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A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation

Mario Iurlaro1, Gabriella Ficz2*, David Oxley3, Eun-Ang Raiber4, Martin Bachman45, Michael J Booth4, Simon Andrews7, Shankar Balasubramanian456 and Wolf Reik189*

Author Affiliations

1 Epigenetics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK

2 Centre for Haemato-Oncology, Barts Cancer Institute, Charterhouse Square, London EC1M 6BQ, UK

3 Proteomics Research Group, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK

4 Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK

5 Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson way, Cambridge CB2 0RE, UK

6 School of Clinical Medicine, The University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0SP, UK

7 Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK

8 Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK

9 1Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK

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Genome Biology 2013, 14:R119  doi:10.1186/gb-2013-14-10-r119

Published: 24 October 2013

Additional files

Additional file 1:

Complete pull-down data. Excel file with table showing all proteins identified by mass spectrometry in the three replicates, with their corresponding spectral counts. Sheet 1 lists proteins identified by the Fgf15 probe, sheet 2 lists proteins identified by the Pax6 probe.

Format: XLSX Size: 152KB Download file

Open Data

Additional file 2:

Pull-down data relative to all proteins with significant enrichment. Excel file with table showing all proteins that passed the significance test, with their corresponding spectral counts in the three replicates and P value. Sheet 1 lists proteins identified by the Fgf15 probe, sheet 2 lists proteins identified by the Pax6 probe.

Format: XLSX Size: 104KB Download file

Open Data

Additional file 3:

DAVID Gene ontology analysis on proteins enriched for C, 5mC and 5hmC on the Fgf15 probe. Enrichment for 5fC is shown in Figure 2b. Results are expressed with their corresponding Benjamini-corrected P value.

Format: PDF Size: 715KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

DAVID Gene ontology analysis on proteins enriched for C, 5mC and 5hmC on the Pax6 probe. 5fC binding proteins showed no significant term enrichment. Results are expressed with their corresponding Benjamini-corrected P value.

Format: PDF Size: 721KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Knockdown efficiency. Bar plots showing knockdown efficiency in mESC. Dark grey bars indicate mRNA levels in the knockdown samples, light grey in the control samples (transfected with non-targeting siRNA).

Format: PDF Size: 630KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

Mass spectrometry of nucleosides data. Excel file showing mass spectrometry data from the knockdown samples (four biological replicates each).

Format: XLSX Size: 55KB Download file

Open Data