Transcriptionally active enhancers in human cancer cells.
Transcriptionally active enhancers in human cancer cells.
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DOI：
10.15252/msb.20209873
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发表时间：
2021-01
影响因子：
9.9
通讯作者：
Lidschreiber M
中科院分区：
文献类型：
--
作者：
Lidschreiber K;Jung LA;von der Emde H;Dave K;Taipale J;Cramer P;Lidschreiber M
人类癌细胞的生长由异常的增强子和基因转录活性驱动。在这里，我们使用瞬时转录组测序（TT-seq）来映射涵盖七种癌症的十四种人类癌细胞系中的数千个转录活性推定增强子。这些增强子与细胞类型特异性基因表达相关，富含易患癌症的遗传变异，并包括功能验证的增强子。通过转录活性的相关性进行的增强子-启动子（E-P）配对揭示了约40，000个推定的E-P对，这些E-P对耗尽了管家基因，并富集了转录因子、癌症相关基因和3D构象邻近性。靶基因的细胞类型特异性和转录活性随着成对增强子数目的增加而增加。我们的研究结果代表了一个丰富的资源，为未来的研究基因调控的增强子和他们在驱动癌细胞生长的作用。TT‐seq在人类癌细胞中以高灵敏度测量全基因组增强子转录。由此产生的假定增强子和增强子-启动子对的全面注释为研究增强子功能提供了宝贵的资源。
The growth of human cancer cells is driven by aberrant enhancer and gene transcription activity. Here, we use transient transcriptome sequencing (TT‐seq) to map thousands of transcriptionally active putative enhancers in fourteen human cancer cell lines covering seven types of cancer. These enhancers were associated with cell type‐specific gene expression, enriched for genetic variants that predispose to cancer, and included functionally verified enhancers. Enhancer–promoter (E–P) pairing by correlation of transcription activity revealed ~ 40,000 putative E–P pairs, which were depleted for housekeeping genes and enriched for transcription factors, cancer‐associated genes, and 3D conformational proximity. The cell type specificity and transcription activity of target genes increased with the number of paired putative enhancers. Our results represent a rich resource for future studies of gene regulation by enhancers and their role in driving cancerous cell growth. TT‐seq measures genome‐wide enhancer transcription with high sensitivity in human cancer cells. The resulting comprehensive annotation of putative enhancers and enhancer‐promoter pairs serves as a valuable resource for studying enhancer function.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
10.5
作者：
Cabili, Moran N.;Trapnell, Cole;Rinn, John L.
通讯作者：
Rinn, John L.
DOI：
10.1073/pnas.0910668107
发表时间：
2010-05-25
影响因子：
11.1
作者：
Ahmadiyeh, Nasim;Pomerantz, Mark M.;Freedman, Matthew L.
通讯作者：
Freedman, Matthew L.
DOI：
10.1126/science.1259418
发表时间：
2015-02-27
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Arner E;Daub CO;Vitting-Seerup K;Andersson R;Lilje B;Drabløs F;Lennartsson A;Rönnerblad M;Hrydziuszko O;Vitezic M;Freeman TC;Alhendi AM;Arner P;Axton R;Baillie JK;Beckhouse A;Bodega B;Briggs J;Brombacher F;Davis M;Detmar M;Ehrlund A;Endoh M;Eslami A;Fagiolini M;Fairbairn L;Faulkner GJ;Ferrai C;Fisher ME;Forrester L;Goldowitz D;Guler R;Ha T;Hara M;Herlyn M;Ikawa T;Kai C;Kawamoto H;Khachigian LM;Klinken SP;Kojima S;Koseki H;Klein S;Mejhert N;Miyaguchi K;Mizuno Y;Morimoto M;Morris KJ;Mummery C;Nakachi Y;Ogishima S;Okada-Hatakeyama M;Okazaki Y;Orlando V;Ovchinnikov D;Passier R;Patrikakis M;Pombo A;Qin XY;Roy S;Sato H;Savvi S;Saxena A;Schwegmann A;Sugiyama D;Swoboda R;Tanaka H;Tomoiu A;Winteringham LN;Wolvetang E;Yanagi-Mizuochi C;Yoneda M;Zabierowski S;Zhang P;Abugessaisa I;Bertin N;Diehl AD;Fukuda S;Furuno M;Harshbarger J;Hasegawa A;Hori F;Ishikawa-Kato S;Ishizu Y;Itoh M;Kawashima T;Kojima M;Kondo N;Lizio M;Meehan TF;Mungall CJ;Murata M;Nishiyori-Sueki H;Sahin S;Nagao-Sato S;Severin J;de Hoon MJ;Kawai J;Kasukawa T;Lassmann T;Suzuki H;Kawaji H;Summers KM;Wells C;FANTOM Consortium;Hume DA;Forrest AR;Sandelin A;Carninci P;Hayashizaki Y
通讯作者：
Hayashizaki Y
影响因子：
10.5
作者：
Ashe, HL;Monks, J;Proudfoot, NJ
通讯作者：
Proudfoot, NJ