The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements.

Abstract:

BACKGROUND:Bread wheat is an allohexaploid species with a 16-Gb genome that has large intergenic regions, which presents a big challenge for pinpointing regulatory elements and further revealing the transcriptional regulatory mechanisms. Chromatin profiling to characterize the combinatorial patterns of chromatin signatures is a powerful means to detect functional elements and clarify regulatory activities in human studies. RESULTS:In the present study, through comprehensive analyses of the open chromatin, DNA methylome, seven major chromatin marks, and transcriptomic data generated for seedlings of allohexaploid wheat, we detected distinct chromatin architectural features surrounding various functional elements, including genes, promoters, enhancer-like elements, and transposons. Thousands of new genic regions and cis-regulatory elements are identified based on the combinatorial pattern of chromatin features. Roughly 1.5% of the genome encodes a subset of active regulatory elements, including promoters and enhancer-like elements, which are characterized by a high degree of chromatin openness and histone acetylation, an abundance of CpG islands, and low DNA methylation levels. A comparison across sub-genomes reveals that evolutionary selection on gene regulation is targeted at the sequence and chromatin feature levels. The divergent enrichment of cis-elements between enhancer-like sequences and promoters implies these functional elements are targeted by different transcription factors. CONCLUSIONS:We herein present a systematic epigenomic map for the annotation of cis-regulatory elements in the bread wheat genome, which provides new insights into the connections between chromatin modifications and cis-regulatory activities in allohexaploid wheat.

journal_name

Genome Biol

journal_title

Genome biology

authors

Li Z,Wang M,Lin K,Xie Y,Guo J,Ye L,Zhuang Y,Teng W,Ran X,Tong Y,Xue Y,Zhang W,Zhang Y

doi

10.1186/s13059-019-1746-8

subject

Has Abstract

pub_date

2019-07-15 00:00:00

pages

139

issue

1

eissn

1474-7596

issn

1474-760X

pii

10.1186/s13059-019-1746-8

journal_volume

20

pub_type

杂志文章
  • High-resolution genomic analysis: the tumor-immune interface comes into focus.

    abstract::A genomic analysis of heterogeneous colorectal tumor samples has uncovered interactions between immunophenotype and various aspects of tumor biology, with implications for informing the choice of immunotherapies for specific patients and guiding the design of personalized neoantigen-based vaccines. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-015-0631-3

    authors: Havel JJ,Chan TA

    更新日期:2015-03-31 00:00:00

  • Histone modifications: from genome-wide maps to functional insights.

    abstract::A large number of histone modifications has been implicated in the regulation of gene expression. Together, these modifications have the potential to form a complex combinatorial regulatory code. Genome-wide mapping approaches provide new opportunities to decipher this code, but they may suffer from systematic biases....

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2005-6-6-113

    authors: van Leeuwen F,van Steensel B

    更新日期:2005-01-01 00:00:00

  • Epigenetic prediction of complex traits and death.

    abstract:BACKGROUND:Genome-wide DNA methylation (DNAm) profiling has allowed for the development of molecular predictors for a multitude of traits and diseases. Such predictors may be more accurate than the self-reported phenotypes and could have clinical applications. RESULTS:Here, penalized regression models are used to deve...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-018-1514-1

    authors: McCartney DL,Hillary RF,Stevenson AJ,Ritchie SJ,Walker RM,Zhang Q,Morris SW,Bermingham ML,Campbell A,Murray AD,Whalley HC,Gale CR,Porteous DJ,Haley CS,McRae AF,Wray NR,Visscher PM,McIntosh AM,Evans KL,Deary IJ,Mar

    更新日期:2018-09-27 00:00:00

  • mirMark: a site-level and UTR-level classifier for miRNA target prediction.

    abstract::MiRNAs play important roles in many diseases including cancers. However computational prediction of miRNA target genes is challenging and the accuracies of existing methods remain poor. We report mirMark, a new machine learning-based method of miRNA target prediction at the site and UTR levels. This method uses experi...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-014-0500-5

    authors: Menor M,Ching T,Zhu X,Garmire D,Garmire LX

    更新日期:2014-01-01 00:00:00

  • Comparative biology and genomics join forces to decipher the diversity of life.

    abstract::A report on the Cold Spring Harbor Laboratory meeting on the Evolution of Developmental Diversity, Cold Spring Harbor, NY, USA, 17-21 April 2002. ...

    journal_title:Genome biology

    pub_type:

    doi:10.1186/gb-2002-3-8-reports4023

    authors: King N

    更新日期:2002-07-15 00:00:00

  • Genomics through the lens of next-generation sequencing.

    abstract::A report on the 23rd annual meeting on 'The Biology of Genomes', 11-15 May 2010, Cold Spring Harbor, USA. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2010-11-6-306

    authors: Capra JA,Carbone L,Riesenfeld SJ,Wall JD

    更新日期:2010-01-01 00:00:00

  • Epigenetic engineering and the art of epigenetic manipulation.

    abstract::A report on the Epigenetic Engineering Meeting hosted by the Barts Institute of Cancer, held in London, UK, May 7, 2014. ...

    journal_title:Genome biology

    pub_type:

    doi:10.1186/gb4179

    authors: Magnani L

    更新日期:2014-01-01 00:00:00

  • An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.

    abstract::How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost vir...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-018-1618-7

    authors: Grubaugh ND,Gangavarapu K,Quick J,Matteson NL,De Jesus JG,Main BJ,Tan AL,Paul LM,Brackney DE,Grewal S,Gurfield N,Van Rompay KKA,Isern S,Michael SF,Coffey LL,Loman NJ,Andersen KG

    更新日期:2019-01-08 00:00:00

  • Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains.

    abstract:BACKGROUND:Francisella tularensis subspecies tularensis and holarctica are pathogenic to humans, whereas the two other subspecies, novicida and mediasiatica, rarely cause disease. To uncover the factors that allow subspecies tularensis and holarctica to be pathogenic to humans, we compared their genome sequences with t...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2007-8-6-r102

    authors: Rohmer L,Fong C,Abmayr S,Wasnick M,Larson Freeman TJ,Radey M,Guina T,Svensson K,Hayden HS,Jacobs M,Gallagher LA,Manoil C,Ernst RK,Drees B,Buckley D,Haugen E,Bovee D,Zhou Y,Chang J,Levy R,Lim R,Gillett W,Guenth

    更新日期:2007-01-01 00:00:00

  • Improved reference genome of the arboviral vector Aedes albopictus.

    abstract:BACKGROUND:The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albop...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-020-02141-w

    authors: Palatini U,Masri RA,Cosme LV,Koren S,Thibaud-Nissen F,Biedler JK,Krsticevic F,Johnston JS,Halbach R,Crawford JE,Antoshechkin I,Failloux AB,Pischedda E,Marconcini M,Ghurye J,Rhie A,Sharma A,Karagodin DA,Jenrette J,Ga

    更新日期:2020-08-26 00:00:00

  • Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds.

    abstract:BACKGROUND:While the song of all songbirds is controlled by the same neural circuit, the hormone dependence of singing behavior varies greatly between species. For this reason, songbirds are ideal organisms to study ultimate and proximate mechanisms of hormone-dependent behavior and neuronal plasticity. RESULTS:We pre...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-014-0578-9

    authors: Frankl-Vilches C,Kuhl H,Werber M,Klages S,Kerick M,Bakker A,de Oliveira EH,Reusch C,Capuano F,Vowinckel J,Leitner S,Ralser M,Timmermann B,Gahr M

    更新日期:2015-01-29 00:00:00

  • Attacking pathogens through their hosts.

    abstract::Through understanding the intricacies of host-pathogen interactions, it is now possible to inhibit the growth of microbes, especially viruses, by targeting host-cell proteins and functions. This new antimicrobial strategy has proved effective in the laboratory and in the clinic, and it has great potential for the futu...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2006-7-1-201

    authors: Kellam P

    更新日期:2006-01-01 00:00:00

  • Genetic subtraction profiling identifies genes essential for Arabidopsis reproduction and reveals interaction between the female gametophyte and the maternal sporophyte.

    abstract:BACKGROUND:The embryo sac contains the haploid maternal cell types necessary for double fertilization and subsequent seed development in plants. Large-scale identification of genes expressed in the embryo sac remains cumbersome because of its inherent microscopic and inaccessible nature. We used genetic subtraction and...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2007-8-10-r204

    authors: Johnston AJ,Meier P,Gheyselinck J,Wuest SE,Federer M,Schlagenhauf E,Becker JD,Grossniklaus U

    更新日期:2007-01-01 00:00:00

  • Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes.

    abstract::Identifying the biochemical basis of microbial phenotypes is a main objective of comparative genomics. Here we present a novel method using multivariate machine learning techniques for comparing automatically derived metabolic reconstructions of sequenced genomes on a large scale. Applying our method to 266 genomes di...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2009-10-3-r28

    authors: Kastenmüller G,Schenk ME,Gasteiger J,Mewes HW

    更新日期:2009-01-01 00:00:00

  • SAGE profiling of the forelimb and hindlimb.

    abstract::A recent study has used serial analysis of gene expression to compare mouse forelimb and hindlimb gene-expression profiles. The method successfully identified known regulators of limb identity and has generated a candidate set of differentially expressed genes that may regulate limb identity. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2002-3-3-reviews1007

    authors: Logan M

    更新日期:2002-01-01 00:00:00

  • Going beyond genetics to discover cancer targets.

    abstract::Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-017-1238-7

    authors: Sandoval GJ,Hahn WC

    更新日期:2017-05-22 00:00:00

  • Is 'big biology' a commercial enterprise?

    abstract::Big projects in biology - such as the human genome project and a number of related and ensuing enterprises - require big funding. A new tradition is growing in which some types of basic research take place within commercial organizations. This article reviews some of the reasons for this and some of the key players, i...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2002-3-4-comment2004

    authors: Swindells M

    更新日期:2002-01-01 00:00:00

  • Transcriptional regulation of metastatic [Id]entity by KLF17.

    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

    authors: Iwanicki MP,Brugge JS

    更新日期:2009-01-01 00:00:00

  • Copy number variation goes clinical.

    abstract::A report of the First Golden Helix Symposium 'Copy Number Variation (CNV) and Genomic Alterations in Health and Disease', Athens, Greece, 28-29 November 2008. ...

    journal_title:Genome biology

    pub_type:

    doi:10.1186/gb-2009-10-1-301

    authors: Le Caignec C,Redon R

    更新日期:2009-01-01 00:00:00

  • The first aurochs genome reveals the breeding history of British and European cattle.

    abstract::The first genome sequence of the extinct European wild aurochs reveals the genetic foundation of native British and Irish landraces of cattle.See related Research article: www.dx.doi.org/10.1186/s13059-015-0790-2. ...

    journal_title:Genome biology

    pub_type: 评论,杂志文章

    doi:10.1186/s13059-015-0793-z

    authors: Orlando L

    更新日期:2015-10-26 00:00:00

  • SWISS: multiplexed orthogonal genome editing in plants with a Cas9 nickase and engineered CRISPR RNA scaffolds.

    abstract::We describe here a CRISPR simultaneous and wide-editing induced by a single system (SWISS), in which RNA aptamers engineered in crRNA scaffold recruit their cognate binding proteins fused with cytidine deaminase and adenosine deaminase to Cas9 nickase target sites to generate multiplexed base editing. By using paired ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-020-02051-x

    authors: Li C,Zong Y,Jin S,Zhu H,Lin D,Li S,Qiu JL,Wang Y,Gao C

    更新日期:2020-06-16 00:00:00

  • Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS.

    abstract:BACKGROUND:There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits. RESULTS:The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expre...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-017-1328-6

    authors: Lin HY,Liu Q,Li X,Yang J,Liu S,Huang Y,Scanlon MJ,Nettleton D,Schnable PS

    更新日期:2017-10-17 00:00:00

  • Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes.

    abstract:BACKGROUND:The genomic binding of CTCF is highly conserved across mammals, but the mechanisms that underlie its stability are poorly understood. One transcription factor known to functionally interact with CTCF in the context of X-chromosome inactivation is the ubiquitously expressed YY1. Because combinatorial transcri...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2013-14-12-r148

    authors: Schwalie PC,Ward MC,Cain CE,Faure AJ,Gilad Y,Odom DT,Flicek P

    更新日期:2013-12-31 00:00:00

  • Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin.

    abstract:BACKGROUND:Aging and sun exposure are the leading causes of skin cancer. It has been shown that epigenetic changes, such as DNA methylation, are well established mechanisms for cancer, and also have emerging roles in aging and common disease. Here, we directly ask whether DNA methylation is altered following skin aging...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-015-0644-y

    authors: Vandiver AR,Irizarry RA,Hansen KD,Garza LA,Runarsson A,Li X,Chien AL,Wang TS,Leung SG,Kang S,Feinberg AP

    更新日期:2015-04-16 00:00:00

  • The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data.

    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

    authors: Hayamizu TF,Mangan M,Corradi JP,Kadin JA,Ringwald M

    更新日期:2005-01-01 00:00:00

  • A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi.

    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

    authors: Hane JK,Rouxel T,Howlett BJ,Kema GH,Goodwin SB,Oliver RP

    更新日期:2011-01-01 00:00:00

  • Dynamic reprogramming of chromatin accessibility during Drosophila embryo development.

    abstract:BACKGROUND:The development of complex organisms is believed to involve progressive restrictions in cellular fate. Understanding the scope and features of chromatin dynamics during embryogenesis, and identifying regulatory elements important for directing developmental processes remain key goals of developmental biology...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2011-12-5-r43

    authors: Thomas S,Li XY,Sabo PJ,Sandstrom R,Thurman RE,Canfield TK,Giste E,Fisher W,Hammonds A,Celniker SE,Biggin MD,Stamatoyannopoulos JA

    更新日期:2011-01-01 00:00:00

  • Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements.

    abstract:BACKGROUND:The mobilization of transposable elements (TEs) is suppressed by host genome defense mechanisms. Recent studies showed that the cis-regulatory region of Arabidopsis thaliana COPIA78/ONSEN retrotransposons contains heat-responsive elements (HREs), which cause their activation during heat stress. However, it r...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-016-1072-3

    authors: Pietzenuk B,Markus C,Gaubert H,Bagwan N,Merotto A,Bucher E,Pecinka A

    更新日期:2016-10-11 00:00:00

  • Sex-specific gene expression in preimplantation mouse embryos.

    abstract::The 3.5-day-old blastocyst-stage mouse embryo consists of two tissues and contains approximately 60 cells. This tiny structure has now been observed to express nearly 600 genes in a sex-specific fashion, including at least one gene (Rhox/Pem) expressed only in females from their paternal X chromosome. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2006-7-2-205

    authors: Eakin GS,Hadjantonakis AK

    更新日期:2006-01-01 00:00:00

  • Fungal biology reaps the benefit of genomics.

    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

    authors: Dean R,Mitchell T,Donofrio N,Jeong JS,Powell A

    更新日期:2005-01-01 00:00:00