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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- Chromosomes and Gene Expression
RNA polymerase II (RNAPII) transcription initiates bidirectionally at many human protein-coding genes. Sense transcription usually dominates and leads to messenger RNA production, whereas antisense transcription rapidly terminates. The basis for this directionality is not fully understood. Here, we show that sense transcriptional initiation is more efficient than in the antisense direction, which establishes initial promoter directionality. After transcription begins, the opposing functions of the endonucleolytic subunit of Integrator, INTS11, and cyclin-dependent kinase 9 (CDK9) maintain directionality. Specifically, INTS11 terminates antisense transcription, whereas sense transcription is protected from INTS11-dependent attenuation by CDK9 activity. Strikingly, INTS11 attenuates transcription in both directions upon CDK9 inhibition, and the engineered recruitment of CDK9 desensitises transcription to INTS11. Therefore, the preferential initiation of sense transcription and the opposing activities of CDK9 and INTS11 explain mammalian promoter directionality.
