Abstract:
:Accelerated evolution of regulatory sequence can alter the expression pattern of target genes, and cause phenotypic changes. In this study, we used DNase I hypersensitive sites (DHSs) to annotate putative regulatory sequences in the human genome, and conducted a genome-wide analysis of the effects of accelerated evolution on regulatory sequences. Working under the assumption that local ancient repeat elements of DHSs are under neutral evolution, we discovered that ∼0.44% of DHSs are under accelerated evolution (ace-DHSs). We found that ace-DHSs tend to be more active than background DHSs, and are strongly associated with epigenetic marks of active transcription. The target genes of ace-DHSs are significantly enriched in neuron-related functions, and their expression levels are positively selected in the human brain. Thus, these lines of evidences strongly suggest that accelerated evolution on regulatory sequences plays important role in the evolution of human-specific phenotypes.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Dong X,Wang X,Zhang F,Tian Wdoi
10.1093/molbev/msw128subject
Has Abstractpub_date
2016-10-01 00:00:00pages
2565-75issue
10eissn
0737-4038issn
1537-1719pii
msw128journal_volume
33pub_type
杂志文章abstract::Gene duplication is a major driving force in genome evolution. Here, we explore the nature and origin of the POT1 gene duplication in Arabidopsis thaliana. Protection of Telomeres (POT1) is a conserved multifunctional protein that modulates telomerase activity and its engagement with telomeres. Arabidopsis thaliana en...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv025
更新日期:2015-05-01 00:00:00
abstract::Some genes have repeatedly been found to control diverse adaptations in a wide variety of organisms. Such gene reuse reveals not only the diversity of phenotypes these unique genes control but also the composition of developmental gene networks and the genetic routes available to and taken by organisms during adaptati...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz194
更新日期:2019-12-01 00:00:00
abstract::Viral genome integration provides a complex route to biological innovation that has rarely but repeatedly occurred in one of the most diverse lineages of organisms on the planet, parasitoid wasps. We describe a novel endogenous virus in braconid wasps derived from pathogenic alphanudiviruses. Limited to a subset of th...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy148
更新日期:2018-10-01 00:00:00
abstract::Phenotypic plasticity results in a diversity of phenotypes from a single genotype in response to environmental cues. To understand the molecular basis of phenotypic plasticity, studies have focused on differential gene expression levels between environmentally determined phenotypes. The extent of alternative splicing ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy095
更新日期:2018-08-01 00:00:00
abstract::The emergence of islands has been linked to spectacular radiations of diverse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary diversifi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz017
更新日期:2019-04-01 00:00:00
abstract::Most of the well-characterized mitochondrial genomes from diverse green algal lineages are circular mapping DNA molecules; however, Chlamydomonas reinhardtii has a linear 15.8 kb unit mitochondrial genome with 580 or 581 bp inverted repeat ends. In mitochondrial-enriched fractions prepared from Polytomella parva (=P. ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004180
更新日期:2002-07-01 00:00:00
abstract::Serum response factor (SRF) and myocyte enhancer factor 2 (MEF2) represent two types of members of the MCM1, AGAMOUS, DEFICIENS, and SRF (MADS)-box transcription factor family present in animals and fungi. Each type has distinct biological functions, which are reflected by the distinct specificities of the proteins bo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq214
更新日期:2011-01-01 00:00:00
abstract::The Piwi-interacting RNA (piRNA) pathway defends animal genomes against the harmful consequences of transposable element (TE) infection by imposing small-RNA-mediated silencing. Because silencing is targeted by TE-derived piRNAs, piRNA production is posited to be central to the evolution of genome defense. We harnesse...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst081
更新日期:2013-08-01 00:00:00
abstract::The evolution of mitochondria from ancestral bacteria required that new protein transport machinery be established. Recent controversy over the evolution of these new molecular machines hinges on the degree to which ancestral bacterial transporters contributed during the establishment of the new protein import pathway...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq305
更新日期:2011-05-01 00:00:00
abstract::Cells react to oxidative stress conditions by launching a defense response through the induction of nuclear gene expression. The advent of microarray technologies allowed monitoring of oxidative stress-dependent changes of transcript levels at a comprehensive and genome-wide scale, resulting in a series of inventories...
journal_title:Molecular biology and evolution
pub_type: 杂志文章,meta分析
doi:10.1093/molbev/msm276
更新日期:2008-03-01 00:00:00
abstract::Human c-Myb proto-oncogene is highly expressed in hematopoietic progenitors as well as leukemia and certain solid tumor. However, the regulatory mechanisms of its expression and biological functions remain largely unclear. Recently, c-Myb has been shown to be targeted by microRNA-150 (miR-150) which thereby controls B...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn165
更新日期:2008-10-01 00:00:00
abstract::The question of multiple sequence alignment quality has received much attention from developers of alignment methods. Less forthcoming, however, are practical measures for addressing alignment quality issues in real life settings. Here, we present a simple methodology to help identify and quantify the uncertainties in...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm060
更新日期:2007-06-01 00:00:00
abstract::The geographic origin and time of dispersal of Austroasiatic (AA) speakers, presently settled in south and southeast Asia, remains disputed. Two rival hypotheses, both assuming a demic component to the language dispersal, have been proposed. The first of these places the origin of Austroasiatic speakers in southeast A...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq288
更新日期:2011-02-01 00:00:00
abstract::The heat shock protein (Hsp) sequences, because of their ubiquity and high degree of conservation, provide useful models for phylogenetic analysis. In this paper I have carried out a global alignment of all available sequences (a total of 31) for the 90-kD heat shock protein (Hsp90) family. The minimum amino acid iden...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040281
更新日期:1995-11-01 00:00:00
abstract::Reconstructing phylogenies from intraspecific data (such as human mitochondrial DNA variation) is often a challenging task because of large sample sizes and small genetic distances between individuals. The resulting multitude of plausible trees is best expressed by a network which displays alternative potential evolut...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026036
更新日期:1999-01-01 00:00:00
abstract::While it is widely accepted that most animals (Metazoa) do not have endogenous cellulases, relying instead on intestinal symbionts for cellulose digestion, the glycosyl hydrolase family 9 (GHF9) cellulases found in the genomes of termites, abalone, and sea squirts could be an exception. Using information from expresse...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi107
更新日期:2005-05-01 00:00:00
abstract::Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity t...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa221
更新日期:2021-01-23 00:00:00
abstract::Genetic variation in contemporary South Asian populations follows a northwest to southeast decreasing cline of shared West Eurasian ancestry. A growing body of ancient DNA evidence is being used to build increasingly more realistic models of demographic changes in the last few thousand years. Through high-quality mode...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz037
更新日期:2019-08-01 00:00:00
abstract::Two recent studies have presented conflicting views on variation present within the 294 base third domain of the 12S rRNA gene in the genus Drosophila, and in D. pseudoobscura in particular. One study suggested that this gene is highly invariant across the genus, while another recovered 22 distinct haplotypes from 22 ...
journal_title:Molecular biology and evolution
pub_type: 评论,杂志文章
doi:10.1093/oxfordjournals.molbev.a026374
更新日期:2000-06-01 00:00:00
abstract::Bacterial populations have been shown to accumulate deleterious mutations during spatial expansions that overall decrease their fitness and ability to grow. However, it is unclear if and how they can respond to selection in face of this mutation load. We examine here if artificial selection can counteract the negative...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz148
更新日期:2019-10-01 00:00:00
abstract::Models of codon evolution have attracted particular interest because of their unique capabilities to detect selection forces and their high fit when applied to sequence evolution. We described here a novel approach for modeling codon evolution, which is based on Kronecker product of matrices. The 61 × 61 codon substit...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu196
更新日期:2014-09-01 00:00:00
abstract::Wolbachia bacteria infect about half of all arthropods, with diverse and extreme consequences ranging from sex-ratio distortion and mating incompatibilities to protection against viruses. These phenotypic effects, combined with efficient vertical transmission from mothers to offspring, satisfactorily explain the invas...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx073
更新日期:2017-05-01 00:00:00
abstract::Gene expression changes contribute to complex trait variations in both individuals and populations. However, the evolution of gene expression underlying complex traits over macroevolutionary timescales remains poorly understood. Snake venoms are proteinaceous cocktails where the expression of each toxin can be quantif...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz125
更新日期:2019-09-01 00:00:00
abstract::The complete mitochondrial DNA (mtDNA) control region was sequenced for 71 individuals from five species of the rodent genus Clethrionomys both to understand patterns of variation and to explore the existence of previously described domains and other elements. Among species, the control region ranged from 942 to 971 b...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003935
更新日期:2001-08-01 00:00:00
abstract::Dissecting the evolutionary genetic processes underlying eye reduction and vision loss in obligate cave-dwelling organisms has been a long-standing challenge in evolutionary biology. Independent vision loss events in related subterranean organisms can provide critical insight into these processes as well as into the n...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy106
更新日期:2018-08-01 00:00:00
abstract::The phylogeny of Anisoptera, dragonflies in the strict sense, has proven to be notoriously difficult to resolve. Based on morphological characters, several recent publications dealing with the phylogeny of dragonflies proposed contradicting inter- and intrafamily relationships. We explored phylogenetic information con...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003717
更新日期:2001-01-01 00:00:00
abstract::We have evaluated the molecular evolution of the chemokine receptor CCR5 in primates. The chemokine receptor CCR5 serves as a major co-receptor for human immunodeficiency virus/simian immunodeficiency virus (HIV/SIV) infection. Knowledge of evolution of the CCR5 molecule and selection on the CCR5 gene may shed light o...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg198
更新日期:2003-10-01 00:00:00
abstract::Heuristic approaches were used to quantify the influence that sequencing errors have on estimates of nucleotide diversity, substitution rate, and the construction of genealogies. Error rates of less than 1 nucleotide/kb probably have little affect on conclusions about the evolutionary history of highly polymorphic org...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040756
更新日期:1992-07-01 00:00:00
abstract::The nucleotide sequences of the 5'-flanking regions of the duplicated Amy genes in eight sibling species belonging to the melanogaster species subgroup are analyzed. In Drosophila melanogaster, a region of about 450 bp immediately upstream of the translation initiation site of the two paralogous genes (the proximal an...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025617
更新日期:1996-04-01 00:00:00
abstract::This study examines molecular relationships across a wide range of species in the mass spawning scleractinian coral genus Acropora. Molecular phylogenies were obtained for 28 species using DNA sequence analyses of two independent markers, a nuclear intron and the mtDNA putative control region. Although the composition...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003916
更新日期:2001-07-01 00:00:00