• an award winning podcast from Genome British Columbia , is back with a thought-provoking Season 3, exploring the many ways genomics impacts the world. (genomebc.ca)
  • Genome BC is a not-for-profit organization supporting world-class genomics research and innovation to grow globally competitive life sciences sectors and deliver sustainable benefits for British Columbia, Canada and beyond. (genomebc.ca)
  • In addition to scientific programming, Genome BC works to integrate genomics into society by supporting responsible research and innovation and foster an understanding and appreciation of the life sciences among educators, students, and the public. (genomebc.ca)
  • The complete sequencing of the human genome, announced in 2001, marked the culmination of unprecedented advances in the science of genomics, the study of the genome and its functions. (who.int)
  • Accordingly, a wide-ranging consultative process was undertaken, engaging scientists, clinicians, ethicists, public and private funders of genomics research, health policy-makers, nongovernmental organizations and civil society groups concerned with the ethical, legal and social implications of genomics. (who.int)
  • Genome structure, comparative genomics, and bioinformatics. (lu.se)
  • Genomics refers to the study of the genome as a whole, including single genes and the interaction of multiple loci and the environment. (cdc.gov)
  • Gene organization in the bacterial chromosome has very well known effects on transcription and a standard example is the organization of genes into operons, which allows for a sophisticated regulation of gene expression [ 9 ]. (biomedcentral.com)
  • These structures are emerging as a paradigm for gene regulation, a highly complex process that requires the dynamic coordination of hundreds of regulatory factors around precise targets in different cell states. (caltech.edu)
  • We describe the discovery of hundreds of RNA-DNA hubs throughout the nucleus that are organized around essential nuclear functions such as RNA processing, centromeric heterochromatin organization, and gene regulation. (caltech.edu)
  • Chromatin looping is important for gene regulation, and studies of 3D chromatin structure across species and cell types have improved our understanding of the principles governing chromatin looping. (nature.com)
  • Professor Dekker's work is at the cutting edge of connecting the structure of DNA with its function, one of the final frontiers in understanding gene regulation," said Terence R. Flotte, MD, the Celia and Isaac Haidak Professor of Medical Education , executive deputy chancellor, provost and dean of the School of Medicine. (umassmed.edu)
  • These differences are achieved through the regulation of individual genes such that they are only on in particular cell types. (ca.gov)
  • For instance, the regulation of specific genes allows skin cells to serve their specialized epidermal function. (ca.gov)
  • Additionally, we find that the ESC genome is organized in such a way as to juxtapose regions of DNA that show similar regulation by demonstrating that spatially associated regions in the genome are associated with the same gene regulatory factors. (ca.gov)
  • This finding adds a new dimension to our understanding of how ESC-specific gene regulation is maintained and how the genome is organized. (ca.gov)
  • 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)
  • Principles for regulation of gene expression through intercellular signalling. (lu.se)
  • Gene regulation in developmental biology and the cell cycle. (lu.se)
  • We sequenced Fv strain 7600 and Fol strain 4287 (Methods, Supplementary Table 1 ) using a whole-genome shotgun approach and assembled the sequence using Arachne ( Table 1 , ref. 6 ). (nature.com)
  • Herein, we conducted an analysis based on whole-genome sequencing. (go.jp)
  • A whole genome screen for HIV restriction factors. (nih.gov)
  • What are whole exome sequencing and whole genome sequencing? (medlineplus.gov)
  • When available, the information provided by whole-genome sequencing projects provides an entry into an understanding of genome structure and evolution and gene discovery, and function. (biomedcentral.com)
  • 2423}. Whole-genome sequencing has ing has shown that more than half of all shown that more than half of all cases cases of MDS-MLD carry mutations in of MDS-MLD carry mutations in genes genes that are also mutated in MDS with that are also mutated in MDS with excess excess blasts and acute myeloid leukae- blasts and acute myeloid leukaemia. (who.int)
  • The degree of organization has been shown to increase with genome size, overall GC composition and the presence of nucleoid-binding proteins [ 1 ]. (biomedcentral.com)
  • Previously, the genome of the cereal pathogen Fg was sequenced and shown to encode a larger number of proteins in pathogenicity related protein families compared to non-pathogenic fungi, including predicted transcription factors, hydrolytic enzymes, and transmembrane transporters 5 . (nature.com)
  • Toward this objective, ChIP-Seq data of 14 S/MAR binding proteins were analyzed and the binding site coordinates of these proteins were used to prepare a non-redundant S/MAR dataset of human genome. (researchgate.net)
  • If genes don't produce the right proteins or don't produce them correctly, a child can have a genetic disorder . (medlineplus.gov)
  • Dispersed between the chromosomes are over 20,000 genes, sometimes separated by vast stretches of non-coding DNA, or that which does not encode proteins. (jove.com)
  • In eukaryotic genomes, genes are separated by large stretches of DNA that do not code for proteins. (jove.com)
  • As observed more broadly in angiosperms, ribosomal proteins have been especially prone to gene loss in the S. latifolia lineage. (biomedcentral.com)
  • Plant mitochondrial genomes contain genes for their own rRNA subunits as well as for some of the ribosomal proteins and tRNAs required for translation (Figure 1 ), but many necessary ribosomal protein and tRNA genes are located in the nuclear genome, so their gene products must be imported into the mitochondrion [ 15 ]. (biomedcentral.com)
  • The technology, unlike the chromosome conformation capture technologies that map interactions genome-wide, will allow scientists to zoom in on small, defined regions of the genome and to identify the proteins and other molecules that bind to the genome to facilitate local folding. (umassmed.edu)
  • Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization. (ca.gov)
  • Additionally, we identified two further levels of genome organization in ESCs characterized by colocalization of regions with high pluripotency factor occupancy and strong enrichment for Polycomb proteins/H3K27me3, respectively. (ca.gov)
  • We need to know more about the proteins that our genes produce. (lu.se)
  • We have around 20 000 genes that can produce at least 500 000 proteins. (lu.se)
  • Most of the human genome is uncharted territory -- entire stretches of sequence with no clear function or purpose," said Jason Lieb, Ph.D., associate professor of biology at UNC, a member of the UNC Lineberger Comprehensive Cancer Center and one of the senior authors of the study. (sciencedaily.com)
  • The first tomato genome sequence was released in 2012, revealing approximately 35,000 genes and facilitating crop improvement efforts. (isaaa.org)
  • Sequence diversity and genomic organization of vomeronasal receptor genes in the mouse. (jax.org)
  • Many EST libraries were constructed from RNA extracted from various genetic backgrounds, thus gene identification from these sources is complicated by the existence of both gene and allele sequence differences. (biomedcentral.com)
  • using a redundancy criterion to identify reproducible sequence differences between related genes within gene families. (biomedcentral.com)
  • Analysis of these sequences revealed single base substitutions and single base indels are the most frequently observed form of sequence variation between genes within families in the dataset. (biomedcentral.com)
  • The more recent duplication event in particular would be expected to result in many paralogous pairs of genes differing by relatively few sequence differences, thus complicating gene identification using ESTs. (biomedcentral.com)
  • In this study, we report the first complete mitochondrial genome sequence from a member of this family, Silene latifolia . (biomedcentral.com)
  • In addition, genes encoding 18S and, especially, 5S rRNA exhibit exceptional sequence divergence relative to other plants. (biomedcentral.com)
  • Gene expression also relies on extensive C-to-U (and sometimes U-to-C) RNA editing, in which substitution of specific pyrimidines in the mRNA sequence restores phylogenetically conserved codons [ 8 ]. (biomedcentral.com)
  • When further modeling DNA as a semifexible polymer explicitly taking into account the structural disorder induced by the sequence, we have provided some evidence that the observed LRC favor the spontaneous formation as well as the cooperative positioning of nucleosomes along the chromosomes including the nucleosome free regions experimentally observed at gene promoters (see figure below). (ens-lyon.fr)
  • Note that the organization of the nucleosomal assembly results from the confinement of nucleosomes between sequence induced high energy barriers corresponding to the nucleosome free regions observed at the promoters and gene ends. (ens-lyon.fr)
  • With tools such as CRISPR/CAS9, researchers at the center will be able to label specific parts of the genome so that they can be visualized in the microscope, and they will be able to make changes to the DNA sequence so that the 3D folding can be perturbed in a highly targeted manner. (umassmed.edu)
  • a , Maximum-likelihood tree using concatenated protein sequences of 100 genes randomly selected from 4,694 Fusarium orthologous genes that have clear 1:1:1:1 correlation among the Fusarium genomes and have unique matches in Magnaporthe grisea , Neurospora crassa and Aspergillus nidulans . (nature.com)
  • The recent development of homologous recombination-mediated gene targeting (GT) techniques has made it easy to modify nucleotide sequences in plant genomes. (go.jp)
  • Large scale gene analysis of most organisms is hampered by incomplete genomic sequences. (biomedcentral.com)
  • The identification of potential gene sequences (pHaps) from soybean allows us to begin to get a picture of the genomic history of the organism as well as begin to observe the evolutionary fates of gene copies in this highly duplicated genome. (biomedcentral.com)
  • We identified approximately 45,000 potential gene sequences (pHaps) from EST sequences of Williams/Williams82, an inbred genotype of soybean ( Glycine max L. Merr. (biomedcentral.com)
  • Functional annotation of gene sequences indicate functional classifications are not randomly distributed among gene families containing few or many genes. (biomedcentral.com)
  • The coding capacity of the genome is not controlled solely by DNA sequences. (duke.edu)
  • Rather, fine tuning is achieved through epigenetic factors that impact the accessibility of DNA sequences for enzymatic modifications, and through factors that participate in genome organization establishing a functional nuclear landscape. (duke.edu)
  • High frequency intra- and intermolecular recombination among large repeated sequences is the rule, generating a heterogeneous pool of genome configurations within a single individual [ 12 - 14 ]. (biomedcentral.com)
  • The availability of genome sequences for many living organisms clearly has important implications for health improvement, and it has been widely predicted that elucidation of the sequences will lead to a revolution in medical research and patient care. (who.int)
  • A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics. (cdc.gov)
  • Past genomic studies have comprehensively described the organization of the bacterial chromosome, for example in terms of gene localization, order and orientation. (biomedcentral.com)
  • This organization of the chromosome can be described as being an adaptive and functional tool, essential for the survival of the bacterial cell. (biomedcentral.com)
  • It has also been shown that neighbouring genes in a bacterial chromosome tend to be co-expressed, even if they are not in the same operon [ 10 ], suggesting the existence of a "supra-operonic" organization [ 11 ]. (biomedcentral.com)
  • and (iv) lysA and argG genes were located on the 2.5-Mb chromosome, in contrast to the argH gene, which was located on the 3.4-Mb chromosome. (elsevierpure.com)
  • The present findings also indicated that the 2.5-Mb chromosome carried various auxotrophic genes with no structural or functional counterparts on the remaining two chromosomes. (elsevierpure.com)
  • To determine how changes in chromosome positioning affect transcription across thousands of genes with minimal perturbation, we characterized nuclear organization and global gene expression in budding yeast containing chromosome fusions. (hal.science)
  • We used computational modeling and single-cell imaging to determine chromosome positions, and integrated these data with genome-wide transcriptional profiles from RNA sequencing. (hal.science)
  • We find that chromosome fusions dramatically alter 3D nuclear organization without leading to strong genome-wide changes in transcription. (hal.science)
  • These data suggest that basal transcriptional activity is sensitive to radial changes in gene position, and provide insight into the functional relevance of budding yeast chromosome-level 3D organization in gene expression. (hal.science)
  • This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. (nih.gov)
  • He developed the chromosome conformation capture technologies, biochemical techniques for determining how DNA segments interact and are linked to one another, which are the heart of the "3C," "5C," "Hi-C" and "Micro-C" tools used by researchers worldwide to map the structure and organization of chromosomes inside cells. (umassmed.edu)
  • Using chromosome conformation capture technologies in conjunction with advanced computational modeling and a range of imaging methods, the center will generate three-dimensional models of the human genome inside fibroblast cells during metaphase and interphase, as well as in embryonic stem cells in undifferentiated and differentiated states. (umassmed.edu)
  • Underlining the independence of these networks and their functional relevance for genome organization, loss of the Polycomb protein Eed diminishes interactions between Polycomb-regulated regions without altering overarching chromosome conformation. (ca.gov)
  • Table 1 provides a summary outline of the gene symbols, chromosomal locations, radiation sensitivity characteristics, immunodeficiencies, chromosome breakage characteristics, and major cancer risk for each of these disorders. (medscape.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)
  • The organisation and evolution of the eukaryotic genomes. (lu.se)
  • They found that the chromatin is more open in the presence of the high risk version of the gene (a T) than in the presence of the non-risk version (an A). Further analysis demonstrated that the risk variant enhanced the activity of the gene, indicating that it may possess functional characteristics that could contribute to disease. (sciencedaily.com)
  • Southern hybridization analysis, allelic exchange mutagenesis of ATCC 17616, and complementation tests demonstrated that all of the genes examined were functional and existed as a single copy within the genome. (elsevierpure.com)
  • Molecular approaches to understanding the functional circuitry of the nervous system promise new insights into the relationship between genes, brain and behaviour. (nih.gov)
  • We used the ESTminer suite of programs to identify potential soybean gene transcripts from a single genetic background allowing us to observe functional classifications between gene families as well as structural differences between genes and gene paralogs within families. (biomedcentral.com)
  • The genomes of eukaryotes can be structured in several functional categories. (jove.com)
  • Beginning with time-series gene expression data, the Local Edge Machine (LEM) seeks to find functional network models capable of generating the dynamic behavior of the data (Fig. 1 ). (biomedcentral.com)
  • Mitochondrial gene loss and functional transfer to the nucleus is an ongoing process in many lineages of plants, resulting in substantial variation across species in mitochondrial gene content. (biomedcentral.com)
  • The genome has also experienced a major reduction in tRNA gene content, including loss of functional tRNAs of both native and chloroplast origin. (biomedcentral.com)
  • The genomes of plant mitochondria, like any organelle genome, depend on highly integrated functional coordination with the nucleus. (biomedcentral.com)
  • 1) "native" tRNAs encoded in the mitochondrial genome and inherited from the α-proteobacterial progenitor of mitochondria, 2) chloroplast-like tRNAs, which are also encoded in the mitochondrial genome but which were acquired by functional gene transfer from the chloroplast genome during land plant evolution, and 3) nuclear-encoded tRNAs imported from the cytosol. (biomedcentral.com)
  • Hence, TADs are believed to represent structural chromosomal units that are of functional importance for the regulatory cross talk that determines gene expression programs. (biomedcentral.com)
  • Despite their importance, a lack of genomic information and resources has hindered the functional characterisation of genes in major crops. (grassroots.tools)
  • 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 23rd pair, the sex chromosomes (X and Y), determines a person's sex as well as containing other functional genes. (msdmanuals.com)
  • The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. (nih.gov)
  • Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (nih.gov)
  • 2002). Expression and genomic organization of the zebrafish chaperonin gene complex . (sgu.edu)
  • The Genetics Society of America is a nonprofit, tax-exempt charitable organization (tax identification number 93-6023830) under Section 501(c)(3) of the Internal Revenue Code. (genetics-gsa.org)
  • The use of genetics in population screening long predates the Human Genome Project. (cdc.gov)
  • The completion of the human genome project has spurred a flurry of research into the exact genetic changes underlying disease. (sciencedaily.com)
  • Now, scientists from the USDA Agricultural Research Service (ARS) and the Boyce Thompson Institute (BTI) have created a pan-genome that captures all of the genetic information of 725 cultivated and closely related wild tomatoes, mapping 4,873 genes that were absent from the original reference genome . (isaaa.org)
  • However, owing to the possibility of unintentional transgene introduction during genetic transformation, analytical methods may be necessary to reliably and comprehensively detect transgenes remaining on a plant genome. (go.jp)
  • Along with the complex arrangement of genetic material in a cell's nucleus, human genes also demonstrate their own unique organization. (jove.com)
  • Once they've generated these 3D genomic models, Dekker's team will use gene editing techniques to biologically validate genetic functions linked to structure. (umassmed.edu)
  • Antimicrobial resistance occurs through different mechanisms, which include spontaneous (natural) genetic mutations and horizontal transfer of resistant genes through deoxyribonucleic acid (DNA). (who.int)
  • Gene technology: basic and applied molecular genetic methods. (lu.se)
  • Here we have developed a map that can guide scientists to regions of the genome that do appear to be functionally relevant, instead of a dead end. (sciencedaily.com)
  • Mutations in this gene have been associated with severe developmental defects on the anterior-posterior (a-p) limb axis. (wikipedia.org)
  • To determine the distribution and organization of the amino acid biosynthetic genes on the genome of this β-proteobacterium, various auxotrophic mutations were isolated using a Tn5 derivative that was convenient not only for the determination of its insertion site on the genome map but also for the structural analysis of the flanking regions. (elsevierpure.com)
  • Genes Dev, 2000 May 15. (nih.gov)
  • Nucleosome occupancy (white corresponding to large occupancy values) for the 2000 shortest S. Cerevisiae genes ordered by increasing length from top to bottom and aligned on the promoter (null distance). (ens-lyon.fr)
  • Finally, our results show the existence of spatial periodic transcriptional patterns in the genome of Buchnera . (biomedcentral.com)
  • Focusing on RNA processing, specifically co-transcriptional splicing, we find that genome-wide organization of active genes near nuclear speckles drives the efficiency of pre-mRNA splicing in a cell-type specific manner. (caltech.edu)
  • The hierarchical levels of genome architecture exert transcriptional control by tuning the accessibility and proximity of genes and regulatory elements. (biomedcentral.com)
  • Transcription factors (TFs) are critical for B-cell differentiation, affecting gene expression both by repres- sion and transcriptional activation. (lu.se)
  • The effect of Buchnera genome evolution on gene expression levels has also been analysed in order to assess the constraints imposed by the obligate symbiosis with aphids, underlining the importance of some gene sets for the survival of the two partners. (biomedcentral.com)
  • This is a perfect illustration of the mutual influence between gene expression levels and chromosomal organization in bacteria. (biomedcentral.com)
  • These variable loops contribute significantly to corresponding gene expression variability across cells and species, possibly by refining sub-TAD-scale loop contacts responsible for cell-type-specific enhancer-promoter interactions. (nature.com)
  • Abstract In eukaryotic cells, the spatial organization of genes within the nucleus is correlated with their expression. (hal.science)
  • To determine how nuclear spatial organization affects gene expression, Di Stefano et al. (hal.science)
  • However, we observe a mild but significant and reproducible increase in the expression of genes displaced away from the periphery. (hal.science)
  • for example, a 10% decrease in the propensity of a gene to reside at the nuclear envelope is accompanied by a 10% increase in gene expression. (hal.science)
  • We describe here an anatomically comprehensive digital atlas containing the expression patterns of approximately 20,000 genes in the adult mouse brain. (nih.gov)
  • GXD's primary emphasis is on endogenous gene expression during development. (jax.org)
  • These elements are involved in control of gene expression which governs the phenotype and also plays role in disease biology. (researchgate.net)
  • As a result, silencers help to regulate gene expression. (jove.com)
  • However, these intergenic regions carry important elements that regulate gene activity, for instance, the promoter where transcription starts, and enhancers and silencers that fine-tune gene expression. (jove.com)
  • In the Yildirim lab, we study how epigenetic mechanisms, particularly those that are mediated by long noncoding RNAs (ncRNAs), complement gene expression, impact genome stability and define cell fate decisions. (duke.edu)
  • We are interested in defining the molecular bases of these interactions and delineating their significance in driving gene expression and genome functions. (duke.edu)
  • Data from genome wide expression profiling studies of various human cancers have provided evidence for altered expression of long ncRNAs. (duke.edu)
  • This female specific dosage compensation mechanism depends on expression of Xist long ncRNA, which coats and transcriptionally silences future inactive X (Xi) balancing X-linked gene expression between XX females and XY males (Fig 1). (duke.edu)
  • In addition to their canonical functions in maintaining nuclear architecture and nucleocytoplasmic trafficking, components of the nuclear envelope (i.e. nuclear pore complex (NPC), nuclear lamina) are also involved in intracellular signaling, DNA repair, and gene expression. (duke.edu)
  • In various organisms, components of the nuclear envelope interact with chromatin that is spatially organized within the nucleus (Fig 2) and subsequently regulate gene expression. (duke.edu)
  • We present a novel approach, the Local Edge Machine, for the inference of regulatory interactions directly from time-series gene expression data. (biomedcentral.com)
  • Temporally dynamic gene expression programs have been observed in a wide variety of organisms. (biomedcentral.com)
  • In the present set of experiments, using gene-expression microarray technology that allowed us to quantify the expression of ~25,000 genes simultaneously, we assessed the gene expression profiles of the best and worst learners from a sample of 60 mice (in two replications). (rutgers.edu)
  • The most consistent pattern of differential expression was found in the prefrontal cortex, here a set of genes associated with the efficacy of dopamine functioning (i.e. (rutgers.edu)
  • This relationship was further verified through a quantitative PCR analysis where we demonstrated a significant correlation between the expression of these prefrontal dopamine genes and the general learning abilities of 48 mice. (rutgers.edu)
  • The goal is to understand how 3D genome structure influences gene expression, cellular function, development and disease. (umassmed.edu)
  • To properly understand how the genome works to coordinate gene expression, it's necessary to understand how and why the genome is organized in space. (umassmed.edu)
  • For wheat, these include gene model annotations, expression atlases and gene networks that provide information about putative function. (grassroots.tools)
  • Dr. Martin has also conducted research on the effect of environmental perturbations and their effects on gene expression and embryonic development. (sgu.edu)
  • 2004). Differential expression of the methyl-cytosine binding protein 2 (MeCP2) gene in embryonic and adult brain of zebrafish . (sgu.edu)
  • 2001). Expression of the chaperonin 10 gene during zebrafish development . (sgu.edu)
  • 1999). Restricted expression of the zebrafish hsp90α gene in slow and fast muscle fibre lineages . (sgu.edu)
  • Methods for analysis of gene expression: microarray, hybridisation, promoter analyses. (lu.se)
  • Strategies for gene therapy and production of medicines via genetically-modified organisms (expression vectors and viral vectors). (lu.se)
  • In the last decade, diagnostic and prognostic evaluation has been facilitated by global gene expression profiling (GEP), provid- ing a new powerful means for the classification, prediction of survival, and response to treatment of lym- phomas. (lu.se)
  • The identified transcription factors influence both the global and specific gene expression of the BCLs and have possible implications for diagnosis and treat- ment. (lu.se)
  • Genomic studies on bacteria have clearly shown the existence of chromosomal organization as regards, for example, to gene localization, order and orientation. (biomedcentral.com)
  • Moreover, transcriptomic analyses have demonstrated that, in free-living bacteria, gene transcription levels and chromosomal organization are mutually influenced. (biomedcentral.com)
  • We have explored the possible conservation of relationships between mRNA abundances and chromosomal organization in the highly reduced genome of Buchnera aphidicola , the primary endosymbiont of the aphids, and a close relative to Escherichia coli . (biomedcentral.com)
  • Despite an important reduction in its genome size and an apparent decay of its capacity for regulating transcription, this work reveals a significant correlation between mRNA abundances and chromosomal organization of the aphid-symbiont Buchnera . (biomedcentral.com)
  • The chromosomal localization of genes was improved, and Human Genome Variation Society (HGVS) notation was used throughout for translocations, insertions, and other gene alterations. (who.int)
  • The asymmetry of the distribution of the genes between the two strands of DNA is explained as being a means of minimizing interruptions in gene transcription due to collisions between the DNA and RNA polymerases. (biomedcentral.com)
  • Our aim is to define the molecular bases of the interactions that are established between chromatin and the components of the nuclear envelope, and determine how they 1) regulate epigenetic state of genes and their transcription, 2) participate in spatial organization of the genome, and 3) contribute to cellular functions during mammalian development. (duke.edu)
  • Dans une étroite relation avec l'expérimentation, les activités de l'équipe visent à l'analyse de la structuration du génome dans les cellules en connexion avec la transcription et la réplication. (ens-lyon.fr)
  • Around these putative origins, genes are abundant and broadly expressed, and their transcription is co-oriented with replication fork progression. (ens-lyon.fr)
  • We have proposed that this specific organization could result from the constraints of accommodating the replication and transcription initiation processes at chromatin level, and reducing head-on collisions between the two machineries. (ens-lyon.fr)
  • Our findings has provided a new model of gene organization in the human genome, which integrates transcription, replication, and chromatin structure as coordinated determinants of genome architecture. (ens-lyon.fr)
  • To exert stimulatory or repressive effects on transcription, accessible regulatory DNA elements must be in close spatial proximity to susceptible genes. (biomedcentral.com)
  • Enhancers promote transcription by providing a binding platform for transcription factors [ 12 ] that can act on (distal) target genes through three-dimensional chromatin looping [ 13 - 15 ]. (biomedcentral.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)
  • Extreme variability among mammalian V1R gene families. (jax.org)
  • Bioinformatics' gives an introductory overview of the underpinning principles of molecular biology that allow the acquisition, analysis and storage of information about genomes, transcriptomes and proteomes. (le.ac.uk)
  • Such EST data form a valuable foundation for the understanding of the gene composition and genomic biology of yet-to-be fully sequenced genomes [ 3 ]. (biomedcentral.com)
  • We've entered what can be considered the third phase of the human genome project," said Job Dekker, PhD, Howard Hughes Medical Institute Investigator , professor of biochemistry & molecular pharmacology and co-director of the Program in Systems Biology. (umassmed.edu)
  • With this new phase we want to understand how the various genes and regulatory elements that make up the genome talk to each other and collaborate together in real-time to influence biology and disease. (umassmed.edu)
  • Other research in the lab focuses on understanding how spatial organization of the genome is achieved through interactions between chromatin and components of the nuclear envelope. (duke.edu)
  • Finally, the center will develop entirely new technology for locally mapping the spatial organization of the genome. (umassmed.edu)
  • More like a ball of cooked spaghetti, the genome folds and loops back on itself so it can fit inside the tight confines of the nucleus. (umassmed.edu)
  • Different cell types, along with turning different genes on and off, organize those genes in the three dimensional (3D) space of the cell nucleus in different configurations. (ca.gov)
  • Modeling suggests that this is due to both deletion of telomeres and to displacement of genes relative to the nuclear periphery. (hal.science)
  • These findings suggest a markedly expanded role for nuclear gene products in the translation of mitochondrial genes in S. latifolia and raise the possibility of altered selective constraints operating on the mitochondrial translational apparatus in this lineage. (biomedcentral.com)
  • For example, translation of mitochondrially-encoded genes requires a mix of nuclear and mitochondrially encoded components. (biomedcentral.com)
  • Together, our data highlight a pluripotency-specific genome organization in which pluripotency factors such as Nanog and H3K27me3 occupy distinct nuclear spaces and reveal a role for cell-type-specific gene-regulatory networks in genome organization. (ca.gov)
  • Here we present the comparative analysis of the genomes of these three species. (nature.com)
  • Unfortunately, the size and complexity of the genomes of many agronomically important species currently hinders the undertaking of such projects. (biomedcentral.com)
  • The polymorphism observed in the organization of the subtelomeric region in the genome of two Penicillium species within the high homogeneous Penicillium subgenus is for the first time reported and perhaps can be employed in future phylogenetic studies. (scielo.br)
  • The mitochondrial genomes of flowering plants exhibit a number of characteristics that distinguish them from the mitochondrial genomes of other eukaryotes [ 1 ]. (biomedcentral.com)
  • We sequenced and constructed the complete genome of an environmental strain CR1 of P. aeruginosa and performed the comparative genomic analysis. (frontiersin.org)
  • Twenty of these genes are known to harbor gene variants associated with type II diabetes. (sciencedaily.com)
  • A genome-wide association study for Hunner-type interstitial cystitis led to amino acid variants in the class II human leukocyte antigen DQ-beta1 and DP-beta1 chain genes. (genomeweb.com)
  • Both observational studies and randomized controlled trials may be required to adequately evaluate health benefits, harms, and costs based on returning or not returning the results of gene variants to patients and providers. (cdc.gov)
  • This means taking different types of cancer, for example, as the starting point and trying to identify the genes and the different protein variants that differ between healthy and ill individuals. (lu.se)
  • The relationship between 3D organization of the genome and gene-regulatory networks is poorly understood. (ca.gov)
  • Each cluster typically encompassed single genes that are active specifically in islet cells. (sciencedaily.com)
  • The purpose of this funding opportunity is to provide support for investigative groups to conduct genome-wide association (GWA) genotyping and/or replication studies using data and samples from human subjects on whom information is available for conditions/traits of public health importance and relevant environmental exposures. (nih.gov)
  • RNA:DNA hybrids such as R-loops affect genome integrity and DNA replication fork progression. (biorxiv.org)
  • Here, we investigate the contributions of RNases HII (RnhB) and HIII (RnhC) to hybrid removal, DNA replication, and mutagenesis genome-wide. (biorxiv.org)
  • Our results resolve the outstanding question of how hybrids in native genomic contexts interact with replication to cause mutagenesis and shape genome organization. (biorxiv.org)
  • Molecular functions of small and large gene families appear to be non-randomly distributed possibly indicating a difference in retention of duplicates or local expansion. (biomedcentral.com)
  • Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. (nih.gov)
  • Our analysis showed that mRNA abundances, gene organization (operon) and gene essentiality are correlated in Buchnera (i.e., the most expressed genes are essential genes organized in operons) whereas no link between mRNA abundances and gene strand bias was found. (biomedcentral.com)
  • The predominance of single nucleotide insertion/deletions and substitution events between genes within families (individual genes and gene paralogs) is consistent with a model of gene amplification followed by single base random mutational events expected under the classical model of duplicated gene evolution. (biomedcentral.com)
  • Divergence in one region of 18S rRNA appears to be the result of a gene conversion event, in which recombination with a homologous gene of chloroplast origin led to the complete replacement of a helix in this ribosomal RNA. (biomedcentral.com)
  • While no one wants to curtail the creativity of fruitfly geneticists, it will be important to ensure that, in the future, no joky names are adopted for human genes where they might cause offence, Ludman adds. (bioedonline.org)
  • Here, we examined long-range chromatin interactions genome-wide in mouse embryonic stem cells (ESCs), iPSCs, and fibroblasts and uncovered a pluripotency-specific genome organization that is gradually reestablished during reprogramming. (ca.gov)
  • Although gradual changes in trait complexity appear to have been facilitated by allelic turnover, key innovations are associated with gene and genome duplications. (lu.se)
  • These findings provide an important connection between the origins of biodiversity, coevolution, and the role of gene and genome duplications as a substrate for novel traits. (lu.se)
  • Several attempts have been made toward identification of S/MARs in genomes of various organisms including human. (researchgate.net)
  • Here, we review current insights into the trans-acting factors that enable the genome to flexibly adopt different functionally relevant conformations. (biomedcentral.com)
  • Gene reduction analysis revealed that the gene deletion processes are under selective pressure, and many of the inactivations are probably related to the organism's interaction with its host environment. (asm.org)
  • To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516. (asm.org)
  • While these observations were made on free-living bacteria, very few data exist on symbiotic bacteria characterized by reduced genomes, shaped by their adaptation to the host metabolic requirements and by their high evolution rate. (biomedcentral.com)
  • However, 3D genome evolution and its relationship with natural selection remains largely unexplored. (nature.com)
  • This module will also illustrate how computers are used to investigate the organisation and evolution of genes and genomes. (le.ac.uk)
  • The size and complexity of plant mitochondrial genomes, especially when compared with animals and fungi, make them powerful models for exploring the forces affecting eukaryotic genome structure and evolution. (biomedcentral.com)
  • Diversity of the hepatitis C virus NS5B gene during HIV co-infection. (cdc.gov)
  • LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. (nature.com)
  • The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number. (nih.gov)
  • Our genome integrity evaluation method could also be applicable to plant lines produced using other genome-editing technologies such as CRISPR/Cas9. (go.jp)
  • The overall impacts of naturally occurring RNA:DNA hybrids on genome integrity, and the relative contributions of ribonucleases H to mitigating the negative effects of hybrids, remain unknown. (biorxiv.org)
  • We identified eight new regions of genomic plasticity and a plasmid pCR1 with a VirB/D4 complex followed by trimeric auto-transporter that can induce virulence phenotype in the genome of strain CR1. (frontiersin.org)
  • Indeed, bacterial genomes carry, on average, from 78% (for genomes containing the polymerase PolC) to 58% (for the other genomes) of their genes on the leading strand [ 3 ]. (biomedcentral.com)
  • Key to the organization of an individual gene is its promoter, to which machinery, especially RNA polymerase, can attach. (jove.com)
  • The genome can be mapped as a 253,413 bp circle, but its structure is complicated by a large repeated region that is present in 6 copies. (biomedcentral.com)
  • UMass Medical School has been awarded a five-year, $15 million grant from the National Institutes of Medicine Common Fund to establish the Center for 3D Structure and Physics of the Genome. (umassmed.edu)
  • Dr. Dekker is a pioneer in the study of the three-dimensional structure of the genome. (umassmed.edu)
  • With this we'll begin to understand which aspects of the 3D structure of the genome control gene function. (umassmed.edu)
  • Methods for gene identification and analysis of gene structure: cloning, PCR, restriction mapping, in situ hybridisation, DNA sequencing. (lu.se)
  • Virulence genotype analysis revealed that strain CR1 lacked hemolytic phospholipase C and D, three genes for LPS biosynthesis and had reduced antibiotic resistance genes when compared with clinical strains. (frontiersin.org)