Pitfalls in global normalization of ChIP-seq data in CD4+ T cells treated with butyrate: A possible solution strategy
Regulatory T cells (Treg) play a central role in the suppression of inflammatory and allergic responses. Colonization of certain gut commensal microbes such as Clostridia class IV and XIVa in the gut can induce development of colonic Treg cells contributing to the maintenance of gut immune homeostas...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2014-12-01
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| Series: | Genomics Data |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2213596014000518 |
| _version_ | 1818849836020006912 |
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| author | Yukihiro Furusawa Takaho A. Endo Yuuki Obata Osamu Ohara Hiroshi Ohno Koji Hase |
| author_facet | Yukihiro Furusawa Takaho A. Endo Yuuki Obata Osamu Ohara Hiroshi Ohno Koji Hase |
| author_sort | Yukihiro Furusawa |
| collection | DOAJ |
| description | Regulatory T cells (Treg) play a central role in the suppression of inflammatory and allergic responses. Colonization of certain gut commensal microbes such as Clostridia class IV and XIVa in the gut can induce development of colonic Treg cells contributing to the maintenance of gut immune homeostasis. Clostridia-derived butyrate promotes the differentiation of naïve T cells into Treg cells through upregulation of Foxp3, the master transcription factor of Treg cells. Chromatin immunoprecipitation-sequencing (ChIP-seq) analysis revealed that treatment of naïve T cells with butyrate induces Treg-polarizing conditions by enhanced histone H3 acetylation in the promoter and conserved non-coding sequence regions of the Foxp3 locus. In general, global normalization was utilized for ChIP-seq analysis to compare the data obtained from two or more samples. However, global normalization is not appropriate for the evaluation of ChIP-seq data when treatment can affect the total amount of target protein. Here, we introduce a unique normalization method for ChIP-seq analysis in cells treated with butyrate, a pan-HDAC inhibitor that is likely to affect total acetylation levels of histone H3. |
| first_indexed | 2024-12-19T06:39:33Z |
| format | Article |
| id | doaj.art-f547577dd7124e889b2b7d30e054d83a |
| institution | Directory Open Access Journal |
| issn | 2213-5960 |
| language | English |
| last_indexed | 2024-12-19T06:39:33Z |
| publishDate | 2014-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Genomics Data |
| spelling | doaj.art-f547577dd7124e889b2b7d30e054d83a2022-12-21T20:32:07ZengElsevierGenomics Data2213-59602014-12-012C17618010.1016/j.gdata.2014.06.018Pitfalls in global normalization of ChIP-seq data in CD4+ T cells treated with butyrate: A possible solution strategyYukihiro Furusawa0Takaho A. Endo1Yuuki Obata2Osamu Ohara3Hiroshi Ohno4Koji Hase5Graduate School of Pharmaceutical Science, Keio University, Tokyo 105-8512, JapanRIKEN Center for Integrative Medical Sciences (IMS-RCAI), Kanagawa 230 0045, JapanGraduate School of Pharmaceutical Science, Keio University, Tokyo 105-8512, JapanRIKEN Center for Integrative Medical Sciences (IMS-RCAI), Kanagawa 230 0045, JapanRIKEN Center for Integrative Medical Sciences (IMS-RCAI), Kanagawa 230 0045, JapanGraduate School of Pharmaceutical Science, Keio University, Tokyo 105-8512, JapanRegulatory T cells (Treg) play a central role in the suppression of inflammatory and allergic responses. Colonization of certain gut commensal microbes such as Clostridia class IV and XIVa in the gut can induce development of colonic Treg cells contributing to the maintenance of gut immune homeostasis. Clostridia-derived butyrate promotes the differentiation of naïve T cells into Treg cells through upregulation of Foxp3, the master transcription factor of Treg cells. Chromatin immunoprecipitation-sequencing (ChIP-seq) analysis revealed that treatment of naïve T cells with butyrate induces Treg-polarizing conditions by enhanced histone H3 acetylation in the promoter and conserved non-coding sequence regions of the Foxp3 locus. In general, global normalization was utilized for ChIP-seq analysis to compare the data obtained from two or more samples. However, global normalization is not appropriate for the evaluation of ChIP-seq data when treatment can affect the total amount of target protein. Here, we introduce a unique normalization method for ChIP-seq analysis in cells treated with butyrate, a pan-HDAC inhibitor that is likely to affect total acetylation levels of histone H3.http://www.sciencedirect.com/science/article/pii/S2213596014000518ChIP-seqMicroarrayButyrateHDACNormalizationRegulatory T cells |
| spellingShingle | Yukihiro Furusawa Takaho A. Endo Yuuki Obata Osamu Ohara Hiroshi Ohno Koji Hase Pitfalls in global normalization of ChIP-seq data in CD4+ T cells treated with butyrate: A possible solution strategy Genomics Data ChIP-seq Microarray Butyrate HDAC Normalization Regulatory T cells |
| title | Pitfalls in global normalization of ChIP-seq data in CD4+ T cells treated with butyrate: A possible solution strategy |
| title_full | Pitfalls in global normalization of ChIP-seq data in CD4+ T cells treated with butyrate: A possible solution strategy |
| title_fullStr | Pitfalls in global normalization of ChIP-seq data in CD4+ T cells treated with butyrate: A possible solution strategy |
| title_full_unstemmed | Pitfalls in global normalization of ChIP-seq data in CD4+ T cells treated with butyrate: A possible solution strategy |
| title_short | Pitfalls in global normalization of ChIP-seq data in CD4+ T cells treated with butyrate: A possible solution strategy |
| title_sort | pitfalls in global normalization of chip seq data in cd4 t cells treated with butyrate a possible solution strategy |
| topic | ChIP-seq Microarray Butyrate HDAC Normalization Regulatory T cells |
| url | http://www.sciencedirect.com/science/article/pii/S2213596014000518 |
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