The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach.
The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach.
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基于RNAPII CTD的磷酸化状态将mRNA表达水平的分类基于综合基因组方法。
DOI：
10.1186/1471-2164-12-516
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发表时间：
2011-10-20
期刊：
影响因子：
4.4
通讯作者：
Ohkawa Y
中科院分区：
文献类型：
--
作者：
Odawara J;Harada A;Yoshimi T;Maehara K;Tachibana T;Okada S;Akashi K;Ohkawa Y
细胞功能由严格调节的mRNA量的平衡来调节。RNA聚合酶II（RNAPII）是一种转录mRNA的酶，根据其催化亚基RPB 1的磷酸化状态，可将RNAPII分为暂停转录状态和激活转录状态。然而，mRNA表达水平和RNAPII磷酸化状态之间的全基因组关联尚不清楚。虽然暂停基因的功能重要性是明确的，例如在小鼠胚胎干细胞分化中，但理解这种关联对于在表达谱数据中区分暂停基因与活跃转录基因至关重要，例如微阵列和RNAseq。因此，我们使用ChIPseq和RNAseq的组合分析来检查RNAPII的磷酸化与mRNA表达水平之间的相关性。我们首先通过在RNAseq中进行优化计算来进行mRNA的精确定量测量。然后，我们可视化了各种磷酸化RNAPII的募集，如Ser2P和Ser5P。使用优化的RNAseq和ChIPseq对磷酸化RNAPII进行的组合分析显示，mRNA水平与RNAPII的各种磷酸化状态相关。我们证明了mRNA的量精确地反映了Ser2和Ser5的阶段性磷酸化。特别是，即使是最“暂停”的基因，只有丝氨酸5磷酸化，在一定水平的mRNA检测。我们的分析表明，根据RNAPII的磷酸化状态，mRNA水平的定量调控的复杂性可以分为三类。
Cellular function is regulated by the balance of stringently regulated amounts of mRNA. Previous reports revealed that RNA polymerase II (RNAPII), which transcribes mRNA, can be classified into the pausing state and the active transcription state according to the phosphorylation state of RPB1, the catalytic subunit of RNAPII. However, genome-wide association between mRNA expression level and the phosphorylation state of RNAPII is unclear. While the functional importance of pausing genes is clear, such as in mouse Embryonic Stem cells for differentiation, understanding this association is critical for distinguishing pausing genes from active transcribing genes in expression profiling data, such as microarrays and RNAseq. Therefore, we examined the correlation between the phosphorylation of RNAPII and mRNA expression levels using a combined analysis by ChIPseq and RNAseq. We first performed a precise quantitative measurement of mRNA by performing an optimized calculation in RNAseq. We then visualized the recruitment of various phosphorylated RNAPIIs, such as Ser2P and Ser5P. A combined analysis using optimized RNAseq and ChIPseq for phosphorylated RNAPII revealed that mRNA levels correlate with the various phosphorylation states of RNAPII. We demonstrated that the amount of mRNA is precisely reflected by the phased phosphorylation of Ser2 and Ser5. In particular, even the most "pausing" genes, for which only Ser5 is phosphorylated, were detectable at a certain level of mRNA. Our analysis indicated that the complexity of quantitative regulation of mRNA levels could be classified into three categories according to the phosphorylation state of RNAPII.
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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：
4.6
作者：
Alder, Olivia;Lavial, Fabrice;Azuara, Veronique
通讯作者：
Azuara, Veronique
影响因子：
5.3
作者：
Dacwag, Caroline S.;Ohkawa, Yasuyuki;Imbalzano, Anthony N.
通讯作者：
Imbalzano, Anthony N.
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：
64.5
作者：
Guenther, Matthew G.;Levine, Stuart S.;Young, Richard A.
通讯作者：
Young, Richard A.