Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize.
Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize.
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玉米中亲本依赖性核小体组织与基因组印记相关
DOI：
10.1101/gr.230201.117
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发表时间：
2018-07
期刊：
影响因子：
7
通讯作者：
Lai J
中科院分区：
文献类型：
--
作者：
Dong X;Chen J;Li T;Li E;Zhang X;Zhang M;Song W;Zhao H;Lai J
基因组印记是指基因的等位基因特异性表达取决于其亲本来源。核小体是染色质的基本单位，在基因转录调控中起着重要作用。然而，目前尚不清楚差异核小体组织是否与印迹基因的等位基因特异性表达有关。在这里，我们产生了一个全基因组的等位基因特异性核小体占用玉米胚乳的地图，并提出了一个综合分析其与父母的起源依赖的基因表达和DNA甲基化的关系。结果表明，玉米胚乳中约有2.3%的核小体具有明显的亲偏性。来源依赖于亲本的核小体大多数以单个分离的核小体存在。父母的来源依赖的核小体显着相关的等位基因特异性表达的印记基因，与核小体优先定位在启动子的非表达等位基因的印记基因。此外，我们发现，大多数父亲特异性定位的核小体（帕特核小体）与父母的起源依赖性差异甲基化区域，这表明母亲的去甲基化和帕特核小体的发生之间的功能联系。母体特异性定位的核小体（垫核小体）是独立的等位基因特异性DNA甲基化，但似乎与等位基因特异性组蛋白修饰。我们的研究提供了第一个全基因组范围内的等位基因特异性核小体占据植物的地图，并提出了染色质组织和基因组印记之间的机械连接。
Genomic imprinting refers to allele-specific expression of genes depending on their parental origin. Nucleosomes, the fundamental units of chromatin, play a critical role in gene transcriptional regulation. However, it remains unknown whether differential nucleosome organization is related to the allele-specific expression of imprinted genes. Here, we generated a genome-wide map of allele-specific nucleosome occupancy in maize endosperm and presented an integrated analysis of its relationship with parent-of-origin-dependent gene expression and DNA methylation. We found that ∼2.3% of nucleosomes showed significant parental bias in maize endosperm. The parent-of-origin-dependent nucleosomes mostly exist as single isolated nucleosomes. Parent-of-origin-dependent nucleosomes were significantly associated with the allele-specific expression of imprinted genes, with nucleosomes positioned preferentially in the promoter of nonexpressed alleles of imprinted genes. Furthermore, we found that most of the paternal specifically positioned nucleosomes (pat-nucleosomes) were associated with parent-of-origin-dependent differential methylated regions, suggesting a functional link between the maternal demethylation and the occurrence of pat-nucleosome. Maternal specifically positioned nucleosomes (mat-nucleosomes) were independent of allele-specific DNA methylation but seem to be associated with allele-specific histone modification. Our study provides the first genome-wide map of allele-specific nucleosome occupancy in plants and suggests a mechanistic connection between chromatin organization and genomic imprinting.
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影响因子：
7.4
作者：
Fincher, Justin A.;Vera, Daniel L.;Bass, Hank W.
通讯作者：
Bass, Hank W.
DOI：
10.1073/pnas.1019273108
发表时间：
2011-02-01
影响因子：
11.1
作者：
Hsieh, Tzung-Fu;Shin, Juhyun;Fischer, Robert L.
通讯作者：
Fischer, Robert L.
DOI：
10.1126/science.1224839
发表时间：
2012-09-14
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Ibarra CA;Feng X;Schoft VK;Hsieh TF;Uzawa R;Rodrigues JA;Zemach A;Chumak N;Machlicova A;Nishimura T;Rojas D;Fischer RL;Tamaru H;Zilberman D
通讯作者：
Zilberman D
影响因子：
14.9
作者：
Collings CK;Waddell PJ;Anderson JN
通讯作者：
Anderson JN
影响因子：
7
作者：
Kelly TK;Liu Y;Lay FD;Liang G;Berman BP;Jones PA
通讯作者：
Jones PA