Developmental Epigenomics

“We aim to understand how cells use their genetic information throughout development, and how these regulatory mechanisms are affected in disease.”

The interest of our laboratory is to understand how the information encoded in the DNA is accurately used by cells to perform the physiological functions that are required for each organism during the different phases of their life cycles. The access to this information is tightly regulated by an intricate system of different regulatory layers involving, for example, the recognition of specific sequences in the DNA by transcription factors, the positioning of nucleosomes and associated histone marks at key locations in the DNA, or the higher-order accessibility and three-dimensional positioning of the chromatin in the nucleus, among others. These determine, for instance, which genes need to be turned on or off at different developmental times, and in response to infectious agents or changes in the environment. The disruption or break down of these regulatory mechanisms are responsible of many developmental disorders and diseases such as cancer. We aim to uncover the functioning of some of these mechanisms, which, in turn, will help us understand the cause of the associated diseases.

To do so, we employ high-throughput genomic techniques such as single-cell multiomics, RNA-seq, ChIP-seq, or Hi-C, that examine not only individual genes, but the genome as a whole, allowing us to measure changes in regulatory mechanisms at a global scale even for individual cells. The computational analysis of these datasets allows us to test hypotheses and draw conclusions from observing specific patterns in the data. Have a look at this video to get an idea of how we do these experiments:

Juanma Vaquerizas holds an Academy of Medical Sciences Professorship.

Selected Publications

Chang NC, Rovira Q, Wells JN, Feschotte C, Vaquerizas JM. Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression. Genome Res. 2022 Jan 5:gr.275655.121. doi: 10.1101/gr.275655.121.

Ing-Simmons E, Rigau M, Vaquerizas JM. Curr Opin Cell Biol. 2022 Emerging mechanisms and dynamics of three-dimensional genome organisation at zygotic genome activation. Jan 19;74:37-46. doi: 10.1016/

Ing-Simmons E, Vaid R, Bing XY, Levine M, Mannervik M, Vaquerizas JM. (2021). Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning. Nature Genetics 53(4):487-499. doi: 10.1038/s41588-021-00799-x. PMID: 33795866; PMCID: PMC8035076.

This research featured on the front cover: 

Kruse K, Hug CB, Vaquerizas JM. (2020). FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data. Genome Biology 21(1):303. doi: 10.1186/s13059-020-02215-9. PMID: 33334380; PMCID: PMC7745377.

Rhodes JDP, Feldman A, Hernandez-Rodriguez B, Diaz N, Brown JM, Fursova NA, Blackledge NP, Prathapan P, Dobrinic P, Huseyin MK, Szczurek A, Kruse K, Nasymth KA, Buckle VJ, Vaquerizas JM, Klose RJ. (2020). Cohesin disrupts Polycomb-dependent chromosome interactions in embryonic stem cells. Cell Reports, doi: 10.1016/j.celrep.2019.12.057.

Galan S, Machnik N, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. (2020). CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics 52(11):1247-1255. doi: 10.1038/s41588-020-00712-y.  PMID: 33077914; PMCID: PMC7610641.

Ing-Simmons E, Vaquerizas JM. (2019). Visualising three-dimensional genome organisation in two dimensions. Development, doi: 10.1242/dev.177162.

Diaz N, Kruse K, Erdmann T, Staiger AM, Ott G, Lenz G, Vaquerizas JM. (2018). Chromatin conformation analysis of primary patient tissue using a low input Hi-C method. Nature Communications, doi: 10.1038/s41467-018-06961-0.

Hug CB, Grimaldi AG, Kruse K, Vaquerizas JM. (2017). Chromatin architecture emerges during zygotic genome activation independent of transcription. Cell, doi: 10.1016/j.cell.2017.03.024

Vaquerizas JM, Torres-Padilla M. (2016). Developmental biology: Panormaic views of the early epigenome. Nature, doi: 10.1038/nature19468.

Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. (2009). A census of human transcription factors: function, expression and evolution. Nature Reviews Geneticsdoi: 10.1038/nrg2538.

All ‘Developmental Epigenomics’ publications:
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