• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4835760)   Today's Articles (102)
For: Gisselbrecht SS, Palagi A, Kurland JV, Rogers JM, Ozadam H, Zhan Y, Dekker J, Bulyk ML. Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts. Mol Cell 2019;77:324-337.e8. [PMID: 31704182 DOI: 10.1016/j.molcel.2019.10.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 08/15/2019] [Accepted: 10/01/2019] [Indexed: 12/26/2022]
Number Cited by Other Article(s)
1
Cui X, Yin Q, Gao Z, Li Z, Chen X, Lv H, Chen S, Liu Q, Zeng W, Jiang R. CREATE: cell-type-specific cis-regulatory element identification via discrete embedding. Nat Commun 2025;16:4607. [PMID: 40382355 PMCID: PMC12085597 DOI: 10.1038/s41467-025-59780-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 05/02/2025] [Indexed: 05/20/2025]  Open
2
Mikulski P, Tehrani SSH, Kogan A, Abdul-Zani I, Shell E, James L, Ryan BJ, Jansen LET. Heritable maintenance of chromatin modifications confers transcriptional memory of interferon-γ signaling. Nat Struct Mol Biol 2025:10.1038/s41594-025-01522-8. [PMID: 40186025 DOI: 10.1038/s41594-025-01522-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/20/2025] [Indexed: 04/07/2025]
3
Regner MJ, Garcia-Recio S, Thennavan A, Wisniewska K, Mendez-Giraldez R, Felsheim B, Spanheimer PM, Parker JS, Perou CM, Franco HL. Defining the regulatory logic of breast cancer using single-cell epigenetic and transcriptome profiling. CELL GENOMICS 2025;5:100765. [PMID: 39914387 PMCID: PMC11872555 DOI: 10.1016/j.xgen.2025.100765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 11/04/2024] [Accepted: 01/08/2025] [Indexed: 02/12/2025]
4
Song W, Ovcharenko I. Abundant repressor binding sites in human enhancers are associated with the fine-tuning of gene regulation. iScience 2025;28:111658. [PMID: 39868043 PMCID: PMC11761325 DOI: 10.1016/j.isci.2024.111658] [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: 02/29/2024] [Revised: 08/04/2024] [Accepted: 11/25/2024] [Indexed: 01/28/2025]  Open
5
Friedman RZ, Ramu A, Lichtarge S, Wu Y, Tripp L, Lyon D, Myers CA, Granas DM, Gause M, Corbo JC, Cohen BA, White MA. Active learning of enhancers and silencers in the developing neural retina. Cell Syst 2025;16:101163. [PMID: 39778579 PMCID: PMC11827711 DOI: 10.1016/j.cels.2024.12.004] [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: 03/26/2024] [Revised: 10/17/2024] [Accepted: 12/06/2024] [Indexed: 01/11/2025]
6
Ozturan D, de Boer CG. Silent silencers: Leave no trace. Mol Cell 2024;84:4473-4475. [PMID: 39642851 DOI: 10.1016/j.molcel.2024.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Revised: 11/07/2024] [Accepted: 11/07/2024] [Indexed: 12/09/2024]
7
Hofbauer L, Pleyer LM, Reiter F, Schleiffer A, Vlasova A, Serebreni L, Huang A, Stark A. A genome-wide screen identifies silencers with distinct chromatin properties and mechanisms of repression. Mol Cell 2024;84:4503-4521.e14. [PMID: 39571581 DOI: 10.1016/j.molcel.2024.10.041] [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: 02/12/2024] [Revised: 08/20/2024] [Accepted: 10/29/2024] [Indexed: 12/08/2024]
8
McDonald JMC, Reed RD. Beyond modular enhancers: new questions in cis-regulatory evolution. Trends Ecol Evol 2024;39:1035-1046. [PMID: 39266441 DOI: 10.1016/j.tree.2024.07.005] [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: 10/26/2023] [Revised: 06/28/2024] [Accepted: 07/08/2024] [Indexed: 09/14/2024]
9
Qiu K, Vu DC, Wang L, Nguyen NN, Bookstaver AK, Sol-Church K, Li H, Dinh TN, Goldfarb AN, Tenen DG, Trinh BQ. Chromatin structure and 3D architecture define the differential functions of PU.1 regulatory elements in blood cell lineages. Epigenetics Chromatin 2024;17:33. [PMID: 39487555 PMCID: PMC11531149 DOI: 10.1186/s13072-024-00556-4] [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: 03/29/2024] [Accepted: 10/22/2024] [Indexed: 11/04/2024]  Open
10
Jores T, Mueth NA, Tonnies J, Char SN, Liu B, Grillo-Alvarado V, Abbitt S, Anand A, Deschamps S, Diehn S, Gordon-Kamm B, Jiao S, Munkvold K, Snowgren H, Sardesai N, Fields S, Yang B, Cuperus JT, Queitsch C. Small DNA elements that act as both insulators and silencers in plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.13.612883. [PMID: 39345455 PMCID: PMC11429706 DOI: 10.1101/2024.09.13.612883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
11
Fu X, Rabadan R. Understanding variants of unknown significance: the computational frontier. Oncologist 2024;29:653-657. [PMID: 38848164 PMCID: PMC11299926 DOI: 10.1093/oncolo/oyae103] [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: 04/07/2024] [Accepted: 04/16/2024] [Indexed: 06/09/2024]  Open
12
Li Y, Tan M, Akkari-Henić A, Zhang L, Kip M, Sun S, Sepers JJ, Xu N, Ariyurek Y, Kloet SL, Davis RP, Mikkers H, Gruber JJ, Snyder MP, Li X, Pang B. Genome-wide Cas9-mediated screening of essential non-coding regulatory elements via libraries of paired single-guide RNAs. Nat Biomed Eng 2024;8:890-908. [PMID: 38778183 PMCID: PMC11310080 DOI: 10.1038/s41551-024-01204-8] [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: 09/05/2023] [Accepted: 03/27/2024] [Indexed: 05/25/2024]
13
Roy Chowdhury N, Gurevich V, Shamay M. KSHV genome harbors both constitutive and lytically induced enhancers. J Virol 2024;98:e0017924. [PMID: 38695538 PMCID: PMC11237633 DOI: 10.1128/jvi.00179-24] [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: 01/30/2024] [Accepted: 04/03/2024] [Indexed: 06/14/2024]  Open
14
Delihas N. Evolution of a Human-Specific De Novo Open Reading Frame and Its Linked Transcriptional Silencer. Int J Mol Sci 2024;25:3924. [PMID: 38612733 PMCID: PMC11011693 DOI: 10.3390/ijms25073924] [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: 02/27/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024]  Open
15
Merrill CB, Titos I, Pabon MA, Montgomery AB, Rodan AR, Rothenfluh A. Iterative assay for transposase-accessible chromatin by sequencing to isolate functionally relevant neuronal subtypes. SCIENCE ADVANCES 2024;10:eadi4393. [PMID: 38536919 PMCID: PMC10971406 DOI: 10.1126/sciadv.adi4393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 02/21/2024] [Indexed: 04/18/2024]
16
Shepherdson JL, Friedman RZ, Zheng Y, Sun C, Oh IY, Granas DM, Cohen BA, Chen S, White MA. Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors. Genome Res 2024;34:243-255. [PMID: 38355306 PMCID: PMC10984388 DOI: 10.1101/gr.278133.123] [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: 05/27/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
17
Ando K, Ou J, Thompson JD, Welsby J, Bangru S, Shen J, Wei X, Diao Y, Poss KD. A screen for regeneration-associated silencer regulatory elements in zebrafish. Dev Cell 2024;59:676-691.e5. [PMID: 38290519 PMCID: PMC10939760 DOI: 10.1016/j.devcel.2024.01.004] [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: 06/24/2023] [Revised: 11/03/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
18
Lim B, Domsch K, Mall M, Lohmann I. Canalizing cell fate by transcriptional repression. Mol Syst Biol 2024;20:144-161. [PMID: 38302581 PMCID: PMC10912439 DOI: 10.1038/s44320-024-00014-z] [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: 09/19/2023] [Revised: 11/28/2023] [Accepted: 12/15/2023] [Indexed: 02/03/2024]  Open
19
Tendolkar A, Mazo-Vargas A, Livraghi L, Hanly JJ, Van Horne KC, Gilbert LE, Martin A. Cis-regulatory modes of Ultrabithorax inactivation in butterfly forewings. eLife 2024;12:RP90846. [PMID: 38261357 PMCID: PMC10945631 DOI: 10.7554/elife.90846] [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] [Indexed: 01/24/2024]  Open
20
Qiu K, Vu D, Wang L, Bookstaver A, Dinh TN, Goldfarb AN, Tenen DG, Trinh BQ. Chromatin structure and 3D architecture define differential functions of PU.1 cis regulatory elements in human blood cell lineages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.01.573782. [PMID: 38260486 PMCID: PMC10802337 DOI: 10.1101/2024.01.01.573782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
21
Shepherdson JL, Friedman RZ, Zheng Y, Sun C, Oh IY, Granas DM, Cohen BA, Chen S, White MA. Pathogenic variants in Crx have distinct cis-regulatory effects on enhancers and silencers in photoreceptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.27.542576. [PMID: 37292699 PMCID: PMC10245955 DOI: 10.1101/2023.05.27.542576] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
22
Edrei Y, Levy R, Kaye D, Marom A, Radlwimmer B, Hellman A. Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variation. Genome Biol 2023;24:264. [PMID: 38012713 PMCID: PMC10683314 DOI: 10.1186/s13059-023-03094-6] [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: 05/23/2022] [Accepted: 10/23/2023] [Indexed: 11/29/2023]  Open
23
Milevskiy MJ, Coughlan HD, Kane SR, Johanson TM, Kordafshari S, Chan WF, Tsai M, Surgenor E, Wilcox S, Allan RS, Chen Y, Lindeman GJ, Smyth GK, Visvader JE. Three-dimensional genome architecture coordinates key regulators of lineage specification in mammary epithelial cells. CELL GENOMICS 2023;3:100424. [PMID: 38020976 PMCID: PMC10667557 DOI: 10.1016/j.xgen.2023.100424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/20/2023] [Accepted: 09/20/2023] [Indexed: 12/01/2023]
24
Mendieta JP, Sangra A, Yan H, Minow MAA, Schmitz RJ. Exploring plant cis-regulatory elements at single-cell resolution: overcoming biological and computational challenges to advance plant research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023;115:1486-1499. [PMID: 37309871 PMCID: PMC10598807 DOI: 10.1111/tpj.16351] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/14/2023]
25
Friedman RZ, Ramu A, Lichtarge S, Myers CA, Granas DM, Gause M, Corbo JC, Cohen BA, White MA. Active learning of enhancer and silencer regulatory grammar in photoreceptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554146. [PMID: 37662358 PMCID: PMC10473580 DOI: 10.1101/2023.08.21.554146] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
26
Chan B, Rubinstein M. Theory of chromatin organization maintained by active loop extrusion. Proc Natl Acad Sci U S A 2023;120:e2222078120. [PMID: 37253009 PMCID: PMC10266055 DOI: 10.1073/pnas.2222078120] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/13/2023] [Indexed: 06/01/2023]  Open
27
Stefan K, Barski A. Cis-regulatory atlas of primary human CD4+ T cells. BMC Genomics 2023;24:253. [PMID: 37170195 PMCID: PMC10173520 DOI: 10.1186/s12864-023-09288-3] [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: 12/30/2022] [Accepted: 03/31/2023] [Indexed: 05/13/2023]  Open
28
Méndez-González ID, Williams TM, Rebeiz M. Changes in locus wide repression underlie the evolution of Drosophila abdominal pigmentation. PLoS Genet 2023;19:e1010722. [PMID: 37134121 PMCID: PMC10184908 DOI: 10.1371/journal.pgen.1010722] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 05/15/2023] [Accepted: 03/28/2023] [Indexed: 05/04/2023]  Open
29
Vermunt MW, Luan J, Zhang Z, Thrasher AJ, Huang A, Saari MS, Khandros E, Beagrie RA, Zhang S, Vemulamada P, Brilleman M, Lee K, Yano JA, Giardine BM, Keller CA, Hardison RC, Blobel GA. Gene silencing dynamics are modulated by transiently active regulatory elements. Mol Cell 2023;83:715-730.e6. [PMID: 36868189 PMCID: PMC10719944 DOI: 10.1016/j.molcel.2023.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 12/05/2022] [Accepted: 02/03/2023] [Indexed: 03/05/2023]
30
Mechanisms of Interaction between Enhancers and Promoters in Three Drosophila Model Systems. Int J Mol Sci 2023;24:ijms24032855. [PMID: 36769179 PMCID: PMC9917889 DOI: 10.3390/ijms24032855] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]  Open
31
Kim S, Wysocka J. Deciphering the multi-scale, quantitative cis-regulatory code. Mol Cell 2023;83:373-392. [PMID: 36693380 PMCID: PMC9898153 DOI: 10.1016/j.molcel.2022.12.032] [Citation(s) in RCA: 116] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/24/2023]
32
Enhancer-promoter entanglement explains their transcriptional interdependence. Proc Natl Acad Sci U S A 2023;120:e2216436120. [PMID: 36656865 PMCID: PMC9942820 DOI: 10.1073/pnas.2216436120] [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] [Indexed: 01/20/2023]  Open
33
Mouri K, Dewey HB, Castro R, Berenzy D, Kales S, Tewhey R. Whole-genome functional characterization of RE1 silencers using a modified massively parallel reporter assay. CELL GENOMICS 2023;3:100234. [PMID: 36777181 PMCID: PMC9903721 DOI: 10.1016/j.xgen.2022.100234] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 09/12/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022]
34
Preissl S, Gaulton KJ, Ren B. Characterizing cis-regulatory elements using single-cell epigenomics. Nat Rev Genet 2023;24:21-43. [PMID: 35840754 PMCID: PMC9771884 DOI: 10.1038/s41576-022-00509-1] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2022] [Indexed: 12/24/2022]
35
Lohia R, Fox N, Gillis J. A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships. Genome Biol 2022;23:238. [PMID: 36352464 PMCID: PMC9647974 DOI: 10.1186/s13059-022-02790-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 10/10/2022] [Indexed: 11/10/2022]  Open
36
Pang B, van Weerd JH, Hamoen FL, Snyder MP. Identification of non-coding silencer elements and their regulation of gene expression. Nat Rev Mol Cell Biol 2022;24:383-395. [DOI: 10.1038/s41580-022-00549-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
37
Xu J, Pratt HE, Moore JE, Gerstein MB, Weng Z. Building integrative functional maps of gene regulation. Hum Mol Genet 2022;31:R114-R122. [PMID: 36083269 PMCID: PMC9585680 DOI: 10.1093/hmg/ddac195] [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: 07/17/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022]  Open
38
Zheng M, Guo T, Yang B, Zhang Z, Huang L. Origin, evolution, and tissue-specific functions of the porcine repetitive element 1. Genet Sel Evol 2022;54:54. [PMID: 35896967 PMCID: PMC9327148 DOI: 10.1186/s12711-022-00745-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022]  Open
39
Keränen SVE, Villahoz-Baleta A, Bruno AE, Halfon MS. REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics. INSECTS 2022;13:618. [PMID: 35886794 PMCID: PMC9323752 DOI: 10.3390/insects13070618] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/29/2022]
40
Boldyreva LV, Andreyeva EN, Pindyurin AV. Position Effect Variegation: Role of the Local Chromatin Context in Gene Expression Regulation. Mol Biol 2022. [DOI: 10.1134/s0026893322030049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
41
Interplay between regulatory elements and chromatin topology in cellular lineage determination. Trends Genet 2022;38:1048-1061. [DOI: 10.1016/j.tig.2022.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/02/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022]
42
Sun DA, Bredeson JV, Bruce HS, Patel NH. Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis. Development 2022;149:275484. [PMID: 35608283 DOI: 10.1242/dev.200793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/21/2022] [Indexed: 12/13/2022]
43
Mulero Hernández J, Fernández-Breis JT. Analysis of the landscape of human enhancer sequences in biological databases. Comput Struct Biotechnol J 2022;20:2728-2744. [PMID: 35685360 PMCID: PMC9168495 DOI: 10.1016/j.csbj.2022.05.045] [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: 03/28/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 12/01/2022]  Open
44
Merrill CB, Montgomery AB, Pabon MA, Shabalin AA, Rodan AR, Rothenfluh A. Harnessing changes in open chromatin determined by ATAC-seq to generate insulin-responsive reporter constructs. BMC Genomics 2022;23:399. [PMID: 35614386 PMCID: PMC9134605 DOI: 10.1186/s12864-022-08637-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 05/12/2022] [Indexed: 01/07/2023]  Open
45
Long-Distance Repression by Human Silencers: Chromatin Interactions and Phase Separation in Silencers. Cells 2022;11:cells11091560. [PMID: 35563864 PMCID: PMC9101175 DOI: 10.3390/cells11091560] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022]  Open
46
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: 58] [Impact Index Per Article: 19.3] [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]
47
Boyling A, Perez-Siles G, Kennerson ML. Structural Variation at a Disease Mutation Hotspot: Strategies to Investigate Gene Regulation and the 3D Genome. Front Genet 2022;13:842860. [PMID: 35401663 PMCID: PMC8990796 DOI: 10.3389/fgene.2022.842860] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/21/2022] [Indexed: 12/18/2022]  Open
48
Akiyama N, Sato S, Tanaka KM, Sakai T, Takahashi A. The role of the epidermis enhancer element in positive and negative transcriptional regulation of ebony in Drosophila melanogaster. G3 (BETHESDA, MD.) 2022;12:jkac010. [PMID: 35100378 PMCID: PMC8895987 DOI: 10.1093/g3journal/jkac010] [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] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/06/2022] [Indexed: 11/15/2022]
49
Luecke D, Rice G, Kopp A. Sex-specific evolution of a Drosophila sensory system via interacting cis- and trans-regulatory changes. Evol Dev 2022;24:37-60. [PMID: 35239254 PMCID: PMC9179014 DOI: 10.1111/ede.12398] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 12/13/2022]
50
Galouzis CC, Furlong EEM. Regulating specificity in enhancer-promoter communication. Curr Opin Cell Biol 2022;75:102065. [PMID: 35240372 DOI: 10.1016/j.ceb.2022.01.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/14/2022]
PrevPage 1 of 2 12Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA