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For: Tsai A, Muthusamy AK, Alves MR, Lavis LD, Singer RH, Stern DL, Crocker J. Nuclear microenvironments modulate transcription from low-affinity enhancers. eLife 2017;6:28975. [PMID: 29095143 PMCID: PMC5695909 DOI: 10.7554/elife.28975] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/29/2017] [Indexed: 02/07/2023]  Open
Number Cited by Other Article(s)
1
Fallacaro S, Mukherjee A, Turner MA, Garcia HG, Mir M. Transcription factor hubs exhibit gene-specific properties that tune expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.07.647578. [PMID: 40291650 PMCID: PMC12026892 DOI: 10.1101/2025.04.07.647578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2025]
2
Liu S, Gomez-Alcala P, Leemans C, Glassford WJ, Melo LA, Lu XJ, Mann RS, Bussemaker HJ. Predicting the DNA binding specificity of transcription factor mutants using family-level biophysically interpretable machine learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.01.24.577115. [PMID: 38352411 PMCID: PMC10862739 DOI: 10.1101/2024.01.24.577115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
3
Pei G, Lyons H, Li P, Sabari BR. Transcription regulation by biomolecular condensates. Nat Rev Mol Cell Biol 2025;26:213-236. [PMID: 39516712 DOI: 10.1038/s41580-024-00789-x] [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] [Accepted: 09/30/2024] [Indexed: 11/16/2024]
4
Ugolini M, Vastenhouw NL. The role of transcription bodies in gene expression: what embryos teach us. Biochem Soc Trans 2025;53:BST20240599. [PMID: 39912709 DOI: 10.1042/bst20240599] [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: 10/14/2024] [Revised: 01/22/2025] [Accepted: 01/24/2025] [Indexed: 02/07/2025]
5
Munshi R, Ling J, Ryabichko S, Wieschaus EF, Gregor T. Transcription factor clusters as information transfer agents. SCIENCE ADVANCES 2025;11:eadp3251. [PMID: 39742495 DOI: 10.1126/sciadv.adp3251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 11/21/2024] [Indexed: 01/03/2025]
6
Berrocal A, Lammers NC, Garcia HG, Eisen MB. Unified bursting strategies in ectopic and endogenous even-skipped expression patterns. eLife 2024;12:RP88671. [PMID: 39651963 PMCID: PMC11627552 DOI: 10.7554/elife.88671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2024]  Open
7
Fallacaro S, Mukherjee A, Ratchasanmuang P, Zinski J, Haloush YI, Shankta K, Mir M. A fine kinetic balance of interactions directs transcription factor hubs to genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589811. [PMID: 38659757 PMCID: PMC11042322 DOI: 10.1101/2024.04.16.589811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
8
Kribelbauer-Swietek JF, Pushkarev O, Gardeux V, Faltejskova K, Russeil J, van Mierlo G, Deplancke B. Context transcription factors establish cooperative environments and mediate enhancer communication. Nat Genet 2024;56:2199-2212. [PMID: 39363017 PMCID: PMC11525195 DOI: 10.1038/s41588-024-01892-7] [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: 05/05/2023] [Accepted: 08/01/2024] [Indexed: 10/05/2024]
9
Kawasaki K, Fukaya T. Regulatory landscape of enhancer-mediated transcriptional activation. Trends Cell Biol 2024;34:826-837. [PMID: 38355349 DOI: 10.1016/j.tcb.2024.01.008] [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: 10/31/2023] [Revised: 12/21/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
10
Munshi R. How Transcription Factor Clusters Shape the Transcriptional Landscape. Biomolecules 2024;14:875. [PMID: 39062589 PMCID: PMC11274464 DOI: 10.3390/biom14070875] [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: 06/01/2024] [Revised: 07/14/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024]  Open
11
Chen PT, Levo M, Zoller B, Gregor T. Gene activity fully predicts transcriptional bursting dynamics. ARXIV 2024:arXiv:2304.08770v3. [PMID: 37131882 PMCID: PMC10153294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
12
Berrocal A, Lammers NC, Garcia HG, Eisen MB. Unified bursting strategies in ectopic and endogenous even-skipped expression patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.09.527927. [PMID: 36798351 PMCID: PMC9934701 DOI: 10.1101/2023.02.09.527927] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
13
Hayward-Lara G, Fischer MD, Mir M. Dynamic microenvironments shape nuclear organization and gene expression. Curr Opin Genet Dev 2024;86:102177. [PMID: 38461773 PMCID: PMC11162947 DOI: 10.1016/j.gde.2024.102177] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/11/2024] [Accepted: 02/14/2024] [Indexed: 03/12/2024]
14
Hwang DW, Maekiniemi A, Singer RH, Sato H. Real-time single-molecule imaging of transcriptional regulatory networks in living cells. Nat Rev Genet 2024;25:272-285. [PMID: 38195868 DOI: 10.1038/s41576-023-00684-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/11/2024]
15
Ugolini M, Kerlin MA, Kuznetsova K, Oda H, Kimura H, Vastenhouw NL. Transcription bodies regulate gene expression by sequestering CDK9. Nat Cell Biol 2024;26:604-612. [PMID: 38589534 PMCID: PMC11021188 DOI: 10.1038/s41556-024-01389-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 02/28/2024] [Indexed: 04/10/2024]
16
Salomone J, Farrow E, Gebelein B. Homeodomain complex formation and biomolecular condensates in Hox gene regulation. Semin Cell Dev Biol 2024;152-153:93-100. [PMID: 36517343 PMCID: PMC10258226 DOI: 10.1016/j.semcdb.2022.11.016] [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: 07/30/2022] [Revised: 10/21/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022]
17
Syed S, Duan Y, Lim B. Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos. eLife 2023;12:e85997. [PMID: 37934571 PMCID: PMC10629816 DOI: 10.7554/elife.85997] [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: 01/06/2023] [Accepted: 10/19/2023] [Indexed: 11/08/2023]  Open
18
Jindal GA, Bantle AT, Solvason JJ, Grudzien JL, D'Antonio-Chronowska A, Lim F, Le SH, Song BP, Ragsac MF, Klie A, Larsen RO, Frazer KA, Farley EK. Single-nucleotide variants within heart enhancers increase binding affinity and disrupt heart development. Dev Cell 2023;58:2206-2216.e5. [PMID: 37848026 PMCID: PMC10720985 DOI: 10.1016/j.devcel.2023.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/07/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023]
19
Gaskill MM, Soluri IV, Branks AE, Boka AP, Stadler MR, Vietor K, Huang HYS, Gibson TJ, Mukherjee A, Mir M, Blythe SA, Harrison MM. Localization of the Drosophila pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression. Dev Cell 2023;58:1610-1624.e8. [PMID: 37478844 PMCID: PMC10528433 DOI: 10.1016/j.devcel.2023.06.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/19/2023] [Accepted: 06/29/2023] [Indexed: 07/23/2023]
20
Mohana G, Dorier J, Li X, Mouginot M, Smith RC, Malek H, Leleu M, Rodriguez D, Khadka J, Rosa P, Cousin P, Iseli C, Restrepo S, Guex N, McCabe BD, Jankowski A, Levine MS, Gambetta MC. Chromosome-level organization of the regulatory genome in the Drosophila nervous system. Cell 2023;186:3826-3844.e26. [PMID: 37536338 PMCID: PMC10529364 DOI: 10.1016/j.cell.2023.07.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 03/31/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023]
21
Theis A, Harrison MM. Reprogramming of three-dimensional chromatin organization in the early embryo. Curr Opin Struct Biol 2023;81:102613. [PMID: 37224641 PMCID: PMC10524315 DOI: 10.1016/j.sbi.2023.102613] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/26/2023]
22
Afzal Z, Lange JJ, Nolte C, McKinney S, Wood C, Paulson A, De Kumar B, Unruh J, Slaughter BD, Krumlauf R. Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube. Development 2023;150:dev201259. [PMID: 37102683 PMCID: PMC10233718 DOI: 10.1242/dev.201259] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/19/2023] [Indexed: 04/28/2023]
23
A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination. Mol Cell 2023;83:681-697.e7. [PMID: 36736317 DOI: 10.1016/j.molcel.2023.01.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 11/04/2022] [Accepted: 01/09/2023] [Indexed: 02/05/2023]
24
van Mierlo G, Pushkarev O, Kribelbauer JF, Deplancke B. Chromatin modules and their implication in genomic organization and gene regulation. Trends Genet 2023;39:140-153. [PMID: 36549923 DOI: 10.1016/j.tig.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 11/04/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022]
25
Lyons H, Veettil RT, Pradhan P, Fornero C, De La Cruz N, Ito K, Eppert M, Roeder RG, Sabari BR. Functional partitioning of transcriptional regulators by patterned charge blocks. Cell 2023;186:327-345.e28. [PMID: 36603581 PMCID: PMC9910284 DOI: 10.1016/j.cell.2022.12.013] [Citation(s) in RCA: 141] [Impact Index Per Article: 70.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 10/15/2022] [Accepted: 12/07/2022] [Indexed: 01/05/2023]
26
Kuznetsova K, Chabot NM, Ugolini M, Wu E, Lalit M, Oda H, Sato Y, Kimura H, Jug F, Vastenhouw NL. Nanog organizes transcription bodies. Curr Biol 2023;33:164-173.e5. [PMID: 36476751 DOI: 10.1016/j.cub.2022.11.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/21/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022]
27
Syed S, Duan Y, Lim B. Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522923. [PMID: 36711729 PMCID: PMC9881968 DOI: 10.1101/2023.01.05.522923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
28
Developmental phenomics suggests that H3K4 monomethylation confers multi-level phenotypic robustness. Cell Rep 2022;41:111832. [PMID: 36516782 PMCID: PMC9764455 DOI: 10.1016/j.celrep.2022.111832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/29/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022]  Open
29
Merabet S, Carnesecchi J. Hox dosage and morphological diversification during development and evolution. Semin Cell Dev Biol 2022:S1084-9521(22)00360-3. [PMID: 36481343 DOI: 10.1016/j.semcdb.2022.11.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/15/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
30
Unveiling dynamic enhancer–promoter interactions in Drosophila melanogaster. Biochem Soc Trans 2022;50:1633-1642. [DOI: 10.1042/bst20220325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022]
31
Gandin V, English BP, Freeman M, Leroux LP, Preibisch S, Walpita D, Jaramillo M, Singer RH. Cap-dependent translation initiation monitored in living cells. Nat Commun 2022;13:6558. [PMID: 36323665 PMCID: PMC9630388 DOI: 10.1038/s41467-022-34052-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 10/06/2022] [Indexed: 11/19/2022]  Open
32
Srivastava M, Payne JL. On the incongruence of genotype-phenotype and fitness landscapes. PLoS Comput Biol 2022;18:e1010524. [PMID: 36121840 PMCID: PMC9521842 DOI: 10.1371/journal.pcbi.1010524] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/29/2022] [Accepted: 08/30/2022] [Indexed: 11/22/2022]  Open
33
Deng H, Lim B. Shared Transcriptional Machinery at Homologous Alleles Leads to Reduced Transcription in Early Drosophila Embryos. Front Cell Dev Biol 2022;10:912838. [PMID: 35898395 PMCID: PMC9311490 DOI: 10.3389/fcell.2022.912838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/21/2022] [Indexed: 02/05/2023]  Open
34
Nollmann M, Bennabi I, Götz M, Gregor T. The Impact of Space and Time on the Functional Output of the Genome. Cold Spring Harb Perspect Biol 2022;14:a040378. [PMID: 34230036 PMCID: PMC8733053 DOI: 10.1101/cshperspect.a040378] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
35
Zhang Y, Lu Y, El Sayyed H, Bian J, Lin J, Li X. Transcription factor dynamics in plants: Insights and technologies for in vivo imaging. PLANT PHYSIOLOGY 2022;189:23-36. [PMID: 35134239 PMCID: PMC9070795 DOI: 10.1093/plphys/kiac042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
36
Levo M, Raimundo J, Bing XY, Sisco Z, Batut PJ, Ryabichko S, Gregor T, Levine MS. Transcriptional coupling of distant regulatory genes in living embryos. Nature 2022;605:754-760. [PMID: 35508662 PMCID: PMC9886134 DOI: 10.1038/s41586-022-04680-7] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 03/23/2022] [Indexed: 02/01/2023]
37
Herrmann JC, Beagrie RA, Hughes JR. Making connections: enhancers in cellular differentiation. Trends Genet 2022;38:395-408. [PMID: 34753603 DOI: 10.1016/j.tig.2021.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 01/23/2023]
38
Tsai A, Crocker J. Nuclear morphogenesis: forming a heterogeneous nucleus during embryogenesis. Development 2022;149:274325. [PMID: 35142344 PMCID: PMC8918797 DOI: 10.1242/dev.200266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/18/2022] [Indexed: 11/20/2022]
39
Farrants H, Tebo AG. Fluorescent chemigenetic actuators and indicators for use in living animals. Curr Opin Pharmacol 2022;62:159-167. [DOI: 10.1016/j.coph.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/03/2021] [Accepted: 12/12/2021] [Indexed: 11/28/2022]
40
Molecular architecture of enhancer–promoter interaction. Curr Opin Cell Biol 2022;74:62-70. [DOI: 10.1016/j.ceb.2022.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/29/2021] [Accepted: 01/10/2022] [Indexed: 12/26/2022]
41
Perelsman O, Asano S, Freifeld L. Expansion Microscopy of Larval Zebrafish Brains and Zebrafish Embryos. Methods Mol Biol 2022;2440:211-222. [PMID: 35218542 DOI: 10.1007/978-1-0716-2051-9_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
42
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]
43
Castells-Garcia A, Ed-Daoui I, González-Almela E, Vicario C, Ottestrom J, Lakadamyali M, Neguembor MV, Cosma MP. Super resolution microscopy reveals how elongating RNA polymerase II and nascent RNA interact with nucleosome clutches. Nucleic Acids Res 2021;50:175-190. [PMID: 34929735 PMCID: PMC8754629 DOI: 10.1093/nar/gkab1215] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 10/13/2021] [Accepted: 11/26/2021] [Indexed: 11/17/2022]  Open
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Carnesecchi J, Boumpas P, van Nierop Y Sanchez P, Domsch K, Pinto HD, Borges Pinto P, Lohmann I. The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II. Nucleic Acids Res 2021;50:763-783. [PMID: 34931250 PMCID: PMC8789087 DOI: 10.1093/nar/gkab1250] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022]  Open
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Olfactory receptor choice: a case study for gene regulation in a multi-enhancer system. Curr Opin Genet Dev 2021;72:101-109. [PMID: 34896807 DOI: 10.1016/j.gde.2021.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/25/2021] [Accepted: 11/11/2021] [Indexed: 12/14/2022]
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Biswas J, Li W, Singer RH, Coleman RA. Imaging Organization of RNA Processing within the Nucleus. Cold Spring Harb Perspect Biol 2021;13:a039453. [PMID: 34127450 PMCID: PMC8635003 DOI: 10.1101/cshperspect.a039453] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Waymack R, Gad M, Wunderlich Z. Molecular competition can shape enhancer activity in the Drosophila embryo. iScience 2021;24:103034. [PMID: 34568782 PMCID: PMC8449247 DOI: 10.1016/j.isci.2021.103034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/27/2021] [Accepted: 08/20/2021] [Indexed: 01/12/2023]  Open
48
Krebs AR. Studying transcription factor function in the genome at molecular resolution. Trends Genet 2021;37:798-806. [DOI: 10.1016/j.tig.2021.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/11/2022]
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Frank F, Liu X, Ortlund EA. Glucocorticoid receptor condensates link DNA-dependent receptor dimerization and transcriptional transactivation. Proc Natl Acad Sci U S A 2021;118:e2024685118. [PMID: 34285072 PMCID: PMC8325269 DOI: 10.1073/pnas.2024685118] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
50
Wagh K, Garcia DA, Upadhyaya A. Phase separation in transcription factor dynamics and chromatin organization. Curr Opin Struct Biol 2021;71:148-155. [PMID: 34303933 DOI: 10.1016/j.sbi.2021.06.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 06/16/2021] [Indexed: 02/07/2023]
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