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For: Maston GA, Landt SG, Snyder M, Green MR. Characterization of enhancer function from genome-wide analyses. Annu Rev Genomics Hum Genet 2012;13:29-57. [PMID: 22703170 DOI: 10.1146/annurev-genom-090711-163723] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Number Cited by Other Article(s)
1
Griffith EC, West AE, Greenberg ME. Neuronal enhancers fine-tune adaptive circuit plasticity. Neuron 2024;112:3043-3057. [PMID: 39208805 PMCID: PMC11550865 DOI: 10.1016/j.neuron.2024.08.002] [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: 05/01/2023] [Revised: 07/22/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
2
Koesterich J, Liu J, Williams SE, Yang N, Kreimer A. Network Analysis of Enhancer-Promoter Interactions Highlights Cell-Type-Specific Mechanisms of Transcriptional Regulation Variation. Int J Mol Sci 2024;25:9840. [PMID: 39337329 PMCID: PMC11432627 DOI: 10.3390/ijms25189840] [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: 08/13/2024] [Revised: 09/08/2024] [Accepted: 09/10/2024] [Indexed: 09/30/2024]  Open
3
Di Nardo M, Musio A. Cohesin - bridging the gap among gene transcription, genome stability, and human diseases. FEBS Lett 2024. [PMID: 38852996 DOI: 10.1002/1873-3468.14949] [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: 02/19/2024] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 06/11/2024]
4
Ye W, Yu Y, Zhu X, Wan W, Liu Y, Zou H, Zhu Z. A Common Functional Variant at the Enhancer of the Rheumatoid Arthritis Risk Gene ORMDL3 Regulates its Expression Through Allele-Specific JunD Binding. PHENOMICS (CHAM, SWITZERLAND) 2023;3:485-495. [PMID: 37881318 PMCID: PMC10593690 DOI: 10.1007/s43657-023-00107-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 10/27/2023]
5
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: 14.0] [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]
6
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]
7
Bene K, Halasz L, Nagy L. Transcriptional repression shapes the identity and function of tissue macrophages. FEBS Open Bio 2021;11:3218-3229. [PMID: 34358410 PMCID: PMC8634859 DOI: 10.1002/2211-5463.13269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/16/2021] [Accepted: 08/05/2021] [Indexed: 12/22/2022]  Open
8
Liou SH, Singh SK, Singer RH, Coleman RA, Liu WL. Structure of the p53/RNA polymerase II assembly. Commun Biol 2021;4:397. [PMID: 33767390 PMCID: PMC7994806 DOI: 10.1038/s42003-021-01934-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 03/02/2021] [Indexed: 02/07/2023]  Open
9
Brown CY, Sadlon T, Hope CM, Wong YY, Wong S, Liu N, Withers H, Brown K, Bandara V, Gundsambuu B, Pederson S, Breen J, Robertson SA, Forrest A, Beyer M, Barry SC. Molecular Insights Into Regulatory T-Cell Adaptation to Self, Environment, and Host Tissues: Plasticity or Loss of Function in Autoimmune Disease. Front Immunol 2020;11:1269. [PMID: 33072063 PMCID: PMC7533603 DOI: 10.3389/fimmu.2020.01269] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 05/19/2020] [Indexed: 12/19/2022]  Open
10
Beer MA, Shigaki D, Huangfu D. Enhancer Predictions and Genome-Wide Regulatory Circuits. Annu Rev Genomics Hum Genet 2020;21:37-54. [PMID: 32443951 DOI: 10.1146/annurev-genom-121719-010946] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
11
Supervised enhancer prediction with epigenetic pattern recognition and targeted validation. Nat Methods 2020;17:807-814. [PMID: 32737473 PMCID: PMC8073243 DOI: 10.1038/s41592-020-0907-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 06/18/2020] [Indexed: 12/20/2022]
12
Novel Approaches for Identifying the Molecular Background of Schizophrenia. Cells 2020;9:cells9010246. [PMID: 31963710 PMCID: PMC7017322 DOI: 10.3390/cells9010246] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/06/2020] [Accepted: 01/16/2020] [Indexed: 12/20/2022]  Open
13
Korkmaz G, Manber Z, Lopes R, Prekovic S, Schuurman K, Kim Y, Teunissen H, Flach K, Wit ED, Galli GG, Zwart W, Elkon R, Agami R. A CRISPR-Cas9 screen identifies essential CTCF anchor sites for estrogen receptor-driven breast cancer cell proliferation. Nucleic Acids Res 2019;47:9557-9572. [PMID: 31372638 PMCID: PMC6765117 DOI: 10.1093/nar/gkz675] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 07/11/2019] [Accepted: 07/24/2019] [Indexed: 01/07/2023]  Open
14
Rezazadeh S, Yang D, Tombline G, Simon M, Regan SP, Seluanov A, Gorbunova V. SIRT6 promotes transcription of a subset of NRF2 targets by mono-ADP-ribosylating BAF170. Nucleic Acids Res 2019;47:7914-7928. [PMID: 31216030 DOI: 10.1093/nar/gkz528] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/22/2019] [Accepted: 06/12/2019] [Indexed: 12/22/2022]  Open
15
Xia JH, Wei GH. Enhancer Dysfunction in 3D Genome and Disease. Cells 2019;8:cells8101281. [PMID: 31635067 PMCID: PMC6830074 DOI: 10.3390/cells8101281] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/10/2019] [Accepted: 10/14/2019] [Indexed: 12/13/2022]  Open
16
Rowe EM, Xing V, Biggar KK. Lysine methylation: Implications in neurodegenerative disease. Brain Res 2019;1707:164-171. [DOI: 10.1016/j.brainres.2018.11.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/13/2018] [Accepted: 11/18/2018] [Indexed: 12/14/2022]
17
Genome-wide identification of enhancer elements in the placenta. Placenta 2018;79:72-77. [PMID: 30268337 DOI: 10.1016/j.placenta.2018.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/03/2018] [Accepted: 09/10/2018] [Indexed: 12/25/2022]
18
Swinstead EE, Paakinaho V, Hager GL. Chromatin reprogramming in breast cancer. Endocr Relat Cancer 2018;25:R385-R404. [PMID: 29692347 PMCID: PMC6029727 DOI: 10.1530/erc-18-0033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 04/24/2018] [Indexed: 02/06/2023]
19
Sadlon T, Brown CY, Bandara V, Hope CM, Schjenken JE, Pederson SM, Breen J, Forrest A, Beyer M, Robertson S, Barry SC. Unravelling the molecular basis for regulatory T-cell plasticity and loss of function in disease. Clin Transl Immunology 2018;7:e1011. [PMID: 29497530 PMCID: PMC5827651 DOI: 10.1002/cti2.1011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/28/2018] [Accepted: 01/29/2018] [Indexed: 12/14/2022]  Open
20
Catarino RR, Stark A. Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation. Genes Dev 2018;32:202-223. [PMID: 29491135 PMCID: PMC5859963 DOI: 10.1101/gad.310367.117] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
21
Nizovtseva EV, Todolli S, Olson WK, Studitsky VM. Towards quantitative analysis of gene regulation by enhancers. Epigenomics 2017;9:1219-1231. [PMID: 28799793 DOI: 10.2217/epi-2017-0061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]  Open
22
Li P, Shi ML, Shen WL, Zhang Z, Xie DJ, Zhang XY, He C, Zhang Y, Zhao ZH. Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017;1860:885-893. [PMID: 28511927 PMCID: PMC7102783 DOI: 10.1016/j.bbagrm.2017.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/21/2017] [Accepted: 05/08/2017] [Indexed: 11/26/2022]
23
Casas-Tintó S, Arnés M, Ferrús A. Drosophila enhancer-Gal4 lines show ectopic expression during development. ROYAL SOCIETY OPEN SCIENCE 2017;4:170039. [PMID: 28405401 PMCID: PMC5383858 DOI: 10.1098/rsos.170039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/27/2017] [Indexed: 06/07/2023]
24
Singh SK, Qiao Z, Song L, Jani V, Rice W, Eng E, Coleman RA, Liu WL. Structural visualization of the p53/RNA polymerase II assembly. Genes Dev 2016;30:2527-2537. [PMID: 27920087 PMCID: PMC5159667 DOI: 10.1101/gad.285692.116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 10/18/2016] [Indexed: 01/03/2023]
25
Gokoolparsadh A, Sutton GJ, Charamko A, Green NFO, Pardy CJ, Voineagu I. Searching for convergent pathways in autism spectrum disorders: insights from human brain transcriptome studies. Cell Mol Life Sci 2016;73:4517-4530. [PMID: 27405608 PMCID: PMC11108267 DOI: 10.1007/s00018-016-2304-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 06/16/2016] [Accepted: 07/05/2016] [Indexed: 01/07/2023]
26
Awazu A. Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition. Bioinformatics 2016;33:42-48. [PMID: 27563027 PMCID: PMC5860184 DOI: 10.1093/bioinformatics/btw562] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/02/2016] [Accepted: 08/19/2016] [Indexed: 11/13/2022]  Open
27
Le JV, Luo Y, Darcy MA, Lucas CR, Goodwin MF, Poirier MG, Castro CE. Probing Nucleosome Stability with a DNA Origami Nanocaliper. ACS NANO 2016;10:7073-84. [PMID: 27362329 PMCID: PMC5460529 DOI: 10.1021/acsnano.6b03218] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
28
Engel KL, Mackiewicz M, Hardigan AA, Myers RM, Savic D. Decoding transcriptional enhancers: Evolving from annotation to functional interpretation. Semin Cell Dev Biol 2016;57:40-50. [PMID: 27224938 DOI: 10.1016/j.semcdb.2016.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/06/2016] [Accepted: 05/18/2016] [Indexed: 12/18/2022]
29
Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic. Genome Res 2016;26:882-95. [PMID: 27197205 PMCID: PMC4937571 DOI: 10.1101/gr.204149.116] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/17/2016] [Indexed: 12/11/2022]
30
Rastegar S, Strähle U. The Zebrafish as Model for Deciphering the Regulatory Architecture of Vertebrate Genomes. GENETICS, GENOMICS AND FISH PHENOMICS 2016;95:195-216. [DOI: 10.1016/bs.adgen.2016.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
31
Kashkin KN, Sverdlov ED. Poised RNA polymerase II and master regulation in Metazoa. Mol Biol 2015. [DOI: 10.1134/s0026893315060114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
32
Mannini L, C Lamaze F, Cucco F, Amato C, Quarantotti V, Rizzo IM, Krantz ID, Bilodeau S, Musio A. Mutant cohesin affects RNA polymerase II regulation in Cornelia de Lange syndrome. Sci Rep 2015;5:16803. [PMID: 26581180 PMCID: PMC4652179 DOI: 10.1038/srep16803] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/20/2015] [Indexed: 01/10/2023]  Open
33
Pacheco MP, John E, Kaoma T, Heinäniemi M, Nicot N, Vallar L, Bueb JL, Sinkkonen L, Sauter T. Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network. BMC Genomics 2015;16:809. [PMID: 26480823 PMCID: PMC4617894 DOI: 10.1186/s12864-015-1984-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 10/06/2015] [Indexed: 01/31/2023]  Open
34
Patrushev LI, Kovalenko TF. Functions of noncoding sequences in mammalian genomes. BIOCHEMISTRY (MOSCOW) 2015;79:1442-69. [PMID: 25749159 DOI: 10.1134/s0006297914130021] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
35
Long-Range Transcriptional Control of the Il2 Gene by an Intergenic Enhancer. Mol Cell Biol 2015;35:3880-91. [PMID: 26351138 DOI: 10.1128/mcb.00592-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/28/2015] [Indexed: 02/08/2023]  Open
36
González-Vallinas J, Pagès A, Singh B, Eyras E. A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cells. BMC Genomics 2015;16:523. [PMID: 26169177 PMCID: PMC4501197 DOI: 10.1186/s12864-015-1704-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 06/15/2015] [Indexed: 02/06/2023]  Open
37
Yao P, Lin P, Gokoolparsadh A, Assareh A, Thang MWC, Voineagu I. Coexpression networks identify brain region-specific enhancer RNAs in the human brain. Nat Neurosci 2015;18:1168-74. [PMID: 26167905 DOI: 10.1038/nn.4063] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/18/2015] [Indexed: 12/17/2022]
38
Lochmann TL, Thomas RR, Bennett JP, Taylor SM. Epigenetic Modifications of the PGC-1α Promoter during Exercise Induced Expression in Mice. PLoS One 2015;10:e0129647. [PMID: 26053857 PMCID: PMC4460005 DOI: 10.1371/journal.pone.0129647] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 05/12/2015] [Indexed: 11/18/2022]  Open
39
Bhatia S, Gordon CT, Foster RG, Melin L, Abadie V, Baujat G, Vazquez MP, Amiel J, Lyonnet S, van Heyningen V, Kleinjan DA. Functional assessment of disease-associated regulatory variants in vivo using a versatile dual colour transgenesis strategy in zebrafish. PLoS Genet 2015;11:e1005193. [PMID: 26030420 PMCID: PMC4452300 DOI: 10.1371/journal.pgen.1005193] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 04/02/2015] [Indexed: 11/26/2022]  Open
40
Shen E, Shulha H, Weng Z, Akbarian S. Regulation of histone H3K4 methylation in brain development and disease. Philos Trans R Soc Lond B Biol Sci 2015;369:rstb.2013.0514. [PMID: 25135975 DOI: 10.1098/rstb.2013.0514] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
41
Melnikova LS, Kostyuchenko MV, Georgiev PG. Functional organization of the white gene enhancer in Drosophila melanogaster. DOKL BIOCHEM BIOPHYS 2015;461:89-93. [PMID: 25937222 DOI: 10.1134/s1607672915020076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Indexed: 11/23/2022]
42
Ceballos-Chávez M, Subtil-Rodríguez A, Giannopoulou EG, Soronellas D, Vázquez-Chávez E, Vicent GP, Elemento O, Beato M, Reyes JC. The chromatin Remodeler CHD8 is required for activation of progesterone receptor-dependent enhancers. PLoS Genet 2015;11:e1005174. [PMID: 25894978 PMCID: PMC4403880 DOI: 10.1371/journal.pgen.1005174] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 03/25/2015] [Indexed: 01/01/2023]  Open
43
Younger ST, Kenzelmann-Broz D, Jung H, Attardi LD, Rinn JL. Integrative genomic analysis reveals widespread enhancer regulation by p53 in response to DNA damage. Nucleic Acids Res 2015;43:4447-62. [PMID: 25883152 PMCID: PMC4482066 DOI: 10.1093/nar/gkv284] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 03/23/2015] [Indexed: 02/04/2023]  Open
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Blatti C, Kazemian M, Wolfe S, Brodsky M, Sinha S. Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism. Nucleic Acids Res 2015;43:3998-4012. [PMID: 25791631 PMCID: PMC4417154 DOI: 10.1093/nar/gkv195] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 02/24/2015] [Indexed: 11/17/2022]  Open
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Pazin MJ. Using the ENCODE Resource for Functional Annotation of Genetic Variants. Cold Spring Harb Protoc 2015;2015:522-36. [PMID: 25762420 DOI: 10.1101/pdb.top084988] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions. Proc Natl Acad Sci U S A 2015;112:3841-6. [PMID: 25755260 DOI: 10.1073/pnas.1502971112] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
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Suryamohan K, Halfon MS. Identifying transcriptional cis-regulatory modules in animal genomes. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2015;4:59-84. [PMID: 25704908 PMCID: PMC4339228 DOI: 10.1002/wdev.168] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/04/2014] [Accepted: 11/16/2014] [Indexed: 11/08/2022]
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Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B. A comparative encyclopedia of DNA elements in the mouse genome. Nature 2015;515:355-64. [PMID: 25409824 PMCID: PMC4266106 DOI: 10.1038/nature13992] [Citation(s) in RCA: 1190] [Impact Index Per Article: 132.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 10/24/2014] [Indexed: 12/11/2022]
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The Maternal-to-Zygotic Transition in C. elegans. Curr Top Dev Biol 2015;113:1-42. [DOI: 10.1016/bs.ctdb.2015.06.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Rad R, Rad L, Wang W, Strong A, Ponstingl H, Bronner IF, Mayho M, Steiger K, Weber J, Hieber M, Veltkamp C, Eser S, Geumann U, Öllinger R, Zukowska M, Barenboim M, Maresch R, Cadiñanos J, Friedrich M, Varela I, Constantino-Casas F, Sarver A, Ten Hoeve J, Prosser H, Seidler B, Bauer J, Heikenwälder M, Metzakopian E, Krug A, Ehmer U, Schneider G, Knösel T, Rümmele P, Aust D, Grützmann R, Pilarsky C, Ning Z, Wessels L, Schmid RM, Quail MA, Vassiliou G, Esposito I, Liu P, Saur D, Bradley A. A conditional piggyBac transposition system for genetic screening in mice identifies oncogenic networks in pancreatic cancer. Nat Genet 2014;47:47-56. [PMID: 25485836 DOI: 10.1038/ng.3164] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/12/2014] [Indexed: 01/02/2023]
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