“Bridging the chromatin structure gap: Sequence-resolved local nucleosome contacts in intact cells”

Sponsoring Department: 
Department of Biochemistry and Molecular Genetics
Dr. Viviana Risca, Stanford University
Event Time: 
Event Location: 
Herman Auditorium, Molecular Biology Research Building, 900 S. Ashland Avenue, Chicago, IL 60607
Contact Email: 

Chromatin structure at the length scale spanning local nucleosome–nucleosome interactions has been proposed to play a crucial role in regulating transcription and access to DNA through variable chromatin compaction. However, it remains poorly understood as compared with the structure of single nucleosomes or with long-range chromosome interactions. This seminar will discuss a new method for mapping chromatin structure in human cells at the 1–3 nucleosome (50–500 bp) scale, obtained using ionizing radiation-induced spatially correlated cleavage of DNA with sequencing (RICC-seq). Analysis of RICC-seq data reveals that DNA fragments characteristic of DNA-DNA contacts between alternating nucleosomes are enriched in transcriptionally repressed genome regions marked by histone H3 lysine 9 trimethylation. These results support a model of chromatin architecture consisting of fibers with local zig-zag order and variable longitudinal compaction that correlates with changes in histone modifications. Future research plans to apply this approach to understanding the mechanisms by which access of transcriptional machinery to DNA is regulated in the context of differentiation-associated random X chromosome inactivation and formation of senescence associated heterochromatic foci will be discussed.