Synthetic CpG islands reveal DNA sequence determinants of chromatin structure
- University of Edinburgh, United Kingdom
- Technische Universitaet Dresden, Germany
Abstract
The mammalian genome is punctuated by CpG islands (CGIs), which differ sharply from the bulk genome by being rich in G+C and the dinucleotide CpG. CGIs often include transcription initiation sites and display 'active' histone marks, notably histone H3 lysine 4 methylation. In embryonic stem cells (ESCs) some CGIs adopt a 'bivalent' chromatin state bearing simultaneous 'active' and 'inactive' chromatin marks. To determine whether CGI chromatin is developmentally programmed at specific genes or is imposed by shared features of CGI DNA, we integrated artificial CGI-like DNA sequences into the ESC genome. We found that bivalency is the default chromatin structure for CpG-rich, G+C-rich DNA. A high CpG density alone is not sufficient for this effect, as A+T-rich sequence settings invariably provoke de novo DNA methylation leading to loss of CGI signature chromatin. We conclude that both CpG-richness and G+C-richness are required for induction of signature chromatin structures at CGIs.
Article and author information
Author details
Reviewing Editor
- Anne C Ferguson-Smith, University of Cambridge, United Kingdom
Version history
- Received: May 16, 2014
- Accepted: September 11, 2014
- Accepted Manuscript published: September 26, 2014 (version 1)
- Version of Record published: October 21, 2014 (version 2)
Copyright
© 2014, Wachter 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.
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Synthetic CpG islands reveal DNA sequence determinants of chromatin structure
eLife 3:e03397.
https://doi.org/10.7554/eLife.03397
Further reading
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- 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.
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- Cancer Biology
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The chromatin-associated protein WD Repeat Domain 5 (WDR5) is a promising target for cancer drug discovery, with most efforts blocking an arginine-binding cavity on the protein called the ‘WIN’ site that tethers WDR5 to chromatin. WIN site inhibitors (WINi) are active against multiple cancer cell types in vitro, the most notable of which are those derived from MLL-rearranged (MLLr) leukemias. Peptidomimetic WINi were originally proposed to inhibit MLLr cells via dysregulation of genes connected to hematopoietic stem cell expansion. Our discovery and interrogation of small-molecule WINi, however, revealed that they act in MLLr cell lines to suppress ribosome protein gene (RPG) transcription, induce nucleolar stress, and activate p53. Because there is no precedent for an anticancer strategy that specifically targets RPG expression, we took an integrated multi-omics approach to further interrogate the mechanism of action of WINi in human MLLr cancer cells. We show that WINi induce depletion of the stock of ribosomes, accompanied by a broad yet modest translational choke and changes in alternative mRNA splicing that inactivate the p53 antagonist MDM4. We also show that WINi are synergistic with agents including venetoclax and BET-bromodomain inhibitors. Together, these studies reinforce the concept that WINi are a novel type of ribosome-directed anticancer therapy and provide a resource to support their clinical implementation in MLLr leukemias and other malignancies.
