Vicente Pelechano Group

Transcriptional basis of non-genetic cellular heterogeneity

One of the biggest challenges in biology is to understand how apparently identical cells respond differently to the same stimulus. In some cases this differential behaviour can be explained by alterations of their genetic material, however in other cases identical (clonal) cells can also display phenotypically heterogeneous responses. We use state of the art genomic technologies to study the regulatory mechanism leading to the appearance of divergent gene expression programs in clonal populations of cells.

In the last few years, the biomedical field has suffered a revolution thanks to the development of the massive parallel sequencing technologies. Now we can obtain the complete genetic information of a person and analyse how this information is being used in a few days and with a limited cost. This technologies makes possible a kind of research that was unthinkable a few years back. In the past we have developed a diversity of novel genome-wide approaches to study eukaryotic gene expression using both budding yeast and mammalian cells. By simultaneously sequencing both the 5’ and 3’ ends of each RNA molecule (TIF-Seq), we showed that the complexity of overlapping transcript isoforms had been greatly underestimated. More recently, we have shown how the existence of widespread co-translational mRNA degradation allows to study ribosome dynamics by sequencing mRNA degradation intermediates (5P-Seq). In addition, we have also developed new approaches for the study of other relevant biological questions, such as chromatin structure, single-cell transcriptomics, RNA polymerase elongation or isoform-specific interactions with RNA binding proteins.

Our group, combining experimental and computational work, aims to develop and apply novel genome-wide techniques to study eukaryotic transcription to address fundamental biological questions with medical implications. We are specially interested in the case of drug-tolerant cancer persister cells that, although genetically sensitive to a drug, do not respond to it. To deliver an integrated view of the mechanisms driving their appearance, as well as to refine our knowledge of the basic process of gene expression, we study both budding yeast and human cell lines at three levels of the gene expression process: epigenetic status, transcript isoform usage and post-transcriptional mRNA regulation

Our group is affiliated to both MTC and the Science for Life Laboratory ( where our lab is located. Group homepage/external homepage:

Selected Publications

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 B, et al
EMBO J. 2018 Oct;():

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;14(7):e1007563

A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage.
Ladds M, van Leeuwen I, Drummond C, Chu S, Healy A, Popova G, et al
Nat Commun 2018 03;9(1):1107

Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis.
Chabbert C, Adjalley S, Steinmetz L, Pelechano V
Methods Mol. Biol. 2018 ;1689():177-194

From transcriptional complexity to cellular phenotypes: Lessons from yeast.
Pelechano V
Yeast 2017 12;34(12):475-482

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, et al
Nucleic Acids Res. 2017 Sep;45(16):9302-9318

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;45(12):7326-7338

A global genetic interaction network maps a wiring diagram of cellular function
M. Costanzo, B. VanderSluis, E. N. Koch, A. Baryshnikova, C. Pons, G. Tan, W. Wang, M. Usaj, J. Hanchard, S. D. Lee, V. Pelechano, E. B. et al
Science, 2016; 353 (6306): aaf1420 DOI: 10.1126/science.aaf1420

Functional interplay between MSL1 and CDK7 controls RNA polymerase II Ser5 phosphorylation.
Chlamydas S, Holz H, Samata M, Chelmicki T, Georgiev P, Pelechano V, et al
Nat. Struct. Mol. Biol. 2016 06;23(6):580-9

Genome-wide quantification of 5'-phosphorylated mRNA degradation intermediates for analysis of ribosome dynamics.
Pelechano V, Wei W, Steinmetz L
Nat Protoc 2016 Feb;11(2):359-76

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics.
Pelechano V, Wei W, Steinmetz L
Cell 2015 Jun;161(6):1400-12

Single-cell polyadenylation site mapping reveals 3' isoform choice variability.
Velten L, Anders S, Pekowska A, Järvelin A, Huber W, Pelechano V, et al
Mol. Syst. Biol. 2015 Jun;11(6):812

A high-throughput ChIP-Seq for large-scale chromatin studies.
Chabbert C, Adjalley S, Klaus B, Fritsch E, Gupta I, Pelechano V, et al
Mol. Syst. Biol. 2015 Jan;11(1):777

Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle.
Jordán-Pla A, Gupta I, de Miguel-Jiménez L, Steinmetz L, Chávez S, Pelechano V, et al
Nucleic Acids Res. 2015 Jan;43(2):787-802

Genome-wide identification of transcript start and end sites by transcript isoform sequencing.
Pelechano V, Wei W, Jakob P, Steinmetz L
Nat Protoc 2014 Jul;9(7):1740-59

Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions.
Gupta I, Clauder-Münster S, Klaus B, Järvelin A, Aiyar R, Benes V, et al
Mol. Syst. Biol. 2014 ;10():719

Extensive transcriptional heterogeneity revealed by isoform profiling.
Pelechano V, Wei W, Steinmetz L
Nature 2013 May;497(7447):127-31

Group Members

Alisa AlekseenkoPhD student, Graduate Student

Susanne HuchPostdoc

Bingnan LiPostdoc

Sueli MarquesSenior lab manager

Lilit NersisyanPostdoc

Yerma Pareja SanchezPhD student, Graduate Student

Vicente Pelechano GarciaAssistant professor

Inka SchröterAssociated

Jingwen WangPostdoc

Xiushan YinSenior research specialist

Yujie ZhangGraduate Student

Tumour Biology