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For: Anderson E, Devenney PS, Hill RE, Lettice LA. Mapping the Shh long-range regulatory domain. Development 2014;141:3934-43. [PMID: 25252942 PMCID: PMC4197689 DOI: 10.1242/dev.108480] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Number Cited by Other Article(s)
1
Bower G, Kvon EZ. Genetic factors mediating long-range enhancer-promoter communication in mammalian development. Curr Opin Genet Dev 2025;90:102282. [PMID: 39579740 DOI: 10.1016/j.gde.2024.102282] [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: 08/20/2024] [Revised: 10/20/2024] [Accepted: 10/28/2024] [Indexed: 11/25/2024]
2
Harke J, Lee JR, Nguyen SC, Arab A, Rakowiecki SM, Hugelier S, Paliou C, Rauseo A, Yunker R, Xu K, Yao Y, Lakadamyali M, Andrey G, Epstein DJ, Joyce EF. Multiple allelic configurations govern long-range Shh enhancer-promoter communication in the embryonic forebrain. Mol Cell 2024;84:4698-4710.e6. [PMID: 39579767 DOI: 10.1016/j.molcel.2024.10.042] [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: 09/13/2023] [Revised: 08/30/2024] [Accepted: 10/30/2024] [Indexed: 11/25/2024]
3
Qiao L, Welch CL, Hernan R, Wynn J, Krishnan US, Zalieckas JM, Buchmiller T, Khlevner J, De A, Farkouh-Karoleski C, Wagner AJ, Heydweiller A, Mueller AC, de Klein A, Warner BW, Maj C, Chung D, McCulley DJ, Schindel D, Potoka D, Fialkowski E, Schulz F, Kipfmuller F, Lim FY, Magielsen F, Mychaliska GB, Aspelund G, Reutter HM, Needelman H, Schnater JM, Fisher JC, Azarow K, Elfiky M, Nöthen MM, Danko ME, Li M, Kosiński P, Wijnen RMH, Cusick RA, Soffer SZ, Cochius-Den Otter SCM, Schaible T, Crombleholme T, Duron VP, Donahoe PK, Sun X, High FA, Bendixen C, Brosens E, Shen Y, Chung WK. Common variants increase risk for congenital diaphragmatic hernia within the context of de novo variants. Am J Hum Genet 2024;111:2362-2381. [PMID: 39332409 PMCID: PMC11568762 DOI: 10.1016/j.ajhg.2024.08.024] [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: 04/23/2024] [Revised: 08/24/2024] [Accepted: 08/30/2024] [Indexed: 09/29/2024]  Open
4
Abnizova I, Stapel C, Boekhorst RT, Lee JTH, Hemberg M. Integrative analysis of transcriptomic and epigenomic data reveals distinct patterns for developmental and housekeeping gene regulation. BMC Biol 2024;22:78. [PMID: 38600550 PMCID: PMC11005181 DOI: 10.1186/s12915-024-01869-2] [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: 08/23/2023] [Accepted: 03/14/2024] [Indexed: 04/12/2024]  Open
5
Sabarís G, Ortíz DM, Laiker I, Mayansky I, Naik S, Cavalli G, Stern DL, Preger-Ben Noon E, Frankel N. The Density of Regulatory Information Is a Major Determinant of Evolutionary Constraint on Noncoding DNA in Drosophila. Mol Biol Evol 2024;41:msae004. [PMID: 38364113 PMCID: PMC10871701 DOI: 10.1093/molbev/msae004] [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: 07/04/2023] [Revised: 11/26/2023] [Accepted: 01/05/2024] [Indexed: 02/18/2024]  Open
6
Zimmermann B, Montenegro JD, Robb SMC, Fropf WJ, Weilguny L, He S, Chen S, Lovegrove-Walsh J, Hill EM, Chen CY, Ragkousi K, Praher D, Fredman D, Schultz D, Moran Y, Simakov O, Genikhovich G, Gibson MC, Technau U. Topological structures and syntenic conservation in sea anemone genomes. Nat Commun 2023;14:8270. [PMID: 38092765 PMCID: PMC10719294 DOI: 10.1038/s41467-023-44080-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023]  Open
7
Yang K, Zhang J, Zhao Y, Shao Y, Zhai M, Liu H, Zhang L. Whole Genome Resequencing Revealed the Genetic Relationship and Selected Regions among Baicheng-You, Beijing-You, and European-Origin Broilers. BIOLOGY 2023;12:1397. [PMID: 37997996 PMCID: PMC10669838 DOI: 10.3390/biology12111397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]
8
Chen Y, Zhou T, Liao Z, Gao W, Wu J, Zhang S, Li Y, Liu H, Zhou H, Xu C, Su P. Hnrnpk is essential for embryonic limb bud development as a transcription activator and a collaborator of insulator protein Ctcf. Cell Death Differ 2023;30:2293-2308. [PMID: 37608075 PMCID: PMC10589297 DOI: 10.1038/s41418-023-01207-z] [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: 03/12/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023]  Open
9
Thomas HF, Buecker C. What is an enhancer? Bioessays 2023;45:e2300044. [PMID: 37256273 PMCID: PMC11475577 DOI: 10.1002/bies.202300044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2023]
10
Luo R, Yan J, Oh JW, Xi W, Shigaki D, Wong W, Cho HS, Murphy D, Cutler R, Rosen BP, Pulecio J, Yang D, Glenn RA, Chen T, Li QV, Vierbuchen T, Sidoli S, Apostolou E, Huangfu D, Beer MA. Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions. Nat Genet 2023;55:1336-1346. [PMID: 37488417 PMCID: PMC11012226 DOI: 10.1038/s41588-023-01450-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 06/20/2023] [Indexed: 07/26/2023]
11
Mach P, Giorgetti L. Integrative approaches to study enhancer-promoter communication. Curr Opin Genet Dev 2023;80:102052. [PMID: 37257410 PMCID: PMC10293802 DOI: 10.1016/j.gde.2023.102052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 06/02/2023]
12
Chen LF, Long HK, Park M, Swigut T, Boettiger AN, Wysocka J. Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus. Mol Cell 2023;83:1446-1461.e6. [PMID: 36996812 DOI: 10.1016/j.molcel.2023.03.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/15/2023] [Accepted: 03/07/2023] [Indexed: 03/31/2023]
13
Luo R, Yan J, Oh JW, Xi W, Shigaki D, Wong W, Cho H, Murphy D, Cutler R, Rosen BP, Pulecio J, Yang D, Glenn R, Chen T, Li QV, Vierbuchen T, Sidoli S, Apostolou E, Huangfu D, Beer MA. Dynamic network-guided CRISPRi screen reveals CTCF loop-constrained nonlinear enhancer-gene regulatory activity in cell state transitions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531569. [PMID: 36945628 PMCID: PMC10028945 DOI: 10.1101/2023.03.07.531569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
14
Chemotherapy suppresses SHH gene expression via a specific enhancer. J Genet Genomics 2023;50:27-37. [PMID: 35998878 DOI: 10.1016/j.jgg.2022.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 02/06/2023]
15
Zhu M, Tabin CJ. The role of timing in the development and evolution of the limb. Front Cell Dev Biol 2023;11:1135519. [PMID: 37200627 PMCID: PMC10185760 DOI: 10.3389/fcell.2023.1135519] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/13/2023] [Indexed: 05/20/2023]  Open
16
Diacou R, Nandigrami P, Fiser A, Liu W, Ashery-Padan R, Cvekl A. Cell fate decisions, transcription factors and signaling during early retinal development. Prog Retin Eye Res 2022;91:101093. [PMID: 35817658 PMCID: PMC9669153 DOI: 10.1016/j.preteyeres.2022.101093] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 12/30/2022]
17
Ringel AR, Szabo Q, Chiariello AM, Chudzik K, Schöpflin R, Rothe P, Mattei AL, Zehnder T, Harnett D, Laupert V, Bianco S, Hetzel S, Glaser J, Phan MHQ, Schindler M, Ibrahim DM, Paliou C, Esposito A, Prada-Medina CA, Haas SA, Giere P, Vingron M, Wittler L, Meissner A, Nicodemi M, Cavalli G, Bantignies F, Mundlos S, Robson MI. Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes. Cell 2022;185:3689-3704.e21. [PMID: 36179666 PMCID: PMC9567273 DOI: 10.1016/j.cell.2022.09.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 06/03/2022] [Accepted: 08/30/2022] [Indexed: 01/26/2023]
18
Cohesin is required for long-range enhancer action at the Shh locus. Nat Struct Mol Biol 2022;29:891-897. [PMID: 36097291 DOI: 10.1038/s41594-022-00821-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 07/20/2022] [Indexed: 11/08/2022]
19
Chua EHZ, Yasar S, Harmston N. The importance of considering regulatory domains in genome-wide analyses - the nearest gene is often wrong! Biol Open 2022;11:274931. [PMID: 35377406 PMCID: PMC9002814 DOI: 10.1242/bio.059091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
20
Zuin J, Roth G, Zhan Y, Cramard J, Redolfi J, Piskadlo E, Mach P, Kryzhanovska M, Tihanyi G, Kohler H, Eder M, Leemans C, van Steensel B, Meister P, Smallwood S, Giorgetti L. Nonlinear control of transcription through enhancer-promoter interactions. Nature 2022;604:571-577. [PMID: 35418676 PMCID: PMC9021019 DOI: 10.1038/s41586-022-04570-y] [Citation(s) in RCA: 221] [Impact Index Per Article: 73.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 02/21/2022] [Indexed: 12/19/2022]
21
Karr JP, Ferrie JJ, Tjian R, Darzacq X. The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer-promoter communication. Genes Dev 2022;36:7-16. [PMID: 34969825 PMCID: PMC8763055 DOI: 10.1101/gad.349160.121] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
22
Ridnik M, Schoenfelder S, Gonen N. Cis-Regulatory Control of Mammalian Sex Determination. Sex Dev 2021;15:317-334. [PMID: 34710870 PMCID: PMC8743899 DOI: 10.1159/000519244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/10/2021] [Indexed: 11/19/2022]  Open
23
Complete lung agenesis caused by complex genomic rearrangements with neo-TAD formation at the SHH locus. Hum Genet 2021;140:1459-1469. [PMID: 34436670 PMCID: PMC8460539 DOI: 10.1007/s00439-021-02344-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/10/2021] [Indexed: 11/05/2022]
24
Crane-Smith Z, Schoenebeck J, Graham KA, Devenney PS, Rose L, Ditzell M, Anderson E, Thomson JI, Klenin N, Kurrasch DM, Lettice LA, Hill RE. A Highly Conserved Shh Enhancer Coordinates Hypothalamic and Craniofacial Development. Front Cell Dev Biol 2021;9:595744. [PMID: 33869166 PMCID: PMC8047142 DOI: 10.3389/fcell.2021.595744] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 02/28/2021] [Indexed: 11/24/2022]  Open
25
Bademci G, Abad C, Cengiz FB, Seyhan S, Incesulu A, Guo S, Fitoz S, Atli EI, Gosstola NC, Demir S, Colbert BM, Seyhan GC, Sineni CJ, Duman D, Gurkan H, Morton CC, Dykxhoorn DM, Walz K, Tekin M. Long-range cis-regulatory elements controlling GDF6 expression are essential for ear development. J Clin Invest 2021;130:4213-4217. [PMID: 32369452 DOI: 10.1172/jci136951] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/29/2020] [Indexed: 12/15/2022]  Open
26
Haslam IS, Zhou G, Xie G, Teng X, Ao X, Yan Z, Smart E, Rutkowski D, Wierzbicka J, Zhou Y, Huang Z, Zhang Y, Farjo N, Farjo B, Paus R, Yue Z. Inhibition of Shh Signaling through MAPK Activation Controls Chemotherapy-Induced Alopecia. J Invest Dermatol 2021;141:334-344. [DOI: 10.1016/j.jid.2020.05.118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 04/16/2020] [Accepted: 05/11/2020] [Indexed: 01/09/2023]
27
A 300-kb microduplication of 7q36.3 in a patient with triphalangeal thumb-polysyndactyly syndrome combined with congenital heart disease and optic disc coloboma: a case report. BMC Med Genomics 2020;13:175. [PMID: 33218365 PMCID: PMC7678048 DOI: 10.1186/s12920-020-00821-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/09/2020] [Indexed: 12/04/2022]  Open
28
Tobias IC, Abatti LE, Moorthy SD, Mullany S, Taylor T, Khader N, Filice MA, Mitchell JA. Transcriptional enhancers: from prediction to functional assessment on a genome-wide scale. Genome 2020;64:426-448. [PMID: 32961076 DOI: 10.1139/gen-2020-0104] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
29
Amano T. Gene regulatory landscape of the sonic hedgehog locus in embryonic development. Dev Growth Differ 2020;62:334-342. [PMID: 32343848 DOI: 10.1111/dgd.12668] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/31/2020] [Accepted: 04/15/2020] [Indexed: 12/22/2022]
30
Robson MI, Ringel AR, Mundlos S. Regulatory Landscaping: How Enhancer-Promoter Communication Is Sculpted in 3D. Mol Cell 2020;74:1110-1122. [PMID: 31226276 DOI: 10.1016/j.molcel.2019.05.032] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/13/2019] [Accepted: 05/23/2019] [Indexed: 10/26/2022]
31
Okuhara S, Birjandi AA, Adel Al-Lami H, Sagai T, Amano T, Shiroishi T, Xavier GM, Liu KJ, Cobourne MT, Iseki S. Temporospatial sonic hedgehog signalling is essential for neural crest-dependent patterning of the intrinsic tongue musculature. Development 2019;146:146/21/dev180075. [PMID: 31719045 DOI: 10.1242/dev.180075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/17/2019] [Indexed: 01/20/2023]
32
Williamson I, Kane L, Devenney PS, Flyamer IM, Anderson E, Kilanowski F, Hill RE, Bickmore WA, Lettice LA. Developmentally regulated Shh expression is robust to TAD perturbations. Development 2019;146:dev179523. [PMID: 31511252 PMCID: PMC7212092 DOI: 10.1242/dev.179523] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/02/2019] [Indexed: 12/26/2022]
33
Mir M, Bickmore W, Furlong EEM, Narlikar G. Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase? Development 2019;146:dev182766. [PMID: 31554625 PMCID: PMC6803379 DOI: 10.1242/dev.182766] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
34
Potuijt JWP, Galjaard RJH, van der Spek PJ, van Nieuwenhoven CA, Ahituv N, Oberg KC, Hovius SER. A multidisciplinary review of triphalangeal thumb. J Hand Surg Eur Vol 2019;44:59-68. [PMID: 30318985 PMCID: PMC6297887 DOI: 10.1177/1753193418803521] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
35
Tan G, Polychronopoulos D, Lenhard B. CNEr: A toolkit for exploring extreme noncoding conservation. PLoS Comput Biol 2019;15:e1006940. [PMID: 31449516 PMCID: PMC6730951 DOI: 10.1371/journal.pcbi.1006940] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 09/06/2019] [Accepted: 06/25/2019] [Indexed: 12/18/2022]  Open
36
Paliou C, Guckelberger P, Schöpflin R, Heinrich V, Esposito A, Chiariello AM, Bianco S, Annunziatella C, Helmuth J, Haas S, Jerković I, Brieske N, Wittler L, Timmermann B, Nicodemi M, Vingron M, Mundlos S, Andrey G. Preformed chromatin topology assists transcriptional robustness of Shh during limb development. Proc Natl Acad Sci U S A 2019;116:12390-12399. [PMID: 31147463 PMCID: PMC6589666 DOI: 10.1073/pnas.1900672116] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
37
Bompadre O, Andrey G. Chromatin topology in development and disease. Curr Opin Genet Dev 2019;55:32-38. [DOI: 10.1016/j.gde.2019.04.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 03/25/2019] [Accepted: 04/15/2019] [Indexed: 12/20/2022]
38
Polychronopoulos D, King JWD, Nash AJ, Tan G, Lenhard B. Conserved non-coding elements: developmental gene regulation meets genome organization. Nucleic Acids Res 2018;45:12611-12624. [PMID: 29121339 PMCID: PMC5728398 DOI: 10.1093/nar/gkx1074] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/24/2017] [Indexed: 12/20/2022]  Open
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Leal F, Cohn MJ. Developmental, genetic, and genomic insights into the evolutionary loss of limbs in snakes. Genesis 2017;56. [DOI: 10.1002/dvg.23077] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/29/2017] [Accepted: 10/06/2017] [Indexed: 12/31/2022]
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Peluso S, Douglas A, Hill A, De Angelis C, Moore BL, Grimes G, Petrovich G, Essafi A, Hill RE. Fibroblast growth factors (FGFs) prime the limb specific Shh enhancer for chromatin changes that balance histone acetylation mediated by E26 transformation-specific (ETS) factors. eLife 2017;6:28590. [PMID: 28949289 PMCID: PMC5659820 DOI: 10.7554/elife.28590] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/25/2017] [Indexed: 01/12/2023]  Open
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Harmston N, Ing-Simmons E, Tan G, Perry M, Merkenschlager M, Lenhard B. Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation. Nat Commun 2017;8:441. [PMID: 28874668 PMCID: PMC5585340 DOI: 10.1038/s41467-017-00524-5] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 07/05/2017] [Indexed: 02/08/2023]  Open
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Norton HK, Phillips-Cremins JE. Crossed wires: 3D genome misfolding in human disease. J Cell Biol 2017;216:3441-3452. [PMID: 28855250 PMCID: PMC5674879 DOI: 10.1083/jcb.201611001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 06/09/2017] [Accepted: 08/16/2017] [Indexed: 12/13/2022]  Open
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Micale M, Embrey B, Hubbell K, Beaudry-Rogers K, Whitten A. Prenatal identification of two discontinuous maternally inherited chromosome 7q36.3 microduplications totaling 507 kb including the sonic hedgehog gene in a fetus with multiple congenital anomalies. Clin Case Rep 2017;5:993-999. [PMID: 28588853 PMCID: PMC5457993 DOI: 10.1002/ccr3.982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/24/2017] [Accepted: 02/13/2017] [Indexed: 12/03/2022]  Open
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Wu C, Hu S, Cheng J, Wang G, Tao K. Smoothened antagonist GDC-0449 (Vismodegib) inhibits proliferation and triggers apoptosis in colon cancer cell lines. Exp Ther Med 2017;13:2529-2536. [PMID: 28565875 DOI: 10.3892/etm.2017.4282] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 02/03/2017] [Indexed: 12/19/2022]  Open
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Evolution of Shh endoderm enhancers during morphological transition from ventral lungs to dorsal gas bladder. Nat Commun 2017;8:14300. [PMID: 28155855 PMCID: PMC5296767 DOI: 10.1038/ncomms14300] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/16/2016] [Indexed: 11/13/2022]  Open
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Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking. Nat Genet 2016;49:65-74. [PMID: 27869826 DOI: 10.1038/ng.3722] [Citation(s) in RCA: 296] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/19/2016] [Indexed: 02/06/2023]
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Symmons O, Pan L, Remeseiro S, Aktas T, Klein F, Huber W, Spitz F. The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances. Dev Cell 2016;39:529-543. [PMID: 27867070 PMCID: PMC5142843 DOI: 10.1016/j.devcel.2016.10.015] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/01/2016] [Accepted: 10/18/2016] [Indexed: 11/18/2022]
48
Ordulu Z, Kammin T, Brand H, Pillalamarri V, Redin CE, Collins RL, Blumenthal I, Hanscom C, Pereira S, Bradley I, Crandall BF, Gerrol P, Hayden MA, Hussain N, Kanengisser-Pines B, Kantarci S, Levy B, Macera MJ, Quintero-Rivera F, Spiegel E, Stevens B, Ulm JE, Warburton D, Wilkins-Haug LE, Yachelevich N, Gusella JF, Talkowski ME, Morton CC. Structural Chromosomal Rearrangements Require Nucleotide-Level Resolution: Lessons from Next-Generation Sequencing in Prenatal Diagnosis. Am J Hum Genet 2016;99:1015-1033. [PMID: 27745839 PMCID: PMC5097935 DOI: 10.1016/j.ajhg.2016.08.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 08/26/2016] [Indexed: 12/27/2022]  Open
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Drew AP, Cutrupi AN, Brewer MH, Nicholson GA, Kennerson ML. A 1.35 Mb DNA fragment is inserted into the DHMN1 locus on chromosome 7q34–q36.2. Hum Genet 2016;135:1269-1278. [DOI: 10.1007/s00439-016-1720-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
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Xuan S, Sussel L. GATA4 and GATA6 regulate pancreatic endoderm identity through inhibition of hedgehog signaling. Development 2016;143:780-6. [PMID: 26932670 DOI: 10.1242/dev.127217] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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