiv.org)
  • The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work. (nih.gov)
  • Our results provide a framework to analyze gene expression profiles to gain novel biological insights, a key goal of systems biology. (biorxiv.org)
  • In this module you will focus on the central dogma of molecular biology: how the information stored in the genome of an organism is expressed. (exeter.ac.uk)
  • Eileen Furlong, head of the Genome Biology Unit at EMBL's Heidelberg site. (embl.org)
  • In this unit we review the state-of-the-art in post-genome biology, from a brief overview of genome sequencing itself through to models of entire systems. (manchester.ac.uk)
  • Here we demonstrate systems for inducible repression of gene expression based on clustered regularly interspaced short palindromic repeats-mediated interference (CRISPRi) in Mycoplasma pneumoniae and synthetic Mycoplasma mycoides, two organisms with reduced genomes actively used in systems biology studies. (jcvi.org)
  • I will present two studies, one focusing on kinetic modeling of a small system of divergent transcription and another focusing on genome scale metabolic flux balance analysis of gut microorganisms. (imsc.res.in)
  • This segmentation reflects the growing significance of the agbio tools segment, which includes sales to academia, service providers, crop companies, livestock companies, biofuel companies, and other institutions for the analysis of plant and animal genomes as well as associated microorganisms, parasites, and any other pest. (genengnews.com)
  • This gene encodes an intracellular F-actin binding protein. (cancerindex.org)
  • The ksgA gene encodes a methylase that modifies 16S rRNA, rendering it vulnerable to inhibition by the antibiotic kasugamycin. (jcvi.org)
  • 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)
  • We use this information to infer the target genes of 70,329 candidate regulatory elements and suggest potential regulatory function for 27,325 noncoding sequence variants associated with 2,117 physiological traits and diseases. (duke.edu)
  • The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. (nih.gov)
  • appreciate the range of non-coding RNAs in the genome, and describe how they can be annotated and how they function in gene expression regulation. (manchester.ac.uk)
  • The differentially expressed genes (DEGs) of the poor and good prognosis groups were screened using the Linear Models for Microarray Data package, and the prognosis‑related genes were screened using univariate Cox regression analysis. (cancerindex.org)
  • HPV gene expression is polycistronic initiating from multiple promoters. (medscape.com)
  • DNA methylation is a frequent epigenetic modification that restricts the activity of regulatory elements, including cell type-specific gene promoters and enhancers. (biomedcentral.com)
  • We recently characterized the phenomenon of Exon-Mediated Activation of Transcription Starts (EMATS), in which the splicing of internal exons impacts the spectrum of promoters used and expression levels of the host gene. (bu.edu)
  • Divergent promoters are the promoters in which upstream reverse oriented transcription occurs in the regions devoid of annotated genes but shows the presence of core promoter elements. (imsc.res.in)
  • Here, we present bromouride labeling and sequencing (Bru-Seq) and bromouridine pulse-chase and sequencing (BruChase-Seq) to assess genome-wide changes to RNA synthesis and stability in human fibroblasts at homeostasis and after exposure to the proinflammatory tumor necrosis factor (TNF). (nih.gov)
  • These controls are critical for the regulation of many genes across human tissues. (wikipedia.org)
  • Researchers built a resource with information on gene regulation from more than 2,000 human brains. (nih.gov)
  • In another paper, a team led by researchers at Yale and the Allen Institute examined how gene regulation changes in the brain over the course of human development. (nih.gov)
  • Methylomics of gene expression in human monocytes. (cdc.gov)
  • Our study provides a detailed description of the epigenetic architecture in human monocytes and its relationship to gene expression. (cdc.gov)
  • Using PCR and Capture-based chromosome conformation capture (3C) approaches, collectively called 4Tran, we take advantage of the repetitive nature of transposons to capture interactions from multiple copies of endogenous retrovirus (ERVs) in the human and mouse genomes. (biomedcentral.com)
  • Androgen treatment significantly influenced the expression of approximately 3,000 genes in immortalized human meibomian gland and conjunctival epithelial cells. (molvis.org)
  • To continue to test our hypothesis, we examined the influence of androgens in gene expression in immortalized human meibomian gland and conjunctival epithelial cells. (molvis.org)
  • Human adenoviruses are widely used as models for studying cellular transformation and regulation of gene expression. (bdbiosciences.com)
  • However, it is clear that further improvements in: vector production, transgene expression and regulation, better characterization of the mechanisms involved in vector integration, and the development of immune response against vector delivered transgenes are required before HIV-1 vectors are considered safe and efficacious enough for human clinical trials. (unc.edu)
  • We experimentally validated the photoreceptors localization of three genes in human retina that had not been previously reported. (whiterose.ac.uk)
  • Dr. Zheng first identified RNA cis-elements in regulation of alternative RNA splicing in papillomavirus in 1996 and has been studying protein-RNA interactions and their consequences in various infections with tumor viruses, including high-risk human papillomaviruses and Kaposi's sarcoma-associated herpesvirus. (cancer.gov)
  • The combinatory analysis of both RNA synthesis and stability using Bru-Seq and BruChase-Seq allows for a much deeper understanding of mechanisms of gene regulation than afforded by the analysis of steady-state total RNA and should be useful in many biological settings. (nih.gov)
  • Development of such a framework would allow perturbation-specific gene regulation mechanisms to be uncoupled from global gene expression control, and allow synthetic gene circuits with complex behaviours to be designed ( 9 , 10 ). (biorxiv.org)
  • and the mechanisms by which antihormones (antiestrogens and antiprogestins) antagonize hormone-dependent gene transcription and cell growth. (illinois.edu)
  • Transcription of endogenous genes also has been detected in late 1-cell mouse embryos where it begins at the end of S-phase. (nih.gov)
  • Targeting of six selected endogenous genes with this system results in lowered transcript levels or reduced growth rates that agree with lack or shortage of data in previous transposon bombardment studies, and now produces actual cells to analyze. (jcvi.org)
  • We demonstrated that SRp20 is a proto-oncogene essential for cell proliferation by regulating genome-wide RNA splicing of several hundred host genes. (cancer.gov)
  • The group utilizes state-of-the-art NextGen genome analysis technologies, bioinformatics, and molecular and genetic methods. (nih.gov)
  • You will first focus on the forms of information within the genome and how these are maintained, before exploring the molecular detail of how the information is expressed. (exeter.ac.uk)
  • Technological advances are providing views of genome organization at unprecedented resolution and are beginning to reveal the ways that cells co-opt the structures of the nuclear periphery for nuclear organization and gene regulation. (nih.gov)
  • We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. (nih.gov)
  • Understanding HPV mRNA expression and its regulation in the different diseases associated with infection may lead to development of novel diagnostic approaches and will reveal key viral and cellular targets for development of novel antiviral therapies. (medscape.com)
  • The flow of the unit is from genome to systems, beginning with the complete genome itself, covering transcriptome, proteome, and integrated systems approaches including consideration of biological networks and protein structure. (manchester.ac.uk)
  • Various approaches and algorithms are being developed to study gene expression in complex diseases like cancer. (grandviewresearch.com)
  • Gene Transfer: Delivery and Expression of DNA and RNA provides the first comprehensive guide to technical approaches for delivering nucleic acids into cells and organisms and of ensuring (even manipulating) appropriate expression. (cshlpress.com)
  • These include viral and nonviral methods of gene delivery, transgenic approaches, strategies for the regulation of transgene expression, and modification of the host response. (cshlpress.com)
  • Conventional transposon bombardment and gene knockout approaches often fail to reveal functions of genes that are essential for viability, where lethality precludes phenotypic characterization. (jcvi.org)
  • The long-term goal is to develop a series of therapeutic approaches to control viral or cellular gene expression for cancer or AIDS treatments and to identify biomarkers for clinical diagnosis and prognosis. (cancer.gov)
  • 2018). Protein condensates formed by transcription factors, co-activators, and RNAPII (via the CTD) are major players in gene expression regulation, notably by providing local environments favorable for the assembly of macromolecular assemblies such as super-enhancers (Boija et al. (ircm.qc.ca)
  • 2018). Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains. (ircm.qc.ca)
  • 2018). Coactivator condensation at super-enhancers links phase separation and gene control. (ircm.qc.ca)
  • It's a complex process but errors are surprisingly rare, so we'd like to understand how this regulation of embryonic genes can be so precise. (embl.org)
  • The heterochromatin protein HP1 has an essential role in establishing several features of the 3D nuclear organization of the genome during early embryonic development in Drosophila . (nature.com)
  • But exactly how these regions of the genome exert their effects on the brain is poorly understood. (nih.gov)
  • These include information on DNA variations and gene expression for about 32,000 cells taken from major regions of the donor brains. (nih.gov)
  • Contrary to expectation, these eMS were not predominately enriched in promoter regions, or CpG islands, but rather in the 3' UTR, gene bodies, CpG shores or 'offshore' sites, and both positive and negative correlations between methylation and expression were observed across all locations. (cdc.gov)
  • With 4Tran-PCR, reads are selectively mapped to unique regions in the genome. (biomedcentral.com)
  • Of all the protein-coding genes in Gencode, 65% are expressed in the retina. (whiterose.ac.uk)
  • Gene expression has emerged as one of the key technologies used in various applications, such as drug discovery and development procedures, clinical diagnostics, biotechnology, microbiology, and others. (grandviewresearch.com)
  • A large U3 deletion causes increased in vivo expression from a nonintegrating lentiviral vector. (unc.edu)
  • Dmitri works on several projects involving CTCF and BORIS that relate to 3D organization of genome, activation/repression of transcription, imprinting control, X chromosome inactivation & transgenerational inheritance. (nih.gov)
  • She carried out the first systematic inactivation of all the genes in any animal, which pioneered genome-wide reverse genetic screening. (cam.ac.uk)
  • Nevertheless, a role for NMD in genome regulation has not been fully assessed, partially because NMD inactivation is lethal in many organisms. (biorxiv.org)
  • We further found that UPF1 inactivation leads to translational repression, manifested by a global shift in mRNAs from polysomes to monosomes and a downregulation of genes involved in translation and ribosome biogenesis. (biorxiv.org)
  • Conditional inactivation of genes is effective for characterizing functions central to cell growth and division, but tools are limited for this purpose in mycoplasmas. (jcvi.org)
  • The facile methods for conditional gene activation and inactivation in mycoplasmas open the door to systematic dissection of genetic programs at the core of cellular life. (jcvi.org)
  • In the presence of genetic or environmental perturbations, differential expression of genes, orchestrated by dedicated regulatory circuits, shapes the physiological responses of the cell. (biorxiv.org)
  • Of the probe sets, 1,597 (representing 1,081 genes) met the criteria for differential expression, of which 82 genes were significantly up-or down-regulated in treated retinas. (molvis.org)
  • Our differential expression and expression quantitative trait locus (eQTL) analysis in SSc was further integrated with epigenetic, expression and eQTL data from skin, monocytes, neutrophils and lymphocytes. (bmj.com)
  • Western blotting, northern blotting, enzyme-linked immunosorbent assays, PCR technology with an emphasis on quantitative PCR, differential protein display, and DNA sequencing and hybridization arrays technology with a focus on macro arrays and microarrays in facilitating gene expression are a few examples of technological advancements for gene expression. (grandviewresearch.com)
  • This enables the identification of transposable element interaction profiles for individual ERV families and integration events specific to particular genomes. (biomedcentral.com)
  • This system plays a major role in the regulation of gene activity, and enables the selective expression of different functions in differentiated cell types. (uni-muenchen.de)
  • Targeting the ksgA gene with CRISPRi removes the lethal effect of kasugamycin and enables cell growth, thereby establishing specific and effective gene modulation with our system. (jcvi.org)
  • Several transcripts deregulated in retinas after a radiation injury play a key role in radiation-induced neurogenic visual loss, especially for genes associated with RGC, glial cell, and cell death. (molvis.org)
  • The ObsT included 77 623 transcripts (23 960 genes) covering 137 Mb (35 Mb new transcribed genome). (whiterose.ac.uk)
  • Most of the transcripts (92%) were multi-exonic: 81% with known isoforms, 16% with new isoforms and 3% belonging to new genes. (whiterose.ac.uk)
  • The RefT included 13 792 genes across 94 521 known transcripts. (whiterose.ac.uk)
  • Mechanical cues from the microenvironment can be efficiently transmitted to the nucleus to engage in the regulation of genome organization and gene expression. (nature.com)
  • The genome is packaged and organized nonrandomly within the 3D space of the nucleus to promote efficient gene expression and to faithfully maintain silencing of heterochromatin. (nih.gov)
  • To understand genome regulation, we need to study the three-dimensional arrangement of regulatory elements and genes within the nucleus of the cell. (embl.org)
  • Single-nucleus Hi-C of embryos, polymer simulations and single-molecule imaging collectively reveal that MCM complexes influence genome folding and gene expression by impeding DNA loop extrusion. (nature.com)
  • Complex formation between the products of oncogenes and tumor suppressor genes are believed to be important in cellular transformation. (bdbiosciences.com)
  • We know that a large part of our genome is involved in regulating gene activity, and differences in this activity are crucial in determining the way cells develop into different cell types, ultimately forming the diverse range of tissues in our body. (embl.org)
  • We sought to determine whether this hormone action involves the regulation of epithelial cell gene expression in these tissues. (molvis.org)
  • The needs to efficiently deliver genetic cargo and to maintain long-term transgene expression in vivo prompted the development of the HIV-1 based vector system. (unc.edu)
  • However we believe that further improvements in: vector production, transgene expression and regulation, and better characterization of the mechanism responsible for the development of immune response against vector delivered transgenes are required before we can consider the use of the lentiviral system in clinical trials. (unc.edu)
  • To allow regulation of transgene expression in vivo we develop tetracycline inducible lentivirus vectors. (unc.edu)
  • Cytosine methylation is a frequent epigenetic modification restricting the activity of gene regulatory elements. (biomedcentral.com)
  • Fluorescent molecules reveal genome regulation in a developing embryo of the fruit fly Drosophila. (embl.org)
  • Scope includes mutations and abnormal protein expression. (cancerindex.org)
  • We are currently characterizing the effects of unique point mutations in the HIV-1 gag and pol genes on the efficiency of vector particles at transducing a variety of primary cells. (unc.edu)
  • Aberrant splicing is a hallmark of leukemias with mutations in splicing factor (SF)-encoding genes. (iscb.org)
  • International Cancer Genome Consortium. (cancerindex.org)
  • In the present study, two messenger ribonucleic acid sequencing datasets of patients with AML were downloaded from the Cancer Genome Atlas and Gene Expression Omnibus databases. (cancerindex.org)
  • Our lab is focused on the development of HIV-1 vectors for gene therapy of genetic diseases such as hemophilia A and B, as well as well as a means of treating prostate cancer. (unc.edu)
  • Transcription Regulation and Genome Rewiring Governing Sensitivity and Resistance to FOXM1 Inhibition in Breast Cancer. (illinois.edu)
  • This growth can be attributed to significant investments in cancer-related research and the increasing demand for advanced interpretation software for cancer gene expression studies. (grandviewresearch.com)
  • For example, projective clustering techniques and ensemble techniques are reported to be used for the integration of cancer gene expression data. (grandviewresearch.com)
  • These early genetic studies resulted in the establishment of functional relationships among various factors in regulation of gene expression through analysis of their genetic interactions. (nih.gov)
  • By comparing them to normal pro-B cells, we found thousands of aberrant local splice variations (LSVs) per sample, with 279 LSVs in 241 genes present in every comparison. (iscb.org)
  • We show that this regulatory scheme, named PCF11-mediated expression regulation through IPA (PEIPA), takes place in cell differentiation, during which downregulation of PCF11 is coupled with upregulation of long genes with functions in cell morphology, adhesion, and migration. (nih.gov)
  • There was prominent upregulation of genes associated with glial cell activation in the treated retina. (molvis.org)
  • They then used machine learning to create a predictive model of the risk for psychiatric disorders based on variations in gene expression and regulation. (nih.gov)
  • The researchers were also able to associate the altered regulation of many genes with specific disorders: 64 for schizophrenia, 11 for bipolar disorder, and 5 for autism spectrum disorder. (nih.gov)
  • In contrast, the messenger ribonucleic acid (mRNA) expression levels of retinal ganglion cell (RGC)-specific genes were low. (molvis.org)
  • Regulation of flavonoid biosynthesis during plant development and plant-pathogen interaction. (psu.edu)