A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster.
Epigenetic research has been focused on cell-type-specific regulation; less is known about common features of epigenetic programming shared by diverse cell types within an organism. Here, we report a modified method for chromatin immunoprecipitation and deep sequencing (ChIP-Seq) and its use to cons...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2011-12-01
|
| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC3240582?pdf=render |
| _version_ | 1828232971792941056 |
|---|---|
| author | Hang Yin Sarah Sweeney Debasish Raha Michael Snyder Haifan Lin |
| author_facet | Hang Yin Sarah Sweeney Debasish Raha Michael Snyder Haifan Lin |
| author_sort | Hang Yin |
| collection | DOAJ |
| description | Epigenetic research has been focused on cell-type-specific regulation; less is known about common features of epigenetic programming shared by diverse cell types within an organism. Here, we report a modified method for chromatin immunoprecipitation and deep sequencing (ChIP-Seq) and its use to construct a high-resolution map of the Drosophila melanogaster key histone marks, heterochromatin protein 1a (HP1a) and RNA polymerase II (polII). These factors are mapped at 50-bp resolution genome-wide and at 5-bp resolution for regulatory sequences of genes, which reveals fundamental features of chromatin modification landscape shared by major adult Drosophila cell types: the enrichment of both heterochromatic and euchromatic marks in transposons and repetitive sequences, the accumulation of HP1a at transcription start sites with stalled polII, the signatures of histone code and polII level/position around the transcriptional start sites that predict both the mRNA level and functionality of genes, and the enrichment of elongating polII within exons at splicing junctions. These features, likely conserved among diverse epigenomes, reveal general strategies for chromatin modifications. |
| first_indexed | 2024-04-12T19:31:51Z |
| format | Article |
| id | doaj.art-43a80ab6c9aa441081d2cfb2aab4fc15 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-12T19:31:51Z |
| publishDate | 2011-12-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-43a80ab6c9aa441081d2cfb2aab4fc152022-12-22T03:19:20ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042011-12-01712e100238010.1371/journal.pgen.1002380A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster.Hang YinSarah SweeneyDebasish RahaMichael SnyderHaifan LinEpigenetic research has been focused on cell-type-specific regulation; less is known about common features of epigenetic programming shared by diverse cell types within an organism. Here, we report a modified method for chromatin immunoprecipitation and deep sequencing (ChIP-Seq) and its use to construct a high-resolution map of the Drosophila melanogaster key histone marks, heterochromatin protein 1a (HP1a) and RNA polymerase II (polII). These factors are mapped at 50-bp resolution genome-wide and at 5-bp resolution for regulatory sequences of genes, which reveals fundamental features of chromatin modification landscape shared by major adult Drosophila cell types: the enrichment of both heterochromatic and euchromatic marks in transposons and repetitive sequences, the accumulation of HP1a at transcription start sites with stalled polII, the signatures of histone code and polII level/position around the transcriptional start sites that predict both the mRNA level and functionality of genes, and the enrichment of elongating polII within exons at splicing junctions. These features, likely conserved among diverse epigenomes, reveal general strategies for chromatin modifications.http://europepmc.org/articles/PMC3240582?pdf=render |
| spellingShingle | Hang Yin Sarah Sweeney Debasish Raha Michael Snyder Haifan Lin A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster. PLoS Genetics |
| title | A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster. |
| title_full | A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster. |
| title_fullStr | A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster. |
| title_full_unstemmed | A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster. |
| title_short | A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster. |
| title_sort | high resolution whole genome map of key chromatin modifications in the adult drosophila melanogaster |
| url | http://europepmc.org/articles/PMC3240582?pdf=render |
| work_keys_str_mv | AT hangyin ahighresolutionwholegenomemapofkeychromatinmodificationsintheadultdrosophilamelanogaster AT sarahsweeney ahighresolutionwholegenomemapofkeychromatinmodificationsintheadultdrosophilamelanogaster AT debasishraha ahighresolutionwholegenomemapofkeychromatinmodificationsintheadultdrosophilamelanogaster AT michaelsnyder ahighresolutionwholegenomemapofkeychromatinmodificationsintheadultdrosophilamelanogaster AT haifanlin ahighresolutionwholegenomemapofkeychromatinmodificationsintheadultdrosophilamelanogaster AT hangyin highresolutionwholegenomemapofkeychromatinmodificationsintheadultdrosophilamelanogaster AT sarahsweeney highresolutionwholegenomemapofkeychromatinmodificationsintheadultdrosophilamelanogaster AT debasishraha highresolutionwholegenomemapofkeychromatinmodificationsintheadultdrosophilamelanogaster AT michaelsnyder highresolutionwholegenomemapofkeychromatinmodificationsintheadultdrosophilamelanogaster AT haifanlin highresolutionwholegenomemapofkeychromatinmodificationsintheadultdrosophilamelanogaster |