Please find a full publication list on google scholar, pubmed and biorxiv.

Selected Publications


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1 Raviram R*Rocha PP*, Luo V, Swanzey E, Miraldi E, Chuong E, Feschotte C, Richard Bonneau R, Skok J (2018) Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate Genome Biology *co-first author.

In this study we adapt chromosome conformation techniques to study how endogenous retroviruses are impacted by the nuclear organization of the genome and how they themselves are able to act like canonical enhancers that are able to loop and physically contact the genes that they regulate.



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2 – Rocha PP*, Raviram R, Fu Y, Kim J, Luo V, Aljoufi A, Swanzey E, Pasquarella A, Balestrini, A, Miraldi ER, Bonneau R, Petrini J, Schotta G, Skok JA. (2016) A damage independent role for 53BP1 that impacts break order and Igh architecture during CSR Cell Reports *co-corresponding author

We described an unanticipated role for the DNA damage sensor protein 53BP1 that is independent of its role in the DNA damage repair pathway. We showed that 53BP1 impacts the local organization of the Igh locus to orchestrate the correct introduction of DNA breaks during recombination. – Fu Y, Rocha PP*, Luo V, Raviram R, Deng Y, Mazzoni, E, Skok JA. (2016) CRISPR-dCas9 and sgRNA scaffolds enable dual-color live imaging of satellite sequences and repeat-enriched individual loci Nature Communications *co-first author and co-corresponding author

This study was spearheaded by a master student (Yi Fu) and we reported a live imaging system based on dCas9 and sgRNAs scaffolds that allows labeling of more than one locus in living cells. We were the first to be able to label single loci (in opposition to repeat regions) with more than one color.Screen Shot 2018-03-25 at 11.51.11 AMeve


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4 – Narenda V, Rocha PP, An D, Raviram R, Skok JA, Mazzoni EO, Reinberg D (2015) CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation Science

In this collaboration with the Reinberg lab we showed how manipulation of a single CTCF site is enough to change the boundary between chromatin domains and impact gene regulation during development.



5 – Rocha PP*, Micsinai M*, Kim JR, Hewitt SL, Souza PP, Trimarchi T, Strino F, Parisi F, Kluger Y, and Skok JA (2012) Close proximity to Igh is a contributin factor to AID-mediated translocations Molecular Cell *co-first authors

We reported one of the first uses of the 4C-Seq. We showed that in recombining B cells, AID off-target loci located in chromosomal domains that frequently contact Igh are more likely to be involved in translocations with Igh.


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6 – Rocha PP, Scholze, M Bleiss W, Schrewe H (2010) MED12 is essential for early mouse development and for canonical and PCP-Wnt signaling Development

In this study we reported the generation of the first in vivo model of the MED12 coregulator protein. MED12 has been shown to be an essential regulator of gene expression and a marker for Super Enhancers. In this study we showed that MED12 is essential during early mouse development for both canonical and PCP-Wnt signaling.