Application of CUT&Tag to the mapping and analysis of VEZF1 binding sites in K562 cells

Wang, Erxuan (2024) Application of CUT&Tag to the mapping and analysis of VEZF1 binding sites in K562 cells. MSc(R) thesis, University of Glasgow.

Abstract

VEZF1 is a highly conserved vertebrate transcription factor that has ubiquitous expression in vertebrates. VEZF1 is essential for the barrier activity of the chicken ẞ globin HS4 insulator, where it prevents de novo DNA methylation. Knock-out of VEZF1 results in lethal haemorrhaging and edema in murine embryos, indicating a role for VEZF1 in the maintenance of vascular integrity.

In this study, the CUT&Tag method, previously reported to be an improvement on CUT&RUN and ChIP-seq, was utilised to map VEZF1 binding sites in K562 cells. The binding sites identified by CUT&Tag are similar to those previously identified using ChIP-seq, but the data generated from CUT&Tag shows significant advantages of lower background and higher peaks. Peak analysis indicates that most of the VEZF1 peaks are associated with promoters or enhancers, and there is strong co-localisation of the binding of VEZF1 and GATA2. VEZF1 tends to recognize and bind to GGGNGGGG motifs, but no difference is found between GGGNGGGG motifs discovered at VEZF1-associated promoters and enhancers. Furthermore, co-localisation of GATA2 does not affect the sequence of the GGGGNGGGG motifs enriched at VEZF1 peaks. Sequence analysis also revealed other motifs that are recognized by a variety of transcription factors, which may act alongside VEZF1 to regulate gene expression in K562 cells.

Our study shows that CUT&Tag is an efficient method for mapping and analyzing the binding sites of transcription factors, and provides new opportunities for research on the interactions between VEZF1 and other transcription factors.

• Item Type: Thesis (MSc(R))
• Qualification Level: Masters
• Subjects: Q Science > QR Microbiology; Q Science > QR Microbiology > QR180 Immunology
• Colleges/Schools: College of Medical Veterinary and Life Sciences > School of Cancer Sciences
• Supervisor's Name: West, Dr. Katherine
• Date of Award: 2024
• Depositing User: Theses Team
• Unique ID: glathesis:2024-84670
• Copyright: Copyright of this thesis is held by the author.
• Date Deposited: 08 Nov 2024 10:12
• Last Modified: 08 Nov 2024 10:14
• Thesis DOI: 10.5525/gla.thesis.84670
• URI: https://theses.gla.ac.uk/id/eprint/84670