Kavitha Sarma, Ph.D.

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Department: Cell and Developmental Biology
Graduate Group Affiliations

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3601 Spruce St. Rm 234
Philadelphia, PA
Lab: 215-898-3970
Ph.D. (Biochemistry)
Rutgers University, 2007.
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Description of Research Expertise

Research Interests: RNA interactions in epigenetic gene regulation and genome organization.

Keywords: epigenetics, chromatin, polycomb, genome organization, non-coding RNA

We are interested in understanding the molecular mechanisms of RNA mediated epigenetic gene regulation. Aberrations in epigenetic gene silencing can be a causal mechanism of numerous human disease and developmental syndromes. The eukaryotic genome is organized into chromatin, a mixture of histone proteins, DNA and RNAs (Figure 1). In recent years, RNAs have emerged as important factors that play critical roles in epigenetic gene regulation and also dictate chromatin architecture. It has also become clear that many protein factors that regulate gene expression interact with RNAs. Our goal is to elucidate the molecular mechanisms and functional implications of RNA interactions in gene regulation and in genome organization.

Figure 1. Chromatin composition in eukaryotes
Figure 1. Chromatin composition in eukaryotes.
The eukaryotic genome is organized into chromatin, a mixture of histone proteins, DNA, and RNAs. RNAs can function as scaffolds to recruit various protein factors to chromatin and can also serve to bridge two protein factors. Many epigenetic regulators have recently been discovered to interact with RNAs. However, the functional significance of many of these associations are unclear.

Our research has focused on an RNA binding chromatin remodeler, ATRX. ATRX is an epigenetic regulator that is mutated in both neurodevelopmental disorders and cancers. Despite its importance in normal development and maintenance of genome instability, how it contributes to these processes is not well understood. ATRX belongs to a unique class of proteins with the capacity to bind the 3 major chromatin components – DNA, histones, and RNA. While its action on DNA and histones have been studied to some extent, the functional significance of its interactions with RNA remains largely unexplored. Our previous studies have shown that ATRX interacts with the Xist long non-coding RNA and plays an important role in the process of X chromosome inactivation. ATRX also regulates the association of the Polycomb repressive complex 2 to the inactive X chromosome as well as many polycomb gene targets genome-wide (Figure 2).

Figure 2. ATRX dependent PRC2 enrichment on the inactive X chromosome
Figure 2. ATRX dependent PRC2 enrichment on the inactive X chromosome.
In wild-type mouse embryonic fibroblasts (top), ATRX (green) is enriched in nuclear foci that correspond to pericentromeres. EZH2 (red), a component of the PRC2 complex, is enriched on the inactive X chromosome (Xi, white arrows). Upon ATRX depletion (bottom), EZH2 enrichment from the Xi is lost.

We have recently discovered an RNA binding region (RBR) within ATRX. We hypothesize that ATRX is initially recruited to heterochromatic regions through its interactions with RNAs that reside at these loci. ATRX is stabilized at these regions through both histone and DNA contacts and functions in transcription repression at these sites to maintain genome stability (Figure 3). Some questions that we are addressing include: What RNAs interact with ATRX? Do RNA interactions dictate ATRX genomic targeting in vivo? How does loss of RNA interactions affect ATRX function in gene regulation and genome stability?

Figure 3. Model for RNA dependent ATRX targeting to heterochromatin
Figure 3. Model for RNA dependent ATRX targeting to heterochromatin.
Low levels of transcription at heterochromatin or other repetitive regulatory regions may serve as a signal for the RNA dependent recruitment of ATRX to these sites. ATRX binding is stabilized by additional interactions with modified histones and repressive proteins (H3K9me3 and HP1 respectively at constitutive heterochromatin), and DNA. These regions may become decondensed due to cellular processes such as DNA replication or damage and result in increased expression of repetitive RNAs. Increased RNA production can function as a signal to recruit ATRX to reinforce silencing at heterochromatin and maintain genome stability.

Another area of investigation in the lab is the impact of RNA associations on chromatin structure. Here we focus on triplex nucleic acid structures known as R-loops, that are comprised of an DNA:RNA hybrid and displaced ssDNA. R-loops are formed during transcription when the mRNA invades dsDNA (forming the DNA:RNA hybrid) and exposes a ssDNA that can then adopt a G quadruplex (G4) structure (Figure 4). Transcription from G rich repetitive regions results in the formation of G4 DNA that impedes the reannealing of DNA strands, promotes DNA:RNA hybridization, and stabilizes R-loops. In addition to known regulatory roles, R-loops are closely linked to increased DNA damage and genome instability. Stable aberrant R-loops have also been discovered in several neurological disorders, neurodegenerative diseases, and cancers. Discovering the genome-wide locations of R-loops is challenging because of the requirement for large sample size and inefficient enrichment using the monoclonal antibody that recognizes the RNA:DNA hybrid within R-loops. We have developed a new antibody independent approach, called MapR, to identify native R-loops genome-wide. Some questions that are interested in exploring are: Where do R-loops form in specific disease states? How do unscheduled R-loops contribute to neurodegenerative diseases and cancers? What are the protein factors that function in R-loop resolution and stabilization? How can R-loops impact gene regulation and genome organization in disease states?

Figure 4. R-loop structure and formation
Figure 4. R-loop structure and formation.
R-loops are triplex nucleic acid structures comprising an RNA-DNA hybrid and displaced ssDNA. They are formed during transcription when the mRNA invades the dsDNA (forming the RNA-DNA hybrid) and exposes an ssDNA that can adopt a G quadruplex (G4) structure. R-loops can also form when specific long non-coding RNAs associate with chromatin to regulate gene expression.

For our studies we use a combination of biochemical, cell biological and functional genomics approaches in embryonic stem cell, neural stem cell, and cancer cell models.

Lab Personnel:
Anna Bieluszewska Ph.D. - Postdoctoral Fellow
John Doherty B.S. - Research Assistant I
Bhanu Karisetty Ph.D. - Postdoctoral Fellow
Phillip Wulfridge Ph.D. - NRSA Postdoctoral Fellow
Qingqing Yan Ph.D. - Postdoctoral Fellow

Nicole Medeiros - Research Assistant III
Devinne Miller - Undergraduate Researcher
Joyce Bian - Undergraduate Researcher
Wenqing Ren- Postdoctoral Fellow Current Affiliation - Associate Researcher, Tongji University, China

Students who have been admitted to a graduate program at the University of Pennsylvania are encouraged to inquire about current rotation projects by sending an email to: ksarma@wistar.org.

Selected Publications

Wulfridge P and Sarma K: A nuclease- and bisulfite-based strategy captures strand-specific R-loops genome-wide. eLife Feb 2021.

Wenqing Ren*,Nicole Medeiros*, Robert Warneford-Thomson, Phillip Wulfridge, Qingqing Yan, Joyce Bian, Simone Sidoli, Benjamin A. Garcia, Emmanuel Skordalakes, Eric Joyce, Roberto Bonasio, Kavitha Sarma: Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function. Nature Communications May 2020.

Qingqing Yan, Emily J. Shields, Roberto Bonasio, Kavitha Sarma: Mapping native R-loops genome-wide using a targeted nuclease approach. Cell Reports Oct 2019.

Sarma Kavitha, Cifuentes-Rojas Catherine, Ergun Ayla, Del Rosario Amanda, Jeon Yesu, White Forest, Sadreyev Ruslan, Lee Jeannie T: ATRX directs binding of PRC2 to Xist RNA and Polycomb targets. Cell 159(4): 869-83, Nov 2014.

Cifuentes-Rojas Catherine, Hernandez Alfredo J, Sarma Kavitha, Lee Jeannie T: Regulatory interactions between RNA and polycomb repressive complex 2. Molecular cell 55(2): 171-85, Jul 2014.

Simon Matthew D, Pinter Stefan F, Fang Rui, Sarma Kavitha, Rutenberg-Schoenberg Michael, Bowman Sarah K, Kesner Barry A, Maier Verena K, Kingston Robert E, Lee Jeannie T: High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation. Nature 504(7480): 465-9, Dec 2013.

Dimitrova Nadya, Zamudio Jesse R, Jong Robyn M, Soukup Dylan, Resnick Rebecca, Sarma Kavitha, Ward Amanda J, Raj Arjun, Lee Jeannie T, Sharp Phillip A, Jacks Tyler: LincRNA-p21 activates p21 in cis to promote Polycomb target gene expression and to enforce the G1/S checkpoint. Molecular cell 54(5): 777-90, Jun 2014.

Zhao Jing, Ohsumi Toshiro K, Kung Johnny T, Ogawa Yuya, Grau Daniel J, Sarma Kavitha, Song Ji Joon, Kingston Robert E, Borowsky Mark, Lee Jeannie T: Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular cell 40(6): 939-53, Dec 2010.

Jeon Yesu, Sarma Kavitha, Lee Jeannie T: New and Xisting regulatory mechanisms of X chromosome inactivation. Current opinion in genetics & development 22(2): 62-71, Apr 2012.

Sarma Kavitha, Levasseur Pierre, Aristarkhov Alexander, Lee Jeannie T: Locked nucleic acids (LNAs) reveal sequence requirements and kinetics of Xist RNA localization to the X chromosome. Proceedings of the National Academy of Sciences of the United States of America 107(51): 22196-201, Dec 2010.

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Last updated: 07/09/2021
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