Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation.
Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation.
复制标题
对二倍体和异源四倍体棉花之间的 H3K4me3 图谱进行全基因组比较分析，以完善基因组注释
DOI：
10.1038/s41598-017-09680-6
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发表时间：
2017-08-22
影响因子：
4.6
通讯作者：
Su Z
中科院分区：
文献类型：
--
作者：
You Q;Yi X;Zhang K;Wang C;Ma X;Zhang X;Xu W;Li F;Su Z
多倍体是植物进化中常见的现象。最近，发表了异源四倍体G. Hirsutum及其供体G.树木园和G.雷蒙迪使棉花成为一种可利用的多倍体模式。本研究使用染色质免疫沉淀结合高通量测序（ChIP-Seq）来研究H3K4me3 inG的全基因组分布。树木园和G. hirsutum的基因组结构，探讨二倍体和异源四倍体棉花基因组结构的保守性和变异性。我们的研究结果表明，H3K4me3修饰在两个棉花中与活跃的转录相关。H3K4me3组蛋白标记主要出现在基因区域，并在基因转录起始位点（TSS）附近富集。我们将H3K4me3的ChIP-seq数据与RNA-seq和ESTs数据相结合，以改进基因结构注释。在G中发现了6，773和12，773个新的转录本。树木园和G. hirsutum，分别。此外，共表达网络与组蛋白修饰和模块化，试图解释差异H3K4me3富集与棉花发育和进化过程中基因转录的变化相关。总之，我们结合表观基因组和转录组数据集，系统地发现功能基因，并比较它们之间的G。树木园和G. hirsutum的研究结果，可能有助于研究基因组庞大、进化复杂的二倍体和异源四倍体植物。
Polyploidy is a common evolutionary occurrence in plants. Recently, published genomes of allotetraploidG. hirsutumand its donorsG. arboreumandG. raimondiimake cotton an accessible polyploid model. This study used chromatin immunoprecipitation with high-throughput sequencing (ChIP-Seq) to investigate the genome-wide distribution of H3K4me3 inG. arboreumandG. hirsutum, and explore the conservation and variation of genome structures between diploid and allotetraploid cotton. Our results showed that H3K4me3 modifications were associated with active transcription in both cottons. The H3K4me3 histone markers appeared mainly in genic regions and were enriched around the transcription start sites (TSSs) of genes. We integrated the ChIP-seq data of H3K4me3 with RNA-seq and ESTs data to refine the genic structure annotation. There were 6,773 and 12,773 new transcripts discovered inG. arboreumandG. hirsutum, respectively. Furthermore, co-expression networks were linked with histone modification and modularized in an attempt to explain differential H3K4me3 enrichment correlated with changes in gene transcription during cotton development and evolution. Taken together, we have combined epigenomic and transcriptomic datasets to systematically discover functional genes and compare them betweenG. arboreumandG. hirsutum, which may be beneficial for studying diploid and allotetraploid plants with large genomes and complicated evolution.
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影响因子：
46.9
作者：
Trapnell C;Williams BA;Pertea G;Mortazavi A;Kwan G;van Baren MJ;Salzberg SL;Wold BJ;Pachter L
通讯作者：
Pachter L
影响因子：
12.3
作者：
Denoeud F;Aury JM;Da Silva C;Noel B;Rogier O;Delledonne M;Morgante M;Valle G;Wincker P;Scarpelli C;Jaillon O;Artiguenave F
通讯作者：
Artiguenave F
影响因子：
11.6
作者：
He, Guangming;Zhu, Xiaopeng;Deng, Xing-Wang
通讯作者：
Deng, Xing-Wang
影响因子：
46.9
作者：
Li, Fuguang;Fan, Guangyi;Yu, Shuxun
通讯作者：
Yu, Shuxun
影响因子：
27.5
作者：
Du, Zhou;Li, Hui;Su, Zhen
通讯作者：
Su, Zhen