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For: Coulon A, Chow CC, Singer RH, Larson DR. Eukaryotic transcriptional dynamics: from single molecules to cell populations. Nat Rev Genet 2013;14:572-84. [PMID: 23835438 DOI: 10.1038/nrg3484] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Number Cited by Other Article(s)
1
Solovei I, Mirny L. Spandrels of the cell nucleus. Curr Opin Cell Biol 2024;90:102421. [PMID: 39180905 DOI: 10.1016/j.ceb.2024.102421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/18/2024] [Accepted: 08/02/2024] [Indexed: 08/27/2024]
2
Vilar JMG, Saiz L. The unreasonable effectiveness of equilibrium gene regulation through the cell cycle. Cell Syst 2024;15:639-648.e2. [PMID: 38981487 DOI: 10.1016/j.cels.2024.06.002] [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: 10/06/2022] [Revised: 06/19/2023] [Accepted: 06/14/2024] [Indexed: 07/11/2024]
3
Kupkova K, Shetty SJ, Hoffman EA, Bekiranov S, Auble DT. Genome-scale chromatin binding dynamics of RNA Polymerase II general transcription machinery components. EMBO J 2024;43:1799-1821. [PMID: 38565951 PMCID: PMC11066129 DOI: 10.1038/s44318-024-00089-2] [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: 08/02/2023] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 04/04/2024]  Open
4
Dixit S, Middelkoop TC, Choubey S. Governing principles of transcriptional logic out of equilibrium. Biophys J 2024;123:1015-1029. [PMID: 38486450 PMCID: PMC11052701 DOI: 10.1016/j.bpj.2024.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 03/24/2024]  Open
5
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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/11/2024]
6
Stortz M, Presman DM, Levi V. Transcriptional condensates: a blessing or a curse for gene regulation? Commun Biol 2024;7:187. [PMID: 38365945 PMCID: PMC10873363 DOI: 10.1038/s42003-024-05892-5] [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: 10/26/2023] [Accepted: 02/06/2024] [Indexed: 02/18/2024]  Open
7
Meeussen JVW, Lenstra TL. Time will tell: comparing timescales to gain insight into transcriptional bursting. Trends Genet 2024;40:160-174. [PMID: 38216391 PMCID: PMC10860890 DOI: 10.1016/j.tig.2023.11.003] [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: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 01/14/2024]
8
Du M, Stitzinger SH, Spille JH, Cho WK, Lee C, Hijaz M, Quintana A, Cissé II. Direct observation of a condensate effect on super-enhancer controlled gene bursting. Cell 2024;187:331-344.e17. [PMID: 38194964 DOI: 10.1016/j.cell.2023.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/29/2023] [Accepted: 12/04/2023] [Indexed: 01/11/2024]
9
Syed S, Lim B. Multi-labeling Live Imaging to Quantify Gene Expression Dynamics During Drosophila Embryonic Development. Methods Mol Biol 2024;2805:137-151. [PMID: 39008179 DOI: 10.1007/978-1-0716-3854-5_9] [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] [Indexed: 07/16/2024]
10
Yavuz S, Kabbech H, van Staalduinen J, Linder S, van Cappellen W, Nigg A, Abraham T, Slotman J, Quevedo M, Poot R, Zwart W, van Royen M, Grosveld F, Smal I, Houtsmuller A. Compartmentalization of androgen receptors at endogenous genes in living cells. Nucleic Acids Res 2023;51:10992-11009. [PMID: 37791849 PMCID: PMC10639085 DOI: 10.1093/nar/gkad803] [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: 04/14/2023] [Revised: 09/06/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023]  Open
11
Keller SH, Deng H, Lim B. Regulation of the dynamic RNA Pol II elongation rate in Drosophila embryos. Cell Rep 2023;42:113225. [PMID: 37837623 PMCID: PMC10842316 DOI: 10.1016/j.celrep.2023.113225] [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: 06/29/2022] [Revised: 08/20/2023] [Accepted: 09/22/2023] [Indexed: 10/16/2023]  Open
12
Junier I, Ghobadpour E, Espeli O, Everaers R. DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling. Front Microbiol 2023;14:1192831. [PMID: 37965550 PMCID: PMC10642903 DOI: 10.3389/fmicb.2023.1192831] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/25/2023] [Indexed: 11/16/2023]  Open
13
Wang Y, He S, Fang X. Emerging roles of phase separation in plant transcription and chromatin organization. CURRENT OPINION IN PLANT BIOLOGY 2023;75:102387. [PMID: 37311366 DOI: 10.1016/j.pbi.2023.102387] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023]
14
Mahat DB, Tippens ND, Martin-Rufino JD, Waterton SK, Fu J, Blatt SE, Sharp PA. Single-cell nascent RNA sequencing using click-chemistry unveils coordinated transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.558015. [PMID: 37745427 PMCID: PMC10516050 DOI: 10.1101/2023.09.15.558015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
15
Kleiner RE. Chemical Approaches To Investigate Post-transcriptional RNA Regulation. ACS Chem Biol 2023;18:1684-1697. [PMID: 37540831 PMCID: PMC11031734 DOI: 10.1021/acschembio.3c00406] [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] [Indexed: 08/06/2023]
16
Kupkova K, Shetty SJ, Hoffman EA, Bekiranov S, Auble DT. Genome-scale chromatin interaction dynamic measurements for key components of the RNA Pol II general transcription machinery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550532. [PMID: 37546819 PMCID: PMC10402067 DOI: 10.1101/2023.07.25.550532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
17
Pownall ME, Miao L, Vejnar CE, M’Saad O, Sherrard A, Frederick MA, Benitez MD, Boswell CW, Zaret KS, Bewersdorf J, Giraldez AJ. Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin. Science 2023;381:92-100. [PMID: 37410825 PMCID: PMC10372697 DOI: 10.1126/science.ade5308] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 05/17/2023] [Indexed: 07/08/2023]
18
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: 2.0] [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]
19
Langenbacher AD, Lu F, Crisman L, Huang ZYS, Chapski DJ, Vondriska TM, Wang Y, Gao C, Chen JN. Rtf1 Transcriptionally Regulates Neonatal and Adult Cardiomyocyte Biology. J Cardiovasc Dev Dis 2023;10:221. [PMID: 37233188 PMCID: PMC10219292 DOI: 10.3390/jcdd10050221] [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: 04/21/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]  Open
20
Goychuk A, Kannan D, Chakraborty AK, Kardar M. Polymer folding through active processes recreates features of genome organization. Proc Natl Acad Sci U S A 2023;120:e2221726120. [PMID: 37155885 PMCID: PMC10194017 DOI: 10.1073/pnas.2221726120] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 04/02/2023] [Indexed: 05/10/2023]  Open
21
Mahdavi S, Salmon GL, Daghlian P, Garcia HG, Phillips R. Flexibility and sensitivity in gene regulation out of equilibrium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536490. [PMID: 37090612 PMCID: PMC10120662 DOI: 10.1101/2023.04.11.536490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
22
Competing constraints shape the nonequilibrium limits of cellular decision-making. Proc Natl Acad Sci U S A 2023;120:e2211203120. [PMID: 36862689 PMCID: PMC10013869 DOI: 10.1073/pnas.2211203120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]  Open
23
Das SK, Lewis BA, Levens D. MYC: a complex problem. Trends Cell Biol 2023;33:235-246. [PMID: 35963793 PMCID: PMC9911561 DOI: 10.1016/j.tcb.2022.07.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/22/2022]
24
Itani A, Shida Y, Ogasawara W. A microfluidic device for simultaneous detection of enzyme secretion and elongation of a single hypha. Front Microbiol 2023;14:1125760. [PMID: 36937311 PMCID: PMC10020217 DOI: 10.3389/fmicb.2023.1125760] [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: 12/16/2022] [Accepted: 02/16/2023] [Indexed: 03/06/2023]  Open
25
Wang K, Escobar M, Li J, Mahata B, Goell J, Shah S, Cluck M, Hilton I. Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions. Nucleic Acids Res 2022;50:7842-7855. [PMID: 35849129 PMCID: PMC9371918 DOI: 10.1093/nar/gkac582] [Citation(s) in RCA: 2] [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: 11/14/2021] [Revised: 06/19/2022] [Accepted: 06/24/2022] [Indexed: 12/29/2022]  Open
26
Forero-Quintero LS, Raymond W, Munsky B, Stasevich TJ. Visualization, Quantification, and Modeling of Endogenous RNA Polymerase II Phosphorylation at a Single-copy Gene in Living Cells. Bio Protoc 2022;12:e4482. [PMID: 36082371 PMCID: PMC9411018 DOI: 10.21769/bioprotoc.4482] [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: 03/17/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 01/05/2023]  Open
27
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: 0.5] [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
28
Guo X, Tang T, Duan M, Zhang L, Ge H. The nonequilibrium mechanism of noise-enhanced drug synergy in HIV latency reactivation. iScience 2022;25:104358. [PMID: 35620426 PMCID: PMC9127169 DOI: 10.1016/j.isci.2022.104358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 03/04/2022] [Accepted: 04/29/2022] [Indexed: 11/29/2022]  Open
29
Wu J, Chen B, Liu Y, Ma L, Huang W, Lin Y. Modulating gene regulation function by chemically controlled transcription factor clustering. Nat Commun 2022;13:2663. [PMID: 35562359 PMCID: PMC9106659 DOI: 10.1038/s41467-022-30397-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 04/29/2022] [Indexed: 12/21/2022]  Open
30
Feric M, Misteli T. Function moves biomolecular condensates in phase space. Bioessays 2022;44:e2200001. [PMID: 35243657 PMCID: PMC9277701 DOI: 10.1002/bies.202200001] [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: 01/03/2022] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 11/08/2022]
31
Johari YB, Scarrott JM, Pohle TH, Liu P, Mayer A, Brown AJ, James DC. Engineering of the CMV promoter for controlled expression of recombinant genes in HEK293 cells. Biotechnol J 2022;17:e2200062. [PMID: 35482470 DOI: 10.1002/biot.202200062] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/07/2022] [Accepted: 04/23/2022] [Indexed: 11/08/2022]
32
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: 159] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [Abstract] [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]
33
Bowles JR, Hoppe C, Ashe HL, Rattray M. Scalable inference of transcriptional kinetic parameters from MS2 time series data. Bioinformatics 2022;38:1030-1036. [PMID: 34788793 PMCID: PMC8796374 DOI: 10.1093/bioinformatics/btab765] [Citation(s) in RCA: 4] [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: 12/06/2020] [Revised: 07/22/2021] [Accepted: 11/03/2021] [Indexed: 02/04/2023]  Open
34
Shang J, He L, Wang J, Tong A, Xiang Y. In Situ Visualizing Nascent RNA by Exploring DNA-Templated Oxidative Amination of 4-Thiouridine. Bioconjug Chem 2022;33:164-171. [PMID: 34910465 DOI: 10.1021/acs.bioconjchem.1c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
35
Yang X, Luo S, Zhang Z, Wang Z, Zhou T, Zhang J. Silent transcription intervals and translational bursting lead to diverse phenotypic switching. Phys Chem Chem Phys 2022;24:26600-26608. [DOI: 10.1039/d2cp03703c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
36
Chen M, Luo S, Cao M, Guo C, Zhou T, Zhang J. Exact distributions for stochastic gene expression models with arbitrary promoter architecture and translational bursting. Phys Rev E 2022;105:014405. [PMID: 35193181 DOI: 10.1103/physreve.105.014405] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/14/2021] [Indexed: 11/07/2022]
37
Jordán-Pla A, Pérez-Ortín JE. High-Resolution Deep Sequencing of Nascent Transcription in Yeast with BioGRO-seq. Methods Mol Biol 2022;2477:57-70. [PMID: 35524111 DOI: 10.1007/978-1-0716-2257-5_4] [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] [Indexed: 06/14/2023]
38
Schweizer G, Wagner A. Both Binding Strength and Evolutionary Accessibility Affect the Population Frequency of Transcription Factor Binding Sequences in Arabidopsis thaliana. Genome Biol Evol 2021;13:6459646. [PMID: 34894231 PMCID: PMC8712246 DOI: 10.1093/gbe/evab273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 11/22/2022]  Open
39
Hu F, Zhu T, Guo X, Yu K, Ma X, Liu C, Liu L, Gao Y, Song M, Wu J, Huang B, Li Y. Generation of duck Tembusu virus using a simple reverse genetic system in duck embryo fibroblast cells. J Virol Methods 2021;300:114385. [PMID: 34843824 DOI: 10.1016/j.jviromet.2021.114385] [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: 09/15/2020] [Revised: 09/04/2021] [Accepted: 11/25/2021] [Indexed: 11/25/2022]
40
Garbuzov FE, Gursky VV. Nonequilibrium model of short-range repression in gene transcription regulation. Phys Rev E 2021;104:014407. [PMID: 34412298 DOI: 10.1103/physreve.104.014407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 06/24/2021] [Indexed: 11/07/2022]
41
Garcia DA, Fettweis G, Presman DM, Paakinaho V, Jarzynski C, Upadhyaya A, Hager GL. Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model. Nucleic Acids Res 2021;49:6605-6620. [PMID: 33592625 DOI: 10.1093/nar/gkab072] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/13/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022]  Open
42
Koch AL, Morisaki T, Stasevich TJ. A Multi-color Bicistronic Biosensor to Compare the Translation Dynamics of Different Open Reading Frames at Single-molecule Resolution in Live Cells. Bio Protoc 2021;11:e4096. [PMID: 34395732 DOI: 10.21769/bioprotoc.4096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/29/2021] [Accepted: 05/16/2021] [Indexed: 11/02/2022]  Open
43
Gene Expression at a Single Molecule Level: Implications for MDS and AML. Blood 2021;138:625-636. [PMID: 34157070 DOI: 10.1182/blood.2019004261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022]  Open
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Forero-Quintero LS, Raymond W, Handa T, Saxton MN, Morisaki T, Kimura H, Bertrand E, Munsky B, Stasevich TJ. Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene. Nat Commun 2021;12:3158. [PMID: 34039974 PMCID: PMC8155019 DOI: 10.1038/s41467-021-23417-0] [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: 01/27/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023]  Open
45
Liu J, Hansen D, Eck E, Kim YJ, Turner M, Alamos S, Garcia HG. Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage. PLoS Comput Biol 2021;17:e1008999. [PMID: 34003867 PMCID: PMC8162642 DOI: 10.1371/journal.pcbi.1008999] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 05/28/2021] [Accepted: 04/23/2021] [Indexed: 12/23/2022]  Open
46
Cvekl A, Eliscovich C. Crystallin gene expression: Insights from studies of transcriptional bursting. Exp Eye Res 2021;207:108564. [PMID: 33894228 DOI: 10.1016/j.exer.2021.108564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/05/2021] [Accepted: 03/22/2021] [Indexed: 01/26/2023]
47
McNamara AV, Awais R, Momiji H, Dunham L, Featherstone K, Harper CV, Adamson AA, Semprini S, Jones NA, Spiller DG, Mullins JJ, Finkenstädt BF, Rand D, White MRH, Davis JRE. Transcription Factor Pit-1 Affects Transcriptional Timing in the Dual-Promoter Human Prolactin Gene. Endocrinology 2021;162:6060060. [PMID: 33388754 PMCID: PMC7871365 DOI: 10.1210/endocr/bqaa249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Indexed: 12/31/2022]
48
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
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A hierarchical regulatory network analysis of the vitamin D induced transcriptome reveals novel regulators and complete VDR dependency in monocytes. Sci Rep 2021;11:6518. [PMID: 33753848 PMCID: PMC7985518 DOI: 10.1038/s41598-021-86032-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/04/2021] [Indexed: 11/11/2022]  Open
50
Larke MSC, Schwessinger R, Nojima T, Telenius J, Beagrie RA, Downes DJ, Oudelaar AM, Truch J, Graham B, Bender MA, Proudfoot NJ, Higgs DR, Hughes JR. Enhancers predominantly regulate gene expression during differentiation via transcription initiation. Mol Cell 2021;81:983-997.e7. [PMID: 33539786 PMCID: PMC7612206 DOI: 10.1016/j.molcel.2021.01.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 09/25/2020] [Accepted: 01/02/2021] [Indexed: 12/16/2022]
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