Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays.
BACKGROUND: Uncovering epigenetic states by chromatin immunoprecipitation and microarray hybridization (ChIP-chip) has significantly contributed to the understanding of gene regulation at the genome-scale level. Many studies have been carried out in mice and humans; however limited high-resolution i...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2010-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3004928?pdf=render |
| _version_ | 1818692328935653376 |
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| author | Leif C Lindeman Andrew H Reiner Sinnakaruppan Mathavan Peter Aleström Philippe Collas |
| author_facet | Leif C Lindeman Andrew H Reiner Sinnakaruppan Mathavan Peter Aleström Philippe Collas |
| author_sort | Leif C Lindeman |
| collection | DOAJ |
| description | BACKGROUND: Uncovering epigenetic states by chromatin immunoprecipitation and microarray hybridization (ChIP-chip) has significantly contributed to the understanding of gene regulation at the genome-scale level. Many studies have been carried out in mice and humans; however limited high-resolution information exists to date for non-mammalian vertebrate species. PRINCIPAL FINDINGS: We report a 2.1-million feature high-resolution Nimblegen tiling microarray for ChIP-chip interrogations of epigenetic states in zebrafish (Danio rerio). The array covers 251 megabases of the genome at 92 base-pair resolution. It includes ∼15 kb of upstream regulatory sequences encompassing all RefSeq promoters, and over 5 kb in the 5' end of coding regions. We identify with high reproducibility, in a fibroblast cell line, promoters enriched in H3K4me3, H3K27me3 or co-enriched in both modifications. ChIP-qPCR and sequential ChIP experiments validate the ChIP-chip data and support the co-enrichment of trimethylated H3K4 and H3K27 on a subset of genes. H3K4me3- and/or H3K27me3-enriched genes are associated with distinct transcriptional status and are linked to distinct functional categories. CONCLUSIONS: We have designed and validated for the scientific community a comprehensive high-resolution tiling microarray for investigations of epigenetic states in zebrafish, a widely used developmental and disease model organism. |
| first_indexed | 2024-12-17T12:56:03Z |
| format | Article |
| id | doaj.art-e67b1427be18455682307893832eb018 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-17T12:56:03Z |
| publishDate | 2010-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-e67b1427be18455682307893832eb0182022-12-21T21:47:28ZengPublic Library of Science (PLoS)PLoS ONE1932-62032010-01-01512e1565110.1371/journal.pone.0015651Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays.Leif C LindemanAndrew H ReinerSinnakaruppan MathavanPeter AleströmPhilippe CollasBACKGROUND: Uncovering epigenetic states by chromatin immunoprecipitation and microarray hybridization (ChIP-chip) has significantly contributed to the understanding of gene regulation at the genome-scale level. Many studies have been carried out in mice and humans; however limited high-resolution information exists to date for non-mammalian vertebrate species. PRINCIPAL FINDINGS: We report a 2.1-million feature high-resolution Nimblegen tiling microarray for ChIP-chip interrogations of epigenetic states in zebrafish (Danio rerio). The array covers 251 megabases of the genome at 92 base-pair resolution. It includes ∼15 kb of upstream regulatory sequences encompassing all RefSeq promoters, and over 5 kb in the 5' end of coding regions. We identify with high reproducibility, in a fibroblast cell line, promoters enriched in H3K4me3, H3K27me3 or co-enriched in both modifications. ChIP-qPCR and sequential ChIP experiments validate the ChIP-chip data and support the co-enrichment of trimethylated H3K4 and H3K27 on a subset of genes. H3K4me3- and/or H3K27me3-enriched genes are associated with distinct transcriptional status and are linked to distinct functional categories. CONCLUSIONS: We have designed and validated for the scientific community a comprehensive high-resolution tiling microarray for investigations of epigenetic states in zebrafish, a widely used developmental and disease model organism.http://europepmc.org/articles/PMC3004928?pdf=render |
| spellingShingle | Leif C Lindeman Andrew H Reiner Sinnakaruppan Mathavan Peter Aleström Philippe Collas Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays. PLoS ONE |
| title | Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays. |
| title_full | Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays. |
| title_fullStr | Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays. |
| title_full_unstemmed | Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays. |
| title_short | Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays. |
| title_sort | tiling histone h3 lysine 4 and 27 methylation in zebrafish using high density microarrays |
| url | http://europepmc.org/articles/PMC3004928?pdf=render |
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