DNA Methylation and Transcription Onset in the Brain

Abstract

Aim: The goal of this study was to test the state of methylation of transcription start positions in DNA that are actively involved in transcription. Materials & methods: We used sequential ChIP-bisulfite-sequencing with an antibody to RNpolII-PS5 to map the state of methylation of actively transcribing transcription start sites (TSS). Results: TSS that RNApolII-PS5 physically bind to, are ubiquitously unmethylated. TSS that appear to be both heavily methylated and transcriptionally active are truly a mixture of unmethylated TSS with bound RNApolII-PS5 in some nuclei and unbound methylated TSS in other nuclei. Conclusion: TSS DNA methylation is universally inconsistent with transcription onset and could therefore serve as a digital count of the fraction of nuclei with methylation-silenced TSS.

Keywords::

• ChIP-bisulfite sequencing
• DNA methylation
• RNAPII
• RNAPII-Ser5
• steady-state mRNA
• transcription onset

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at:www.tandfonline.com/doi/full/10.2217/epi-2016-0184

M Szyf conceived and supervised the study. M Szyf, M Suderman and R Massart wrote the main manuscript text. R Massart and V Mongrain performed experiments. R Massart and M Suderman analyzed the data.

Financial & competing interests disclosure

This study was supported by a grant from the Canadian Institute of Health Research to MS (MOP-42411). Illumina sequencing was performed at Institut de Recherches Cliniques de Montreal (IRCM). The raw sequencing data were submitted to GEO, accession number: GSE60658. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

Brains were derived from animals that were previously sacrificed as controls for other experiments that were approved by Ethical Committee for Animal Experimentation of the Hôpital du Sacré-Coeur de Montréal.

Additional information

Funding

This study was supported by a grant from the Canadian Institute of Health Research to MS (MOP-42411). Illumina sequencing was performed at Institut de Recherches Cliniques de Montreal (IRCM). The raw sequencing data were submitted to GEO, accession number: GSE60658. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.