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Items: 42

1.

Publisher Correction: A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage.

Ladds MJGW, van Leeuwen IMM, Drummond CJ, Chu S, Healy AR, Popova G, Pastor Fernández A, Mollick T, Darekar S, Sedimbi SK, Nekulova M, Sachweh MCC, Campbell J, Higgins M, Tuck C, Popa M, Safont MM, Gelebart P, Fandalyuk Z, Thompson AM, Svensson R, Gustavsson AL, Johansson L, Färnegårdh K, Yngve U, Saleh A, Haraldsson M, D'Hollander ACA, Franco M, Zhao Y, Håkansson M, Walse B, Larsson K, Peat EM, Pelechano V, Lunec J, Vojtesek B, Carmena M, Earnshaw WC, McCarthy AR, Westwood NJ, Arsenian-Henriksson M, Lane DP, Bhatia R, McCormack E, Laín S.

Nat Commun. 2018 May 22;9(1):2071. doi: 10.1038/s41467-018-04198-5.

2.

A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage.

Ladds MJGW, van Leeuwen IMM, Drummond CJ, Chu S, Healy AR, Popova G, Pastor Fernández A, Mollick T, Darekar S, Sedimbi SK, Nekulova M, Sachweh MCC, Campbell J, Higgins M, Tuck C, Popa M, Safont MM, Gelebart P, Fandalyuk Z, Thompson AM, Svensson R, Gustavsson AL, Johansson L, Färnegårdh K, Yngve U, Saleh A, Haraldsson M, D'Hollander ACA, Franco M, Zhao Y, Håkansson M, Walse B, Larsson K, Peat EM, Pelechano V, Lunec J, Vojtesek B, Carmena M, Earnshaw WC, McCarthy AR, Westwood NJ, Arsenian-Henriksson M, Lane DP, Bhatia R, McCormack E, Laín S.

Nat Commun. 2018 Mar 16;9(1):1107. doi: 10.1038/s41467-018-03441-3. Erratum in: Nat Commun. 2018 May 22;9(1):2071.

3.

Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis.

Chabbert CD, Adjalley SH, Steinmetz LM, Pelechano V.

Methods Mol Biol. 2018;1689:177-194. doi: 10.1007/978-1-4939-7380-4_16.

PMID:
29027175
4.

From transcriptional complexity to cellular phenotypes: Lessons from yeast.

Pelechano V.

Yeast. 2017 Dec;34(12):475-482. doi: 10.1002/yea.3277. Epub 2017 Oct 11. Review.

PMID:
28866863
5.

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.

6.

eIF5A facilitates translation termination globally and promotes the elongation of many non polyproline-specific tripeptide sequences.

Pelechano V, Alepuz P.

Nucleic Acids Res. 2017 Jul 7;45(12):7326-7338. doi: 10.1093/nar/gkx479.

7.

A global genetic interaction network maps a wiring diagram of cellular function.

Costanzo M, VanderSluis B, Koch EN, Baryshnikova A, Pons C, Tan G, Wang W, Usaj M, Hanchard J, Lee SD, Pelechano V, Styles EB, Billmann M, van Leeuwen J, van Dyk N, Lin ZY, Kuzmin E, Nelson J, Piotrowski JS, Srikumar T, Bahr S, Chen Y, Deshpande R, Kurat CF, Li SC, Li Z, Usaj MM, Okada H, Pascoe N, San Luis BJ, Sharifpoor S, Shuteriqi E, Simpkins SW, Snider J, Suresh HG, Tan Y, Zhu H, Malod-Dognin N, Janjic V, Przulj N, Troyanskaya OG, Stagljar I, Xia T, Ohya Y, Gingras AC, Raught B, Boutros M, Steinmetz LM, Moore CL, Rosebrock AP, Caudy AA, Myers CL, Andrews B, Boone C.

Science. 2016 Sep 23;353(6306). pii: aaf1420.

8.

Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters.

Chen Y, Pai AA, Herudek J, Lubas M, Meola N, Järvelin AI, Andersson R, Pelechano V, Steinmetz LM, Jensen TH, Sandelin A.

Nat Genet. 2016 Sep;48(9):984-94. doi: 10.1038/ng.3616. Epub 2016 Jul 25.

9.

Functional interplay between MSL1 and CDK7 controls RNA polymerase II Ser5 phosphorylation.

Chlamydas S, Holz H, Samata M, Chelmicki T, Georgiev P, Pelechano V, Dündar F, Dasmeh P, Mittler G, Cadete FT, Ramírez F, Conrad T, Wei W, Raja S, Manke T, Luscombe NM, Steinmetz LM, Akhtar A.

Nat Struct Mol Biol. 2016 Jun;23(6):580-9. doi: 10.1038/nsmb.3233. Epub 2016 May 16.

PMID:
27183194
10.

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.

PMID:
27001033
11.

Landscape and Dynamics of Transcription Initiation in the Malaria Parasite Plasmodium falciparum.

Adjalley SH, Chabbert CD, Klaus B, Pelechano V, Steinmetz LM.

Cell Rep. 2016 Mar 15;14(10):2463-75. doi: 10.1016/j.celrep.2016.02.025. Epub 2016 Mar 3.

12.

Genome-wide quantification of 5'-phosphorylated mRNA degradation intermediates for analysis of ribosome dynamics.

Pelechano V, Wei W, Steinmetz LM.

Nat Protoc. 2016 Feb;11(2):359-76. doi: 10.1038/nprot.2016.026. Epub 2016 Jan 28.

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.

14.

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.

PMID:
26483020
15.

Genome-Wide Identification of Alternative Polyadenylation Events Using 3'T-Fill.

Wilkening S, Pelechano V, Steinmetz LM.

Methods Mol Biol. 2016;1358:295-302. doi: 10.1007/978-1-4939-3067-8_18.

PMID:
26463391
16.

The Nuclear PolyA-Binding Protein Nab2p Is Essential for mRNA Production.

Schmid M, Olszewski P, Pelechano V, Gupta I, Steinmetz LM, Jensen TH.

Cell Rep. 2015 Jul 7;12(1):128-139. doi: 10.1016/j.celrep.2015.06.008. Epub 2015 Jun 25.

17.

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics.

Pelechano V, Wei W, Steinmetz LM.

Cell. 2015 Jun 4;161(6):1400-12. doi: 10.1016/j.cell.2015.05.008.

18.

Single-cell polyadenylation site mapping reveals 3' isoform choice variability.

Velten L, Anders S, Pekowska A, Järvelin AI, Huber W, Pelechano V, Steinmetz LM.

Mol Syst Biol. 2015 Jun 3;11(6):812. doi: 10.15252/msb.20156198.

19.

A high-throughput ChIP-Seq for large-scale chromatin studies.

Chabbert CD, Adjalley SH, Klaus B, Fritsch ES, Gupta I, Pelechano V, Steinmetz LM.

Mol Syst Biol. 2015 Jan 12;11(1):777. doi: 10.15252/msb.20145776.

20.

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.

21.

Genome-wide identification of transcript start and end sites by transcript isoform sequencing.

Pelechano V, Wei W, Jakob P, Steinmetz LM.

Nat Protoc. 2014 Jul;9(7):1740-59. doi: 10.1038/nprot.2014.121. Epub 2014 Jun 26.

22.

Association of condensin with chromosomes depends on DNA binding by its HEAT-repeat subunits.

Piazza I, Rutkowska A, Ori A, Walczak M, Metz J, Pelechano V, Beck M, Haering CH.

Nat Struct Mol Biol. 2014 Jun;21(6):560-8. doi: 10.1038/nsmb.2831. Epub 2014 May 18.

PMID:
24837193
23.

Dynamic remodeling of histone modifications in response to osmotic stress in Saccharomyces cerevisiae.

Magraner-Pardo L, Pelechano V, Coloma MD, Tordera V.

BMC Genomics. 2014 Mar 30;15:247. doi: 10.1186/1471-2164-15-247.

24.

Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions.

Gupta I, Clauder-Münster S, Klaus B, Järvelin AI, Aiyar RS, Benes V, Wilkening S, Huber W, Pelechano V, Steinmetz LM.

Mol Syst Biol. 2014 Feb 25;10:719. doi: 10.1002/msb.135068. Print 2014.

25.

Gene regulation by antisense transcription.

Pelechano V, Steinmetz LM.

Nat Rev Genet. 2013 Dec;14(12):880-93. doi: 10.1038/nrg3594. Epub 2013 Nov 12. Review.

PMID:
24217315
26.

Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality.

Ntini E, Järvelin AI, Bornholdt J, Chen Y, Boyd M, Jørgensen M, Andersson R, Hoof I, Schein A, Andersen PR, Andersen PK, Preker P, Valen E, Zhao X, Pelechano V, Steinmetz LM, Sandelin A, Jensen TH.

Nat Struct Mol Biol. 2013 Aug;20(8):923-8. doi: 10.1038/nsmb.2640. Epub 2013 Jul 14.

PMID:
23851456
27.

Extensive transcriptional heterogeneity revealed by isoform profiling.

Pelechano V, Wei W, Steinmetz LM.

Nature. 2013 May 2;497(7447):127-31. doi: 10.1038/nature12121. Epub 2013 Apr 24.

28.

An efficient method for genome-wide polyadenylation site mapping and RNA quantification.

Wilkening S, Pelechano V, Järvelin AI, Tekkedil MM, Anders S, Benes V, Steinmetz LM.

Nucleic Acids Res. 2013 Mar 1;41(5):e65. doi: 10.1093/nar/gks1249. Epub 2013 Jan 7. Erratum in: Nucleic Acids Res. 2013 Jul;41(12):6370.

29.

Genome-wide polyadenylation site mapping.

Pelechano V, Wilkening S, Järvelin AI, Tekkedil MM, Steinmetz LM.

Methods Enzymol. 2012;513:271-96. doi: 10.1016/B978-0-12-391938-0.00012-4.

PMID:
22929774
30.

Rrp6p controls mRNA poly(A) tail length and its decoration with poly(A) binding proteins.

Schmid M, Poulsen MB, Olszewski P, Pelechano V, Saguez C, Gupta I, Steinmetz LM, Moore C, Jensen TH.

Mol Cell. 2012 Jul 27;47(2):267-80. doi: 10.1016/j.molcel.2012.05.005. Epub 2012 Jun 7.

31.

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.

32.

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.

33.

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.

PMID:
21819946
34.

Functional consequences of bidirectional promoters.

Wei W, Pelechano V, Järvelin AI, Steinmetz LM.

Trends Genet. 2011 Jul;27(7):267-76. doi: 10.1016/j.tig.2011.04.002. Epub 2011 May 24. Review.

35.

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.

PMID:
21468983
36.

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.

37.

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.

38.

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.

39.

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.

40.

The transcriptional inhibitor thiolutin blocks mRNA degradation in yeast.

Pelechano V, Pérez-Ortín JE.

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

41.

A genomic study of the inter-ORF distances in Saccharomyces cerevisiae.

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

Yeast. 2006 Jul 15;23(9):689-99.

42.

[Personality and behavior therapy: a method of relations analysis].

Pelechano V.

Arch Neurobiol (Madr). 1972 Nov-Dec;35(6):489-516. Spanish. No abstract available.

PMID:
4680476

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