Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements.
Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements.
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DOI：
10.1093/nar/gkt1366
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发表时间：
2014-04
影响因子：
14.9
通讯作者：
Iyer VR
中科院分区：
文献类型：
--
作者：
Park D;Morris AR;Battenhouse A;Iyer VR
理解调控因子结合、染色质结构、顺式调控元件和rna调控机制之间的关系依赖于转录起始位点（TSS）和聚腺苷酸化位点（PAS）的准确信息。虽然有几种方法已经确定了酵母中的转录本末端，但分辨率和覆盖范围的限制仍然存在，并且尚未实现单核苷酸分辨率的TSS和PAS的最终鉴定。我们开发了SMORE-seq（通过测序同时定位RNA末端），并使用它同时鉴定了5207个（90%）基因的最强TSS和5277个（91%）基因的最强PAS。SMORE-seq鉴定的新转录本注释与tata样调控元件、核小体位置和活性RNA聚合酶的距离关系有所改善。我们发现150个基因的TSS位于注释起始密码子的下游，并且对进化保护和核糖体足迹的进一步分析表明，这些蛋白质编码序列可能被错误注释。SMORE-seq检测到正常条件下野生型细胞中1000多个启动子的短非编码rna转录差异。这些不同的非编码rna在包含规范TATA盒子的启动子上不太明显，这表明RNAPII在启动子上的转录起始是双向的，TATA元件限制起始的方向性。
Understanding the relationships between regulatory factor binding, chromatin structure, cis-regulatory elements and RNA-regulation mechanisms relies on accurate information about transcription start sites (TSS) and polyadenylation sites (PAS). Although several approaches have identified transcript ends in yeast, limitations of resolution and coverage have remained, and definitive identification of TSS and PAS with single-nucleotide resolution has not yet been achieved. We developed SMORE-seq (simultaneous mapping of RNA ends by sequencing) and used it to simultaneously identify the strongest TSS for 5207 (90%) genes and PAS for 5277 (91%) genes. The new transcript annotations identified by SMORE-seq showed improved distance relationships with TATA-like regulatory elements, nucleosome positions and active RNA polymerase. We found 150 genes whose TSS were downstream of the annotated start codon, and additional analysis of evolutionary conservation and ribosome footprinting suggests that these protein-coding sequences are likely to be mis-annotated. SMORE-seq detected short non-coding RNAs transcribed divergently from more than a thousand promoters in wild-type cells under normal conditions. These divergent non-coding RNAs were less evident at promoters containing canonical TATA boxes, suggesting a model where transcription initiation at promoters by RNAPII is bidirectional, with TATA elements serving to constrain the directionality of initiation.
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DOI：
10.1073/pnas.93.11.5208
发表时间：
1996-05-28
影响因子：
11.1
作者：
Iyer, V;Struhl, K
通讯作者：
Struhl, K
影响因子：
64.8
作者：
Kellis, M;Patterson, N;Lander, ES
通讯作者：
Lander, ES
影响因子：
64.5
作者：
Basehoar, AD;Zanton, SJ;Pugh, BF
通讯作者：
Pugh, BF
影响因子：
3.7
作者：
Itoh M;Kojima M;Nagao-Sato S;Saijo E;Lassmann T;Kanamori-Katayama M;Kaiho A;Lizio M;Kawaji H;Carninci P;Forrest AR;Hayashizaki Y
通讯作者：
Hayashizaki Y
影响因子：
64.5
作者：
Jenal, Mathias;Elkon, Ran;Agami, Reuven
通讯作者：
Agami, Reuven