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The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins.

Blasco-Moreno B, de Campos-Mata L, Böttcher R, García-Martínez J, Jungfleisch J, Nedialkova DD, Chattopadhyay S, Gas ME, Oliva B, Pérez-Ortín JE, Leidel SA, Choder M, Díez J.

Nat Commun. 2019 Mar 21;10(1):1298. doi: 10.1038/s41467-019-09199-6.


Measuring RNA polymerase activity genome-wide with high-resolution run-on-based methods.

Jordán-Pla A, Pérez-Martínez ME, Pérez-Ortín JE.

Methods. 2019 Feb 2. pii: S1046-2023(18)30295-0. doi: 10.1016/j.ymeth.2019.01.017. [Epub ahead of print] Review.


A role for Mog1 in H2Bub1 and H3K4me3 regulation affecting RNAPII transcription and mRNA export.

Oliete-Calvo P, Serrano-Quílez J, Nuño-Cabanes C, Pérez-Martínez ME, Soares LM, Dichtl B, Buratowski S, Pérez-Ortín JE, Rodríguez-Navarro S.

EMBO Rep. 2018 Nov;19(11). pii: e45992. doi: 10.15252/embr.201845992. Epub 2018 Sep 24.


The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally.

García-Molinero V, García-Martínez J, Reja R, Furió-Tarí P, Antúnez O, Vinayachandran V, Conesa A, Pugh BF, Pérez-Ortín JE, Rodríguez-Navarro S.

Epigenetics Chromatin. 2018 Mar 29;11(1):13. doi: 10.1186/s13072-018-0184-2.


Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning.

Gutiérrez G, Millán-Zambrano G, Medina DA, Jordán-Pla A, Pérez-Ortín JE, Peñate X, Chávez S.

Epigenetics Chromatin. 2017 Dec 7;10(1):58. doi: 10.1186/s13072-017-0165-x.


Asymmetric cell division requires specific mechanisms for adjusting global transcription.

Mena A, Medina DA, García-Martínez J, Begley V, Singh A, Chávez S, Muñoz-Centeno MC, Pérez-Ortín JE.

Nucleic Acids Res. 2017 Dec 1;45(21):12401-12412. doi: 10.1093/nar/gkx974.


The ribosome assembly gene network is controlled by the feedback regulation of transcription elongation.

Gómez-Herreros F, Margaritis T, Rodríguez-Galán O, Pelechano V, Begley V, Millán-Zambrano G, Morillo-Huesca M, Muñoz-Centeno MC, Pérez-Ortín JE, de la Cruz J, Holstege FCP, Chávez S.

Nucleic Acids Res. 2017 Sep 19;45(16):9302-9318. doi: 10.1093/nar/gkx529.


Modulation of protein synthesis and degradation maintains proteostasis during yeast growth at different temperatures.

Benet M, Miguel A, Carrasco F, Li T, Planells J, Alepuz P, Tordera V, Pérez-Ortín JE.

Biochim Biophys Acta Gene Regul Mech. 2017 Jul;1860(7):794-802. doi: 10.1016/j.bbagrm.2017.04.003. Epub 2017 Apr 29.


Corrigendum to "External conditions inversely change the RNA polymerase II elongation rate and density in yeast" [Biochim. Biophys. Acta 1829/11 (2013) 1248-1255].

Miguel A, Montón F, Li T, Gómez-Herreros F, Chávez S, Alepuz P, Pérez-Ortín JE.

Biochim Biophys Acta Gene Regul Mech. 2017 Feb;1860(2):289. doi: 10.1016/j.bbagrm.2016.11.003. Epub 2016 Dec 24. No abstract available.


Growth rate controls mRNA turnover in steady and non-steady states.

García-Martínez J, Troulé K, Chávez S, Pérez-Ortín JE.

RNA Biol. 2016 Dec;13(12):1175-1181. Epub 2016 Sep 20.


The importance of controlling mRNA turnover during cell proliferation.

Chávez S, García-Martínez J, Delgado-Ramos L, Pérez-Ortín JE.

Curr Genet. 2016 Nov;62(4):701-710. Epub 2016 Mar 23. Review.


Rpb1 foot mutations demonstrate a major role of Rpb4 in mRNA stability during stress situations in yeast.

Garrido-Godino AI, García-López MC, García-Martínez J, Pelechano V, Medina DA, Pérez-Ortín JE, Navarro F.

Biochim Biophys Acta. 2016 May;1859(5):731-43. doi: 10.1016/j.bbagrm.2016.03.008. Epub 2016 Mar 18.


The mRNA cap-binding protein Cbc1 is required for high and timely expression of genes by promoting the accumulation of gene-specific activators at promoters.

Li T, De Clercq N, Medina DA, Garre E, Sunnerhagen P, Pérez-Ortín JE, Alepuz P.

Biochim Biophys Acta. 2016 Feb;1859(2):405-19. doi: 10.1016/j.bbagrm.2016.01.002. Epub 2016 Jan 13.


The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons.

García-Martínez J, Delgado-Ramos L, Ayala G, Pelechano V, Medina DA, Carrasco F, González R, Andrés-León E, Steinmetz L, Warringer J, Chávez S, Pérez-Ortín JE.

Nucleic Acids Res. 2016 May 5;44(8):3643-58. doi: 10.1093/nar/gkv1512. Epub 2015 Dec 29.


Biotin-Genomic Run-On (Bio-GRO): A High-Resolution Method for the Analysis of Nascent Transcription in Yeast.

Jordán-Pla A, Miguel A, Serna E, Pelechano V, Pérez-Ortín JE.

Methods Mol Biol. 2016;1361:125-39. doi: 10.1007/978-1-4939-3079-1_8.


A web application for the unspecific detection of differentially expressed DNA regions in strand-specific expression data.

Juanes JM, Miguel A, Morales LJ, Pérez-Ortín JE, Arnau V.

Bioinformatics. 2015 Oct 1;31(19):3228-30. doi: 10.1093/bioinformatics/btv343. Epub 2015 Jun 2.


Impact of high pH stress on yeast gene expression: A comprehensive analysis of mRNA turnover during stress responses.

Canadell D, García-Martínez J, Alepuz P, Pérez-Ortín JE, Ariño J.

Biochim Biophys Acta. 2015 Jun;1849(6):653-64. doi: 10.1016/j.bbagrm.2015.04.001. Epub 2015 Apr 18.


Comparative transcriptomic analysis reveals similarities and dissimilarities in Saccharomyces cerevisiae wine strains response to nitrogen availability.

Barbosa C, García-Martínez J, Pérez-Ortín JE, Mendes-Ferreira A.

PLoS One. 2015 Apr 17;10(4):e0122709. doi: 10.1371/journal.pone.0122709. eCollection 2015.


Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle.

Jordán-Pla A, Gupta I, de Miguel-Jiménez L, Steinmetz LM, Chávez S, Pelechano V, Pérez-Ortín JE.

Nucleic Acids Res. 2015 Jan;43(2):787-802. doi: 10.1093/nar/gku1349. Epub 2014 Dec 29.


Cytoplasmic 5'-3' exonuclease Xrn1p is also a genome-wide transcription factor in yeast.

Medina DA, Jordán-Pla A, Millán-Zambrano G, Chávez S, Choder M, Pérez-Ortín JE.

Front Genet. 2014 Feb 6;5:1. doi: 10.3389/fgene.2014.00001. eCollection 2014.


What do you mean by transcription rate?: the conceptual difference between nascent transcription rate and mRNA synthesis rate is essential for the proper understanding of transcriptomic analyses.

Pérez-Ortín JE, Medina DA, Chávez S, Moreno J.

Bioessays. 2013 Dec;35(12):1056-62. doi: 10.1002/bies.201300057. Epub 2013 Sep 17.


External conditions inversely change the RNA polymerase II elongation rate and density in yeast.

Miguel A, Montón F, Li T, Gómez-Herreros F, Chávez S, Alepuz P, Pérez-Ortín JE.

Biochim Biophys Acta. 2013 Nov;1829(11):1248-55. doi: 10.1016/j.bbagrm.2013.09.008. Epub 2013 Oct 6. Erratum in: Biochim Biophys Acta. 2017 Feb;1860(2):289.


Topoisomerase II regulates yeast genes with singular chromatin architectures.

Nikolaou C, Bermúdez I, Manichanh C, García-Martinez J, Guigó R, Pérez-Ortín JE, Roca J.

Nucleic Acids Res. 2013 Nov;41(20):9243-56. doi: 10.1093/nar/gkt707. Epub 2013 Aug 9.


Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis.

Haimovich G, Medina DA, Causse SZ, Garber M, Millán-Zambrano G, Barkai O, Chávez S, Pérez-Ortín JE, Darzacq X, Choder M.

Cell. 2013 May 23;153(5):1000-11. doi: 10.1016/j.cell.2013.05.012.


Nonsense-mediated mRNA decay controls the changes in yeast ribosomal protein pre-mRNAs levels upon osmotic stress.

Garre E, Romero-Santacreu L, Barneo-Muñoz M, Miguel A, Pérez-Ortín JE, Alepuz P.

PLoS One. 2013 Apr 19;8(4):e61240. doi: 10.1371/journal.pone.0061240. Print 2013.


Eukaryotic mRNA decay: methodologies, pathways, and links to other stages of gene expression.

Pérez-Ortín JE, Alepuz P, Chávez S, Choder M.

J Mol Biol. 2013 Oct 23;425(20):3750-75. doi: 10.1016/j.jmb.2013.02.029. Epub 2013 Mar 4. Review.


mRNAStab--a web application for mRNA stability analysis.

Alic A, Pérez-Ortín JE, Moreno J, Arnau V.

Bioinformatics. 2013 Mar 15;29(6):813-4. doi: 10.1093/bioinformatics/btt040. Epub 2013 Jan 25.


The relative importance of transcription rate, cryptic transcription and mRNA stability on shaping stress responses in yeast.

García-Martínez J, Ayala G, Pelechano V, Chávez S, Herrero E, Pérez-Ortín JE.

Transcription. 2012 Jan-Feb;3(1):39-44. doi: 10.4161/trns.3.1.19416.


Genome-wide studies of mRNA synthesis and degradation in eukaryotes.

Pérez-Ortín JE, de Miguel-Jiménez L, Chávez S.

Biochim Biophys Acta. 2012 Jun;1819(6):604-15. doi: 10.1016/j.bbagrm.2011.12.002. Epub 2011 Dec 11. Review.


The conserved foot domain of RNA pol II associates with proteins involved in transcriptional initiation and/or early elongation.

García-López MC, Pelechano V, Mirón-García MC, Garrido-Godino AI, García A, Calvo O, Werner M, Pérez-Ortín JE, Navarro F.

Genetics. 2011 Dec;189(4):1235-48. doi: 10.1534/genetics.111.133215. Epub 2011 Sep 27.


A genomic view of mRNA turnover in yeast.

Pérez-Ortín JE, Jordán-Pla A, Pelechano V.

C R Biol. 2011 Aug-Sep;334(8-9):647-54. doi: 10.1016/j.crvi.2011.05.013. Epub 2011 Jul 5. Review.


Genomic-wide methods to evaluate transcription rates in yeast.

García-Martínez J, Pelechano V, Pérez-Ortín JE.

Methods Mol Biol. 2011;734:25-44. doi: 10.1007/978-1-61779-086-7_2.


Global estimation of mRNA stability in yeast.

Marín-Navarro J, Jauhiainen A, Moreno J, Alepuz P, Pérez-Ortín JE, Sunnerhagen P.

Methods Mol Biol. 2011;734:3-23. doi: 10.1007/978-1-61779-086-7_1.


Heat shock response in yeast involves changes in both transcription rates and mRNA stabilities.

Castells-Roca L, García-Martínez J, Moreno J, Herrero E, Bellí G, Pérez-Ortín JE.

PLoS One. 2011 Feb 25;6(2):e17272. doi: 10.1371/journal.pone.0017272.


Genomic insights into the different layers of gene regulation in yeast.

Pérez-Ortín JE, Medina DA, Jordán-Pla A.

Genet Res Int. 2011;2011:989303. doi: 10.4061/2011/989303. Epub 2011 Nov 22.


A complete set of nascent transcription rates for yeast genes.

Pelechano V, Chávez S, Pérez-Ortín JE.

PLoS One. 2010 Nov 16;5(11):e15442. doi: 10.1371/journal.pone.0015442. Erratum in: PLoS One. 2014;9(12):e115560.


A method for genome-wide analysis of DNA helical tension by means of psoralen-DNA photobinding.

Bermúdez I, García-Martínez J, Pérez-Ortín JE, Roca J.

Nucleic Acids Res. 2010 Oct;38(19):e182. doi: 10.1093/nar/gkq687. Epub 2010 Aug 4.


The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors.

Rodríguez-Gil A, García-Martínez J, Pelechano V, Muñoz-Centeno Mde L, Geli V, Pérez-Ortín JE, Chávez S.

Nucleic Acids Res. 2010 Aug;38(14):4651-64. doi: 10.1093/nar/gkq215. Epub 2010 Apr 12.


There is a steady-state transcriptome in exponentially growing yeast cells.

Pelechano V, Pérez-Ortín JE.

Yeast. 2010 Jul;27(7):413-22. doi: 10.1002/yea.1768.


Regulon-specific control of transcription elongation across the yeast genome.

Pelechano V, Jimeno-González S, Rodríguez-Gil A, García-Martínez J, Pérez-Ortín JE, Chávez S.

PLoS Genet. 2009 Aug;5(8):e1000614. doi: 10.1371/journal.pgen.1000614. Epub 2009 Aug 21.


Specific and global regulation of mRNA stability during osmotic stress in Saccharomyces cerevisiae.

Romero-Santacreu L, Moreno J, Pérez-Ortín JE, Alepuz P.

RNA. 2009 Jun;15(6):1110-20. doi: 10.1261/rna.1435709. Epub 2009 Apr 15.


Chimeric genomes of natural hybrids of Saccharomyces cerevisiae and Saccharomyces kudriavzevii.

Belloch C, Pérez-Torrado R, González SS, Pérez-Ortín JE, García-Martínez J, Querol A, Barrio E.

Appl Environ Microbiol. 2009 Apr;75(8):2534-44. doi: 10.1128/AEM.02282-08. Epub 2009 Feb 27.


The inner nuclear membrane protein Src1 associates with subtelomeric genes and alters their regulated gene expression.

Grund SE, Fischer T, Cabal GG, Antúnez O, Pérez-Ortín JE, Hurt E.

J Cell Biol. 2008 Sep 8;182(5):897-910. doi: 10.1083/jcb.200803098. Epub 2008 Sep 1.


Whole genome analysis of a wine yeast strain.

Hauser NC, Fellenberg K, Gil R, Bastuck S, Hoheisel JD, Pérez-Ortín JE.

Comp Funct Genomics. 2001;2(2):69-79. doi: 10.1002/cfg.73.


Mitochondrial inheritance and fermentative : oxidative balance in hybrids between Saccharomyces cerevisiae and Saccharomyces uvarum.

Solieri L, Antúnez O, Pérez-Ortín JE, Barrio E, Giudici P.

Yeast. 2008 Jul;25(7):485-500. doi: 10.1002/yea.1600.


Comprehensive transcriptional analysis of the oxidative response in yeast.

Molina-Navarro MM, Castells-Roca L, Bellí G, García-Martínez J, Marín-Navarro J, Moreno J, Pérez-Ortín JE, Herrero E.

J Biol Chem. 2008 Jun 27;283(26):17908-18. doi: 10.1074/jbc.M800295200. Epub 2008 Apr 17.


Genomics of mRNA turnover.

Pérez-Ortín JE.

Brief Funct Genomic Proteomic. 2007 Dec;6(4):282-91. doi: 10.1093/bfgp/elm029. Epub 2008 Jan 22. Review.


Common gene expression strategies revealed by genome-wide analysis in yeast.

García-Martínez J, González-Candelas F, Pérez-Ortín JE.

Genome Biol. 2007;8(10):R222.


The transcriptional inhibitor thiolutin blocks mRNA degradation in yeast.

Pelechano V, Pérez-Ortín JE.

Yeast. 2008 Feb;25(2):85-92.


Saccharomyces cerevisiae signature genes for predicting nitrogen deficiency during alcoholic fermentation.

Mendes-Ferreira A, del Olmo M, García-Martínez J, Jiménez-Martí E, Leão C, Mendes-Faia A, Pérez-Ortín JE.

Appl Environ Microbiol. 2007 Aug;73(16):5363-9. Epub 2007 Jun 29.

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