Abstract:
:Mammalian genomes are partitioned into domains that replicate in a defined temporal order. These domains can replicate at similar times in all cell types (constitutive) or at cell type-specific times (developmental). Genome-wide chromatin conformation capture (Hi-C) has revealed sub-megabase topologically associating domains (TADs), which are the structural counterparts of replication domains. Hi-C also segregates inter-TAD contacts into defined 3D spatial compartments that align precisely to genome-wide replication timing profiles. Determinants of the replication-timing program are re-established during early G1 phase of each cell cycle and lost in G2 phase, but it is not known when TAD structure and inter-TAD contacts are re-established after their elimination during mitosis. Here, we use multiplexed 4C-seq to study dynamic changes in chromatin organization during early G1. We find that both establishment of TADs and their compartmentalization occur during early G1, within the same time frame as establishment of the replication-timing program. Once established, this 3D organization is preserved either after withdrawal into quiescence or for the remainder of interphase including G2 phase, implying 3D structure is not sufficient to maintain replication timing. Finally, we find that developmental domains are less well compartmentalized than constitutive domains and display chromatin properties that distinguish them from early and late constitutive domains. Overall, this study uncovers a strong connection between chromatin re-organization during G1, establishment of replication timing, and its developmental control.
journal_name
Genome Resjournal_title
Genome researchauthors
Dileep V,Ay F,Sima J,Vera DL,Noble WS,Gilbert DMdoi
10.1101/gr.183699.114subject
Has Abstractpub_date
2015-08-01 00:00:00pages
1104-13issue
8eissn
1088-9051issn
1549-5469pii
gr.183699.114journal_volume
25pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::The most polymorphic part of the human genome, the MHC, encodes over 160 proteins of diverse function. Half of them, including the HLA class I and II genes, are directly involved in immune responses. Consequently, the MHC region strongly associates with numerous diseases and clinical therapies. Notoriously, the MHC re...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.213538.116
更新日期:2017-05-01 00:00:00
abstract::As part of an effort to identify the gene responsible for the predominant form of polycystic kidney disease (PKD1), we used a gridded human P1 library for contig assembly. The interval of interest, a 700-kb segment on chromosome 16p13.3, can be physically delineated by the genetic markers D16S125 and D16S84 and chromo...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.6.515
更新日期:1996-06-01 00:00:00
abstract::Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here, we present sequential ChIP-bisulfite-sequencing (ChIP-BS-seq) as an approach to quantitatively assess DNA methylat...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.133728.111
更新日期:2012-06-01 00:00:00
abstract::Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using integrated artificial transposons and automated fluorescent sequencing. Mapping and assembly tools represent important compone...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7.5.551
更新日期:1997-05-01 00:00:00
abstract::Sequencing of the human Y chromosome has uncovered the peculiarities of the genomic organization of a heterogametic sex chromosome of old evolutionary age, and has led to many insights into the evolutionary changes that occurred during its long history. We have studied the genomic organization of the medaka fish Y chr...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5016106
更新日期:2006-07-01 00:00:00
abstract::The str family of genes encoding seven-transmembrane G-protein-coupled or serpentine receptors related to the ODR-10 diacetyl chemoreceptor is very large, with at least 197 members in the Caenorhabditis elegans genome. The closely related stl family has 43 genes, and both families are distantly related to the srd fami...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.8.5.449
更新日期:1998-05-01 00:00:00
abstract::Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and r...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.223727.117
更新日期:2017-12-01 00:00:00
abstract::We have constructed a detailed map of the genomic region containing the ETS-variant gene 6 (ETV6), involved in translocations and deletions associated with hematologic malignancies. Thirty-eight cosmids were characterized belonging to two contigs spanning 340 kb, and an EcoRl restriction map was developed. The gap bet...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.5.404
更新日期:1996-05-01 00:00:00
abstract::Plasticity of gene regulatory encryption can permit DNA sequence divergence without loss of function. Functional information is preserved through conservation of the composition of transcription factor binding sites (TFBS) in a regulatory element. We have developed a method that can accurately identify pairs of functi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.119016.110
更新日期:2011-07-01 00:00:00
abstract::Alternative splicing is a major mechanism for gene product regulation in many multicellular organisms. By using different exon combinations, some coding regions can encode amino acids in multiple reading frames in different transcripts. Here we performed a systematic search through a set of high-quality human transcri...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4246506
更新日期:2006-02-01 00:00:00
abstract::Essential genes refer to those whose null mutation leads to lethality or sterility. Theoretical reasoning and empirical data both suggest that the fatal effect of inactivating an essential gene can be attributed to either the loss of indispensable core cellular function (Type I), or the gain of fatal side effects afte...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.205955.116
更新日期:2016-10-01 00:00:00
abstract::Mutation rates of microsatellites vary greatly among loci. The causes of this heterogeneity remain largely enigmatic yet are crucial for understanding numerous human neurological diseases and genetic instability in cancer. In this first genome-wide study, the relative contributions of intrinsic features and regional g...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7113408
更新日期:2008-01-01 00:00:00
abstract::A DNA mutation detection protocol able to identify and characterize a previously unknown change in a given sequence in a rapid, efficient, sensitive, and inexpensive manner is required to take advantage of the resources now available to researchers through the genome sequencing projects. We have developed a method bas...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.gr-1578r
更新日期:2002-09-01 00:00:00
abstract::With the genomic sequencing of Arabidopsis nearing completion and rice sequencing very much in its infancy, a key question is whether we can exploit the Arabidopsis sequence to identify candidate genes for traits in cereal crops using a map-based approach. This requires the existence of colinearity between the Arabido...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.9.9.825
更新日期:1999-09-01 00:00:00
abstract::The world of noncoding RNAs (ncRNAs) is composed of an enormous and growing number of transcripts, ranging in length from tens of bases to tens of kilobases, involved in all biological processes and altered in expression and/or function in many types of human disorders. The premise of this review is the concept that n...
journal_title:Genome research
pub_type: 杂志文章,评审
doi:10.1101/gr.247239.118
更新日期:2019-09-01 00:00:00
abstract::The gastrointestinal microbiome undergoes shifts in species and strain abundances, yet dynamics involving closely related microorganisms remain largely unknown because most methods cannot resolve them. We developed new metagenomic methods and utilized them to track species and strain level variations in microbial comm...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.142315.112
更新日期:2013-01-01 00:00:00
abstract::Microsatellites--tandem repeats of short DNA motifs--are abundant in the human genome and have high mutation rates. While microsatellite instability is implicated in numerous genetic diseases, the molecular processes involved in their emergence and disappearance are still not well understood. Microsatellites are hypot...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.122937.111
更新日期:2011-12-01 00:00:00
abstract::One of the first useful products from the human genome will be a set of predicted genes. Besides its intrinsic scientific interest, the accuracy and completeness of this data set is of considerable importance for human health and medicine. Though progress has been made on computational gene identification in terms of ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.122800
更新日期:2000-10-01 00:00:00
abstract::Cot-based cloning and sequencing (CBCS) is a powerful tool for isolating and characterizing the various repetitive components of any genome, combining the established principles of DNA reassociation kinetics with high-throughput sequencing. CBCS was used to generate sequence libraries representing the high, middle, an...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2438004
更新日期:2005-01-01 00:00:00
abstract::LSH, a member of the SNF2 family of chromatin remodeling ATPases encoded by the Hells gene, is essential for normal levels of DNA methylation in the mammalian genome. While the role of LSH in the methylation of repetitive DNA sequences is well characterized, its contribution to the regulation of DNA methylation and th...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.108498.110
更新日期:2011-01-01 00:00:00
abstract::A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of 107 known nuclear domain families used for the analysis. Most of the novel domains are present in all major eukaryotic l...
journal_title:Genome research
pub_type: 信件
doi:10.1101/gr.203201
更新日期:2002-01-01 00:00:00
abstract::Transcriptional networks have been shown to evolve very rapidly, prompting questions as to how such changes arise and are tolerated. Recent comparisons of transcriptional networks across species have implicated variations in the cis-acting DNA sequences near genes as the main cause of divergence. What is less clear is...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.111765.110
更新日期:2010-12-01 00:00:00
abstract::Molecular evolution studies are usually based on the analysis of individual genes and thus reflect only small-range variations in genomic sequences. A complementary approach is to study the evolutionary history of rearrangements in entire genomes based on the analysis of gene orders. The progress in whole genome seque...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3002305
更新日期:2005-01-01 00:00:00
abstract::Transcription factors (TFs) are key mediators that propagate extracellular and intracellular signals through to changes in gene expression profiles. However, the rules by which promoters decode the amount of active TF into target gene expression are not well understood. To determine the mapping between promoter DNA se...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.212316.116
更新日期:2017-01-01 00:00:00
abstract::The association of subclasses of Alu repetitive elements with various classes of trinucleotide and tetranucleotide microsatellites was characterized as a first step toward advancing our understanding of the evolution of microsatellite repeats. In addition, information regarding the association of specific classes of m...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7.7.716
更新日期:1997-07-01 00:00:00
abstract::The use of high-density oligonucleotide arrays to measure the expression levels of thousands of genes in parallel has become commonplace. To take further advantage of the growing body of data, we developed a method, termed "GeSNP," to mine the detailed hybridization patterns in oligonucleotide array expression data fo...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6307307
更新日期:2007-08-01 00:00:00
abstract::The need to translate genes to function has positioned the rat as an invaluable animal model for genomic research. The significant increase in genomic resources in recent years has had an immediate functional application in the rat. Many of the resources for translational research are already in place and are ready to...
journal_title:Genome research
pub_type: 杂志文章,评审
doi:10.1101/gr.3744005
更新日期:2005-12-01 00:00:00
abstract::Mouse chromosome 7F4/F5, where the imprinting domain is located, is syntenic to human 11p15.5, the locus for Beckwith-Wiedemann syndrome. The domain is thought to consist of the two subdomains Kip2 (p57(kip2))/Lit1 and Igf2/H19. Because DNA methylation is believed to be a key factor in genomic imprinting, we performed...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.110702
更新日期:2002-12-01 00:00:00
abstract::The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes (cis-eQTLs). More research is needed to identify effects of genetic variation on distant genes (trans-eQTLs) and understand their...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.216754.116
更新日期:2017-11-01 00:00:00
abstract::The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the nonr...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.215186.116
更新日期:2017-07-01 00:00:00