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For: Jordán-Pla A, Gupta I, de Miguel-Jiménez L, Steinmetz LM, Chávez S, Pelechano V, Pérez-Ortín JE. Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle. Nucleic Acids Res 2014;43:787-802. [PMID: 25550430 PMCID: PMC4333398 DOI: 10.1093/nar/gku1349] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
Number Cited by Other Article(s)
1
Kelbert M, Jordán-Pla A, de Miguel-Jiménez L, García-Martínez J, Selitrennik M, Guterman A, Henig N, Granneman S, Pérez-Ortín JE, Chávez S, Choder M. The zinc-finger transcription factor Sfp1 imprints specific classes of mRNAs and links their synthesis to cytoplasmic decay. eLife 2024;12:RP90766. [PMID: 39356734 PMCID: PMC11446548 DOI: 10.7554/elife.90766] [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: 10/04/2024]  Open
2
Rajkumar MS, Tembhare K, Garg R, Jain M. Genome-wide mapping of DNase I hypersensitive sites revealed differential chromatin accessibility and regulatory DNA elements under drought stress in rice cultivars. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024;119:2063-2079. [PMID: 38859561 DOI: 10.1111/tpj.16864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 04/08/2024] [Accepted: 05/22/2024] [Indexed: 06/12/2024]
3
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]
4
Cheon Y, Han S, Kim T, Hwang D, Lee D. The chromatin remodeler Ino80 mediates RNAPII pausing site determination. Genome Biol 2021;22:294. [PMID: 34663418 PMCID: PMC8524862 DOI: 10.1186/s13059-021-02500-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/15/2021] [Indexed: 11/25/2022]  Open
5
Shukla A, Bhalla P, Potdar PK, Jampala P, Bhargava P. Transcription-dependent enrichment of the yeast FACT complex influences nucleosome dynamics on the RNA polymerase III-transcribed genes. RNA (NEW YORK, N.Y.) 2020;27:rna.077974.120. [PMID: 33277439 PMCID: PMC7901838 DOI: 10.1261/rna.077974.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/30/2020] [Indexed: 05/04/2023]
6
Begley V, Jordán-Pla A, Peñate X, Garrido-Godino AI, Challal D, Cuevas-Bermúdez A, Mitjavila A, Barucco M, Gutiérrez G, Singh A, Alepuz P, Navarro F, Libri D, Pérez-Ortín JE, Chávez S. Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration. RNA Biol 2020;18:1310-1323. [PMID: 33138675 DOI: 10.1080/15476286.2020.1845504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]  Open
7
Martínez-Fernández V, Cuevas-Bermúdez A, Gutiérrez-Santiago F, Garrido-Godino AI, Rodríguez-Galán O, Jordán-Pla A, Lois S, Triviño JC, de la Cruz J, Navarro F. Prefoldin-like Bud27 influences the transcription of ribosomal components and ribosome biogenesis in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2020;26:1360-1379. [PMID: 32503921 PMCID: PMC7491330 DOI: 10.1261/rna.075507.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/28/2020] [Indexed: 05/08/2023]
8
Fischer J, Song YS, Yosef N, di Iulio J, Churchman LS, Choder M. The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5' and 3' gene regions. J Biol Chem 2020;295:11435-11454. [PMID: 32518159 DOI: 10.1074/jbc.ra120.013426] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/05/2020] [Indexed: 11/06/2022]  Open
9
Jordán-Pla A, Pérez-Martínez ME, Pérez-Ortín JE. Measuring RNA polymerase activity genome-wide with high-resolution run-on-based methods. Methods 2019;159-160:177-182. [PMID: 30716396 DOI: 10.1016/j.ymeth.2019.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 02/05/2023]  Open
10
Gutiérrez G, Millán-Zambrano G, Medina DA, Jordán-Pla A, Pérez-Ortín JE, Peñate X, Chávez S. Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning. Epigenetics Chromatin 2017;10:58. [PMID: 29212533 PMCID: PMC5719526 DOI: 10.1186/s13072-017-0165-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/29/2017] [Indexed: 12/16/2022]  Open
11
Shukla A, Bhargava P. Regulation of tRNA gene transcription by the chromatin structure and nucleosome dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017;1861:295-309. [PMID: 29313808 DOI: 10.1016/j.bbagrm.2017.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 01/19/2023]
12
Cohen E, Zafrir Z, Tuller T. A code for transcription elongation speed. RNA Biol 2017;15:81-94. [PMID: 29165040 DOI: 10.1080/15476286.2017.1384118] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]  Open
13
Van Bortle K, Phanstiel DH, Snyder MP. Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation. Genome Biol 2017;18:180. [PMID: 28931413 PMCID: PMC5607496 DOI: 10.1186/s13059-017-1310-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/25/2017] [Indexed: 12/11/2022]  Open
14
Transcription by RNA polymerase III: insights into mechanism and regulation. Biochem Soc Trans 2017;44:1367-1375. [PMID: 27911719 PMCID: PMC5095917 DOI: 10.1042/bst20160062] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 07/07/2016] [Accepted: 07/13/2016] [Indexed: 12/13/2022]
15
Wahba L, Costantino L, Tan FJ, Zimmer A, Koshland D. S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation. Genes Dev 2017;30:1327-38. [PMID: 27298336 PMCID: PMC4911931 DOI: 10.1101/gad.280834.116] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/11/2016] [Indexed: 12/16/2022]
16
TORC1-dependent sumoylation of Rpc82 promotes RNA polymerase III assembly and activity. Proc Natl Acad Sci U S A 2017;114:1039-1044. [PMID: 28096404 DOI: 10.1073/pnas.1615093114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
17
Orioli A. tRNA biology in the omics era: Stress signalling dynamics and cancer progression. Bioessays 2016;39. [PMID: 28026052 DOI: 10.1002/bies.201600158] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
18
Turowski TW, Leśniewska E, Delan-Forino C, Sayou C, Boguta M, Tollervey D. Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts. Genome Res 2016;26:933-44. [PMID: 27206856 PMCID: PMC4937561 DOI: 10.1101/gr.205492.116] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/20/2016] [Indexed: 01/25/2023]
19
Jimeno-González S, Reyes JC. Chromatin structure and pre-mRNA processing work together. Transcription 2016;7:63-8. [PMID: 27028548 PMCID: PMC4984687 DOI: 10.1080/21541264.2016.1168507] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/14/2016] [Accepted: 03/14/2016] [Indexed: 10/22/2022]  Open
20
Booth GT, Wang IX, Cheung VG, Lis JT. Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast. Genome Res 2016;26:799-811. [PMID: 27197211 PMCID: PMC4889974 DOI: 10.1101/gr.204578.116] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/19/2016] [Indexed: 12/29/2022]
21
Chávez S, García-Martínez J, Delgado-Ramos L, Pérez-Ortín JE. The importance of controlling mRNA turnover during cell proliferation. Curr Genet 2016;62:701-710. [PMID: 27007479 DOI: 10.1007/s00294-016-0594-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 12/13/2022]
22
Jordán-Pla A, Miguel A, Serna E, Pelechano V, Pérez-Ortín JE. Biotin-Genomic Run-On (Bio-GRO): A High-Resolution Method for the Analysis of Nascent Transcription in Yeast. Methods Mol Biol 2016;1361:125-39. [PMID: 26483020 DOI: 10.1007/978-1-4939-3079-1_8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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