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For: Farley EK, Olson KM, Levine MS. Regulatory Principles Governing Tissue Specificity of Developmental Enhancers. Cold Spring Harb Symp Quant Biol 2018;80:27-32. [PMID: 27325706 DOI: 10.1101/sqb.2015.80.027227] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Number Cited by Other Article(s)
1
Lim F, Solvason JJ, Ryan GE, Le SH, Jindal GA, Steffen P, Jandu SK, Farley EK. Affinity-optimizing enhancer variants disrupt development. Nature 2024;626:151-159. [PMID: 38233525 PMCID: PMC10830414 DOI: 10.1038/s41586-023-06922-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 11/30/2023] [Indexed: 01/19/2024]
2
Johannesson K, Leder EH, André C, Dupont S, Eriksson SP, Harding K, Havenhand JN, Jahnke M, Jonsson PR, Kvarnemo C, Pavia H, Rafajlović M, Rödström EM, Thorndyke M, Blomberg A. Ten years of marine evolutionary biology-Challenges and achievements of a multidisciplinary research initiative. Evol Appl 2023;16:530-541. [PMID: 36793681 PMCID: PMC9923476 DOI: 10.1111/eva.13389] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/08/2022] [Accepted: 04/21/2022] [Indexed: 11/26/2022]  Open
3
MacKenzie A, Hay EA, McEwan AR. Context-dependant enhancers as a reservoir of functional polymorphisms and epigenetic markers linked to alcohol use disorders and comorbidities. ADDICTION NEUROSCIENCE 2022;2:None. [PMID: 35712020 PMCID: PMC9101288 DOI: 10.1016/j.addicn.2022.100014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/18/2022] [Accepted: 03/22/2022] [Indexed: 10/25/2022]
4
Kaplow IM, Schäffer DE, Wirthlin ME, Lawler AJ, Brown AR, Kleyman M, Pfenning AR. Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin. BMC Genomics 2022;23:291. [PMID: 35410163 PMCID: PMC8996547 DOI: 10.1186/s12864-022-08450-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/07/2022] [Indexed: 11/10/2022]  Open
5
Martinez-Ara M, Comoglio F, van Arensbergen J, van Steensel B. Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome. Mol Cell 2022;82:2519-2531.e6. [PMID: 35594855 PMCID: PMC9278412 DOI: 10.1016/j.molcel.2022.04.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/17/2022] [Accepted: 04/05/2022] [Indexed: 12/12/2022]
6
Secchia S, Forneris M, Heinen T, Stegle O, Furlong EEM. Simultaneous cellular and molecular phenotyping of embryonic mutants using single-cell regulatory trajectories. Dev Cell 2022;57:496-511.e8. [PMID: 35176234 PMCID: PMC8893321 DOI: 10.1016/j.devcel.2022.01.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/04/2021] [Accepted: 01/26/2022] [Indexed: 11/09/2022]
7
Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling. Genome Res 2021;31:1680-1692. [PMID: 34330790 PMCID: PMC8415375 DOI: 10.1101/gr.275684.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/28/2021] [Indexed: 11/25/2022]
8
Niederhuber MJ, McKay DJ. Mechanisms underlying the control of dynamic regulatory element activity and chromatin accessibility during metamorphosis. CURRENT OPINION IN INSECT SCIENCE 2021;43:21-28. [PMID: 32979530 PMCID: PMC7985040 DOI: 10.1016/j.cois.2020.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/25/2020] [Indexed: 05/10/2023]
9
van der Veeken J, Glasner A, Zhong Y, Hu W, Wang ZM, Bou-Puerto R, Charbonnier LM, Chatila TA, Leslie CS, Rudensky AY. The Transcription Factor Foxp3 Shapes Regulatory T Cell Identity by Tuning the Activity of trans-Acting Intermediaries. Immunity 2020;53:971-984.e5. [PMID: 33176163 DOI: 10.1016/j.immuni.2020.10.010] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/06/2020] [Accepted: 10/14/2020] [Indexed: 12/16/2022]
10
McEwan AR, MacKenzie A. Perspective: Quality Versus Quantity; Is It Important to Assess the Role of Enhancers in Complex Disease from an In Vivo Perspective? Int J Mol Sci 2020;21:E7856. [PMID: 33113946 PMCID: PMC7660172 DOI: 10.3390/ijms21217856] [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: 08/25/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022]  Open
11
On the specificity of gene regulatory networks: How does network co-option affect subsequent evolution? Curr Top Dev Biol 2020;139:375-405. [PMID: 32450967 DOI: 10.1016/bs.ctdb.2020.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
12
Ryan GE, Farley EK. Functional genomic approaches to elucidate the role of enhancers during development. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2020;12:e1467. [PMID: 31808313 PMCID: PMC7027484 DOI: 10.1002/wsbm.1467] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/02/2019] [Accepted: 10/11/2019] [Indexed: 12/22/2022]
13
Zeiske T, Baburajendran N, Kaczynska A, Brasch J, Palmer AG, Shapiro L, Honig B, Mann RS. Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites. Cell Rep 2020;24:2221-2230. [PMID: 30157419 DOI: 10.1016/j.celrep.2018.07.100] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/14/2018] [Accepted: 07/28/2018] [Indexed: 11/26/2022]  Open
14
Cohen DM, Lim HW, Won KJ, Steger DJ. Shared nucleotide flanks confer transcriptional competency to bZip core motifs. Nucleic Acids Res 2019;46:8371-8384. [PMID: 30085281 PMCID: PMC6144830 DOI: 10.1093/nar/gky681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/17/2018] [Indexed: 12/31/2022]  Open
15
Bhakta M, Padanad MS, Harris JP, Lubczyk C, Amatruda JF, Munshi NV. pouC Regulates Expression of bmp4 During Atrioventricular Canal Formation in Zebrafish. Dev Dyn 2018;248:173-188. [PMID: 30444277 DOI: 10.1002/dvdy.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/04/2018] [Accepted: 10/24/2018] [Indexed: 01/04/2023]  Open
16
Chromatin dependencies in cancer and inflammation. Nat Rev Mol Cell Biol 2017;19:245-261. [DOI: 10.1038/nrm.2017.113] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
17
Isoda T, Moore AJ, He Z, Chandra V, Aida M, Denholtz M, Piet van Hamburg J, Fisch KM, Chang AN, Fahl SP, Wiest DL, Murre C. Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate. Cell 2017;171:103-119.e18. [PMID: 28938112 DOI: 10.1016/j.cell.2017.09.001] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/24/2017] [Accepted: 08/30/2017] [Indexed: 01/01/2023]
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