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For: Davie K, Jacobs J, Atkins M, Potier D, Christiaens V, Halder G, Aerts S. Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PLoS Genet 2015;11:e1004994. [PMID: 25679813 PMCID: PMC4334524 DOI: 10.1371/journal.pgen.1004994] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 01/08/2015] [Indexed: 01/24/2023]  Open
Number Cited by Other Article(s)
1
García-Loredo JA, Santoyo-Suarez MG, Rodríguez-Nuñez O, Benitez Chao DF, Garza-Treviño EN, Zapata-Morin PA, Padilla-Rivas GR, Islas JF. Is the Cis-Element CACCC-Box a Master Regulatory Element during Cardiovascular Disease? A Bioinformatics Approach from the Perspective of the Krüppel-like Family of Transcription Factors. Life (Basel) 2024;14:493. [PMID: 38672763 PMCID: PMC11051458 DOI: 10.3390/life14040493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/03/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024]  Open
2
Jin K, McCoy BM, Goldman EA, Usova V, Tkachev V, Chitsazan AD, Kakebeen A, Jeffery U, Creevy KE, Wills A, Snyder‐Mackler N, Promislow DEL. DNA methylation and chromatin accessibility predict age in the domestic dog. Aging Cell 2024;23:e14079. [PMID: 38263575 PMCID: PMC11019125 DOI: 10.1111/acel.14079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024]  Open
3
Chan S, Wang Y, Luo Y, Zheng M, Xie F, Xue M, Yang X, Xue P, Zha C, Fang M. Differential Regulation of Male-Hormones-Related Enhancers Revealed by Chromatin Accessibility and Transcriptional Profiles in Pig Liver. Biomolecules 2024;14:427. [PMID: 38672444 PMCID: PMC11048672 DOI: 10.3390/biom14040427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024]  Open
4
Guo X, Wang C, Zhang Y, Wei R, Xi R. Cell-fate conversion of intestinal cells in adult Drosophila midgut by depleting a single transcription factor. Nat Commun 2024;15:2656. [PMID: 38531872 DOI: 10.1038/s41467-024-46956-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 03/14/2024] [Indexed: 03/28/2024]  Open
5
Liu X, Chen M, Qu X, Liu W, Dou Y, Liu Q, Shi D, Jiang M, Li H. Cis-Regulatory Elements in Mammals. Int J Mol Sci 2023;25:343. [PMID: 38203513 PMCID: PMC10779164 DOI: 10.3390/ijms25010343] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024]  Open
6
Tisi A, Palaniappan S, Maccarrone M. Advanced Omics Techniques for Understanding Cochlear Genome, Epigenome, and Transcriptome in Health and Disease. Biomolecules 2023;13:1534. [PMID: 37892216 PMCID: PMC10605747 DOI: 10.3390/biom13101534] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023]  Open
7
Nowling RJ, Njoya K, Peters JG, Riehle MM. Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique. Front Cell Infect Microbiol 2023;13:1182567. [PMID: 37600946 PMCID: PMC10433755 DOI: 10.3389/fcimb.2023.1182567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023]  Open
8
Huynh K, Smith BR, Macdonald SJ, Long AD. Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster. PLoS Genet 2023;19:e1010439. [PMID: 37146087 PMCID: PMC10191298 DOI: 10.1371/journal.pgen.1010439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 05/17/2023] [Accepted: 04/20/2023] [Indexed: 05/07/2023]  Open
9
Zhang GW, Wang L, Wu J, Ye Y, Zhao J, Du Y, Tu Y, Luo Z, Fu S, Zuo F. Evaluation of MYBL1 as the master regulator for pachytene spermatocyte genes dysregulated in interspecific hybrid dzo. J Dairy Sci 2023;106:4366-4379. [PMID: 37059660 DOI: 10.3168/jds.2022-22963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/08/2022] [Indexed: 04/16/2023]
10
Chin HG, Vishnu US, Sun Z, Ponnaluri VKC, Zhang G, Xu SY, Benoukraf T, Cejas P, Spracklin G, Estève PO, Long HW, Pradhan S. Universal NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cells. Methods Mol Biol 2023;2611:39-52. [PMID: 36807062 DOI: 10.1007/978-1-0716-2899-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
11
Ye B, Shen W, Li Y, Wang D, Zhang Y, Li P, Yin M, Wang Y, Xie D, Shi S, Yao T, Chen J, Xu P, Zhao Z. FAIRE-MS reveals mitotic retention of transcriptional regulators on a proteome-wide scale. FASEB J 2023;37:e22724. [PMID: 36583687 DOI: 10.1096/fj.202201038rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022]
12
Athanasopoulou K, Daneva GN, Boti MA, Dimitroulis G, Adamopoulos PG, Scorilas A. The Transition from Cancer "omics" to "epi-omics" through Next- and Third-Generation Sequencing. LIFE (BASEL, SWITZERLAND) 2022;12:life12122010. [PMID: 36556377 PMCID: PMC9785810 DOI: 10.3390/life12122010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
13
Merrill CB, Pabon MA, Montgomery AB, Rodan AR, Rothenfluh A. Optimized assay for transposase-accessible chromatin by sequencing (ATAC-seq) library preparation from adult Drosophila melanogaster neurons. Sci Rep 2022;12:6043. [PMID: 35411004 PMCID: PMC9001676 DOI: 10.1038/s41598-022-09869-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/14/2022] [Indexed: 01/07/2023]  Open
14
Zhang Z, Lin L, Chen H, Ye W, Dong S, Zheng X, Wang Y. ATAC-Seq Reveals the Landscape of Open Chromatin and cis-Regulatory Elements in the Phytophthora sojae Genome. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022;35:301-310. [PMID: 35037783 DOI: 10.1094/mpmi-11-21-0291-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
15
Bourbon HMG, Benetah MH, Guillou E, Mojica-Vazquez LH, Baanannou A, Bernat-Fabre S, Loubiere V, Bantignies F, Cavalli G, Boube M. A shared ancient enhancer element differentially regulates the bric-a-brac tandem gene duplicates in the developing Drosophila leg. PLoS Genet 2022;18:e1010083. [PMID: 35294439 PMCID: PMC8959175 DOI: 10.1371/journal.pgen.1010083] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/28/2022] [Accepted: 02/07/2022] [Indexed: 11/18/2022]  Open
16
Salavati M, Woolley SA, Cortés Araya Y, Halstead MM, Stenhouse C, Johnsson M, Ashworth CJ, Archibald AL, Donadeu FX, Hassan MA, Clark EL. Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions. G3 (BETHESDA, MD.) 2022;12:6460335. [PMID: 34897420 PMCID: PMC9210303 DOI: 10.1093/g3journal/jkab424] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
17
Logeay R, Géminard C, Lassus P, Rodríguez-Vázquez M, Kantar D, Heron-Milhavet L, Fischer B, Bray SJ, Colinge J, Djiane A. Mechanisms underlying the cooperation between loss of epithelial polarity and Notch signaling during neoplastic growth in Drosophila. Development 2022;149:274230. [PMID: 35005772 DOI: 10.1242/dev.200110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/17/2021] [Indexed: 12/16/2022]
18
Jauregui-Lozano J, Hall H, Stanhope SC, Bakhle K, Marlin MM, Weake VM. The Clock:Cycle complex is a major transcriptional regulator of Drosophila photoreceptors that protects the eye from retinal degeneration and oxidative stress. PLoS Genet 2022;18:e1010021. [PMID: 35100266 PMCID: PMC8830735 DOI: 10.1371/journal.pgen.1010021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/10/2022] [Accepted: 01/08/2022] [Indexed: 12/28/2022]  Open
19
Zhou B, Stueve TR, Mihalakakos EA, Miao L, Mullen D, Wang Y, Liu Y, Luo J, Tran E, Siegmund KD, Lynch SK, Ryan AL, Offringa IA, Borok Z, Marconett CN. Comprehensive epigenomic profiling of human alveolar epithelial differentiation identifies key epigenetic states and transcription factor co-regulatory networks for maintenance of distal lung identity. BMC Genomics 2021;22:906. [PMID: 34922464 PMCID: PMC8684104 DOI: 10.1186/s12864-021-08152-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 11/05/2021] [Indexed: 12/22/2022]  Open
20
Dillard C, Reis JGT, Rusten TE. RasV12; scrib-/- Tumors: A Cooperative Oncogenesis Model Fueled by Tumor/Host Interactions. Int J Mol Sci 2021;22:ijms22168873. [PMID: 34445578 PMCID: PMC8396170 DOI: 10.3390/ijms22168873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 12/19/2022]  Open
21
Dreos R, Sloutskin A, Malachi N, Ideses D, Bucher P, Juven-Gershon T. Computational identification and experimental characterization of preferred downstream positions in human core promoters. PLoS Comput Biol 2021;17:e1009256. [PMID: 34383743 PMCID: PMC8384218 DOI: 10.1371/journal.pcbi.1009256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 08/24/2021] [Accepted: 07/07/2021] [Indexed: 12/02/2022]  Open
22
Dpp and Hedgehog promote the glial response to neuronal apoptosis in the developing Drosophila visual system. PLoS Biol 2021;19:e3001367. [PMID: 34379617 PMCID: PMC8396793 DOI: 10.1371/journal.pbio.3001367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/27/2021] [Accepted: 07/16/2021] [Indexed: 11/19/2022]  Open
23
Chawla A, Nagy C, Turecki G. Chromatin Profiling Techniques: Exploring the Chromatin Environment and Its Contributions to Complex Traits. Int J Mol Sci 2021;22:7612. [PMID: 34299232 PMCID: PMC8305586 DOI: 10.3390/ijms22147612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 01/04/2023]  Open
24
Deregulation of Transcriptional Enhancers in Cancer. Cancers (Basel) 2021;13:cancers13143532. [PMID: 34298745 PMCID: PMC8303223 DOI: 10.3390/cancers13143532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/29/2021] [Accepted: 07/08/2021] [Indexed: 12/14/2022]  Open
25
Li Z, Wei Y, Shao Y, Tang L, Gong J. Multi-omics analysis of intertumoral heterogeneity within medulloblastoma uncharted-pathway subtypes. Brain Tumor Pathol 2021;38:234-242. [PMID: 34180021 DOI: 10.1007/s10014-021-00400-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/07/2021] [Indexed: 11/25/2022]
26
Jauregui-Lozano J, Bakhle K, Weake VM. In vivo tissue-specific chromatin profiling in Drosophila melanogaster using GFP-tagged nuclei. Genetics 2021;218:6281219. [PMID: 34022041 DOI: 10.1093/genetics/iyab079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/17/2021] [Indexed: 12/23/2022]  Open
27
Lozoya OA, Xu F, Grenet D, Wang T, Grimm SA, Godfrey V, Waidyanatha S, Woychik RP, Santos JH. Single Nucleotide Resolution Analysis Reveals Pervasive, Long-Lasting DNA Methylation Changes by Developmental Exposure to a Mitochondrial Toxicant. Cell Rep 2021;32:108131. [PMID: 32937126 PMCID: PMC7553240 DOI: 10.1016/j.celrep.2020.108131] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 03/16/2020] [Accepted: 08/20/2020] [Indexed: 02/08/2023]  Open
28
Zhou M, Li H, Wang X, Guan Y. Evidence of widespread, independent sequence signature for transcription factor cobinding. Genome Res 2021;31:265-278. [PMID: 33303494 PMCID: PMC7849410 DOI: 10.1101/gr.267310.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/03/2020] [Indexed: 01/03/2023]
29
Minnoye L, Marinov GK, Krausgruber T, Pan L, Marand AP, Secchia S, Greenleaf WJ, Furlong EEM, Zhao K, Schmitz RJ, Bock C, Aerts S. Chromatin accessibility profiling methods. NATURE REVIEWS. METHODS PRIMERS 2021;1:10. [PMID: 38410680 PMCID: PMC10895463 DOI: 10.1038/s43586-020-00008-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/01/2020] [Indexed: 02/06/2023]
30
Ruiz JL, Ranford-Cartwright LC, Gómez-Díaz E. The regulatory genome of the malaria vector Anopheles gambiae: integrating chromatin accessibility and gene expression. NAR Genom Bioinform 2021;3:lqaa113. [PMID: 33987532 PMCID: PMC8092447 DOI: 10.1093/nargab/lqaa113] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/15/2020] [Accepted: 12/26/2020] [Indexed: 12/12/2022]  Open
31
Schwartz M, Portugez AS, Attia BZ, Tannenbaum M, Cohen L, Loza O, Chase E, Turman Y, Kaplan T, Salah Z, Hakim O. Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation. Commun Biol 2020;3:696. [PMID: 33239721 PMCID: PMC7809021 DOI: 10.1038/s42003-020-01398-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 10/16/2020] [Indexed: 12/15/2022]  Open
32
Reddington JP, Garfield DA, Sigalova OM, Karabacak Calviello A, Marco-Ferreres R, Girardot C, Viales RR, Degner JF, Ohler U, Furlong EEM. Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis. Dev Cell 2020;55:648-664.e9. [PMID: 33171098 DOI: 10.1016/j.devcel.2020.10.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 08/04/2020] [Accepted: 10/09/2020] [Indexed: 02/01/2023]
33
Rogerson C, Ogden S, Britton E, Ang Y, Sharrocks AD. Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to oesophageal adenocarcinoma. eLife 2020;9:e57189. [PMID: 32880368 PMCID: PMC7544504 DOI: 10.7554/elife.57189] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022]  Open
34
Guo X, Wang C, Wang TY. Chromatin-modifying elements for recombinant protein production in mammalian cell systems. Crit Rev Biotechnol 2020;40:1035-1043. [PMID: 32777953 DOI: 10.1080/07388551.2020.1805401] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
35
Malladi VS, Nagari A, Franco HL, Kraus WL. Total Functional Score of Enhancer Elements Identifies Lineage-Specific Enhancers That Drive Differentiation of Pancreatic Cells. Bioinform Biol Insights 2020;14:1177932220938063. [PMID: 32655276 PMCID: PMC7331761 DOI: 10.1177/1177932220938063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 06/02/2020] [Indexed: 01/10/2023]  Open
36
Hamaratoglu F, Atkins M. Rounding up the Usual Suspects: Assessing Yorkie, AP-1, and Stat Coactivation in Tumorigenesis. Int J Mol Sci 2020;21:E4580. [PMID: 32605129 PMCID: PMC7370090 DOI: 10.3390/ijms21134580] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022]  Open
37
Chen X, Gu J, Neuwald AF, Hilakivi-Clarke L, Clarke R, Xuan J. BICORN: An R package for integrative inference of de novo cis-regulatory modules. Sci Rep 2020;10:7960. [PMID: 32409786 PMCID: PMC7224214 DOI: 10.1038/s41598-020-63043-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/15/2020] [Indexed: 12/18/2022]  Open
38
Bravo González‐Blas C, Quan X, Duran‐Romaña R, Taskiran II, Koldere D, Davie K, Christiaens V, Makhzami S, Hulselmans G, de Waegeneer M, Mauduit D, Poovathingal S, Aibar S, Aerts S. Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics. Mol Syst Biol 2020;16:e9438. [PMID: 32431014 PMCID: PMC7237818 DOI: 10.15252/msb.20209438] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 01/02/2023]  Open
39
Pongor LS, Gross JM, Vera Alvarez R, Murai J, Jang SM, Zhang H, Redon C, Fu H, Huang SY, Thakur B, Baris A, Marino-Ramirez L, Landsman D, Aladjem MI, Pommier Y. BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks. Epigenetics Chromatin 2020;13:21. [PMID: 32321568 PMCID: PMC7175505 DOI: 10.1186/s13072-020-00343-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/11/2020] [Indexed: 12/12/2022]  Open
40
Thompson BJ. YAP/TAZ: Drivers of Tumor Growth, Metastasis, and Resistance to Therapy. Bioessays 2020;42:e1900162. [DOI: 10.1002/bies.201900162] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 02/11/2020] [Indexed: 01/17/2023]
41
Salces-Ortiz J, Vargas-Chavez C, Guio L, Rech GE, González J. Transposable elements contribute to the genomic response to insecticides in Drosophila melanogaster. Philos Trans R Soc Lond B Biol Sci 2020;375:20190341. [PMID: 32075557 PMCID: PMC7061994 DOI: 10.1098/rstb.2019.0341] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
42
Brückner A, Parker J. Molecular evolution of gland cell types and chemical interactions in animals. ACTA ACUST UNITED AC 2020;223:223/Suppl_1/jeb211938. [PMID: 32034048 DOI: 10.1242/jeb.211938] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
43
Villanueva-Cañas JL, Horvath V, Aguilera L, González J. Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in Drosophila melanogaster. Nucleic Acids Res 2020;47:6842-6857. [PMID: 31175824 PMCID: PMC6649756 DOI: 10.1093/nar/gkz490] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/20/2019] [Accepted: 05/22/2019] [Indexed: 12/25/2022]  Open
44
Loubiere V, Papadopoulos GL, Szabo Q, Martinez AM, Cavalli G. Widespread activation of developmental gene expression characterized by PRC1-dependent chromatin looping. SCIENCE ADVANCES 2020;6:eaax4001. [PMID: 31950077 PMCID: PMC6954061 DOI: 10.1126/sciadv.aax4001] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 11/06/2019] [Indexed: 05/21/2023]
45
Klein DC, Hainer SJ. Genomic methods in profiling DNA accessibility and factor localization. Chromosome Res 2019;28:69-85. [PMID: 31776829 PMCID: PMC7125251 DOI: 10.1007/s10577-019-09619-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/10/2019] [Accepted: 10/15/2019] [Indexed: 12/24/2022]
46
Vitobello A, Perner J, Beil J, Zhu J, Del Río-Espínola A, Morawiec L, Westphal M, Dubost V, Altorfer M, Naumann U, Mueller A, Kapur K, Borowsky M, Henderson C, Wolf CR, Schwarz M, Moggs J, Terranova R. Drug-induced chromatin accessibility changes associate with sensitivity to liver tumor promotion. Life Sci Alliance 2019;2:e201900461. [PMID: 31615920 PMCID: PMC6795216 DOI: 10.26508/lsa.201900461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/26/2019] [Accepted: 09/26/2019] [Indexed: 12/27/2022]  Open
47
Morris JP, Yashinskie JJ, Koche R, Chandwani R, Tian S, Chen CC, Baslan T, Marinkovic ZS, Sánchez-Rivera FJ, Leach SD, Carmona-Fontaine C, Thompson CB, Finley LWS, Lowe SW. α-Ketoglutarate links p53 to cell fate during tumour suppression. Nature 2019;573:595-599. [PMID: 31534224 DOI: 10.1038/s41586-019-1577-5] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/13/2019] [Indexed: 12/14/2022]
48
Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks. Cell Rep 2019;23:376-388. [PMID: 29641998 PMCID: PMC5987223 DOI: 10.1016/j.celrep.2018.03.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/12/2018] [Accepted: 03/12/2018] [Indexed: 12/31/2022]  Open
49
Sun Y, Miao N, Sun T. Detect accessible chromatin using ATAC-sequencing, from principle to applications. Hereditas 2019;156:29. [PMID: 31427911 PMCID: PMC6696680 DOI: 10.1186/s41065-019-0105-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/12/2019] [Indexed: 02/07/2023]  Open
50
Sato S, Arimura Y, Kujirai T, Harada A, Maehara K, Nogami J, Ohkawa Y, Kurumizaka H. Biochemical analysis of nucleosome targeting by Tn5 transposase. Open Biol 2019;9:190116. [PMID: 31409230 PMCID: PMC6731594 DOI: 10.1098/rsob.190116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
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