Investigating 3D genome organisation in Caenorhabditis elegans with Accessible Region Conformation Capture (ARC-C)

3C and its derivatives have been applied in various organisms to study chromatin architecture. However, these methods have limitations: most of them are limited to restriction-fragment resolution and all of them, with the exception of Hi-C, only survey a pre-defined subset of the genome. I developed a variant of Hi-C, named Accessible Region Conformation Capture (ARC-C), in C. elegans, which interrogates genome organisation at multiple scales genome-wide - from domains and compartments to high resolution interactions between regulatory elements. I applied ARC-C in wild-type Bristol N2, met-2 set-25 mutants that have no H3K9 methylation to study the effects on domain and compartment formation. In these mutants, compartmentalisation (i.e. inter-domain interactions) between H3K27me3-enriched regulated domains is reduced. I also used ARC-C in blmp-1 mutants to understand the role of BLMP-1 in chromatin looping. In blmp-1 mutants, interactions between putative BLMP-1 mediated loops for downregulated genes are significantly reduced. In wild-type worms, when surveying significant interactions at 500 bp resolution, I observe the presence of dense clusters of significant interactions anchored at high occupancy target (HOT) regions that I call “hubs.” Interestingly, the deletion of these hubs does not affect the transcription of linked or local genes. However, local interactions are altered and some extent of redundancy is observed. To improve our ARC-C protocol, I tested several variations with different enzymes and biotin-mediated streptavidin beads pulldown. In all, ARC-C revealed insights into genome organisation in C. elegans and I have made progress toward a next-generation version of the method.

Name dc:type.qualificationname

Doctor of Philosophy (PhD)

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

University of Cambridge

Year dc:date.issued

2019

Author dc:creator

• Seow, Wei Qiang

Advisor dc:contributor.advisor

• Ahringer, Julie

• Hi-C
• c. elegans
• ARC-C
• conformation-capture
• genome organisation
• genome architecture
• regulatory elements
• regulatory interactions

Licence

• https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/68bc739b-59ce-48ba-995c-ab676e25cba5/download
• https://creativecommons.org/licenses/by-nc-nd/4.0/

Language dc:language

en

DOI dc:identifier.doi

https://doi.org/10.17863/CAM.41320

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/294221