Abstract:
:Understanding the molecular basis for phenotypic differences between humans and other primates remains an outstanding challenge. Mutations in non-coding regulatory DNA that alter gene expression have been hypothesized as a key driver of these phenotypic differences. This has been supported by differential gene expression analyses in general, but not by the identification of specific regulatory elements responsible for changes in transcription and phenotype. To identify the genetic source of regulatory differences, we mapped DNaseI hypersensitive (DHS) sites, which mark all types of active gene regulatory elements, genome-wide in the same cell type isolated from human, chimpanzee, and macaque. Most DHS sites were conserved among all three species, as expected based on their central role in regulating transcription. However, we found evidence that several hundred DHS sites were gained or lost on the lineages leading to modern human and chimpanzee. Species-specific DHS site gains are enriched near differentially expressed genes, are positively correlated with increased transcription, show evidence of branch-specific positive selection, and overlap with active chromatin marks. Species-specific sequence differences in transcription factor motifs found within these DHS sites are linked with species-specific changes in chromatin accessibility. Together, these indicate that the regulatory elements identified here are genetic contributors to transcriptional and phenotypic differences among primate species.
journal_name
PLoS Genetjournal_title
PLoS geneticsauthors
Shibata Y,Sheffield NC,Fedrigo O,Babbitt CC,Wortham M,Tewari AK,London D,Song L,Lee BK,Iyer VR,Parker SC,Margulies EH,Wray GA,Furey TS,Crawford GEdoi
10.1371/journal.pgen.1002789subject
Has Abstractpub_date
2012-06-01 00:00:00pages
e1002789issue
6eissn
1553-7390issn
1553-7404pii
PGENETICS-D-11-02600journal_volume
8pub_type
杂志文章相关文献
PLoS Genetics文献大全abstract::Shifts between epigenetic states of transcriptional activity are typically correlated with changes in epigenetic marks. However, exceptions to this rule suggest the existence of additional, as yet uncharacterized, layers of epigenetic regulation. MOM1, a protein of 2,001 amino acids that acts as a transcriptional sile...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1002484
更新日期:2012-02-01 00:00:00
abstract::Association mapping is a powerful approach for dissecting the genetic architecture of complex quantitative traits using high-density SNP markers in maize. Here, we expanded our association panel size from 368 to 513 inbred lines with 0.5 million high quality SNPs using a two-step data-imputation method which combines ...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1004573
更新日期:2014-09-11 00:00:00
abstract::Genome-wide association studies (GWAS) have identified chromosomal loci that affect risk of coronary heart disease (CHD) independent of classical risk factors. One such association signal has been identified at 6q23.2 in both Caucasians and East Asians. The lead CHD-associated polymorphism in this region, rs12190287, ...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1004263
更新日期:2014-03-27 00:00:00
abstract::A fundamental step in the evolution of the visual system is the gene duplication of visual opsins and differentiation between the duplicates in absorption spectra and expression pattern in the retina. However, our understanding of the mechanism of expression differentiation is far behind that of spectral tuning of ops...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1001245
更新日期:2010-12-16 00:00:00
abstract::Adipose tissue lipolysis occurs during the development of heart failure as a consequence of chronic adrenergic stimulation. However, the impact of enhanced adipose triacylglycerol hydrolysis mediated by adipose triglyceride lipase (ATGL) on cardiac function is unclear. To investigate the role of adipose tissue lipolys...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1007171
更新日期:2018-01-10 00:00:00
abstract::Progesterone, via the progesterone receptor (PGR), is essential for endometrial stromal cell decidualization, a cellular transformation event in which stromal fibroblasts differentiate into decidual cells. Uterine decidualization supports embryo implantation and placentation as well as subsequent events, which togethe...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1005937
更新日期:2016-04-01 00:00:00
abstract::Chromosome breakage is a major threat to genome integrity. The most accurate way to repair DNA double strand breaks (DSB) is homologous recombination (HR) with an intact copy of the broken locus. Mobility of the broken DNA has been seen to increase during the search for a donor copy. Observing chromosome dynamics duri...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1004187
更新日期:2014-03-13 00:00:00
abstract::The requirements for oocyte meiotic cytokinesis during polar body extrusion are not well understood. In particular, the relationship between the oocyte meiotic spindle and polar body contractile ring dynamics remains largely unknown. We have used live cell imaging and spindle assembly defective mutants lacking the fun...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1008751
更新日期:2020-10-07 00:00:00
abstract::Genome-wide association studies (GWAS) have now been conducted for hundreds of phenotypes of relevance to human health. Many such GWAS involve multiple closely-related phenotypes collected on the same samples. However, the vast majority of these GWAS have been analyzed using simple univariate analyses, which consider ...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1008431
更新日期:2019-10-09 00:00:00
abstract::Fanconi Anemia (FA) is a rare autosomal recessive disorder characterized by hypersensitivity to inter-strand crosslinks (ICLs). FANCD2, a central factor of the FA pathway, is essential for the repair of double strand breaks (DSBs) generated during fork collapse at ICLs. While lesions different from ICLs can also trigg...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1005792
更新日期:2016-01-14 00:00:00
abstract::Centromere sequences are not conserved between species, and there is compelling evidence for epigenetic regulation of centromere identity, with location being dictated by the presence of chromatin containing the histone H3 variant CENP-A. Paradoxically, in most organisms CENP-A chromatin generally occurs on particular...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1004986
更新日期:2015-03-04 00:00:00
abstract::More than 5% of alternatively spliced internal exons in the human genome are derived from Alu elements in a process termed exonization. Alus are comprised of two homologous arms separated by an internal polypyrimidine tract (PPT). In most exonizations, splice sites are selected from within the same arm. We hypothesize...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000717
更新日期:2009-11-01 00:00:00
abstract::Almost 60 years ago, Severo Ochoa was awarded the Nobel Prize in Physiology or Medicine for his discovery of the enzymatic synthesis of RNA by polynucleotide phosphorylase (PNPase). Although this discovery provided an important tool for deciphering the genetic code, subsequent work revealed that the predominant functi...
journal_title:PLoS genetics
pub_type: 杂志文章,评审
doi:10.1371/journal.pgen.1007654
更新日期:2018-10-11 00:00:00
abstract::Recent genome-wide meta-analyses identified 157 loci associated with cross-sectional lipid traits. Here we tested whether these loci associate (singly and in trait-specific genetic risk scores [GRS]) with longitudinal changes in total cholesterol (TC) and triglyceride (TG) levels in a population-based prospective coho...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1004388
更新日期:2014-06-12 00:00:00
abstract::It is now widely recognized that robustness is an inherent property of biological systems [1],[2],[3]. The contribution of close sequence homologs to genetic robustness against null mutations has been previously demonstrated in simple organisms [4],[5]. In this paper we investigate in detail the contribution of gene d...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000014
更新日期:2008-03-14 00:00:00
abstract::Significant interest has emerged in mapping genetic susceptibility for complex traits through whole-genome association studies. These studies rely on the extent of association, i.e., linkage disequilibrium (LD), between single nucleotide polymorphisms (SNPs) across the human genome. LD describes the nonrandom associat...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.0020142
更新日期:2006-09-08 00:00:00
abstract::Centrioles are microtubule-based organelles important for the formation of cilia, flagella and centrosomes. Despite progress in understanding the underlying assembly mechanisms, how centriole integrity is ensured is incompletely understood, including in sperm cells, where such integrity is particularly critical. We id...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1004777
更新日期:2014-11-20 00:00:00
abstract::Homology-dependent repair of DNA double-strand breaks (DSBs) by gene conversion involves short tracts of DNA synthesis and limited loss of heterozygosity (LOH). For DSBs that present only one end, repair occurs by invasion into a homologous sequence followed by replication to the end of the chromosome resulting in ext...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1001007
更新日期:2010-07-08 00:00:00
abstract::Genome-wide association studies (GWAS) have become increasingly common due to advances in technology and have permitted the identification of differences in single nucleotide polymorphism (SNP) alleles that are associated with diseases. However, while typical GWAS analysis techniques treat markers individually, comple...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1002101
更新日期:2011-06-01 00:00:00
abstract::HSPB7 is a member of the small heat-shock protein (HSPB) family and is expressed in the cardiomyocytes from cardiogenesis onwards. A dramatic increase in HSPB7 is detected in the heart and blood plasma immediately after myocardial infarction. Additionally, several single-nucleotide polymorphisms of HSPB7 have been ide...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1006984
更新日期:2017-08-21 00:00:00
abstract::RNA silencing is a defense system against "genomic parasites" such as transposable elements (TE), which are potentially harmful to host genomes. In plants, transcripts from TEs induce production of double-stranded RNAs (dsRNAs) and are processed into small RNAs (small interfering RNAs, siRNAs) that suppress TEs by RNA...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1002953
更新日期:2012-09-01 00:00:00
abstract::Nephrolithiasis is a common nephrologic disorder with complex etiology. To identify the genetic factor(s) for nephrolithiasis, we conducted a three-stage genome-wide association study (GWAS) using a total of 5,892 nephrolithiasis cases and 17,809 controls of Japanese origin. Here we found three novel loci for nephroli...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1002541
更新日期:2012-01-01 00:00:00
abstract::Genome-wide association studies have shown that pleiotropy is a common phenomenon that can potentially be exploited for enhanced detection of susceptibility loci. We propose heritability informed power optimization (HIPO) for conducting powerful pleiotropic analysis using summary-level association statistics. We find ...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1007549
更新日期:2018-10-05 00:00:00
abstract::Homolog pairing, which plays a critical role in meiosis, poses a potential risk if it occurs in inappropriate tissues or between nonallelic sites, as it can lead to changes in gene expression, chromosome entanglements, and loss-of-heterozygosity due to mitotic recombination. This is particularly true in Drosophila, wh...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1004013
更新日期:2013-01-01 00:00:00
abstract::Breast cancer is the most common cancer in women in developed countries, and the contribution of genetic susceptibility to breast cancer development has been well-recognized. However, a great proportion of these hereditary predisposing factors still remain unidentified. To examine the contribution of rare copy number ...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1002734
更新日期:2012-01-01 00:00:00
abstract::Microbial populations founded by a single clone and propagated under resource limitation can become polymorphic. We sought to elucidate genetic mechanisms whereby a polymorphism evolved in Escherichia coli under glucose limitation and persisted because of cross-feeding among multiple adaptive clones. Apart from a 29 k...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000713
更新日期:2009-11-01 00:00:00
abstract::The gene encoding the GroEL chaperonin is duplicated in nearly 30% of bacterial genomes; and although duplicated groEL genes have been comprehensively determined to have distinct physiological functions in different species, the mechanisms involved have not been characterized to date. Myxococcus xanthus DK1622 has two...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1003306
更新日期:2013-01-01 00:00:00
abstract::Physical activity (PA) may modify the genetic effects that give rise to increased risk of obesity. To identify adiposity loci whose effects are modified by PA, we performed genome-wide interaction meta-analyses of BMI and BMI-adjusted waist circumference and waist-hip ratio from up to 200,452 adults of European (n = 1...
journal_title:PLoS genetics
pub_type: 杂志文章,meta分析
doi:10.1371/journal.pgen.1006528
更新日期:2017-04-27 00:00:00
abstract::Rhizobial infection of legume root hairs requires a rearrangement of the actin cytoskeleton to enable the establishment of plant-made infection structures called infection threads. In the SCAR/WAVE (Suppressor of cAMP receptor defect/WASP family verpolin homologous protein) actin regulatory complex, the conserved N-te...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1005623
更新日期:2015-10-30 00:00:00
abstract::X-linked myotubular myopathy (XLMTM) is a congenital disorder caused by mutations of the myotubularin gene, MTM1. Myotubularin belongs to a large family of conserved lipid phosphatases that include both catalytically active and inactive myotubularin-related proteins (i.e., "MTMRs"). Biochemically, catalytically inacti...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1003583
更新日期:2013-06-01 00:00:00