Events

Transposable element-driven origin of new transcriptional enhancer

While RNA transposons can act as important developmental enhancers in mammals, it is unclear if this phenomenon can be generalized to other vertebrates. By examining the transcriptome and epigenome of osteoblastic cells from the amphibian Xenopus tropicalis, we identify thousands of active and poised enhancers, half of which are occupied by DNA transposon-derived MITEs. We show that bursts of MITEs have repeatedly bombarded the Xenopus genomes with nucleosome-free CpG islands, directly contributing to the emergence of de novo enhancers.

Seminar of Daniel Rico from the Institute of Cellular Medicine, Newcastle University (UK).

Title: Network approaches to understand chromatin interactions and gene regulation

Place: Campus of Luminy. Seminar room TPR2, Bloc 5. November 20th @ 11h00

Summary

Our research focuses in understanding how to read the genome so we can identify the instructions for building different cell types. We develop and apply new computational methods to integrate genomic, epigenomic and transcriptomic data to decode these instructions. We collaborate with colleagues at Newcastle University and the Great North Children Hospital to understand which mutations can cause “typos” in these instructions, leading to diseases. We are particularly interested in the immune system, where we are investigating how chromatin contributes to sex-specific immune responses. In addition, we have exciting collaborations where we are trying to understand the functional role of chromatin dynamics during mitosis and the interplay of chromatin and genomic translocations in leukemias.

Website: https://www.ncl.ac.uk/icm/people/profile/danielrico

Selected publications

* Rigau M, Juan D, Valencia A, Rico D. Widespread population variability of intron size in evolutionary old genes: implications for gene expression variability. BioRxiv 2017, Epub ahead of print.

* Pancaldi V, Carrillo-de-Santa-Pau E, Javierre BM, Juan D, Fraser P, Valencia A, Rico D. Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity. Genome Biology 2016, 17, 152.

* Carrillo-de-Santa-Pau E, Juan D, Pancaldi V, Were F, Martin-Subero I, Rico D, Valencia A, The BLUEPRINT Consortium. Automatic identification of informative regions with epigenomic changes associated to hematopoiesis. Nucleic Acids Research 2017, 45(16), 9244-9259.