Simple and accurate transcriptional start site identification using Smar2C2 and examination of conserved promoter features.
Simple and accurate transcriptional start site identification using Smar2C2 and examination of conserved promoter features.
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DOI：
10.1111/tpj.15957
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发表时间：
2022-10
期刊：
影响因子：
7.2
通讯作者：
Schmitz, Robert J.
中科院分区：
文献类型：
--
作者：
Murray, Andrew;Mendieta, John Pablo;Vollmers, Chris;Schmitz, Robert J.
关键词：
转录起始位点（TSS）的精确和准确的识别和定量是理解转录控制的关键。核心启动子由TSS和近端非编码序列组成，它们在转录调控中至关重要。因此，准确鉴定TSSs对于理解转录的分子调控具有重要意义。现有的TSS鉴定方案具有挑战性且昂贵，只为一小部分生物体提供高质量的数据。这种数据的稀疏性损害了跨组织或在进化背景下TSS使用的研究。为了解决这些缺点，我们开发了Smart-Seq 2滚动环到串联共识（Smar 2C 2），它可以识别和量化TSS和转录终止位点。Smar 2C 2结合了独特的分子标识符，可以识别多达7000万个位点，没有已知的上限。我们还从低至40 pg的总RNA生成了TSS数据集，这是测试的最小输入。在这项研究中，我们使用Smar 2C 2在大豆（大豆），水稻（水稻），高粱（高粱），小麦（小麦）和玉米（玉米）的多个组织中鉴定TSS。这一广泛的植物TSS面板促进了进化上保守的功能，如新的模式，组成的启动子元件（Inr），与所有物种的启动子表达水平相关的二核苷酸鉴定。我们还发现了已知启动子基序的序列变异，这些基序可靠地靠近TSS，如TATA框和Inr中的差异，这可能对我们理解和控制转录起始具有重要意义。Smar 2C 2允许对这些关键序列进行简单的研究，提供了一种便于发现的工具。我们已经开发了一种称为Smar 2C 2的技术，并使用它来确定玉米，水稻，高粱，大豆和小麦中的转录起始位点。这组广泛的植物TSS促进了进化上保守特征的鉴定，例如组成起始元件的二核苷酸的模式和TATA-box序列基序的差异，这可能对理解和控制转录起始具有重要意义。
The precise and accurate identification and quantification of transcriptional start sites (TSSs) is key to understanding the control of transcription. The core promoter consists of the TSS and proximal non‐coding sequences, which are critical in transcriptional regulation. Therefore, the accurate identification of TSSs is important for understanding the molecular regulation of transcription. Existing protocols for TSS identification are challenging and expensive, leaving high‐quality data available for a small subset of organisms. This sparsity of data impairs study of TSS usage across tissues or in an evolutionary context. To address these shortcomings, we developed Smart‐Seq2 Rolling Circle to Concatemeric Consensus (Smar2C2), which identifies and quantifies TSSs and transcription termination sites. Smar2C2 incorporates unique molecular identifiers that allowed for the identification of as many as 70 million sites, with no known upper limit. We have also generated TSS data sets from as little as 40 pg of total RNA, which was the smallest input tested. In this study, we used Smar2C2 to identify TSSs in Glycine max (soybean), Oryza sativa (rice), Sorghum bicolor (sorghum), Triticum aestivum (wheat) and Zea mays (maize) across multiple tissues. This wide panel of plant TSSs facilitated the identification of evolutionarily conserved features, such as novel patterns in the dinucleotides that compose the initiator element (Inr), that correlated with promoter expression levels across all species examined. We also discovered sequence variations in known promoter motifs that are positioned reliably close to the TSS, such as differences in the TATA box and in the Inr that may prove significant to our understanding and control of transcription initiation. Smar2C2 allows for the easy study of these critical sequences, providing a tool to facilitate discovery. We have developed a technique called Smar2C2 and used it to identify transcription start sites in maize, rice, sorghum, soybean and wheat. This wide panel of plant TSSs facilitated the identification of evolutionarily conserved features, such as patterns in the dinucleotides that compose the initiator element and differences in the TATA‐box sequence motif, that may prove significant to understanding and controlling transcription initiation.
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影响因子：
14.8
作者：
Islam, Saiful;Kjallquist, Una;Linnarsson, Sten
通讯作者：
Linnarsson, Sten
影响因子：
--
作者：
Kadonaga, James T.
通讯作者：
Kadonaga, James T.
影响因子：
18
作者：
Jores, Tobias;Tonnies, Jackson;Wrightsman, Travis;Buckler, Edward S.;Cuperus, Josh T.;Fields, Stanley;Queitsch, Christine
通讯作者：
Queitsch, Christine
影响因子：
14.9
作者：
Bailey TL;Johnson J;Grant CE;Noble WS
通讯作者：
Noble WS
DOI：
10.1038/s41580-018-0028-8
发表时间：
2018-10
期刊：
Nature reviews. Molecular cell biology
影响因子：
--
作者：
Haberle V;Stark A
通讯作者：
Stark A