Open Access Highly Accessed Research article

CpG islands under selective pressure are enriched with H3K4me3, H3K27ac and H3K36me3 histone modifications

Most Mauluda Akhtar14*, Giovanni Scala123, Sergio Cocozza14, Gennaro Miele123 and Antonella Monticelli15

Author Affiliations

1 “Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale, Università di Napoli “Federico II” - Università di Salerno, Naples, Italy

2 Dipartimento di Fisica, Università degli Studi di Napoli “Federico II”, Naples, Italy

3 Istituto Nazionale di Fisica Nucleare – Sezione di Napoli, Naples, Italy

4 Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli “Federico II”, Naples, Italy

5 CNR, Istituto di Endocrinologia ed Oncologia Sperimentale IEOS, Naples, Italy

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BMC Evolutionary Biology 2013, 13:145  doi:10.1186/1471-2148-13-145

Published: 10 July 2013

Additional files

Additional file 1: Table S1:

Characteristics of cell lines used in this study.

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Additional file 2: Table S2:

Raw data used to calculate CGIs enriched with H3K4me3, H3K27ac and H3K36me3 in different cell lines.

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Additional file 3:

Euler diagram showing the overlaps among CGIs localized in the regions under selective pressure detected by the three methods used.

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Additional file 4: Table S3:

Raw data used to calculate CGIs enriched with H3K4me3, H3K27ac and H3K36me3 at 5’, intragenic, 3’ and intergenic locations in different cell lines.

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Additional file 5:

Enrichment of H3K4me3 modification in 5’ CpG islands under selective pressure. Black bars represent the fraction of CGIs containing histone modification marks within regions that show signatures of natural selection (HIRs, CEs and 5LSRs). Grey bars represent the fraction of CGIs containing histone modification marks within regions that do not show signatures of selective events. The X-axis indicates the analyzed cell lines. An asterisk (*) above a bar indicates a statistically non-significant difference.

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Additional file 6:

Enrichment of H3K27ac modification in 5’ CpG islands under selective pressure. Same notation as Additional file 5.

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Additional file 7:

Enrichment of H3K36me3 modification in 5’ CpG islands under selective pressure. Same notation as Additional file 5.

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Additional file 8:

Enrichment of H3K36me3 modification in intragenic CpG islands under selective pressure. Same notation as Additional file 5.

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Additional file 9:

Enrichment of H3K36me3 modification in 3’ CpG islands under selective pressure. Same notation as Additional file 5.

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Additional file 10:

Enrichment of H3K4me3 modification in intragenic CpG islands under selective pressure. Same notation as Additional file 5.

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Additional file 11:

Enrichment of H3K4me3 modification in 3’ CpG islands under selective pressure. Same notation as Additional file 5.

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Additional file 12:

Enrichment of H3K27ac modification in intragenic CpG islands under selective pressure. Same notation as Additional file 5.

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Additional file 13:

Enrichment of H3K27ac modification in 3’ CpG islands under selective pressure. Same notation as Additional file 5.

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Additional file 14:

Enrichment of H3K4me3 modification in intergenic CpG islands under selective pressure. Same notation as Additional file 5.

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Additional file 15:

Enrichment of H3K27ac modification in intergenic CpG islands under selective pressure. Same notation as Additional file 5.

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Additional file 16:

Enrichment of H3K36me3 modification in intergenic CpG islands under selective pressure. Same notation as Additional file 5.

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Additional file 17:

Enrichment of H3K4me3 modification in hypo-deaminated CpG islands under selective pressure. Same notation as Additional file 5.

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Additional file 18:

Enrichment of H3K4me3 modification in BGC CpG islands under selective pressure. Same notation as Additional file 5.

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Additional file 19:

Enrichment of H3K27ac modification in hypo-deaminated CpG islands under selective pressure. Same notation as Additional file 5.

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Additional file 20:

Enrichment of H3K27ac modification in BGC CpG islands under selective pressure. Same notation as Additional file 5.

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Additional file 21:

Enrichment of H3K36me3 modification in hypo-deaminated CpG islands under selective pressure. Same notation as Additional file 5.

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Additional file 22:

Enrichment of H3K36me3 modification in BGC CpG islands under selective pressure. Same notation as Additional file 5.

Format: PDF Size: 559KB Download file

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Additional file 23: Table S4:

Raw data used to calculate CGIs enriched with H3K4me3, H3K27ac and H3K36me3 in different cell lines according to the CGIs evolutionary model.

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Additional file 24: Table S5:

Lists number of PS genes that are present in each class defined by the possible presence of each signature of selection (“+” stands for presence, “-” stands for absence) and by the membership to DE set (“+” stands for belonging, “-” stands for not belonging). The exact Fisher’s test p-values are reported, highlighting the statistical significant ones.

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Additional file 25: Table S6:

Lists percentages of PS genes for classes defined by the possible presence of each signature of selection (“+” stands for presence, “-” stands for absence) and by the membership to DE set (“+” stands for belonging, “-” stands for not belonging). For each selection signature we give the p-value for the percentages of PS genes in case of DE + compared with DE - (p-values are reported on the same row), and in case of DE + considering the classes of genes under selection or not under selection (p-values are reported on the same column). The p-values are obtained by means of an exact Fisher’s test, highlighting the statistical significant values.

Format: XLS Size: 12KB Download file

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