Nucleosome deposition and DNA methylation at coding region boundaries.
Nucleosome deposition and DNA methylation at coding region boundaries.
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DOI：
10.1186/gb-2009-10-9-r89
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发表时间：
2009
期刊：
影响因子：
12.3
通讯作者：
Kim YJ
中科院分区：
文献类型：
--
作者：
Choi JK;Bae JB;Lyu J;Kim TY;Kim YJ
在全基因组调查中，已经观察到核小体和甲基化在蛋白质编码单位的两端达到峰值。转录起始下游的核小体沉积和基因体中的DNA甲基化表明，转录延伸的控制是表观遗传调控的一个关键方面。在这里，我们报告了一个全基因组的观察核小体和甲基化在蛋白质编码单位的两端的不同峰。延伸聚合酶倾向于在紧邻表观遗传峰上游的两个编码末端附近暂停，导致延伸效率显著降低。潜在的蛋白质编码序列中的保守特征似乎决定了它们在多个物种中的进化保守性。核小体和甲基化标记通常与高序列编码的DNA弯曲倾向相关，但与CpG密度有差异。随着基因变长，表观遗传密码似乎从可变的内部序列转移到边界区域，使高峰在高等生物中更加突出。最近的研究表明，转录延伸的表观遗传抑制促进了RNA剪接过程中组成型外显子的包含。我们在这里确定的表观遗传标记似乎可以确保第一个和最后一个编码外显子不被外显子跳跃，因为它们是准确翻译所不可或缺的。
Nucleosomes and methylation have been observed to peak at both ends of protein coding units in a genome-wide survey. Nucleosome deposition downstream of transcription initiation and DNA methylation in the gene body suggest that control of transcription elongation is a key aspect of epigenetic regulation. Here we report a genome-wide observation of distinct peaks of nucleosomes and methylation at both ends of a protein coding unit. Elongating polymerases tend to pause near both coding ends immediately upstream of the epigenetic peaks, causing a significant reduction in elongation efficiency. Conserved features in underlying protein coding sequences seem to dictate their evolutionary conservation across multiple species. The nucleosomal and methylation marks are commonly associated with high sequence-encoded DNA-bending propensity but differentially with CpG density. As the gene grows longer, the epigenetic codes seem to be shifted from variable inner sequences toward boundary regions, rendering the peaks more prominent in higher organisms. Recent studies suggest that epigenetic inhibition of transcription elongation facilitates the inclusion of constitutive exons during RNA splicing. The epigenetic marks we identified here seem to secure the first and last coding exons from exon skipping as they are indispensable for accurate translation.
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DOI：
10.1073/pnas.93.16.8334
发表时间：
1996-08-06
影响因子：
11.1
作者：
Hohn, T;Corsten, S;Rothnie, H
通讯作者：
Rothnie, H
影响因子：
16.8
作者：
Lorincz, MC;Dickerson, DR;Groudine, M
通讯作者：
Groudine, M
影响因子：
30.8
作者：
Ioshikhes, Ilya P.;Albert, Istvan;Pugh, B. Franklin
通讯作者：
Pugh, B. Franklin
影响因子：
30.8
作者：
Kolasinska-Zwierz P;Down T;Latorre I;Liu T;Liu XS;Ahringer J
通讯作者：
Ahringer J
DOI：
10.1073/pnas.0605645103
发表时间：
2006-11-21
影响因子：
11.1
作者：
Miura, Fumihito;Kawaguchi, Noriko;Ito, Takashi
通讯作者：
Ito, Takashi