Abstract:
BACKGROUND:CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive. RESULTS:We carry out an experimental and computational study that exploits the natural genetic variation across five closely related species to assess how CTCF binding patterns stably fixed by evolution in each species contribute to the establishment and evolutionary dynamics of TAD boundaries. We perform CTCF ChIP-seq in multiple mouse species to create genome-wide binding profiles and associate them with TAD boundaries. Our analyses reveal that CTCF binding is maintained at TAD boundaries by a balance of selective constraints and dynamic evolutionary processes. Regardless of their conservation across species, CTCF binding sites at TAD boundaries are subject to stronger sequence and functional constraints compared to other CTCF sites. TAD boundaries frequently harbor dynamically evolving clusters containing both evolutionarily old and young CTCF sites as a result of the repeated acquisition of new species-specific sites close to conserved ones. The overwhelming majority of clustered CTCF sites colocalize with cohesin and are significantly closer to gene transcription start sites than nonclustered CTCF sites, suggesting that CTCF clusters particularly contribute to cohesin stabilization and transcriptional regulation. CONCLUSIONS:Dynamic conservation of CTCF site clusters is an apparently important feature of CTCF binding evolution that is critical to the functional stability of a higher-order chromatin structure.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Kentepozidou E,Aitken SJ,Feig C,Stefflova K,Ibarra-Soria X,Odom DT,Roller M,Flicek Pdoi
10.1186/s13059-019-1894-xsubject
Has Abstractpub_date
2020-01-07 00:00:00pages
5issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-019-1894-xjournal_volume
21pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract:BACKGROUND:Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alp...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02080-6
更新日期:2020-07-02 00:00:00
abstract:BACKGROUND:The influence of genetic variation on complex diseases is potentially mediated through a range of highly dynamic epigenetic processes exhibiting temporal variation during development and later life. Here we present a catalogue of the genetic influences on DNA methylation (methylation quantitative trait loci ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-016-0926-z
更新日期:2016-03-31 00:00:00
abstract::A report on the Cold Spring Harbor Laboratory/Wellcome Trust conference on Network Biology, Hinxton, UK, 27-31 August 2008. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2008-9-10-324
更新日期:2008-10-27 00:00:00
abstract::Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats, frequently making Hi-C analyses tedious and time-consuming. Here, we p...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02215-9
更新日期:2020-12-17 00:00:00
abstract:BACKGROUND:Short-term laboratory evolution of bacteria followed by genomic sequencing provides insight into the mechanism of adaptive evolution, such as the number of mutations needed for adaptation, genotype-phenotype relationships, and the reproducibility of adaptive outcomes. RESULTS:In the present study, we descri...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-10-r118
更新日期:2009-01-01 00:00:00
abstract:BACKGROUND:Understanding the embryonic stem cell (ESC) fate decision between self-renewal and proper differentiation is important for developmental biology and regenerative medicine. Attention has focused on mechanisms involving histone modifications, alternative pre-messenger RNA splicing, and cell-cycle progression. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1512-3
更新日期:2018-09-14 00:00:00
abstract:BACKGROUND:Long noncoding enhancer RNAs (lnc-eRNAs) are a subset of stable eRNAs identified from annotated lncRNAs. They might act as enhancer activity-related therapeutic targets in cancer. However, the underlying mechanism of epigenetic activation and their function in cancer initiation and progression remain largely...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02186-x
更新日期:2020-11-03 00:00:00
abstract:BACKGROUND:Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1479-0
更新日期:2018-08-17 00:00:00
abstract:BACKGROUND:Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasingly difficult task of assimilating the knowledge contained in the biomedical literature. We present ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-s2-s9
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:The role played by microRNAs (miRs) as common regulators in physiologic processes such as development and various disease states was recently highlighted. Retinitis pigmentosa (RP) linked to RHO (which encodes rhodopsin) is the most frequent form of inherited retinal degeneration that leads to blindness, for...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-11-r248
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. RESULTS...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-4-r40
更新日期:2011-01-01 00:00:00
abstract::A report on the 23rd Fungal Genetics Conference, Pacific Grove, USA, 15-20 March 2005. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2005-6-8-336
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets. We analyzed archaeal phylogeny using two concatenated datasets consistin...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2004-5-3-r17
更新日期:2004-01-01 00:00:00
abstract::Transposable elements (TEs) are notable drivers of genetic innovation. Over evolutionary time, TE insertions can supply new promoter, enhancer, and insulator elements to protein-coding genes and establish novel, species-specific gene regulatory networks. Conversely, ongoing TE-driven insertional mutagenesis, nonhomolo...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/s13059-016-0965-5
更新日期:2016-05-09 00:00:00
abstract::Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA. ...
journal_title:Genome biology
pub_type: 历史文章,杂志文章,评审
doi:10.1186/s13059-015-0866-z
更新日期:2016-01-11 00:00:00
abstract:BACKGROUND:Hemispheric asymmetry in neuronal processes is a fundamental feature of the human brain and drives symptom lateralization in Parkinson's disease (PD), but its molecular determinants are unknown. Here, we identify divergent epigenetic patterns involved in hemispheric asymmetry by profiling DNA methylation in ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-01960-1
更新日期:2020-03-09 00:00:00
abstract:BACKGROUND:Circular RNAs are a class of endogenous RNAs with various functions in eukaryotic cells. Worthy of note, circular RNAs play a critical role in cancer. Currently, nothing is known about their role in head and neck squamous cell carcinoma (HNSCC). The identification of circular RNAs in HNSCC might become usefu...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1368-y
更新日期:2017-12-20 00:00:00
abstract:BACKGROUND:Growth rate is central to the development of cells in all organisms. However, little is known about the impact of changing growth rates. We used continuous cultures to control growth rate and studied the transcriptional program of the model eukaryote Saccharomyces cerevisiae, with generation times varying be...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-11-r107
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:DNA damage leads to cellular responses that include the increased expression of DNA repair genes, repression of DNA replication and alterations in cellular metabolism. Archaeal information processing pathways resemble those in eukaryotes, but archaeal damage response pathways remain poorly understood. RESUL...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-10-r220
更新日期:2007-01-01 00:00:00
abstract::We have developed an ontology to provide standardized nomenclature for anatomical terms in the postnatal mouse. The Adult Mouse Anatomical Dictionary is structured as a directed acyclic graph, and is organized hierarchically both spatially and functionally. The ontology will be used to annotate and integrate different...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2005-6-3-r29
更新日期:2005-01-01 00:00:00
abstract::Bisulfite sequencing (BS-seq) is the gold standard for studying genome-wide DNA methylation. We developed MOABS to increase the speed, accuracy, statistical power and biological relevance of BS-seq data analysis. MOABS detects differential methylation with 10-fold coverage at single-CpG resolution based on a Beta-Bino...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-2-r38
更新日期:2014-02-24 00:00:00
abstract::We develop PIRCh-seq, a method which enables a comprehensive survey of chromatin-associated RNAs in a histone modification-specific manner. We identify hundreds of chromatin-associated RNAs in several cell types with substantially less contamination by nascent transcripts. Non-coding RNAs are found enriched on chromat...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1880-3
更新日期:2019-12-20 00:00:00
abstract::The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics. ...
journal_title:Genome biology
pub_type: 信件
doi:10.1186/gb-2008-9-3-402
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:Although genetic or epigenetic alterations have been shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed. RESULTS:Here, we explore whether chromatin conformation can be used to classify human leu...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-4-r60
更新日期:2014-04-30 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition. So far, identification of miRNAs has been limited to a few model plant species, such as Arabidopsis, rice and Populus, whose genomes have been sequenc...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-6-r96
更新日期:2007-01-01 00:00:00
abstract::The circadian clock determines the rhythmic expression of many different genes throughout a 24-hour period. A recent study investigating the circadian regulation of liver proteins reveals multiple levels of regulation, including transcriptional, post-transcriptional and post-translational mechanisms. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2006-7-9-234
更新日期:2006-01-01 00:00:00
abstract::A novel in vivo screening approach has identified KLF17 as a key metastasis suppressor gene that acts through regulation of Id1 transcription factor-dependent induction of the epithelial-to-mesenchymal transition. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2009-10-11-244
更新日期:2009-01-01 00:00:00
abstract::Single-cell RNA-sequencing (scRNA-seq) has emerged as a revolutionary tool that allows us to address scientific questions that eluded examination just a few years ago. With the advantages of scRNA-seq come computational challenges that are just beginning to be addressed. In this article, we highlight the computational...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/s13059-016-0927-y
更新日期:2016-04-07 00:00:00
abstract:BACKGROUND:Gene loss, inversions, translocations, and other chromosomal rearrangements vary among species, resulting in different rates of structural genome evolution. Major chromosomal rearrangements are rare in most eukaryotes, giving large regions with the same genes in the same order and orientation across species....
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-5-r45
更新日期:2011-01-01 00:00:00
abstract::Map based cloning in Arabidopsis thaliana can be a difficult and time-consuming process, specifically if the phenotype is subtle and scoring labour intensive. Here, we have re-sequenced the 120-Mb genome of a novel Arabidopsis clock mutant early bird (ebi-1) in Wassilewskija (Ws-2). We demonstrate the utility of seque...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-3-r28
更新日期:2011-01-01 00:00:00