Ruchisree Garuda
Pronouns: She/Her
Research Mentor(s): Mats Ljungman
Co-Presenter:
Research Mentor School/College/Department: Radiation Oncology / Medicine
Presentation Date: April 20
Presentation Type: Poster
Session: Session 5 – 3:40pm – 4:30 pm
Room: League Ballroom
Authors: Ariel McShane, Ruchisree Garuda
Presenter: 57
Abstract
A cell’s genome is organized in 3D space at many levels, one of which is chromatin loop domains. Previous research has shown a role for chromatin loop domains in bringing together certain genomic elements, such as enhancers and promoters. However, no significant change in genome-wide homeostatic transcription was observed when loop domains anchored by CTCF and cohesin were disrupted. Given these observations, we were interested if these chromatin loops played a role in transcription induced by stress conditions and transcriptional stimuli. To investigate this question, we used a modified HCT116 cell line with an auxin inducible degron system that allowed us to degrade the proteins RAD21, a component of the cohesin complex, and CTCF allowing us to disrupt these loop domains. We then treated the cells with heat shock, ionizing radiation, and TNFa to induce transcriptional changes, and asked if the disruption of loop domains affected the cell’s ability to respond to these treatments. We performed Bru-seq, a nascent RNA sequencing technique, to study gene expression and Bru-UV-seq to study enhancer expression, to explore the effect that the loss of loop domains has on induced transcription. Although dramatic transcriptional changes occurred after these treatments, we found no significant effect of disrupted loop domains which led us to conclude that loop domains do not play a significant role regulating induced transcription. Future work will focus on exploring transcription and enhancer activity following these cell stresses.
Biomedical Sciences
