Pedro P. Rocha, Ph.D.

Stadtman Investigator

Unit on Genome Structure and Regulation


NIHBC 06B 2B216


Research Topics

Packing two meters of DNA inside ten-micron nuclei creates a very crowded environment. This is an extraordinary feat of compaction and organization because cellular processes such as replication, transcription, and DNA repair must occur within such a dense setting. We have all seen how electric cables become invariably entangled and non-functional inside our drawers. Cells face the same problems, and therefore developed mechanisms that organize the physical structure of the genome, and ensure its regulation and integrity. Our lab studies how the mechanisms that fold and compact the genome, help ensure precise spatial-temporal activation of gene expression.

Our goal is to understand the regulatory mechanisms that ensure accurate specification of the first mammalian cell lineages, which are essential to support healthy pregnancies. For this we combine cutting-edge genetic, genomic and imaging approaches. Visit to learn more about our research and available positions.


I studied Microbiology and Genetics in Portugal, at Lisbon University and graduated in 2005. I then moved to Germany for my PhD where I worked in the lab of Heiner Schrewe at the Max-Planck Institute for Molecular Genetics in Berlin, studying the role of transcriptional co-regulatory complexes during mouse development, as part of a Marie Curie-sponsored international consortium. For my postdoctoral training I moved to the United States and joined the lab of Jane Skok at New York University, to explore multiple ways by which nuclear organization maintains genomic integrity. Our lab at NIH, started in May of 2018 and we focus on understanding how the mechanisms that fold the genome contribute to regulation of gene expression and cell-fate decisions.

Selected Publications

  1. Thompson JJ, Lee DJ, Mitra A, Frail S, Dale RK, Rocha PP. Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages. Nat Commun. 2022;13(1):4257.
  2. Kurotaki D, Kikuchi K, Cui K, Kawase W, Saeki K, Fukumoto J, Nishiyama A, Nagamune K, Zhao K, Ozato K, Rocha PP, Tamura T. Chromatin structure undergoes global and local reorganization during murine dendritic cell development and activation. Proc Natl Acad Sci U S A. 2022;119(34):e2207009119.
  3. Zuo Z, Rocha PP. Repetitive Elements: Different Subtypes Hint at Distinct Functions. Trends Genet. 2020;36(6):385-387.
  4. Xie G, Lee JE, Senft AD, Park YK, Jang Y, Chakraborty S, Thompson JJ, McKernan K, Liu C, Macfarlan TS, Rocha PP, Peng W, Ge K. MLL3/MLL4 methyltransferase activities control early embryonic development and embryonic stem cell differentiation in a lineage-selective manner. Nat Genet. 2023;55(4):693-705.
  5. Chakraborty S, Kopitchinski N, Zuo Z, Eraso A, Awasthi P, Chari R, Mitra A, Tobias IC, Moorthy SD, Dale RK, Mitchell JA, Petros TJ, Rocha PP. Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness. Nat Genet. 2023;55(2):280-290.

Related Scientific Focus Areas

This page was last updated on Monday, November 20, 2023