Research

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.

Figure 1: Extensive variation in transcript start and end sites revealed by TIF-Seq

Figure 1: Extensive variation in transcript start and end sites revealed by TIF-Seq, a novel technique for transcript isoform profiling (Pelechano et al., Nature 2013)

5PSeq

Figure 2: Widespread co-translational mRNA decay produces an in vivo ribosomal footprint and reveals ribosome dynamics (Pelechano et al. 2015 Cell)

BarChip

Figure 3: Bar-ChIP provides a rapid and accurate genome‐wide profiling of epigenetic marks by multiplex immuno‐precipitation of barcoded chromatin samples (Chabbert, Adjalley et al MSB 2015).

Introduction to our research