Genome-wide nucleosome mapping of <it>Plasmodium falciparum </it>reveals histone-rich coding and histone-poor intergenic regions and chromatin remodeling of core and subtelomeric genes
<p>Abstract</p> <p>Background</p> <p>Epigenetic modifications of histones and regulation of chromatin structure have been implicated in regulation of virulence gene families in <it>P. falciparum</it>. To better understand chromatin-mediated gene regulation,...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2009-12-01
|
| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/10/610 |
| _version_ | 1818807880379269120 |
|---|---|
| author | Winzeler Elizabeth Dharia Neekesh Cui Long Westenberger Scott J Cui Liwang |
| author_facet | Winzeler Elizabeth Dharia Neekesh Cui Long Westenberger Scott J Cui Liwang |
| author_sort | Winzeler Elizabeth |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Epigenetic modifications of histones and regulation of chromatin structure have been implicated in regulation of virulence gene families in <it>P. falciparum</it>. To better understand chromatin-mediated gene regulation, we used a high-density oligonucleotide microarray to map the position and enrichment of nucleosomes across the entire genome of <it>P. falciparum </it>at three time points of the intra-erythrocytic developmental cycle (IDC) in vitro. We used an unmodified histone H4 antibody for chromatin immunoprecipitation of nucleosome-bound DNA.</p> <p>Results</p> <p>We observed generally low nucleosomal occupancy of intergenic regions and higher occupancy of protein coding regions. In contract to the overall small fluctuation of nucleosomal occupancy in most coding regions throughout the IDC, subtelomeric genes encoding surface proteins such as <it>var </it>and <it>rif</it>, as well as some core chromosomal genes such as transcription factors, showed large changes in chromatin structure. Telomeres harbored a region with the highest nucleosomal occupancy of the genome and also exhibited large changes with higher nucleosomal occupancy at schizont stages. While many of these subtelomeric genes were previously shown to be modified by H3K9 trimethylation, we also identified some housekeeping genes in core chromosome regions that showed extensive changes in chromatin structure but do not contain this modification. tRNA and basal transcription factor genes showed low nucleosomal occupancy at all times, suggesting of an open chromatin structure that might be permissive for constitutively high levels of expression. Generally, nucleosomal occupancy was not correlated with the steady-state mRNA levels. Several <it>var </it>genes were exceptions: the <it>var </it>gene with the highest expression level showed the lowest nucleosomal occupancy, and selection of parasites for <it>var2CSA </it>expression resulted in lower nucleosomal occupancy at the <it>var2CSA </it>locus. We identified nucleosome-free regions in intergenic regions that may serve as transcription start sites or transcription factor binding sites. Using the nucleosomal occupancy data as the baseline, we further mapped the genome-wide enrichment of H3K9 acetylation and detected general enrichment of this mark in intergenic regions.</p> <p>Conclusions</p> <p>These data on nucleosome enrichment changes add to our understanding of the influence of chromatin structure on the regulation of gene expression. Histones are generally enriched in coding regions, and relatively poor in intergenic regions. Histone enrichment patterns allow for identification of new putative gene-coding regions. Most genes do not show correlation between chromatin structure and steady-state mRNA levels, indicating the dominant roles of other regulatory mechanisms. We present a genome-wide nucleosomal occupancy map, which can be used as a reference for future experiments of histone modification mapping.</p> |
| first_indexed | 2024-12-18T19:32:41Z |
| format | Article |
| id | doaj.art-dafedb367f4e44e396bcd18b5eb3c829 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-18T19:32:41Z |
| publishDate | 2009-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-dafedb367f4e44e396bcd18b5eb3c8292022-12-21T20:55:41ZengBMCBMC Genomics1471-21642009-12-0110161010.1186/1471-2164-10-610Genome-wide nucleosome mapping of <it>Plasmodium falciparum </it>reveals histone-rich coding and histone-poor intergenic regions and chromatin remodeling of core and subtelomeric genesWinzeler ElizabethDharia NeekeshCui LongWestenberger Scott JCui Liwang<p>Abstract</p> <p>Background</p> <p>Epigenetic modifications of histones and regulation of chromatin structure have been implicated in regulation of virulence gene families in <it>P. falciparum</it>. To better understand chromatin-mediated gene regulation, we used a high-density oligonucleotide microarray to map the position and enrichment of nucleosomes across the entire genome of <it>P. falciparum </it>at three time points of the intra-erythrocytic developmental cycle (IDC) in vitro. We used an unmodified histone H4 antibody for chromatin immunoprecipitation of nucleosome-bound DNA.</p> <p>Results</p> <p>We observed generally low nucleosomal occupancy of intergenic regions and higher occupancy of protein coding regions. In contract to the overall small fluctuation of nucleosomal occupancy in most coding regions throughout the IDC, subtelomeric genes encoding surface proteins such as <it>var </it>and <it>rif</it>, as well as some core chromosomal genes such as transcription factors, showed large changes in chromatin structure. Telomeres harbored a region with the highest nucleosomal occupancy of the genome and also exhibited large changes with higher nucleosomal occupancy at schizont stages. While many of these subtelomeric genes were previously shown to be modified by H3K9 trimethylation, we also identified some housekeeping genes in core chromosome regions that showed extensive changes in chromatin structure but do not contain this modification. tRNA and basal transcription factor genes showed low nucleosomal occupancy at all times, suggesting of an open chromatin structure that might be permissive for constitutively high levels of expression. Generally, nucleosomal occupancy was not correlated with the steady-state mRNA levels. Several <it>var </it>genes were exceptions: the <it>var </it>gene with the highest expression level showed the lowest nucleosomal occupancy, and selection of parasites for <it>var2CSA </it>expression resulted in lower nucleosomal occupancy at the <it>var2CSA </it>locus. We identified nucleosome-free regions in intergenic regions that may serve as transcription start sites or transcription factor binding sites. Using the nucleosomal occupancy data as the baseline, we further mapped the genome-wide enrichment of H3K9 acetylation and detected general enrichment of this mark in intergenic regions.</p> <p>Conclusions</p> <p>These data on nucleosome enrichment changes add to our understanding of the influence of chromatin structure on the regulation of gene expression. Histones are generally enriched in coding regions, and relatively poor in intergenic regions. Histone enrichment patterns allow for identification of new putative gene-coding regions. Most genes do not show correlation between chromatin structure and steady-state mRNA levels, indicating the dominant roles of other regulatory mechanisms. We present a genome-wide nucleosomal occupancy map, which can be used as a reference for future experiments of histone modification mapping.</p>http://www.biomedcentral.com/1471-2164/10/610 |
| spellingShingle | Winzeler Elizabeth Dharia Neekesh Cui Long Westenberger Scott J Cui Liwang Genome-wide nucleosome mapping of <it>Plasmodium falciparum </it>reveals histone-rich coding and histone-poor intergenic regions and chromatin remodeling of core and subtelomeric genes BMC Genomics |
| title | Genome-wide nucleosome mapping of <it>Plasmodium falciparum </it>reveals histone-rich coding and histone-poor intergenic regions and chromatin remodeling of core and subtelomeric genes |
| title_full | Genome-wide nucleosome mapping of <it>Plasmodium falciparum </it>reveals histone-rich coding and histone-poor intergenic regions and chromatin remodeling of core and subtelomeric genes |
| title_fullStr | Genome-wide nucleosome mapping of <it>Plasmodium falciparum </it>reveals histone-rich coding and histone-poor intergenic regions and chromatin remodeling of core and subtelomeric genes |
| title_full_unstemmed | Genome-wide nucleosome mapping of <it>Plasmodium falciparum </it>reveals histone-rich coding and histone-poor intergenic regions and chromatin remodeling of core and subtelomeric genes |
| title_short | Genome-wide nucleosome mapping of <it>Plasmodium falciparum </it>reveals histone-rich coding and histone-poor intergenic regions and chromatin remodeling of core and subtelomeric genes |
| title_sort | genome wide nucleosome mapping of it plasmodium falciparum it reveals histone rich coding and histone poor intergenic regions and chromatin remodeling of core and subtelomeric genes |
| url | http://www.biomedcentral.com/1471-2164/10/610 |
| work_keys_str_mv | AT winzelerelizabeth genomewidenucleosomemappingofitplasmodiumfalciparumitrevealshistonerichcodingandhistonepoorintergenicregionsandchromatinremodelingofcoreandsubtelomericgenes AT dharianeekesh genomewidenucleosomemappingofitplasmodiumfalciparumitrevealshistonerichcodingandhistonepoorintergenicregionsandchromatinremodelingofcoreandsubtelomericgenes AT cuilong genomewidenucleosomemappingofitplasmodiumfalciparumitrevealshistonerichcodingandhistonepoorintergenicregionsandchromatinremodelingofcoreandsubtelomericgenes AT westenbergerscottj genomewidenucleosomemappingofitplasmodiumfalciparumitrevealshistonerichcodingandhistonepoorintergenicregionsandchromatinremodelingofcoreandsubtelomericgenes AT cuiliwang genomewidenucleosomemappingofitplasmodiumfalciparumitrevealshistonerichcodingandhistonepoorintergenicregionsandchromatinremodelingofcoreandsubtelomericgenes |