Coupling high-throughput mapping with proteomics analysis delineates cis-regulatory elements at high resolution.
Coupling high-throughput mapping with proteomics analysis delineates cis-regulatory elements at high resolution.
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DOI：
10.1093/nar/gkab890
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发表时间：
2022-01-11
影响因子：
14.9
通讯作者：
Li G
中科院分区：
文献类型：
--
作者：
Wu T;Jiang D;Zou M;Sun W;Wu D;Cui J;Huntress I;Peng X;Li G
越来越多的证据表明，功能性顺式调控元件（cis-REs）不仅存在于人类基因组的表观遗传标记位点，也存在于人类基因组的未标记位点。虽然已经很难在表观遗传标记位点中识别顺式RE，但询问未标记位点内的顺式RE更具挑战性。在这里，我们报告适应Reel-seq，在体外高通量（HTP）技术，精细映射顺式RE在高分辨率在一个大区域的人类基因组中的系统和连续的方式。使用Reel-seq，作为原理验证，我们通过在携带p16 INK 4 a的衰老相关CDKN 2A/B基因座上定位58 kb核心区域，鉴定了408个候选顺式RE。通过将Reel-seq与蛋白质组学分析技术FREP-MS相结合，我们表征了两个顺式RE，一个在表观遗传标记位点，另一个在表观遗传未标记位点。这些元件通过募集poly（A）结合蛋白PABPC 1和转录因子FOXC 2来调节p16 INK 4a表达超过100 kb的距离。PABPC 1或FOXC 2在人内皮细胞（EC）中的下调可诱导p16 INK 4a依赖的细胞衰老。因此，我们证实了Reel-seq和FREP-MS分析在人类基因组的大区域上以高分辨率系统鉴定顺式RE的实用性。
Growing evidence suggests that functional cis-regulatory elements (cis-REs) not only exist in epigenetically marked but also in unmarked sites of the human genome. While it is already difficult to identify cis-REs in the epigenetically marked sites, interrogating cis-REs residing within the unmarked sites is even more challenging. Here, we report adapting Reel-seq, an in vitro high-throughput (HTP) technique, to fine-map cis-REs at high resolution over a large region of the human genome in a systematic and continuous manner. Using Reel-seq, as a proof-of-principle, we identified 408 candidate cis-REs by mapping a 58 kb core region on the aging-related CDKN2A/B locus that harbors p16INK4a. By coupling Reel-seq with FREP-MS, a proteomics analysis technique, we characterized two cis-REs, one in an epigenetically marked site and the other in an epigenetically unmarked site. These elements are shown to regulate the p16INK4a expression over an ∼100 kb distance by recruiting the poly(A) binding protein PABPC1 and the transcription factor FOXC2. Downregulation of either PABPC1 or FOXC2 in human endothelial cells (ECs) can induce the p16INK4a-dependent cellular senescence. Thus, we confirmed the utility of Reel-seq and FREP-MS analyses for the systematic identification of cis-REs at high resolution over a large region of the human genome.
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影响因子：
64.8
作者：
Baker DJ;Childs BG;Durik M;Wijers ME;Sieben CJ;Zhong J;Saltness RA;Jeganathan KB;Verzosa GC;Pezeshki A;Khazaie K;Miller JD;van Deursen JM
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van Deursen JM
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30.8
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Li G;Martínez-Bonet M;Wu D;Yang Y;Cui J;Nguyen HN;Cunin P;Levescot A;Bai M;Westra HJ;Okada Y;Brenner MB;Raychaudhuri S;Hendrickson EA;Maas RL;Nigrovic PA
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Nigrovic PA
影响因子：
48
作者：
Diao Y;Fang R;Li B;Meng Z;Yu J;Qiu Y;Lin KC;Huang H;Liu T;Marina RJ;Jung I;Shen Y;Guan KL;Ren B
通讯作者：
Ren B
影响因子：
30.8
作者：
Fulco, Charles P.;Nasser, Joseph;Engreitz, Jesse M.
通讯作者：
Engreitz, Jesse M.
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影响因子：
7.8
作者：
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通讯作者：
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