Author ORCID Identifier

https://orcid.org/0000-0002-3644-1284

Date of Graduation

8-2019

Document Type

Thesis (MS)

Program Affiliation

Biomedical Sciences

Degree Name

Masters of Science (MS)

Advisor/Committee Chair

Wenbo Li

Committee Member

Darren Boehning

Committee Member

Leng Han

Committee Member

Chunru Lin

Committee Member

Dung-Fang Lee

Abstract

Metazoans utilize a constellation of distal regulatory elements to control gene transcription, and therefore they have to forge highly complex chromatin loops to spatially bridge these regulatory elements and genes in the three-dimensional (3D) genome. However, the hierarchy of chromatin contacts and their underlying mechanisms are not well-understood. SMC complexes including Cohesin complex and Condensin complex has been widely proposed to organize 3D genome structure, and further regulate metazoans’ gene transcription. Here, we aim to dissect the direct functions of SMC complexes (both Cohesin and Condensin) in transcriptional regulation and 3D genome organization, by utilizing an inducible protein degradation system. Nascent transcriptome analysis revealed that Cohesin acute depletion impacts the nascent transcription at promoter regions rather than at the entire gene bodies, indicating a potential role of Cohesin in RNA polymerase II pause-release. Combined analysis with MYC degradation nascent transcriptome showed Cohesin complex and MYC are co-regulating a large portion of MYC targeted genes. Moreover, our nascent transcriptome with different signals’ stimulus demonstrated Cohesin complex is generally not required for TNF-alpha and heat-shock stimulated transcriptional events. To further understand the hierarchy of 3D genome, high-resolution H3K27ac HiChIP analysis after Cohesin depletion revealed that there is a large portion of regulatory chromatin loops persist after Cohesin depletion. This is a significant finding suggesting that Cohesin is not a universal organizer of short-range enhancer-gene loops. We further showed that Cohesin-antagonized extra-long-distance super-enhancer loops are mediated by BRD4 phase separation, validating an emerging hypothesis that LLPS (Liquid-liquid phase separation) can drive chromatin contacts. For Condensin complex, our nascent transcriptome data after Condensin I depletion indicated that Condensin I modulates TNF-alpha stimulated transcription, but not the basal transcription program. Also, Hi-C analysis after Condensin I depletion revealed that Condensin I has a role in counteracting A/B compartmental interaction. Our work has provided a functional dissection of roles played by human SMC complexes in transcription regulation and 3D genome organization.

Keywords

Transcription, 3D Genome, Enhancer, Cohesin, Condensin

Available for download on Thursday, August 13, 2020

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