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For: Brodsky S, Jana T, Barkai N. Order through disorder: The role of intrinsically disordered regions in transcription factor binding specificity. Curr Opin Struct Biol 2021;71:110-115. [PMID: 34303077 DOI: 10.1016/j.sbi.2021.06.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/31/2021] [Accepted: 06/14/2021] [Indexed: 02/07/2023]
Number Cited by Other Article(s)
1
Jonas F, Navon Y, Barkai N. Intrinsically disordered regions as facilitators of the transcription factor target search. Nat Rev Genet 2025;26:424-435. [PMID: 39984675 DOI: 10.1038/s41576-025-00816-3] [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: 01/14/2025] [Indexed: 02/23/2025]
2
Wen Y, Li Z, Ye J, Wang X, Jiang M, Deng Z, Cao C, He X. Discovery and Characterization of Actinosynnelassin: An Anti-Pseudomonas fluorescens Lasso Peptide Derived from a Large Precursor Open Reading Frame. JOURNAL OF NATURAL PRODUCTS 2025. [PMID: 40387067 DOI: 10.1021/acs.jnatprod.5c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2025]
3
Wang W, Han F, Qi Z, Yan C, Su B, Wang J. Phase Separation: Orchestrating Biological Adaptations to Environmental Fluctuations. Int J Mol Sci 2025;26:4614. [PMID: 40429758 PMCID: PMC12110863 DOI: 10.3390/ijms26104614] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2025] [Revised: 04/23/2025] [Accepted: 05/08/2025] [Indexed: 05/29/2025]  Open
4
Muñoz V, Goluguri RR, Ghosh C, Tanielian B, Sadqi M. Mechanisms for DNA Interplay in Eukaryotic Transcription Factors. Annu Rev Biophys 2025;54:121-139. [PMID: 39879549 DOI: 10.1146/annurev-biophys-071524-111008] [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: 01/31/2025]
5
Cerrato CP, Krkoška M, Sun Y, Liaño-Pons J, Neo QY, Vosselman T, Alzrigat M, Vojtěšek B, Lane DP, Arsenian Henriksson M, Miserez A, Landreh M. Engineered Peptide Coacervates Enable Efficient Intracellular Delivery of the MYC Inhibitor omoMYC. Mol Pharm 2025. [PMID: 40304302 DOI: 10.1021/acs.molpharmaceut.5c00468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2025]
6
Lambourne L, Mattioli K, Santoso C, Sheynkman G, Inukai S, Kaundal B, Berenson A, Spirohn-Fitzgerald K, Bhattacharjee A, Rothman E, Shrestha S, Laval F, Carroll BS, Plassmeyer SP, Emenecker RJ, Yang Z, Bisht D, Sewell JA, Li G, Prasad A, Phanor S, Lane R, Moyer DC, Hunt T, Balcha D, Gebbia M, Twizere JC, Hao T, Holehouse AS, Frankish A, Riback JA, Salomonis N, Calderwood MA, Hill DE, Sahni N, Vidal M, Bulyk ML, Fuxman Bass JI. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. Mol Cell 2025;85:1445-1466.e13. [PMID: 40147441 PMCID: PMC12121496 DOI: 10.1016/j.molcel.2025.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 12/06/2024] [Accepted: 03/05/2025] [Indexed: 03/29/2025]
7
Wang L, Brasnett C, Borges-Araújo L, Souza PCT, Marrink SJ. Martini3-IDP: improved Martini 3 force field for disordered proteins. Nat Commun 2025;16:2874. [PMID: 40128232 PMCID: PMC11933364 DOI: 10.1038/s41467-025-58199-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Accepted: 03/14/2025] [Indexed: 03/26/2025]  Open
8
Zhang L, Hodgins L, Sakib S, Verbeem A, Mahmood A, Perez-Romero C, Marmion RA, Dostatni N, Fradin C. Both the transcriptional activator, Bcd, and repressor, Cic, form small mobile oligomeric clusters. Biophys J 2025;124:980-995. [PMID: 39164967 PMCID: PMC11947476 DOI: 10.1016/j.bpj.2024.08.011] [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: 02/02/2024] [Revised: 07/11/2024] [Accepted: 08/15/2024] [Indexed: 08/22/2024]  Open
9
He C, Liang Y, Chen R, Shen Y, Li R, Sun T, Du X, Ni X, Shang J, He Y, Bao M, Luo H, Wang J, Liao P, Kang C, Yuan YW, Ning G. Boosting transcriptional activities by employing repeated activation domains in transcription factors. THE PLANT CELL 2025;37:koae315. [PMID: 39657052 PMCID: PMC11823830 DOI: 10.1093/plcell/koae315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 10/24/2024] [Accepted: 10/28/2024] [Indexed: 12/17/2024]
10
Datta RR, Akdogan D, Tezcan EB, Onal P. Versatile roles of disordered transcription factor effector domains in transcriptional regulation. FEBS J 2025. [PMID: 39888268 DOI: 10.1111/febs.17424] [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: 09/01/2024] [Revised: 11/25/2024] [Accepted: 01/21/2025] [Indexed: 02/01/2025]
11
Kodali S, Sands CM, Guo L, Huang Y, Di Stefano B. Biomolecular condensates in immune cell fate. Nat Rev Immunol 2025:10.1038/s41577-025-01130-z. [PMID: 39875604 DOI: 10.1038/s41577-025-01130-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2025] [Indexed: 01/30/2025]
12
Mindel V, Brodsky S, Yung H, Manadre W, Barkai N. Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors. Nucleic Acids Res 2024;52:12093-12111. [PMID: 39187372 PMCID: PMC11551773 DOI: 10.1093/nar/gkae718] [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: 05/15/2024] [Revised: 07/08/2024] [Accepted: 08/09/2024] [Indexed: 08/28/2024]  Open
13
Spector B, Santana J, Pufall M, Price D. DFF-ChIP: a method to detect and quantify complex interactions between RNA polymerase II, transcription factors, and chromatin. Nucleic Acids Res 2024;52:e88. [PMID: 39248105 PMCID: PMC11472042 DOI: 10.1093/nar/gkae760] [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: 12/22/2023] [Revised: 07/30/2024] [Accepted: 08/20/2024] [Indexed: 09/10/2024]  Open
14
Lu Y, Berenson A, Lane R, Guelin I, Li Z, Chen Y, Shah S, Yin M, Soto-Ugaldi LF, Fiszbein A, Fuxman Bass JI. A large-scale cancer-specific protein-DNA interaction network. Life Sci Alliance 2024;7:e202402641. [PMID: 39013578 PMCID: PMC11252446 DOI: 10.26508/lsa.202402641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/18/2024]  Open
15
Valbuena R, Nigam A, Tycko J, Suzuki P, Spees K, Aradhana, Arana S, Du P, Patel RA, Bintu L, Kundaje A, Bassik MC. Prediction and design of transcriptional repressor domains with large-scale mutational scans and deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.21.614253. [PMID: 39386603 PMCID: PMC11463546 DOI: 10.1101/2024.09.21.614253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
16
Dhillon N, Kamakaka RT. Transcriptional silencing in Saccharomyces cerevisiae: known unknowns. Epigenetics Chromatin 2024;17:28. [PMID: 39272151 PMCID: PMC11401328 DOI: 10.1186/s13072-024-00553-7] [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: 07/02/2024] [Accepted: 09/02/2024] [Indexed: 09/15/2024]  Open
17
Zeng W, Dou Y, Pan L, Xu L, Peng S. Improving prediction performance of general protein language model by domain-adaptive pretraining on DNA-binding protein. Nat Commun 2024;15:7838. [PMID: 39244557 PMCID: PMC11380688 DOI: 10.1038/s41467-024-52293-7] [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: 12/18/2023] [Accepted: 08/29/2024] [Indexed: 09/09/2024]  Open
18
Hurieva B, Kumar DK, Morag R, Lupo O, Carmi M, Barkai N, Jonas F. Disordered sequences of transcription factors regulate genomic binding by integrating diverse sequence grammars and interaction types. Nucleic Acids Res 2024;52:8763-8777. [PMID: 38908024 PMCID: PMC11347154 DOI: 10.1093/nar/gkae521] [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: 11/28/2023] [Revised: 04/25/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]  Open
19
Xu C, Kleinschmidt H, Yang J, Leith EM, Johnson J, Tan S, Mahony S, Bai L. Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1. Mol Cell 2024;84:2838-2855.e10. [PMID: 39019045 PMCID: PMC11334613 DOI: 10.1016/j.molcel.2024.06.022] [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: 01/09/2024] [Revised: 04/23/2024] [Accepted: 06/21/2024] [Indexed: 07/19/2024]
20
Ozkan-Nikitaras T, Grzesik DJ, Romano LEL, Chapple JP, King PJ, Shoulders CC. N-SREBP2 Provides a Mechanism for Dynamic Control of Cellular Cholesterol Homeostasis. Cells 2024;13:1255. [PMID: 39120286 PMCID: PMC11311687 DOI: 10.3390/cells13151255] [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: 06/14/2024] [Revised: 07/05/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024]  Open
21
von Ehr J, Oberstrass L, Yazgan E, Schnaubelt LI, Blümel N, McNicoll F, Weigand JE, Zarnack K, Müller-McNicoll M, Korn SM, Schlundt A. Arid5a uses disordered extensions of its core ARID domain for distinct DNA- and RNA-recognition and gene regulation. J Biol Chem 2024;300:107457. [PMID: 38866324 PMCID: PMC11262183 DOI: 10.1016/j.jbc.2024.107457] [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: 04/10/2024] [Revised: 05/23/2024] [Accepted: 06/01/2024] [Indexed: 06/14/2024]  Open
22
Yao YM, Miodownik I, O’Hagan MP, Jbara M, Afek A. Deciphering the dynamic code: DNA recognition by transcription factors in the ever-changing genome. Transcription 2024;15:114-138. [PMID: 39033307 PMCID: PMC11810102 DOI: 10.1080/21541264.2024.2379161] [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: 03/15/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024]  Open
23
Panagaki F, Tapia-Rojo R, Zhu T, Milmoe N, Paracuellos P, Board S, Mora M, Walker J, Rostkova E, Stannard A, Infante E, Garcia-Manyes S. Structural anisotropy results in mechano-directional transport of proteins across nuclear pores. NATURE PHYSICS 2024;20:1180-1193. [PMID: 39036650 PMCID: PMC11254768 DOI: 10.1038/s41567-024-02438-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 02/08/2024] [Indexed: 07/23/2024]
24
Zhang K, Jiang Z, Li X, Wang D, Hong J. Enhancing simultaneous saccharification and co-fermentation of corncob by Kluyveromyces marxianus through overexpression of putative transcription regulator. BIORESOURCE TECHNOLOGY 2024;399:130627. [PMID: 38522677 DOI: 10.1016/j.biortech.2024.130627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 03/26/2024]
25
Lambourne L, Mattioli K, Santoso C, Sheynkman G, Inukai S, Kaundal B, Berenson A, Spirohn-Fitzgerald K, Bhattacharjee A, Rothman E, Shrestha S, Laval F, Yang Z, Bisht D, Sewell JA, Li G, Prasad A, Phanor S, Lane R, Campbell DM, Hunt T, Balcha D, Gebbia M, Twizere JC, Hao T, Frankish A, Riback JA, Salomonis N, Calderwood MA, Hill DE, Sahni N, Vidal M, Bulyk ML, Fuxman Bass JI. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584681. [PMID: 38617209 PMCID: PMC11014633 DOI: 10.1101/2024.03.12.584681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
26
Ertl HA, Bayala EX, Siddiq MA, Wittkopp PJ. Divergence of Grainy head affects chromatin accessibility, gene expression, and embryonic viability in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.07.588430. [PMID: 38645200 PMCID: PMC11030446 DOI: 10.1101/2024.04.07.588430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
27
Mindel V, Brodsky S, Cohen A, Manadre W, Jonas F, Carmi M, Barkai N. Intrinsically disordered regions of the Msn2 transcription factor encode multiple functions using interwoven sequence grammars. Nucleic Acids Res 2024;52:2260-2272. [PMID: 38109289 PMCID: PMC10954448 DOI: 10.1093/nar/gkad1191] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/04/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]  Open
28
Gibson TJ, Larson ED, Harrison MM. Protein-intrinsic properties and context-dependent effects regulate pioneer factor binding and function. Nat Struct Mol Biol 2024;31:548-558. [PMID: 38365978 PMCID: PMC11261375 DOI: 10.1038/s41594-024-01231-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
29
Holehouse AS, Kragelund BB. The molecular basis for cellular function of intrinsically disordered protein regions. Nat Rev Mol Cell Biol 2024;25:187-211. [PMID: 37957331 PMCID: PMC11459374 DOI: 10.1038/s41580-023-00673-0] [Citation(s) in RCA: 192] [Impact Index Per Article: 192.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
30
Lu Y, Berenson A, Lane R, Guelin I, Li Z, Chen Y, Shah S, Yin M, Soto-Ugaldi LF, Fiszbein A, Fuxman Bass JI. A large-scale cancer-specific protein-DNA interaction network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577099. [PMID: 38352498 PMCID: PMC10862707 DOI: 10.1101/2024.01.24.577099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
31
Martinsen E, Jinnurine T, Subramani S, Rogne M. Advances in RNA therapeutics for modulation of 'undruggable' targets. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024;204:249-294. [PMID: 38458740 DOI: 10.1016/bs.pmbts.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
32
Ray M, Zaborowsky J, Mahableshwarkar P, Vaidyanathan S, Shum J, Viswanathan R, Huang A, Wang SH, Johnson V, Wake N, Conard AM, Conicella AE, Puterbaugh R, Fawzi NL, Larschan E. Dual DNA/RNA-binding factor regulates dynamics of hnRNP splicing condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575216. [PMID: 38260450 PMCID: PMC10802580 DOI: 10.1101/2024.01.11.575216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
33
Xing YH, Dong R, Lee L, Rengarajan S, Riggi N, Boulay G, Rivera MN. DisP-seq reveals the genome-wide functional organization of DNA-associated disordered proteins. Nat Biotechnol 2024;42:52-64. [PMID: 37037903 PMCID: PMC10791585 DOI: 10.1038/s41587-023-01737-4] [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: 07/06/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023]
34
Leslie BJ, Lang B, Babu MM. A genome-wide view of disordered proteins. Nat Biotechnol 2024;42:32-34. [PMID: 37783848 DOI: 10.1038/s41587-023-01955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
35
Shahrajabian MH, Sun W. Characterization of Intrinsically Disordered Proteins in Healthy and Diseased States by Nuclear Magnetic Resonance. Rev Recent Clin Trials 2024;19:176-188. [PMID: 38409704 DOI: 10.2174/0115748871271420240213064251] [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: 09/13/2023] [Revised: 11/10/2023] [Accepted: 12/13/2023] [Indexed: 02/28/2024]
36
Mann RS, Glassford WJ. Hox genes: The original body builders. Semin Cell Dev Biol 2024;152-153:1-3. [PMID: 37291029 PMCID: PMC10949336 DOI: 10.1016/j.semcdb.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
37
Xu C, Kleinschmidt H, Yang J, Leith E, Johnson J, Tan S, Mahony S, Bai L. Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566246. [PMID: 37986839 PMCID: PMC10659273 DOI: 10.1101/2023.11.08.566246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
38
Wagh K, Stavreva DA, Upadhyaya A, Hager GL. Transcription Factor Dynamics: One Molecule at a Time. Annu Rev Cell Dev Biol 2023;39:277-305. [PMID: 37540844 DOI: 10.1146/annurev-cellbio-022823-013847] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
39
Kumar A, Madhurima K, Naganathan AN, Vallurupalli P, Sekhar A. Probing excited state 1Hα chemical shifts in intrinsically disordered proteins with a triple resonance-based CEST experiment: Application to a disorder-to-order switch. Methods 2023;218:198-209. [PMID: 37607621 PMCID: PMC7615522 DOI: 10.1016/j.ymeth.2023.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/24/2023]  Open
40
Brown AD, Lynch K, Langelaan DN. The C-terminal transactivation domain of MITF interacts promiscuously with co-activator CBP/p300. Sci Rep 2023;13:16094. [PMID: 37752231 PMCID: PMC10522771 DOI: 10.1038/s41598-023-43207-6] [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: 07/18/2023] [Accepted: 09/21/2023] [Indexed: 09/28/2023]  Open
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Lupo O, Kumar DK, Livne R, Chappleboim M, Levy I, Barkai N. The architecture of binding cooperativity between densely bound transcription factors. Cell Syst 2023;14:732-745.e5. [PMID: 37527656 DOI: 10.1016/j.cels.2023.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/23/2023] [Accepted: 06/27/2023] [Indexed: 08/03/2023]
42
Karlsson E, Ottoson C, Ye W, Andersson E, Jemth P. Intrinsically Disordered Flanking Regions Increase the Affinity of a Transcriptional Coactivator Interaction across Vertebrates. Biochemistry 2023;62:2710-2716. [PMID: 37647499 PMCID: PMC10515491 DOI: 10.1021/acs.biochem.3c00285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/16/2023] [Indexed: 09/01/2023]
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Oda M. Analysis of the Structural Dynamics of Proteins in the Ligand-Unbound and -Bound States by Diffracted X-ray Tracking. Int J Mol Sci 2023;24:13717. [PMID: 37762021 PMCID: PMC10531450 DOI: 10.3390/ijms241813717] [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: 08/17/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]  Open
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Jonas F, Carmi M, Krupkin B, Steinberger J, Brodsky S, Jana T, Barkai N. The molecular grammar of protein disorder guiding genome-binding locations. Nucleic Acids Res 2023;51:4831-4844. [PMID: 36938874 PMCID: PMC10250222 DOI: 10.1093/nar/gkad184] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/25/2023] [Accepted: 03/15/2023] [Indexed: 03/21/2023]  Open
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Kumar DK, Jonas F, Jana T, Brodsky S, Carmi M, Barkai N. Complementary strategies for directing in vivo transcription factor binding through DNA binding domains and intrinsically disordered regions. Mol Cell 2023;83:1462-1473.e5. [PMID: 37116493 DOI: 10.1016/j.molcel.2023.04.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/17/2023] [Accepted: 01/30/2023] [Indexed: 04/30/2023]
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Gibson TJ, Harrison MM. Protein-intrinsic properties and context-dependent effects regulate pioneer-factor binding and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.18.533281. [PMID: 37066406 PMCID: PMC10103944 DOI: 10.1101/2023.03.18.533281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
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Chuang CK, Chen SF, Su YH, Chen WH, Lin WM, Wang IC, Shyue SK. The Role of SCL Isoforms in Embryonic Hematopoiesis. Int J Mol Sci 2023;24:ijms24076427. [PMID: 37047400 PMCID: PMC10094407 DOI: 10.3390/ijms24076427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 03/16/2023] [Accepted: 03/26/2023] [Indexed: 04/01/2023]  Open
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Chadwick BJ, Ross BE, Lin X. Molecular Dissection of Crz1 and Its Dynamic Subcellular Localization in Cryptococcus neoformans. J Fungi (Basel) 2023;9:jof9020252. [PMID: 36836365 PMCID: PMC9963361 DOI: 10.3390/jof9020252] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/01/2023] [Accepted: 02/08/2023] [Indexed: 02/17/2023]  Open
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Patil A. Enrichment patterns of intrinsic disorder in proteins. Biophys Rev 2022;14:1487-1493. [PMID: 36659984 PMCID: PMC9842814 DOI: 10.1007/s12551-022-01016-7] [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: 09/01/2022] [Accepted: 11/07/2022] [Indexed: 11/21/2022]  Open
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Samulevich ML, Shamilov R, Aneskievich BJ. Thermostable Proteins from HaCaT Keratinocytes Identify a Wide Breadth of Intrinsically Disordered Proteins and Candidates for Liquid-Liquid Phase Separation. Int J Mol Sci 2022;23:ijms232214323. [PMID: 36430801 PMCID: PMC9692912 DOI: 10.3390/ijms232214323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/08/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022]  Open
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