University of Cambridge
Primate-specific KRAB zinc finger proteins and their targets rewire regulatory networks related to inflammation and pancreas development
Abstract
dc:description.abstractTransposable elements (TEs) comprise about 50% of the human genome. While a few are still active and can accumulate copies in new locations of the genome, most of these mobile elements have invaded the genome of our ancestors a long time ago in successive waves during evolution. The largest subfamily of DNA binding factors in human, KRAB Zinc Finger proteins (KZFPs), leads to the epigenetic silencing of their bound loci and have been recently shown to mainly target repetitive regions of the genome, mostly TEs. Interestingly most TEs targeted by KZFPs have lost their ability to transpose and pose no threat to the host’s genomic integrity. TEs are known to contain docking sites for host’s transcription factors and contain transcription regulatory elements including promoters, enhancers and silencers. The differential expression patterns observed for members of the KZFP subfamily amongst different biological contexts, have led us to hypothesise that KZFPs participate in gene regulatory networks by toggling chromatin accessibility on their targeted regions. With approximately 400 KZFP protein coding loci in human genome and only a few functionally described, in this thesis we aim to characterise the function of two KZFPs, ZNF808 and ZNF267. ZNF808 was found to be homozygous knock out in patients diagnosed with pancreatic agenesis, presenting neonatal diabetes with insufficient pancreatic exocrine function. Expression and ChIP data for ZNF808 show that it is upregulated during the early stages of pancreatic development and binds on members of primate conserved MER11 elements leading to their epigenetic silencing. On the other hand, ZNF267 is already highly expressed in monocytes and macrophages but it is further upregulated by inflammatory stimuli. ZNF267 ChIP data show that it mainly targets and silences members of the primate specific THE1 and MSTA TE families. Interestingly, despite both KZFPs being primate specific along with their targeted TEs, they are involved in important biological processes. Our study shows that ZNF808 is implicated in the orchestration of gene regulatory networks involved in pancreatic development whereas ZNF267 demonstrates a profile of transcription regulator and promoter/enhancer silencer in monocytes and macrophages. Notably, ZNF808 and ZNF267 expression is regulated by the same TFs which bind on their targeted TEs suggesting a complex gene regulatory network related the respective biological processes. CRISPR knock outs created for ZNF808 in H1 cell line demonstrate changes in their transcriptome where genes implicated in liver development are upregulated during the early stages of their differentiation to pancreatic cells. These changes are coupled with epigenetic activation of nearby MER11 elements known to be bound by ZNF808. Observations in H1 cells were also confirmed in patient derived ZNF808 knock out iPSCs. Similarly, we generated ZNF267 CRISPR knock outs in monocytic cell line U-937 and studied their transcriptome and epigenome as well as in macrophages treated with LPS. Notably, in both cellular contexts we observed transcripts emerging from THE1 elements in the knockouts, suggesting that ZNF267 silences promoter potential of these elements. This thesis presents the contribution of KZFPs in the evolution of novel gene regulatory networks related to key biological processes.
Degree
thesis:*- Name dc:type.qualificationname
- Doctor of Philosophy (PhD)
- Level dc:type.qualificationlevel
- Doctoral
- Grantor dc:publisher.institution
- University of Cambridge
- Year dc:date.issued
- 2022
Author and committee
dc:creator, dc:contributor.*- Author dc:creator
-
- Triantou, Athina Nikoleta
- Advisor dc:contributor.advisor
-
- Imbeault, Michael
Subjects
dc:subject × 26Rights
dc:rightsIdentifiers
dc:identifier.*- DOI dc:identifier.doi
- https://doi.org/10.17863/CAM.108608
- OAI identifier oai:identifier
- oai:www.repository.cam.ac.uk:1810/368395