Publications – pelechanolab

Current preprints

Barcode-free prediction of cell lineages from scRNA-seq datasets. S. Eisele, M. Tarbier, A.A. Dormann,V. Pelechano, D.M. Suter. bioRxiv 2022.09.20.508646; doi: https://doi.org/10.1101/2022.09.20.508646
The association of the RSC remodeler complex with chromatin depends on prefoldin-like Bud27 and determines nucleosome positioning and polyadenylation sites usage in Saccharomyces cerevisiae. Abel Cuevas-Bermudez, Veronica Martinez-Fernandez, Ana I Garrido-Godino, Antonio Jordan Pla, Xenia Penate, Manuel Martin-Exposito, Gabriel Gutierrez, Chhabi Govind,Sebastian Chavez, Vicent Pelechano, Francisco Navarro. bioRxiv 2023.03.21.533665 https://doi.org/10.1101/2023.03.21.533665
Pedro Tomaz da Silva, Yujie Zhang, Evangelos Theodorakis, Laura D. Martens, Vicente A. Yépez, Vicent Pelechano, Julien Gagneur. Cellular energy regulates mRNA translation and degradation in a codon-specific manner. bioRxiv 2023.04.06.535836; doi: https://doi.org/10.1101/2023.04.06.535836

Selected recent research articles

Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs. Tayyab M*, Barrett D*, van Riel G, Liu S, Reinius B, Scharfe C, Griffin P, Steinmetz LM#, Javanmard M#, Pelechano V#. Sci. Adv. 9, eadi4997(2023).
Atlas of mRNA translation and decay for bacteria. Huch, S., Nersisyan, L., et al. Nat Microbiol (2023). https://doi.org/10.1038/s41564-023-01393-z
Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation. Li, B., Zeis, P., Zhang, Y. et al. Nat Commun 14, 910 (2023).
Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events. Allen, G., Weiss, B., Panasenko, O.O. et al. Genome Biol 24, 30 (2023).
A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation resulting in pro-metastatic NF-κB signaling. Altea-Manzano P, Doglioni G, Liu Y, Cuadros AM, Nolan E, Fernández-García J, Wu Q, Planque M, Laue KJ, Cidre-Aranaz F, Liu XZ, Marin-Bejar O, Van Elsen J, Vermeire I, Broekaert D, Demeyer S, Spotbeen X, Idkowiak J, Montagne A, Demicco M, Alkan HF, Rabas N, Riera-Domingo C, Richard F, Geukens T, De Schepper M, Leduc S, Hatse S, Lambrechts Y, Kay EJ, Lilla S, Alekseenko A, Geldhof V, Boeckx B, de la Calle Arregui C, Floris G, Swinnen JV, Marine JC, Lambrechts D, Pelechano V, Mazzone M, Zanivan S, Cools J, Wildiers H, Baud V, Grünewald TGP, Ben-David U, Desmedt C, Malanchi I, Fendt SM. Nat Cancer. 2023 Feb 2. doi: 10.1038/s43018-023-00513-2.
OPUSeq simplifies detection of low-frequency DNA variants and uncovers fragmentase-associated artifacts. Alekseenko A, Wang J, Barrett D, Pelechano V. NAR Genom Bioinform. 2022 Jun 27;4(2):lqac048.
Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics. Crowe-McAuliffe C*, Murina V*, Turnbull KJ, Huch S, Kasari M, Takada H, Nersisyan L, Sundsfjord A, Hegstad K, Atkinson GC, Pelechano V, Wilson DN#, Hauryliuk V#. Nature communications 2022 13;1 1860-
Not4 and Not5 modulate translation elongation by Rps7A ubiquitination, Rli1 moonlighting, and condensates that exclude eIF5A. Allen GE*, Panasenko OO*, Villanyi Z, Zagatti M, Weiss B, Pagliazzo L, Huch S, Polte C, Zahoran S, Hughes CS, Pelechano V, Ignatova Z, Collart MA. Cell Rep. 2021 Aug 31;36(9):109633. doi: 10.1016/j.celrep.2021.109633.
Sample-to-answer COVID-19 nucleic acid testing using a low-cost centrifugal microfluidic platform with bead-based signal enhancement and smartphone read-out. Soares RRG, Akhtar AS, Pinto IF, Lapins N, Barrett D, Sandh G, Yin X, Pelechano V, Russom A. Lab Chip. 2021 Jun 11. doi: 10.1039/d1lc00266j.
High-throughput 5′P sequencing enables the study of degradation-associated ribosome stalls. Yujie Zhang, Vicent Pelechano. Cell Reports Methods, Available online 2 April 2021, Pages 100001 https://doi.org/10.1016/j.crmeth.2021.100001
Application of high-throughput 5′P sequencing for the study of co-translational mRNA decay. Yujie Zhang, Vicent Pelechano. STAR Protocols, Volume 2, Issue 2, 18 June 2021, Pages 100447 https://doi.org/10.1016/j.xpro.2021.100447
Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples. Kubik S, Marques AC, Xing X, Silvery J, Bertelli C, De Maio F, Pournaras S, Burr T, Duffourd Y, Siemens H, Alloui C, Song L, Wenger Y, Saitta A, Macheret M, Smith EW, Menu P, Brayer M, Steinmetz LM, Si-Mohammed A, Chuisseu J, Stevens R, Constantoulakis P, Sali M, Greub G, Tiemann C, Pelechano V, Willig A, Xu Z. Clin Microbiol Infect. 2021 Apr 1:S1198-743X(21)00164-6. doi: 10.1016/j.cmi.2021.03.029. Epub ahead of print. PMID: 33813118.

Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples. Alekseenko A*, Barrett D*, Pareja-Sanchez Y*, Howard RJ, Strandback E, Ampah-Korsah H, Rovšnik U, Zuniga-Veliz S, Klenov A, Malloo J, Ye S, Liu X, Reinius B, Elsässer SJ, Nyman T, Sandh G, Yin X, Pelechano V. Sci Rep. 2021 Jan 19;11(1):1820. doi: 10.1038/s41598-020-80352-8.
High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts. Chia M, Li C, Marques S, Pelechano V, Luscombe NM, van Werven FJ. Genome Biol. 2021 Jan 14;22(1):34. doi: 10.1186/s13059-020-02245-3
A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae Olga Rodríguez-Galán, Juan J García-Gómez, Iván V Rosado, Wu Wei, Alfonso Méndez-Godoy, Benjamin Pillet, Alisa Alekseenko, Lars M Steinmetz, Vicent Pelechano, Dieter Kressler, Jesús de la Cruz, , Nucleic Acids Research, , gkaa1200, https://doi.org/10.1093/nar/gkaa1200
Improved computational analysis of ribosome dynamics from 5′P degradome data using fivepseq. Lilit Nersisyan, Maria Ropat & Vicent Pelechano. NAR Genomics and Bioinformatics, Volume 2, Issue 4, December 2020, lqaa099, https://doi.org/10.1093/nargab/lqaa099
Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast. A.I. Garrido-Godino, I. Gupta, F Gutiérrez-Santiago, A.B. Martínez-Padilla, A. Alekseenko, L.M. Steinmetz, J.E. Pérez-Ortín, V. Pelechano & F. Navarro. RNA Biology, 2020 DOI: 10.1080/15476286.2020.1839229
TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes. Wang J, Li B, Marques S, Steinmetz LM, Wei W, Pelechano V. Nucleic Acids Res. 2020;gkaa691. doi:10.1093/nar/gkaa691
Transcriptional mutagenesis dramatically alters genome-wide p53 transactivation landscape.Liang S, Ezerskyte M, Wang J, Pelechano V, Dreij K. Sci Rep. 2020;10(1):13513. Published 2020 Aug 11. doi:10.1038/s41598-020-70412-4
The RNA exosome shapes the expression of key protein-coding genes. Wu M, Karadoulama E, Lloret-Llinares M, Rouviere JO, Vaagensø CS, Moravec M, Li B, Wang J, Wu G, Gockert M, Pelechano V, Jensen TH, Sandelin A.
Nucleic Acids Res. 2020 Jul 25:gkaa594. doi: 10.1093/nar/gkaa594.
Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis. Thomas QA, Ard R, Liu J, Li B, Wang J,Pelechano V, Marquardt S. Nat Commun. 2020 May 22;11(1):2589. doi: 10.1038/s41467-020-16390-7.
Rapid detection of COVID-19 coronavirus using a reverse transcriptional loop-mediated isothermal amplification (RT-LAMP) diagnostic platform. Lin Yu, Shanshan Wu, Xiaowen Hao, Xue Dong, Lingling Mao, Vicent Pelechano, Wei-Hua Chen, Xiushan Yin. Clinical Chemistry, hvaa102, https://doi.org/10.1093/clinchem/hvaa102
Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast. Wei W, Hennig BP, Wang J, Zhang Y, Ilaria Piazza, Pareja Sanchez Y, Chabbert CD, Adjalley SH, Steinmetz LM, Pelechano V. Genome Res. 2019 Nov 18. doi:10.1101/gr.243378.118
Transcription-driven Chromatin repression of Intragenic transcription start sites. Nielsen M, Ard R, Leng X, Ivanov M, Kindgren P, Pelechano V, Marquardt S. PLoS Genet. 2019 Feb 1;15(2):e1007969. doi: 10.1371/journal.pgen.1007969.
Tumor suppressor PNRC1 blocks rRNA maturation by recruiting the decapping complex to the nucleolus. Gaviraghi M, Vivori C, Pareja Sanchez Y, Invernizzi F, Cattaneo A, Santoliquido BM, Frenquelli M, Segalla S, Bachi A, Doglioni C, Pelechano V, Cittaro D, Tonon G. EMBO J. 2018 Oct 29. pii: e99179. doi: 10.15252/embj.201899179
The Lsm1-7/Pat1 complex binds to stress-activated mRNAs and modulates the response to hyperosmotic shock. Garre E, Pelechano V, Sánchez Del Pino M, Alepuz P, Sunnerhagen P. PLoS Genet. 2018 Jul 30;14(7):e1007563. doi: 10.1371/journal.pgen.1007563.
From transcriptional complexity to cellular phenotypes: lessons from yeast. Pelechano V. Yeast. 2017 Sep 3. doi:10.1002/yea.3277
eIF5A facilitates translation termination globally and promotes the elongation of many non polyproline-specific tripeptide sequences. Pelechano V^# and Alepuz P^#. Nucleic Acids Res. 2017 May 26. doi: 10.1093/nar/gkx479.
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.
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.
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.
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
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.
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.
Widespread co-translational RNA decay reveals ribosome dynamics. Pelechano V*, Wei W*, and Steinmetz LM. Cell. 2015 Jun 4;161(6):1400-12.
Single cell polyadenylation site mapping reveals isoform choice variability. Velten L, Anders S, Pekowska A, Järvelin AI, Huber W, Pelechano V, and Steinmetz LM. Mol Syst Biol. 2015 Jun 3;11(6):812.
High-throughput ChIP-Seq for large-scale chromatin studies. Chabbert CD*, Adjalley SH*, Klaus B, Fritsch ES, Gupta I, Pelechano V^#, and Steinmetz LM^#. Mol Syst Biol. 2015 Jan 12;11(1):777.
Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle. Jordan-Pla A, Gupta I, de Miguel-Jiménez L, Steinmetz LM, Chavez S^#, Pelechano V^#, and Perez-Ortin JE^#. Nucleic Acids Res. 2015 Jan 30;43(2):787-802.
Genome-wide identification of transcript start and end sites by Transcript Isoform Sequencing, TIF-Seq. Pelechano V, Wei W, Jakob P, and Steinmetz LM. Nat. Protocols. 2014 Jun;9(7):1740-59.
Alternative polyadenylation diversifies post-transcriptional regulation through selective RNA-protein interactions. Gupta I, Clauder-Münster S, Klaus B, Järvelin AI, Aiyar RS, Benes V, Huber W, Pelechano V^# and Steinmetz LM^#. Mol Syst Biol. 2014 Feb 25;10(2):719.
Extensive transcriptional heterogeneity revealed by isoform profiling. Pelechano V*, Wei W*, Steinmetz LM. Nature. 2013 May 2;497(7447):127-31 (*co-first authors).
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
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.
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. Epub 2009 Aug 21.

Selected review articles

Gene regulation by antisense transcription. Pelechano V. and Steinmetz LM. Nat Rev Genetics. 2013. Dec;14(12):880-93. Epub 2013 Nov 12.
Functional consequences of bidirectional promoters. Wei W*, Pelechano V*, Järvelin AI*, Steinmetz LM. Trends Genet. 2011 Jul;27(7):267-76. Epub 2011 May 24.

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