• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (5081042)   Today's Articles (1103)
For: Teytelman L, Thurtle DM, Rine J, van Oudenaarden A. Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proc Natl Acad Sci U S A 2013;110:18602-7. [PMID: 24173036 DOI: 10.1073/pnas.1316064110] [Citation(s) in RCA: 291] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
Number Cited by Other Article(s)
1
Wang R, Wu Y, Zhou Z, Ma Y, Zhang W, Wang Z, Luo W, Hua P. Benchmark of chromatin-protein interaction methods in haploid round spermatids. Front Cell Dev Biol 2025;13:1572405. [PMID: 40433546 PMCID: PMC12106302 DOI: 10.3389/fcell.2025.1572405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Accepted: 04/15/2025] [Indexed: 05/29/2025]  Open
2
Ruiz SE, Maul RW, Gearhart PJ. Optimized CUT&RUN protocol for activated primary mouse B cells. PLoS One 2025;20:e0322139. [PMID: 40273386 PMCID: PMC12021426 DOI: 10.1371/journal.pone.0322139] [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: 08/21/2024] [Accepted: 03/17/2025] [Indexed: 04/26/2025]  Open
3
Abbasova L, Urbanaviciute P, Hu D, Ismail JN, Schilder BM, Nott A, Skene NG, Marzi SJ. CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks. Nat Commun 2025;16:2993. [PMID: 40148272 PMCID: PMC11950320 DOI: 10.1038/s41467-025-58137-2] [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: 07/28/2022] [Accepted: 03/13/2025] [Indexed: 03/29/2025]  Open
4
Ren Z, Way LE, Wang X. SMC translocation is unaffected by an excess of nucleoid associated proteins in vivo. Sci Rep 2025;15:2447. [PMID: 39828741 PMCID: PMC11743769 DOI: 10.1038/s41598-025-86946-4] [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: 10/31/2024] [Accepted: 01/15/2025] [Indexed: 01/22/2025]  Open
5
Shireen H, Batool F, Khatoon H, Parveen N, Sehar NU, Hussain I, Ali S, Abbasi AA. Predicting genome-wide tissue-specific enhancers via combinatorial transcription factor genomic occupancy analysis. FEBS Lett 2025;599:100-119. [PMID: 39367524 DOI: 10.1002/1873-3468.15030] [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: 07/14/2024] [Revised: 08/27/2024] [Accepted: 09/13/2024] [Indexed: 10/06/2024]
6
VanBelzen J, Sakelaris B, Brickner DG, Marcou N, Riecke H, Mangan NM, Brickner JH. Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kinetics. eLife 2024;13:RP100764. [PMID: 39607887 PMCID: PMC11604220 DOI: 10.7554/elife.100764] [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] [Indexed: 11/30/2024]  Open
7
Hudaiberdiev S, Ovcharenko I. Functional characteristics and computational model of abundant hyperactive loci in the human genome. eLife 2024;13:RP95170. [PMID: 39535534 PMCID: PMC11560132 DOI: 10.7554/elife.95170] [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] [Indexed: 11/16/2024]  Open
8
Ferraioli S, Sarigol F, Prakash C, Filipczak D, Foisner R, Naetar N. LAP2alpha facilitates myogenic gene expression by preventing nucleoplasmic lamin A/C from spreading to active chromatin regions. Nucleic Acids Res 2024;52:11500-11518. [PMID: 39228367 PMCID: PMC11514464 DOI: 10.1093/nar/gkae752] [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: 01/11/2024] [Revised: 08/06/2024] [Accepted: 08/20/2024] [Indexed: 09/05/2024]  Open
9
VanBelzen J, Sakelaris B, Brickner DG, Marcou N, Riecke H, Mangan N, Brickner JH. Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kinetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602535. [PMID: 39026809 PMCID: PMC11257477 DOI: 10.1101/2024.07.08.602535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
10
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]
11
Hudaiberdiev S, Ovcharenko I. Functional characteristics and computational model of abundant hyperactive loci in the human genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.05.527203. [PMID: 36945558 PMCID: PMC10028745 DOI: 10.1101/2023.02.05.527203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
12
Pepin AS, Schneider R. Emerging toolkits for decoding the co-occurrence of modified histones and chromatin proteins. EMBO Rep 2024;25:3202-3220. [PMID: 39095610 PMCID: PMC11316037 DOI: 10.1038/s44319-024-00199-2] [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: 02/28/2024] [Revised: 05/10/2024] [Accepted: 06/10/2024] [Indexed: 08/04/2024]  Open
13
Soll DR. White-opaque switching in Candida albicans: cell biology, regulation, and function. Microbiol Mol Biol Rev 2024;88:e0004322. [PMID: 38546228 PMCID: PMC11332339 DOI: 10.1128/mmbr.00043-22] [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: 06/28/2024]  Open
14
Abdel-Fattah WR, Carlsson M, Hu GZ, Singh A, Vergara A, Aslam R, Ronne H, Björklund S. Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes. Nucleic Acids Res 2024;52:6220-6233. [PMID: 38613396 PMCID: PMC11194063 DOI: 10.1093/nar/gkae266] [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: 01/08/2024] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024]  Open
15
Cissé OH, Curran SJ, Folco HD, Liu Y, Bishop L, Wang H, Fischer ER, Davis AS, Combs C, Thapar S, Dekker JP, Grewal S, Cushion M, Ma L, Kovacs JA. Regional centromere configuration in the fungal pathogens of the Pneumocystis genus. mBio 2024;15:e0318523. [PMID: 38380929 PMCID: PMC10936427 DOI: 10.1128/mbio.03185-23] [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: 11/29/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024]  Open
16
Xu J, Gao J, Ni P, Gerstein M. Less-is-more: selecting transcription factor binding regions informative for motif inference. Nucleic Acids Res 2024;52:e20. [PMID: 38214231 PMCID: PMC10899791 DOI: 10.1093/nar/gkad1240] [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: 12/08/2022] [Revised: 12/06/2023] [Accepted: 12/17/2023] [Indexed: 01/13/2024]  Open
17
Akdogan-Ozdilek B, George-Alexander LEMM, Scharer CD. Epigenomic Profiling of B Cell Subsets by CUT&Tag. Methods Mol Biol 2024;2826:65-77. [PMID: 39017886 PMCID: PMC11753148 DOI: 10.1007/978-1-0716-3950-4_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] [Indexed: 07/18/2024]
18
Liorni N, Napoli A, Adinolfi M, Vinciguerra M, Mazza T. Integrative Analysis of CUT&Tag and RNA-Seq Data Through Bioinformatics: A Unified Workflow for Enhanced Insights. Methods Mol Biol 2024;2846:191-213. [PMID: 39141238 DOI: 10.1007/978-1-0716-4071-5_13] [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: 08/15/2024]
19
Wen Y, Latham CM, Moore AN, Thomas NT, Lancaster BD, Reeves KA, Keeble AR, Fry CS, Johnson DL, Thompson KL, Noehren B, Fry JL. Vitamin D status associates with skeletal muscle loss after anterior cruciate ligament reconstruction. JCI Insight 2023;8:e170518. [PMID: 37856482 PMCID: PMC10795826 DOI: 10.1172/jci.insight.170518] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/17/2023] [Indexed: 10/21/2023]  Open
20
van Breugel ME, van Kruijsbergen I, Mittal C, Lieftink C, Brouwer I, van den Brand T, Kluin RJC, Hoekman L, Menezes RX, van Welsem T, Del Cortona A, Malik M, Beijersbergen RL, Lenstra TL, Verstrepen KJ, Pugh BF, van Leeuwen F. Locus-specific proteome decoding reveals Fpt1 as a chromatin-associated negative regulator of RNA polymerase III assembly. Mol Cell 2023;83:4205-4221.e9. [PMID: 37995691 PMCID: PMC11289708 DOI: 10.1016/j.molcel.2023.10.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/27/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
21
Miller G, Rollosson LM, Saada C, Wade SJ, Schulz D. Adaptation of CUT&RUN for use in African trypanosomes. PLoS One 2023;18:e0292784. [PMID: 37988382 PMCID: PMC10662711 DOI: 10.1371/journal.pone.0292784] [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: 06/22/2023] [Accepted: 09/28/2023] [Indexed: 11/23/2023]  Open
22
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]
23
Ma CH, Kumar D, Jayaram M, Ghosh SK, Iyer VR. The selfish yeast plasmid exploits a SWI/SNF-type chromatin remodeling complex for hitchhiking on chromosomes and ensuring high-fidelity propagation. PLoS Genet 2023;19:e1010986. [PMID: 37812641 PMCID: PMC10586699 DOI: 10.1371/journal.pgen.1010986] [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: 06/29/2023] [Revised: 10/19/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023]  Open
24
Penzo A, Dubarry M, Brocas C, Zheng M, Mangione RM, Rougemaille M, Goncalves C, Lautier O, Libri D, Simon MN, Géli V, Dubrana K, Palancade B. A R-loop sensing pathway mediates the relocation of transcribed genes to nuclear pore complexes. Nat Commun 2023;14:5606. [PMID: 37730746 PMCID: PMC10511428 DOI: 10.1038/s41467-023-41345-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023]  Open
25
Wilcher KE, Page ERH, Privette Vinnedge LM. The impact of the chromatin binding DEK protein in hematopoiesis and acute myeloid leukemia. Exp Hematol 2023;123:18-27. [PMID: 37172756 PMCID: PMC10330528 DOI: 10.1016/j.exphem.2023.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/03/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023]
26
Chowdhary K, Benoist C. A variegated model of transcription factor function in the immune system. Trends Immunol 2023;44:530-541. [PMID: 37258360 PMCID: PMC10332489 DOI: 10.1016/j.it.2023.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 06/02/2023]
27
Petrie MV, He Y, Gan Y, Ostrow AZ, Aparicio OM. Broadly Applicable Control Approaches Improve Accuracy of ChIP-Seq Data. Int J Mol Sci 2023;24:9271. [PMID: 37298223 PMCID: PMC10252487 DOI: 10.3390/ijms24119271] [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: 04/25/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]  Open
28
Bondra ER, Rine J. Context dependent function of the transcriptional regulator Rap1 in gene silencing and activation in Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539937. [PMID: 37214837 PMCID: PMC10197613 DOI: 10.1101/2023.05.08.539937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
29
Morin A, Chu ECP, Sharma A, Adrian-Hamazaki A, Pavlidis P. Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets. Genome Res 2023;33:763-778. [PMID: 37308292 PMCID: PMC10317128 DOI: 10.1101/gr.277273.122] [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: 08/31/2022] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
30
Su S, Xue Y, Lee SK, Zhang Y, Fan J, De S, Sharov A, Wang W. A dual-activity topoisomerase complex promotes both transcriptional activation and repression in response to starvation. Nucleic Acids Res 2023;51:2415-2433. [PMID: 36794732 PMCID: PMC10018333 DOI: 10.1093/nar/gkad086] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/17/2023]  Open
31
Banigan EJ, Tang W, van den Berg AA, Stocsits RR, Wutz G, Brandão HB, Busslinger GA, Peters JM, Mirny LA. Transcription shapes 3D chromatin organization by interacting with loop extrusion. Proc Natl Acad Sci U S A 2023;120:e2210480120. [PMID: 36897969 PMCID: PMC10089175 DOI: 10.1073/pnas.2210480120] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/03/2022] [Indexed: 03/12/2023]  Open
32
Abid D, Brent MR. NetProphet 3: a machine learning framework for transcription factor network mapping and multi-omics integration. Bioinformatics 2023;39:7000334. [PMID: 36692138 PMCID: PMC9912366 DOI: 10.1093/bioinformatics/btad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 01/11/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023]  Open
33
Wang H, Wang Y, Luo Z, Lin X, Liu M, Wu F, Shao H, Zhang W. Advances in Off-Target Detection for CRISPR-Based Genome Editing. Hum Gene Ther 2023;34:112-128. [PMID: 36453226 DOI: 10.1089/hum.2022.198] [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: 12/02/2022]  Open
34
Sheu YJ, Kawaguchi RK, Gillis J, Stillman B. Prevalent and dynamic binding of the cell cycle checkpoint kinase Rad53 to gene promoters. eLife 2022;11:e84320. [PMID: 36520028 PMCID: PMC9797190 DOI: 10.7554/elife.84320] [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] [Received: 10/20/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022]  Open
35
He F, Yu Q, Wang M, Wang R, Gong X, Ge F, Yu X, Li S. SESAME-catalyzed H3T11 phosphorylation inhibits Dot1-catalyzed H3K79me3 to regulate autophagy and telomere silencing. Nat Commun 2022;13:7526. [PMID: 36473858 PMCID: PMC9726891 DOI: 10.1038/s41467-022-35182-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]  Open
36
Antony C, George SS, Blum J, Somers P, Thorsheim CL, Wu-Corts DJ, Ai Y, Gao L, Lv K, Tremblay MG, Moss T, Tan K, Wilusz JE, Ganley ARD, Pimkin M, Paralkar VR. Control of ribosomal RNA synthesis by hematopoietic transcription factors. Mol Cell 2022;82:3826-3839.e9. [PMID: 36113481 PMCID: PMC9588704 DOI: 10.1016/j.molcel.2022.08.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/23/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022]
37
Xu J, Pratt HE, Moore JE, Gerstein MB, Weng Z. Building integrative functional maps of gene regulation. Hum Mol Genet 2022;31:R114-R122. [PMID: 36083269 PMCID: PMC9585680 DOI: 10.1093/hmg/ddac195] [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: 07/17/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022]  Open
38
Giacoman-Lozano M, Meléndez-Ramírez C, Martinez-Ledesma E, Cuevas-Diaz Duran R, Velasco I. Epigenetics of neural differentiation: Spotlight on enhancers. Front Cell Dev Biol 2022;10:1001701. [PMID: 36313573 PMCID: PMC9606577 DOI: 10.3389/fcell.2022.1001701] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/03/2022] [Indexed: 11/28/2022]  Open
39
Staller MV. Transcription factors perform a 2-step search of the nucleus. Genetics 2022;222:iyac111. [PMID: 35939561 PMCID: PMC9526044 DOI: 10.1093/genetics/iyac111] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/14/2022] [Indexed: 01/02/2023]  Open
40
Angelov D, Boopathi R, Lone IN, Menoni H, Dimitrov S, Cadet J. Capturing Protein-Nucleic Acid Interactions by High-Intensity Laser-Induced Covalent Crosslinking. Photochem Photobiol 2022;99:296-312. [PMID: 35997098 DOI: 10.1111/php.13699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022]
41
An improved CUT&RUN method for regulation network reconstruction of low abundance transcription factor. Cell Signal 2022;96:110361. [DOI: 10.1016/j.cellsig.2022.110361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/20/2022]
42
Yashar WM, Kong G, VanCampen J, Curtiss BM, Coleman DJ, Carbone L, Yardimci GG, Maxson JE, Braun TP. GoPeaks: histone modification peak calling for CUT&Tag. Genome Biol 2022;23:144. [PMID: 35788238 PMCID: PMC9252088 DOI: 10.1186/s13059-022-02707-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 06/15/2022] [Indexed: 12/27/2022]  Open
43
Ashby E, Paddock L, Betts HL, Liao J, Miller G, Porter A, Rollosson LM, Saada C, Tang E, Wade SJ, Hardin J, Schulz D. Genomic Occupancy of the Bromodomain Protein Bdf3 Is Dynamic during Differentiation of African Trypanosomes from Bloodstream to Procyclic Forms. mSphere 2022;7:e0002322. [PMID: 35642518 PMCID: PMC9241505 DOI: 10.1128/msphere.00023-22] [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: 01/11/2022] [Accepted: 05/05/2022] [Indexed: 12/05/2022]  Open
44
Morse RH. Function and dynamics of the Mediator complex: novel insights and new frontiers. Transcription 2022;13:39-52. [PMID: 35708525 PMCID: PMC9467533 DOI: 10.1080/21541264.2022.2085502] [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] [Indexed: 11/04/2022]  Open
45
Karimzadeh M, Hoffman MM. Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome. Genome Biol 2022;23:126. [PMID: 35681170 PMCID: PMC9185870 DOI: 10.1186/s13059-022-02690-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/16/2022] [Indexed: 11/29/2022]  Open
46
Liu Z, Naler LB, Zhu Y, Deng C, Zhang Q, Zhu B, Zhou Z, Sarma M, Murray A, Xie H, Lu C. nMOWChIP-seq: low-input genome-wide mapping of non-histone targets. NAR Genom Bioinform 2022;4:lqac030. [PMID: 35402909 PMCID: PMC8988714 DOI: 10.1093/nargab/lqac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022]  Open
47
Wei YB, Luo D, Xiong X, Huang YL, Xie M, Lu W, Li D. Biomimetic mimicry of formaldehyde-induced DNA-protein crosslinks in the confined space of a metal-organic framework. Chem Sci 2022;13:4813-4820. [PMID: 35655868 PMCID: PMC9067591 DOI: 10.1039/d2sc00188h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/18/2022] [Indexed: 02/05/2023]  Open
48
He L, Gao M, Pratt H, Weng Z, Struhl K. MafB, WDR77, and ß-catenin interact with each other and have similar genome association profiles. PLoS One 2022;17:e0264799. [PMID: 35482762 PMCID: PMC9049301 DOI: 10.1371/journal.pone.0264799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/15/2022] [Indexed: 11/19/2022]  Open
49
Jing F, Zhang SW, Zhang S. Prediction of the transcription factor binding sites with meta-learning. Methods 2022;203:207-213. [DOI: 10.1016/j.ymeth.2022.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 04/01/2022] [Accepted: 04/17/2022] [Indexed: 11/26/2022]  Open
50
Wei L, Lai EC. Regulation of the Alternative Neural Transcriptome by ELAV/Hu RNA Binding Proteins. Front Genet 2022;13:848626. [PMID: 35281806 PMCID: PMC8904962 DOI: 10.3389/fgene.2022.848626] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/01/2022] [Indexed: 11/30/2022]  Open
PrevPage 1 of 6 123456Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA