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For: Kulkarni MM, Arnosti DN. Information display by transcriptional enhancers. Development 2004;130:6569-75. [PMID: 14660545 DOI: 10.1242/dev.00890] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Number Cited by Other Article(s)
1
Beernink BM, Vogel JP, Lei L. Enhancers in Plant Development, Adaptation and Evolution. PLANT & CELL PHYSIOLOGY 2025;66:461-476. [PMID: 39412125 PMCID: PMC12085095 DOI: 10.1093/pcp/pcae121] [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] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 09/13/2024] [Accepted: 10/09/2024] [Indexed: 05/18/2025]
2
Jatzlau J, Do SN, Mees RA, Mendez PL, Khan RJ, Maas L, Ruiz L, Martin-Malpartida P, Macias MJ, Knaus P. Rare but specific: 5-bp composite motifs define SMAD binding in BMP signaling. BMC Biol 2025;23:79. [PMID: 40082964 PMCID: PMC11907993 DOI: 10.1186/s12915-025-02183-1] [Citation(s) in RCA: 1] [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: 07/16/2024] [Accepted: 03/03/2025] [Indexed: 03/16/2025]  Open
3
Batool F, Shireen H, Malik MF, Abrar M, Abbasi AA. The combinatorial binding syntax of transcription factors in forebrain-specific enhancers. Biol Open 2025;14:BIO061751. [PMID: 39976127 PMCID: PMC11876843 DOI: 10.1242/bio.061751] [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: 09/30/2024] [Accepted: 01/24/2025] [Indexed: 02/21/2025]  Open
4
Pampari A, Shcherbina A, Kvon EZ, Kosicki M, Nair S, Kundu S, Kathiria AS, Risca VI, Kuningas K, Alasoo K, Greenleaf WJ, Pennacchio LA, Kundaje A. ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.12.25.630221. [PMID: 39829783 PMCID: PMC11741299 DOI: 10.1101/2024.12.25.630221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
5
Baniulyte G, McCann AA, Woodstock DL, Sammons MA. Crosstalk between paralogs and isoforms influences p63-dependent regulatory element activity. Nucleic Acids Res 2024;52:13812-13831. [PMID: 39565223 DOI: 10.1093/nar/gkae1143] [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: 05/17/2024] [Revised: 10/04/2024] [Accepted: 11/01/2024] [Indexed: 11/21/2024]  Open
6
Maritato R, Medugno A, D'Andretta E, De Riso G, Lupo M, Botta S, Marrocco E, Renda M, Sofia M, Mussolino C, Bacci ML, Surace EM. A DNA base-specific sequence interposed between CRX and NRL contributes to RHODOPSIN expression. Sci Rep 2024;14:26313. [PMID: 39487168 PMCID: PMC11530525 DOI: 10.1038/s41598-024-76664-8] [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: 07/05/2024] [Accepted: 10/15/2024] [Indexed: 11/04/2024]  Open
7
Kliesmete Z, Orchard P, Lee VYK, Geuder J, Krauß SM, Ohnuki M, Jocher J, Vieth B, Enard W, Hellmann I. Evidence for compensatory evolution within pleiotropic regulatory elements. Genome Res 2024;34:1528-1539. [PMID: 39255977 PMCID: PMC11534155 DOI: 10.1101/gr.279001.124] [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: 01/17/2024] [Accepted: 08/19/2024] [Indexed: 09/12/2024]
8
Jores T, Tonnies J, Mueth NA, Romanowski A, Fields S, Cuperus JT, Queitsch C. Plant enhancers exhibit both cooperative and additive interactions among their functional elements. THE PLANT CELL 2024;36:2570-2586. [PMID: 38513612 PMCID: PMC11218779 DOI: 10.1093/plcell/koae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/16/2024] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
9
Moeckel C, Mouratidis I, Chantzi N, Uzun Y, Georgakopoulos-Soares I. Advances in computational and experimental approaches for deciphering transcriptional regulatory networks: Understanding the roles of cis-regulatory elements is essential, and recent research utilizing MPRAs, STARR-seq, CRISPR-Cas9, and machine learning has yielded valuable insights. Bioessays 2024;46:e2300210. [PMID: 38715516 PMCID: PMC11444527 DOI: 10.1002/bies.202300210] [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: 10/31/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
10
Vaknin I, Willinger O, Mandl J, Heuberger H, Ben-Ami D, Zeng Y, Goldberg S, Orenstein Y, Amit R. A universal system for boosting gene expression in eukaryotic cell-lines. Nat Commun 2024;15:2394. [PMID: 38493141 PMCID: PMC10944472 DOI: 10.1038/s41467-024-46573-5] [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: 07/27/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024]  Open
11
Mahendrawada L, Warfield L, Donczew R, Hahn S. Surprising connections between DNA binding and function for the near-complete set of yeast transcription factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550593. [PMID: 37546716 PMCID: PMC10402042 DOI: 10.1101/2023.07.25.550593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
12
Smith GD, Ching WH, Cornejo-Páramo P, Wong ES. Decoding enhancer complexity with machine learning and high-throughput discovery. Genome Biol 2023;24:116. [PMID: 37173718 PMCID: PMC10176946 DOI: 10.1186/s13059-023-02955-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023]  Open
13
Georgakopoulos-Soares I, Deng C, Agarwal V, Chan CSY, Zhao J, Inoue F, Ahituv N. Transcription factor binding site orientation and order are major drivers of gene regulatory activity. Nat Commun 2023;14:2333. [PMID: 37087538 PMCID: PMC10122648 DOI: 10.1038/s41467-023-37960-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/06/2023] [Indexed: 04/24/2023]  Open
14
Martinez-Corral R, Park M, Biette KM, Friedrich D, Scholes C, Khalil AS, Gunawardena J, DePace AH. Transcriptional kinetic synergy: A complex landscape revealed by integrating modeling and synthetic biology. Cell Syst 2023;14:324-339.e7. [PMID: 37080164 PMCID: PMC10472254 DOI: 10.1016/j.cels.2023.02.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 08/22/2022] [Accepted: 02/10/2023] [Indexed: 04/22/2023]
15
Reiter F, de Almeida BP, Stark A. Enhancers display constrained sequence flexibility and context-specific modulation of motif function. Genome Res 2023;33:346-358. [PMID: 36941077 PMCID: PMC10078294 DOI: 10.1101/gr.277246.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 02/14/2023] [Indexed: 03/23/2023]
16
Zhao Y. TFSyntax: a database of transcription factors binding syntax in mammalian genomes. Nucleic Acids Res 2022;51:D306-D314. [PMID: 36200824 PMCID: PMC9825613 DOI: 10.1093/nar/gkac849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/10/2022] [Accepted: 09/21/2022] [Indexed: 01/29/2023]  Open
17
Sipani R, Joshi R. Hox genes collaborate with helix-loop-helix factor Grainyhead to promote neuroblast apoptosis along the anterior-posterior axis of the Drosophila larval central nervous system. Genetics 2022;222:6632667. [DOI: 10.1093/genetics/iyac101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/21/2022] [Indexed: 11/14/2022]  Open
18
DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers. Nat Genet 2022;54:613-624. [PMID: 35551305 DOI: 10.1038/s41588-022-01048-5] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 03/08/2022] [Indexed: 02/06/2023]
19
Schmitz RJ, Grotewold E, Stam M. Cis-regulatory sequences in plants: Their importance, discovery, and future challenges. THE PLANT CELL 2022;34:718-741. [PMID: 34918159 PMCID: PMC8824567 DOI: 10.1093/plcell/koab281] [Citation(s) in RCA: 166] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/20/2021] [Indexed: 05/19/2023]
20
Ray-Jones H, Spivakov M. Transcriptional enhancers and their communication with gene promoters. Cell Mol Life Sci 2021;78:6453-6485. [PMID: 34414474 PMCID: PMC8558291 DOI: 10.1007/s00018-021-03903-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022]
21
Gillard GB, Grønvold L, Røsæg LL, Holen MM, Monsen Ø, Koop BF, Rondeau EB, Gundappa MK, Mendoza J, Macqueen DJ, Rohlfs RV, Sandve SR, Hvidsten TR. Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication. Genome Biol 2021;22:103. [PMID: 33849620 PMCID: PMC8042706 DOI: 10.1186/s13059-021-02323-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022]  Open
22
Transcriptional Silencers: Driving Gene Expression with the Brakes On. Trends Genet 2021;37:514-527. [PMID: 33712326 DOI: 10.1016/j.tig.2021.02.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/15/2022]
23
Jindal GA, Farley EK. Enhancer grammar in development, evolution, and disease: dependencies and interplay. Dev Cell 2021;56:575-587. [PMID: 33689769 PMCID: PMC8462829 DOI: 10.1016/j.devcel.2021.02.016] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/19/2022]
24
Avsec Ž, Weilert M, Shrikumar A, Krueger S, Alexandari A, Dalal K, Fropf R, McAnany C, Gagneur J, Kundaje A, Zeitlinger J. Base-resolution models of transcription-factor binding reveal soft motif syntax. Nat Genet 2021;53:354-366. [PMID: 33603233 PMCID: PMC8812996 DOI: 10.1038/s41588-021-00782-6] [Citation(s) in RCA: 321] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023]
25
Koo PK, Ploenzke M. Improving representations of genomic sequence motifs in convolutional networks with exponential activations. NAT MACH INTELL 2021;3:258-266. [PMID: 34322657 DOI: 10.1038/s42256-020-00291-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
26
Harmston N. Regulation in common: Sponge to zebrafish. Science 2020;370:657-658. [PMID: 33154124 DOI: 10.1126/science.abe9317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
27
Chen L, Capra JA. Learning and interpreting the gene regulatory grammar in a deep learning framework. PLoS Comput Biol 2020;16:e1008334. [PMID: 33137083 PMCID: PMC7660921 DOI: 10.1371/journal.pcbi.1008334] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 11/12/2020] [Accepted: 09/12/2020] [Indexed: 12/12/2022]  Open
28
Zeitlinger J. Seven myths of how transcription factors read the cis-regulatory code. CURRENT OPINION IN SYSTEMS BIOLOGY 2020;23:22-31. [PMID: 33134611 PMCID: PMC7592701 DOI: 10.1016/j.coisb.2020.08.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
29
Liu J, Shively CA, Mitra RD. Quantitative analysis of transcription factor binding and expression using calling cards reporter arrays. Nucleic Acids Res 2020;48:e50. [PMID: 32133534 PMCID: PMC7229839 DOI: 10.1093/nar/gkaa141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/31/2020] [Accepted: 02/25/2020] [Indexed: 12/13/2022]  Open
30
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]
31
Catizone AN, Uzunbas GK, Celadova P, Kuang S, Bose D, Sammons MA. Locally acting transcription factors regulate p53-dependent cis-regulatory element activity. Nucleic Acids Res 2020;48:4195-4213. [PMID: 32133495 PMCID: PMC7192610 DOI: 10.1093/nar/gkaa147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/27/2020] [Accepted: 02/26/2020] [Indexed: 01/03/2023]  Open
32
King DM, Hong CKY, Shepherdson JL, Granas DM, Maricque BB, Cohen BA. Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in mouse embryonic stem cells. eLife 2020;9:41279. [PMID: 32043966 PMCID: PMC7077988 DOI: 10.7554/elife.41279] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/07/2020] [Indexed: 01/08/2023]  Open
33
Deciphering eukaryotic gene-regulatory logic with 100 million random promoters. Nat Biotechnol 2019;38:56-65. [PMID: 31792407 PMCID: PMC6954276 DOI: 10.1038/s41587-019-0315-8] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 10/16/2019] [Indexed: 11/26/2022]
34
Orlomoski R, Bogle A, Loss J, Simons R, Dresch JM, Drewell RA, Spratt DE. Rapid and efficient purification of Drosophila homeodomain transcription factors for biophysical characterization. Protein Expr Purif 2019;158:9-14. [PMID: 30738927 DOI: 10.1016/j.pep.2019.02.001] [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: 01/04/2019] [Accepted: 02/03/2019] [Indexed: 10/27/2022]
35
Bentovim L, Harden TT, DePace AH. Transcriptional precision and accuracy in development: from measurements to models and mechanisms. Development 2017;144:3855-3866. [PMID: 29089359 PMCID: PMC5702068 DOI: 10.1242/dev.146563] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
36
Brown AJ, Gibson SJ, Hatton D, James DC. In silico design of context-responsive mammalian promoters with user-defined functionality. Nucleic Acids Res 2017;45:10906-10919. [PMID: 28977454 PMCID: PMC5737543 DOI: 10.1093/nar/gkx768] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/22/2017] [Indexed: 12/19/2022]  Open
37
Khoueiry P, Girardot C, Ciglar L, Peng PC, Gustafson EH, Sinha S, Furlong EE. Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity. eLife 2017;6. [PMID: 28792889 PMCID: PMC5550276 DOI: 10.7554/elife.28440] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/21/2017] [Indexed: 12/15/2022]  Open
38
Vockley CM, McDowell IC, D'Ippolito AM, Reddy TE. A long-range flexible billboard model of gene activation. Transcription 2017;8:261-267. [PMID: 28598247 DOI: 10.1080/21541264.2017.1317694] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]  Open
39
Enhancer decommissioning by Snail1-induced competitive displacement of TCF7L2 and down-regulation of transcriptional activators results in EPHB2 silencing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016;1859:1353-1367. [PMID: 27504909 DOI: 10.1016/j.bbagrm.2016.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 07/25/2016] [Accepted: 08/04/2016] [Indexed: 12/20/2022]
40
Fiore C, Cohen BA. Interactions between pluripotency factors specify cis-regulation in embryonic stem cells. Genome Res 2016;26:778-86. [PMID: 27197208 PMCID: PMC4889965 DOI: 10.1101/gr.200733.115] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/13/2016] [Indexed: 01/06/2023]
41
Quantitatively predictable control of Drosophila transcriptional enhancers in vivo with engineered transcription factors. Nat Genet 2016;48:292-8. [DOI: 10.1038/ng.3509] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 01/15/2016] [Indexed: 12/13/2022]
42
Zhao B, Kokoza VA, Saha TT, Wang S, Roy S, Raikhel AS. Regulation of the gut-specific carboxypeptidase: a study using the binary Gal4/UAS system in the mosquito Aedes aegypti. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014;54:1-10. [PMID: 25152428 PMCID: PMC4426967 DOI: 10.1016/j.ibmb.2014.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/31/2014] [Accepted: 08/03/2014] [Indexed: 05/26/2023]
43
Waardenberg AJ, Ramialison M, Bouveret R, Harvey RP. Genetic networks governing heart development. Cold Spring Harb Perspect Med 2014;4:a013839. [PMID: 25280899 PMCID: PMC4208705 DOI: 10.1101/cshperspect.a013839] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Slattery M, Zhou T, Yang L, Dantas Machado AC, Gordân R, Rohs R. Absence of a simple code: how transcription factors read the genome. Trends Biochem Sci 2014;39:381-99. [PMID: 25129887 DOI: 10.1016/j.tibs.2014.07.002] [Citation(s) in RCA: 367] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 12/21/2022]
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Regulatory codewords. Nat Genet 2014;46:801. [DOI: 10.1038/ng.3059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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A comparison of midline and tracheal gene regulation during Drosophila development. PLoS One 2014;9:e85518. [PMID: 24465586 PMCID: PMC3896416 DOI: 10.1371/journal.pone.0085518] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 11/28/2013] [Indexed: 11/19/2022]  Open
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Novel Genetic and Molecular Tools for the Investigation and Control of Dengue Virus Transmission by Mosquitoes. CURRENT TROPICAL MEDICINE REPORTS 2014;1:21-31. [PMID: 24693489 DOI: 10.1007/s40475-013-0007-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Teng L, He B, Gao P, Gao L, Tan K. Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets. Nucleic Acids Res 2013;42:e24. [PMID: 24217919 PMCID: PMC3936738 DOI: 10.1093/nar/gkt1105] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
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Harmston N, Baresic A, Lenhard B. The mystery of extreme non-coding conservation. Philos Trans R Soc Lond B Biol Sci 2013;368:20130021. [PMID: 24218634 PMCID: PMC3826495 DOI: 10.1098/rstb.2013.0021] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
50
Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nat Genet 2013;45:1021-1028. [PMID: 23892608 DOI: 10.1038/ng.2713] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 06/28/2013] [Indexed: 12/12/2022]
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