Publications

Please find a full list on Google Scholar , Pubmed and Biorxiv.

  • Raviram R*, Rocha PP*, Luo V, Swanzey E, Miraldi E, Chuong E, Feschotte C, Bonneau R, Skok JA. (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. 
    Capture Hi-C 4Tran Ifng Interferon gamma
  • 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.

    53BP1 Igh Class Switch 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.
     
  • 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.
    4C-Seq Hox CTCF
  • 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.
    Igh Translocations 4C
  • 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.
    Shh Fzd3 Vangl2 Wnt5a Beta-Catenin Vangl2 Prickle1
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