High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions
- Friedrich Miescher Institute, Switzerland
- Friedrich Miescher Institute, Basel, Switzerland
Abstract
The majority of mammalian promoters are CpG islands; regions of high CG density that require protection from DNA methylation to be functional. Importantly, how sequence architecture mediates this unmethylated state remains unclear. To address this question in a comprehensive manner, we developed a method to interrogate methylation states of hundreds of sequence variants inserted at the same genomic site in mouse embryonic stem cells. Using this assay, we were able to quantify the contribution of various sequence motifs towards the resulting DNA methylation state. Surprisingly, modeling of this comprehensive dataset revealed that CG density alone is a minor determinant of their unmethylated state. Instead, these data argue for a principal role for transcription factor binding sites, a prediction confirmed by testing synthetic mutant libraries. Taken together, these findings establish the hierarchy between the two cis-encoded mechanisms that define the DNA methylation state and thus the transcriptional competence of CpG islands.
Article and author information
Author details
Reviewing Editor
- Anne C Ferguson-Smith, University of Cambridge, United Kingdom
Version history
- Received: July 18, 2014
- Accepted: September 24, 2014
- Accepted Manuscript published: September 26, 2014 (version 1)
- Version of Record published: October 21, 2014 (version 2)
Copyright
© 2014, Krebs et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 4,940
- views
-
- 554
- downloads
-
- 65
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions
eLife 3:e04094.
https://doi.org/10.7554/eLife.04094
Further reading
-
- Chromosomes and Gene Expression
- Genetics and Genomics
Inserting artificially-generated ‘DNA islands’ into a genome has shed new light on why some DNA sequences are methylated and others are not.
-
- Chromosomes and Gene Expression
Extrachromosomal DNA is a common cause of oncogene amplification in cancer. The non-chromosomal inheritance of ecDNA enables tumors to rapidly evolve, contributing to treatment resistance and poor outcome for patients. The transcriptional context in which ecDNAs arise and progress, including chromosomally-driven transcription, is incompletely understood. We examined gene expression patterns of 870 tumors of varied histological types, to identify transcriptional correlates of ecDNA. Here, we show that ecDNA-containing tumors impact four major biological processes. Specifically, ecDNA-containing tumors up-regulate DNA damage and repair, cell cycle control, and mitotic processes, but down-regulate global immune regulation pathways. Taken together, these results suggest profound alterations in gene regulation in ecDNA-containing tumors, shedding light on molecular processes that give rise to their development and progression.
