Pioneer activity distinguishes activating from non-activating SOX2 binding sites.
Pioneer activity distinguishes activating from non-activating SOX2 binding sites.
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DOI：
10.15252/embj.2022113150
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发表时间：
2023-10-16
期刊：
影响因子：
11.4
通讯作者：
de Wit, Elzo
中科院分区：
文献类型：
--
作者：
Maresca, Michela;van den Brand, Teun;Li, Hangpeng;Teunissen, Hans;Davies, James;de Wit, Elzo
关键词：
全基因组转录活动涉及许多转录因子 (TF) 与基因组中数千个位点的结合。先锋 TF 是一类保持开放染色质并允许非先锋 TF 访问其目标位点的 TF。确定哪些 TF 结合位点直接驱动转录仍然是一个挑战。在这里，我们使用先锋 TF SOX2 的急性蛋白质消耗来确定其维持染色质可及性的功能。我们发现，在蛋白质耗尽的一小时内，数千个可访问的位点就会丢失，这表明在缺乏先锋因素的情况下这些位点会快速周转。为了了解与转录的关系，我们进行了新生转录分析，发现与所有其他 SOX2 结合位点相比，SOX2 维持的开放染色质位点高度预测基因表达。我们在 Klf2 基因座中使用 CRISPR-Cas9 基因组编辑来对预测的调控元件进行功能验证。我们的结论是，SOX2 的调节活性主要在其保持可及性的位点发挥作用，而其他结合位点对于基因调节来说在很大程度上是可有可无的。 SOX2 的急性耗竭表明，维持染色质可及性（而不是单独的 DNA 结合）对于小鼠胚胎干细胞的基因调控非常重要。
Genome‐wide transcriptional activity involves the binding of many transcription factors (TFs) to thousands of sites in the genome. Pioneer TFs are a class of TFs that maintain open chromatin and allow non‐pioneer TFs access to their target sites. Determining which TF binding sites directly drive transcription remains a challenge. Here, we use acute protein depletion of the pioneer TF SOX2 to establish its functionality in maintaining chromatin accessibility. We show that thousands of accessible sites are lost within an hour of protein depletion, indicating rapid turnover of these sites in the absence of the pioneer factor. To understand the relationship with transcription, we performed nascent transcription analysis and found that open chromatin sites that are maintained by SOX2 are highly predictive of gene expression, in contrast to all other SOX2 binding sites. We use CRISPR‐Cas9 genome editing in the Klf2 locus to functionally validate a predicted regulatory element. We conclude that the regulatory activity of SOX2 is exerted mainly at sites where it maintains accessibility and that other binding sites are largely dispensable for gene regulation. Acute depletion of SOX2 shows that maintaining chromatin accessibility, rather than DNA binding alone, is important for gene regulation in mouse embryonic stem cells.
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影响因子：
48
作者：
Huber W;Carey VJ;Gentleman R;Anders S;Carlson M;Carvalho BS;Bravo HC;Davis S;Gatto L;Girke T;Gottardo R;Hahne F;Hansen KD;Irizarry RA;Lawrence M;Love MI;MacDonald J;Obenchain V;Oleś AK;Pagès H;Reyes A;Shannon P;Smyth GK;Tenenbaum D;Waldron L;Morgan M
通讯作者：
Morgan M
影响因子：
14.9
作者：
Gillespie M;Jassal B;Stephan R;Milacic M;Rothfels K;Senff-Ribeiro A;Griss J;Sevilla C;Matthews L;Gong C;Deng C;Varusai T;Ragueneau E;Haider Y;May B;Shamovsky V;Weiser J;Brunson T;Sanati N;Beckman L;Shao X;Fabregat A;Sidiropoulos K;Murillo J;Viteri G;Cook J;Shorser S;Bader G;Demir E;Sander C;Haw R;Wu G;Stein L;Hermjakob H;D'Eustachio P
通讯作者：
D'Eustachio P
影响因子：
64.5
作者：
Blat, Y;Kleckner, N
通讯作者：
Kleckner, N
DOI：
10.1093/bioinformatics/btad197
发表时间：
2023-05-04
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
通讯作者：
--
影响因子：
64.5
作者：
Boija A;Klein IA;Sabari BR;Dall'Agnese A;Coffey EL;Zamudio AV;Li CH;Shrinivas K;Manteiga JC;Hannett NM;Abraham BJ;Afeyan LK;Guo YE;Rimel JK;Fant CB;Schuijers J;Lee TI;Taatjes DJ;Young RA
通讯作者：
Young RA