Repository logo
 

Genomic properties of variably methylated retrotransposons in mouse

Published version
Peer-reviewed

Change log

Authors

Ferguson-Smith, Anne  ORCID logo  https://orcid.org/0000-0003-4996-9990
Elmer, Jessica 
Hay, Amir 

Abstract

Background: Transposable elements (TEs) are enriched in cytosine methylation, preventing their mobility within the genome. We previously identified a genome-wide repertoire of candidate intracisternal A particle (IAP) TEs in mice that exhibit interindividual variability in this methylation (VM-IAPs) with implications for genome function. Results: Here we validate these metastable epialleles and discover a novel class that exhibit tissue specificity (tsVM-IAPs) in addition to those with uniform methylation in all tissues (constitutive- or cVM-IAPs); both types have the potential to regulate genes in cis . Screening for variable methylation at other TEs shows that this phenomenon is largely limited to IAPs, which are amongst the youngest and most active endogenous retroviruses. We identify sequences enriched within cVM-IAPs, but determine that these are not sufficient to confer epigenetic variability. CTCF is enriched at VM-IAPs with binding inversely correlated with DNA methylation. We uncover dynamic physical interactions between cVM-IAPs with low methylation ranges and other genomic loci, suggesting that VM-IAPs have the potential for long-range regulation. Conclusion: Our findings indicate that a recently evolved interplay between genetic sequence, CTCF binding, and DNA methylation at young TEs can result in inter-individual variability in transcriptional outcomes with implications for phenotypic variation.

Description

Keywords

CTCF, Chromatin conformation, DNA methylation, Endogenous retrovirus, Intracisternal A particle, Metastable epiallele, Retrotransposon

Journal Title

Mobile DNA

Conference Name

Journal ISSN

1759-8753
1759-8753

Volume Title

Publisher

BioMed Central
Sponsorship
Medical Research Council (MR/R009791/1)
Biotechnology and Biological Sciences Research Council (BB/R009996/1)
Wellcome Trust (210757/Z/18/Z)
Biotechnology and Biological Sciences Research Council (BB/G020930/1)
Relationships
Is derived from: