Exploring the roles of RNAPII in genome organization

by Shu Zhang
Doctoral thesis
Date of Examination:2022-12-06
Date of issue:2022-12-16
Advisor:Prof. Dr. Argyris Papantonis
Referee:Prof. Dr. Argyris Papantonis
Referee:Prof. Dr. Tim Beißbarth
Persistent Address: http://dx.doi.org/10.53846/goediss-9632

 

 

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Abstract

English

The role of RNAPII in 3D genome organization has been heavily debated over the last two decades. Here, in situ Hi-C and Micro-C data were used to conclusively address this debate. I discovered that: 1) using cell population in situ Hi-C data, longer loops with enhanced signal appear upon RNAPII depletion. Together with a rewired-loop pattern of gained loops in the absence of RNAPII, I can suggest that RNAPII may impede cohesin extrusion in human cells; 2) using in situ Hi-C data in G1-sorted cells, I observed loops with longer length, stronger signal, and stronger insulation, which are in line with the cell population in situ Hi-C data. Moreover, a diffuse signal pattern emerges upon RNAPII depletion in this data. Taken together, my data indicate RNAPII impeding cohesin extrusion in interphase. 3) using Micro-C data, transcription-level loops are captured, which show much weaker signal and insulation than CTCF loops. Moreover, on average, ~20% reduction in chromatin-bound CTCF and cohesin is seen in the absence of RNAPII. While this degree of loss does not affect loop detection in Micro-C maps, “transcription only” loops (especially enhancer-anchored loops) are severely weakened or lost in the absence of RNAPII. In addition, enhancer-bound cohesin is reduced by ~50%. Surprisingly, promoter-anchored loops are more stable than enhancer-anchored ones in the absence of RNAPII. Collectively, RNAPII is required for the formation of enhancer-anchored loops; and 4) using in situ Hi-C data from cells entering G1 after mitosis, ~20% reduction of chromatin-bound CTCF and cohesin is seen in the absence of RNAPII and loop formation is affected genome-wide during reentry into G1. Interestingly, as observed in Micro-C data, cohesin occupancy is reduced more at enhancers than promoters upon RNAPII degradation in this transition. Moreover, compartmentalization was also affected in the absence of RNAPII upon reentry G1. Thus, I can conclude that RNAPII is required to properly refold the genome during the mitosis to G1 transition.
Keywords: 3D genome organization; RNAPII; enhancer-promoter interactions; loop extrusion
 
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