当前位置： SCI文献检索 > BMC EVOLUTIONARY BIOLOGY期刊下所有文献 > CpG islands under selective pressure are enriched with H3K4me3, H3K27ac and H3K36me3 histone modifications.

CpG islands under selective pressure are enriched with H3K4me3, H3K27ac and H3K36me3 histone modifications.

Abstract：

BACKGROUND:Histone modification is an epigenetic mechanism that influences gene regulation in eukaryotes. In particular, histone modifications in CpG islands (CGIs) are associated with different chromatin states and with transcription activity. Changes in gene expression play a crucial role in adaptation and evolution. RESULTS:In this paper, we have studied, using a computational biology approach, the relationship between histone modifications in CGIs and selective pressure in Homo sapiens. We considered three histone modifications: histone H3 lysine 4 trimethylation (H3K4me3), histone H3 lysine 27 acetylation (H3K27ac) and histone H3 lysine 36 trimethylation (H3K36me3), and we used the publicly available genomic-scale histone modification data of thirteen human cell lines. To define regions under selective pressure, we used three distinct signatures that mark selective events from different evolutionary periods. We found that CGIs under selective pressure showed significant enrichments for histone modifications. CONCLUSION:Our result suggests that, CGIs that have undergone selective events are characterized by epigenetic signatures, in particular, histone modifications that are distinct from CGIs with no evidence of selection.

journal_name

BMC Evol Biol

journal_title

BMC evolutionary biology

authors

Akhtar MM,Scala G,Cocozza S,Miele G,Monticelli A

doi

10.1186/1471-2148-13-145

subject

Has Abstract

pub_date

2013-07-10 00:00:00

pages

145

issn

1471-2148

pii

1471-2148-13-145

journal_volume

13

pub_type

杂志文章

相关文献

BMC EVOLUTIONARY BIOLOGY文献大全
  • Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment.

    abstract：BACKGROUND:The past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph ...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/s12862-015-0415-0

    authors： Eytan RI,Evans BR,Dornburg A,Lemmon AR,Lemmon EM,Wainwright PC,Near TJ

    更新日期：2015-06-14 00:00:00

  • Molecular evolution of Adh and LEAFY and the phylogenetic utility of their introns in Pyrus (Rosaceae).

    abstract：BACKGROUND:The genus Pyrus belongs to the tribe Pyreae (the former subfamily Maloideae) of the family Rosaceae, and includes one of the most important commercial fruit crops, pear. The phylogeny of Pyrus has not been definitively reconstructed. In our previous efforts, the internal transcribed spacer region (ITS) revea...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/1471-2148-11-255

    authors： Zheng X,Hu C,Spooner D,Liu J,Cao J,Teng Y

    更新日期：2011-09-14 00:00:00

  • Comparative phylogeography of the plateau zokor (Eospalax baileyi) and its host-associated flea (Neopsylla paranoma) in the Qinghai-Tibet Plateau.

    abstract：BACKGROUND:Specific host-parasite systems often embody a particular co-distribution phenomenon, in which the parasite's phylogeographic pattern is dependent on its host. In practice, however, both congruent and incongruent phylogeographic patterns between the host and the parasite have been reported. Here, we compared ...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/s12862-014-0180-5

    authors： Lin G,Zhao F,Chen H,Deng X,Su J,Zhang T

    更新日期：2014-08-17 00:00:00

  • Transgenerational plasticity following a dual pathogen and stress challenge in fruit flies.

    abstract：BACKGROUND:Phenotypic plasticity operates across generations, when the parental environment affects phenotypic expression in the offspring. Recent studies in invertebrates have reported transgenerational plasticity in phenotypic responses of offspring when the mothers had been previously exposed to either live or heat-...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/s12862-016-0737-6

    authors： Nystrand M,Cassidy EJ,Dowling DK

    更新日期：2016-08-27 00:00:00

  • Ongoing niche differentiation under high gene flow in a polymorphic brackish water threespine stickleback (Gasterosteus aculeatus) population.

    abstract：BACKGROUND:Marine threespine sticklebacks colonized and adapted to brackish and freshwater environments since the last Pleistocene glacial. Throughout the Holarctic, three lateral plate morphs are observed; the low, partial and completely plated morph. We test if the three plate morphs in the brackish water Lake Engerv...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/s12862-018-1128-y

    authors： Østbye K,Taugbøl A,Ravinet M,Harrod C,Pettersen RA,Bernatchez L,Vøllestad LA

    更新日期：2018-02-05 00:00:00

  • Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae).

    abstract：BACKGROUND:Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/s12862-016-0714-0

    authors： Young AD,Lemmon AR,Skevington JH,Mengual X,Ståhls G,Reemer M,Jordaens K,Kelso S,Lemmon EM,Hauser M,De Meyer M,Misof B,Wiegmann BM

    更新日期：2016-06-29 00:00:00

  • Spatial turnover in host-plant availability drives host-associated divergence in a South African leafhopper (Cephalelus uncinatus).

    abstract：BACKGROUND:The evolution of reproductive isolation between herbivorous insect populations is often initiated by shifts to novel host-plants, a process that underlies some of the best examples of ecological speciation. However, it is not well understood why host-shifts occur. Arguably the most common hypothesis is that ...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/s12862-017-0916-0

    authors： Augustyn WJ,Anderson B,van der Merwe JF,Ellis AG

    更新日期：2017-03-09 00:00:00

  • The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella.

    abstract：BACKGROUND:Publication of the first diatom genome, that of Thalassiosira pseudonana, established it as a model species for experimental and genomic studies of diatoms. Virtually every ensuing study has treated T. pseudonana as a marine diatom, with genomic and experimental data valued for their insights into the ecolog...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/1471-2148-11-125

    authors： Alverson AJ,Beszteri B,Julius ML,Theriot EC

    更新日期：2011-05-14 00:00:00

  • The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution.

    abstract：BACKGROUND:Bacteria occur in facultative association and intracellular symbiosis with a diversity of eukaryotic hosts. Recently, we have helped to characterise an intracellular nitrogen fixing bacterium, the so-called spheroid body, located within the diatom Rhopalodia gibba. Spheroid bodies are of cyanobacterial origi...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/1471-2148-8-30

    authors： Kneip C,Voss C,Lockhart PJ,Maier UG

    更新日期：2008-01-28 00:00:00

  • Cooperators Unite! Assortative linking promotes cooperation particularly for medium sized associations.

    abstract：BACKGROUND:Evolution of cooperative behaviour is widely studied in different models where interaction is heterogeneous, although static among individuals. However, in nature individuals can often recognize each other and chose, besides to cooperate or not, to preferentially associate with or to avoid certain individual...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/1471-2148-10-173

    authors： Kun A,Boza G,Scheuring I

    更新日期：2010-06-11 00:00:00

  • Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level.

    abstract：BACKGROUND:The functional repertoire of the human proteome is an incremental collection of functions accomplished by protein domains evolved along the Homo sapiens lineage. Therefore, knowledge on the origin of these functionalities provides a better understanding of the domain and protein evolution in human. The lack ...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/1471-2148-6-91

    authors： Pal LR,Guda C

    更新日期：2006-11-07 00:00:00

  • Identification of the notothenioid sister lineage illuminates the biogeographic history of an Antarctic adaptive radiation.

    abstract：BACKGROUND:Antarctic notothenioids are an impressive adaptive radiation. While they share recent common ancestry with several species-depauperate lineages that exhibit a relictual distribution in areas peripheral to the Southern Ocean, an understanding of their evolutionary origins and biogeographic history is limited ...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/s12862-015-0362-9

    authors： Near TJ,Dornburg A,Harrington RC,Oliveira C,Pietsch TW,Thacker CE,Satoh TP,Katayama E,Wainwright PC,Eastman JT,Beaulieu JM

    更新日期：2015-06-11 00:00:00

  • A-to-I editing of Malacoherpesviridae RNAs supports the antiviral role of ADAR1 in mollusks.

    abstract：BACKGROUND:Adenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and thus alter both structural properties and the coding potential of their substrates. Acting on exogenous dsRNAs, ADAR1 exerts a pro- or anti-viral role in vertebrates and Drosophila. RES...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/s12862-019-1472-6

    authors： Rosani U,Bai CM,Maso L,Shapiro M,Abbadi M,Domeneghetti S,Wang CM,Cendron L,MacCarthy T,Venier P

    更新日期：2019-07-23 00:00:00

  • Patterns of genetic variation among geographic and host-plant associated populations of the peach fruit moth Carposina sasakii (Lepidoptera: Carposinidae).

    abstract：BACKGROUND:Populations of herbivorous insects may become genetically differentiated because of local adaptation to different hosts and climates as well as historical processes, and further genetic divergence may occur following the development of reproductive isolation among populations. Here we investigate the populat...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/s12862-017-1116-7

    authors： Wang YZ,Li BY,Hoffmann AA,Cao LJ,Gong YJ,Song W,Zhu JY,Wei SJ

    更新日期：2017-12-20 00:00:00

  • The soft explosive model of placental mammal evolution.

    abstract：BACKGROUND:Recent molecular dating estimates for placental mammals echo fossil inferences for an explosive interordinal diversification, but typically place this event some 10-20 million years earlier than the Paleocene fossils, among apparently more "primitive" mammal faunas. RESULTS:However, current models of molecu...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/s12862-018-1218-x

    authors： Phillips MJ,Fruciano C

    更新日期：2018-07-03 00:00:00

  • Hypervariable antigen genes in malaria have ancient roots.

    abstract：BACKGROUND:The var genes of the human malaria parasite Plasmodium falciparum are highly polymorphic loci coding for the erythrocyte membrane proteins 1 (PfEMP1), which are responsible for the cytoaherence of P. falciparum infected red blood cells to the human vasculature. Cytoadhesion, coupled with differential express...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/1471-2148-13-110

    authors： Zilversmit MM,Chase EK,Chen DS,Awadalla P,Day KP,McVean G

    更新日期：2013-05-31 00:00:00

  • Origin, evolution, and divergence of plant class C GH9 endoglucanases.

    abstract：BACKGROUND:Glycoside hydrolases of the GH9 family encode cellulases that predominantly function as endoglucanases and have wide applications in the food, paper, pharmaceutical, and biofuel industries. The partitioning of plant GH9 endoglucanases, into classes A, B, and C, is based on the differential presence of transm...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/s12862-018-1185-2

    authors： Kundu S,Sharma R

    更新日期：2018-05-30 00:00:00

  • Whole genome duplications and expansion of the vertebrate GATA transcription factor gene family.

    abstract：BACKGROUND:GATA transcription factors influence many developmental processes, including the specification of embryonic germ layers. The GATA gene family has significantly expanded in many animal lineages: whereas diverse cnidarians have only one GATA transcription factor, six GATA genes have been identified in many ver...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/1471-2148-9-207

    authors： Gillis WQ,St John J,Bowerman B,Schneider SQ

    更新日期：2009-08-20 00:00:00

  • Home-field advantage? evidence of local adaptation among plants, soil, and arbuscular mycorrhizal fungi through meta-analysis.

    abstract：BACKGROUND:Local adaptation, the differential success of genotypes in their native versus foreign environment, arises from various evolutionary processes, but the importance of concurrent abiotic and biotic factors as drivers of local adaptation has only recently been investigated. Local adaptation to biotic interactio...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章,meta分析

    doi：10.1186/s12862-016-0698-9

    authors： Rúa MA,Antoninka A,Antunes PM,Chaudhary VB,Gehring C,Lamit LJ,Piculell BJ,Bever JD,Zabinski C,Meadow JF,Lajeunesse MJ,Milligan BG,Karst J,Hoeksema JD

    更新日期：2016-06-10 00:00:00

  • SmTRC1, a novel Schistosoma mansoni DNA transposon, discloses new families of animal and fungi transposons belonging to the CACTA superfamily.

    abstract：BACKGROUND:The CACTA (also called En/Spm) superfamily of DNA-only transposons contain the core sequence CACTA in their Terminal Inverted Repeats (TIRs) and so far have only been described in plants. Large transcriptome and genome sequence data have recently become publicly available for Schistosoma mansoni, a digenetic...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/1471-2148-6-89

    authors： DeMarco R,Venancio TM,Verjovski-Almeida S

    更新日期：2006-11-07 00:00:00

  • Deep phylogenomics of a tandem-repeat galectin regulating appendicular skeletal pattern formation.

    abstract：BACKGROUND:A multiscale network of two galectins Galectin-1 (Gal-1) and Galectin-8 (Gal-8) patterns the avian limb skeleton. Among vertebrates with paired appendages, chondrichthyan fins typically have one or more cartilage plates and many repeating parallel endoskeletal elements, actinopterygian fins have more varied ...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/s12862-016-0729-6

    authors： Bhat R,Chakraborty M,Glimm T,Stewart TA,Newman SA

    更新日期：2016-08-18 00:00:00

  • Molecular circumscription and major evolutionary lineages of the fern genus Dryopteris (Dryopteridaceae).

    abstract：BACKGROUND:The fern genus Dryopteris (Dryopteridaceae) is among the most common and species rich fern genera in temperate forests in the northern hemisphere containing 225-300 species worldwide. The circumscription of Dryopteris has been controversial and various related genera have, over the time, been included in and...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/1471-2148-12-180

    authors： Zhang LB,Zhang L,Dong SY,Sessa EB,Gao XF,Ebihara A

    更新日期：2012-09-13 00:00:00

  • Population size may shape the accumulation of functional mutations following domestication.

    abstract：BACKGROUND:Population genetics theory predicts an important role of differences in the effective population size (N e ) among species on shaping the accumulation of functional mutations by regulating the selection efficiency. However, this correlation has never been tested in domesticated animals. RESULTS:Here, we syn...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/s12862-018-1120-6

    authors： Chen J,Ni P,Li X,Han J,Jakovlić I,Zhang C,Zhao S

    更新日期：2018-01-19 00:00:00

  • Genome trees constructed using five different approaches suggest new major bacterial clades.

    abstract：BACKGROUND:The availability of multiple complete genome sequences from diverse taxa prompts the development of new phylogenetic approaches, which attempt to incorporate information derived from comparative analysis of complete gene sets or large subsets thereof. Such attempts are particularly relevant because of the ma...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/1471-2148-1-8

    authors： Wolf YI,Rogozin IB,Grishin NV,Tatusov RL,Koonin EV

    更新日期：2001-10-20 00:00:00

  • Sex differences in the genetic architecture of lifespan in a seed beetle: extreme inbreeding extends male lifespan.

    abstract：BACKGROUND:Sex differences in lifespan are ubiquitous throughout the animal kingdom but the causes underlying this phenomenon remain poorly understood. Several explanations based on asymmetrical inheritance patterns (sex chromosomes or mitochondrial DNA) have been proposed, but these ideas have rarely been tested exper...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/1471-2148-9-33

    authors： Bilde T,Maklakov AA,Meisner K,la Guardia L,Friberg U

    更新日期：2009-02-06 00:00:00

  • Ecological niche and phylogeography elucidate complex biogeographic patterns in Loxosceles rufescens (Araneae, Sicariidae) in the Mediterranean Basin.

    abstract：BACKGROUND:Understanding the evolutionary history of morphologically cryptic species complexes is difficult, and made even more challenging when geographic distributions have been modified by human-mediated dispersal. This situation is common in the Mediterranean Basin where, aside from the environmental heterogeneity ...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/s12862-014-0195-y

    authors： Planas E,Saupe EE,Lima-Ribeiro MS,Peterson AT,Ribera C

    更新日期：2014-10-09 00:00:00

  • Beneficial laggards: multilevel selection, cooperative polymorphism and division of labour in threshold public good games.

    abstract：BACKGROUND:The origin and stability of cooperation is a hot topic in social and behavioural sciences. A complicated conundrum exists as defectors have an advantage over cooperators, whenever cooperation is costly so consequently, not cooperating pays off. In addition, the discovery that humans and some animal populatio...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/1471-2148-10-336

    authors： Boza G,Számadó S

    更新日期：2010-11-02 00:00:00

  • Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul.

    abstract：BACKGROUND:Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by systematists is likely a product of the difficulties in assessing morphologi...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/s12862-020-01639-y

    authors： de Abreu-Jr EF,Pavan SE,Tsuchiya MTN,Wilson DE,Percequillo AR,Maldonado JE

    更新日期：2020-06-26 00:00:00

  • Timing the origin of human malarias: the lemur puzzle.

    abstract：BACKGROUND:Timing the origin of human malarias has been a focus of great interest. Previous studies on the mitochondrial genome concluded that Plasmodium in primates, including those parasitic to humans, radiated relatively recently during a process where host switches were common. Those investigations, however, assume...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/1471-2148-11-299

    authors： Pacheco MA,Battistuzzi FU,Junge RE,Cornejo OE,Williams CV,Landau I,Rabetafika L,Snounou G,Jones-Engel L,Escalante AA

    更新日期：2011-10-12 00:00:00

  • Mid-day siesta in natural populations of D. melanogaster from Africa exhibits an altitudinal cline and is regulated by splicing of a thermosensitive intron in the period clock gene.

    abstract：BACKGROUND:Many diurnal animals exhibit a mid-day 'siesta', generally thought to be an adaptive response aimed at minimizing exposure to heat on warm days, suggesting that in regions with cooler climates mid-day siestas might be a less prominent feature of animal behavior. Drosophila melanogaster exhibits thermal plast...

    journal_title：BMC evolutionary biology

    pub_type： 杂志文章

    doi：10.1186/s12862-017-0880-8

    authors： Cao W,Edery I

    更新日期：2017-01-23 00:00:00