Tor of the Laboratory of Genome Architecture and Dynamics a L Ic E G a Dau

Issue 158 April 2019 A NEWSLETTER OF THE ROCKEFELLER UNIVERSITY COMMUNITY Natural Selections Interviews Rockefeller’s Viviana Risca, Principal Investiga- tor of the Laboratory of Genome Architecture and Dynamics A LICE G A DAU At the age of fourteen, Viviana Risca spent her summer break unlike most teenag- ers. Every morning, she took the train from Long Island to work in Dr. Daniel Eich- inger’s parasitology laboratory at New York University. Despite the cabinet full of dead worms in formaldehyde she had to pass every morning, this first exposure to biological research was highly influential in propelling her into a lifetime of research. Since then she has been excited about using molecular techniques to understand the processes that occur in cells. NATURAL SELECTIONS NATURAL Viviana has now joined the Rockefell- | er community as one of the two new tenure- track assistant professors hired in 2018. Af- ter completing her Ph.D. in Biophysics at the University of California, Berkeley, she continued her scientific career as a postdoctoral ALICE GADAU scholar at Stanford University with Profes- sor William J. Greenleaf. Viviana is interest- Viviana Risca ed in the biophysical rules that contribute to the dynamics and stability of the genome. In they express different sets of genes that give therapies and diagnostics. addition, she wants to understand how the rise to their unique identities. As a postdoc at Stanford, I worked three-dimensional genome architecture can My lab seeks to understand how on exploring how the landscape of enzyme- regulate DNA-based processes. three-dimensional chromatin structure con- accessible chromatin can give us insights trols the ways in which various proteins, into the regulatory networks that control Alice Gadau: What is the central ques- including those involved in transcription, gene expression in several cell types, includ- tion you are trying to address in your lab, access their binding sites on DNA in order ing a cancer model, using a popular method and how is this an expansion from your past to perform their biological functions. One called ATAC-seq. I also did a lot of technol- work? of the driving hypotheses of our work is that ogy development, which resulted in RICC- Viviana Risca: The three-dimensional chromatin structure acts as an integrator of seq, a method for mapping chromatin fiber structure of the genome is controlled by its many molecular inputs to modulate access structure at high resolution, and ChAR-seq, association with a variety of proteins, to- to DNA. I am particularly interested in how a method for mapping contacts between gether making up a DNA-protein complex chromatin modifications, inter-molecular RNA and DNA genome-wide. In my own we call chromatin. Through the efforts of interactions, and polymer effects give rise lab, we will continue to use and develop large-scale sequencing projects, we now to specialized parts of the cell’s nucleus that these technologies, applying them toward know much of the linear sequence of bases stably repress transcription and help main- the goal of understanding the basic biophys- that make up the human genome, but we tain cell identity and normal cell function. ical and molecular mechanisms responsible are still far from fully understanding the Both chromatin structure and the processes for stable transcriptional repression and mechanisms that control how and when the that shape it are often perturbed in cancer, overall control of access to genomic DNA. information encoded in DNA sequence is as well as during aging, and I hope that our read out by transcription. A skin cell and a work on these fundamental processes will muscle cell contain the same genome, but provide useful leads toward better cancer CONTINUED TO P. 2 - 1 CONTINUED FROM P. 1 - tentially phase-separated domains like the nucleolus. How this long-range organization AG: How does three-dimensional ge- relates to short-range chromatin folding is Editorial Board nome architecture contribute to DNA regula- also an area that my lab plans to explore. tory processes? Sarah Baker Editor-in-Chief, VR: Since the 1920s when Emil Heitz AG: What is RICC-seq and how can it Managing Editor, Webmaster coined the terms euchromatin and hetero- accurately examine short range DNA con- chromatin, we have known that the cell nu- tacts? Jim Keller cleus is divided between regions of high and VR: RICC-seq stands for ionizing Ra- Editor-at-Large low chromatin density. Since then, we have diation-Induced Correlated Cleavage. In the Megan Elizabeth Kelley learned that organization of chromatin is far 1990s, it was shown that the pattern of DNA Associate Editor, Communication from random—it is in fact organized at mul- damage induced by X-rays or gamma-rays tiple length scales. on a cell’s genome is shaped by the way the Emma Garst Editorial Assistant At short length scales, every 150- DNA is folded into chromatin. RICC-seq 200 bp of eukaryotic genomes is wrapped takes advantage of this convenient property Nicole Infarinato around roughly 10 nm-wide histone com- of chromatin. We irradiate cells with X-rays Copy Editor, Distribution plexes called nucleosomes. Regions of DNA or gamma rays, carefully extract the short Melissa Jarmel that are depleted of nucleosomes tend to be pieces of resulting single-stranded DNA, Copy Editor, Website Traffic hyper-accessible to exogenous enzymes we and then sequence those pieces. Their ends use to probe them, and we interpret these tell us about the pattern of DNA damage Donna Tallent regions to be also accessible to endogenous and consequently, about the way the DNA Copy Editor proteins like transcription factors, chroma- was folded in the original cell. This method Nan Pang tin remodelers and polymerases. Indeed, works well for mapping high-resolution Guadalupe Astorga many of these proteins seem to localize to DNA-DNA contacts on the order of less Designers nucleosome-depleted DNA. We also know than 10 nm and less than a thousand base that some histone modifications, like lysine pairs, making it complementary to other selections.rockefeller.edu acetylation, is associated with low-density, three-dimensional structure mapping meth- [email protected] euchromatic regions of the genome that ods like Hi-C, which work better for con- tend to be more accessible to protein bind- tacts spanning thousands of kilobases. ing. The high-density, heterochromatic parts with chromatin engineers to develop pertur- of the genome are less well understood, AG: What makes RICC-seq novel from bations that will help us dissect causal and from a structural standpoint, and many other sequencing techniques? functional relationships between molecular labs, including my own, are currently try- VR: RICC-seq has two unique ad- factors and chromatin structure. ing to decipher the mechanisms that drive vantages. First, it can be performed on liv- the exclusion of transcriptional machinery ing cells that are not fixed or permeabilized. AG: Are there other hobbies you have from these silent genomic regions. Candi- Therefore, we can probe chromatin struc- that incorporate science? date mechanisms that have been proposed ture in its native state. Second, it uses hy- VR: I’ve long loved incorporating skills include occlusion of binding sites by DNA droxyl radicals generated by radiation as its that I pick up in the lab into my other hob- buried in compacted chromatin, chemical probe. The radiation can penetrate all areas bies. When I learned microscopy and optics, exclusion by phase-separated liquid do- of the nucleus, no matter how dense, and the I also took up photography in my spare time, mains, and simple volume exclusion from radicals are smaller than water and can eas- because the basic concepts are the same. I high density regions. ily diffuse. Therefore, we can get data from love art in general and see a lot of parallels We also know that there is functional not only the low-density euchromatin in the between the lives of scientists and artists. We communication between genomic regions at nucleus, but also from highly compacted, are both seeking fundamental truths, and much longer length scales spanning tens of dense heterochromatin. both need to continually find ways to nur- thousands and sometimes hundreds of thou- ture our creativity. I also love to cook. I often sands of kilobases. Enhancer elements in the AG: What other tools are you incorpo- use it to relax because it uses many of the genome, which are acetylated, hyperacces- rating in your lab to understand genome ar- same skills as biochemistry or molecular bi- sible, and bound by transcription factors chitecture? ology, but you can usually determine failure when active, somehow must communicate VR: RICC-seq is not a single-cell or success more rapidly than at the bench, with gene promoter regions because they method and requires quite a bit of input ma- and it is also easier to share your successes regulate these promoters. This is thought terial, so we will be combining it with lower- with your friends. to happen via DNA looping interactions in input methods like single cell or bulk ATAC- Lastly, I love science outreach and three dimensions, but the exact nature and seq and RNA-seq, as well new cutting-edge communications, but I would not call those dynamics of these contacts are an active technologies as they emerge. We will also hobbies. I think all of us as scientists have area of research and not yet understood. be complementing this work with protein a responsibility to share our work with the Lastly, we also know that the cell nucleus is binding measurements like ChIP-seq or public that, after all, supports our work divided up into regions with different func- CUT&RUN, and microscopy that can tell through taxes and donations, to advocate for tional profiles, through associations with us about the long-range organization of the the societal benefits of basic research, and to the nuclear lamina or self-association of po- nucleus.

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