WL lab winter rotation
2022-01-06
2021 Winter, UCI CMB program rotation
Author: Runhang Shu, PhD student
Affiliation: University of California, Irvine
Contact: darsonshu@gmail.com
Date started: 2021-01-06
Date end (last modified): 2021-01-06
This work is licensed under a Creative Commons Attribution 4.0 International License.
Introduction:
Notebook for rotation in Dr. Wei Li lab. It’ll log notes, ideas and inspirations from papers I read; Save a copy of bioinformatic and statistical analysis I did for reproducible science!
Table of contents
- Page 1: 2022-01-06 Basics of DNA methylation
- Most CpG dinucleotides are methylated with the exception of those within in CpG islands (CGIs), which are usually unmethylated.
- Human have ~30,000 CGIs. More than 10,000 CGIs occur at genes’ promoters and nearly always remain unmethylated.
- In mammalian genomes, CGIs are typically 300–3,000 base pairs in length, and have been found in or near approximately 40% of promoters of mammalian genes. Over 60% of human genes and almost all house-keeping genes have their promoters embedded in CpG islands.
Howver, not all 30,000 CGIs are unmethylated. ~9,000 CGIs within gene bodies (intragenic) are more likely to become methylated, serving a role to regulate transcritional activity during differentiation and disease (Jeziorska et al., 2017).
Large undermethylated regions (average methylation <10%) that are longer than 3,500 bp are terms as “canyon” (10 times larger than a typical CGI of ~300 bp)