Journal article
Sex-specific chromatin landscapes in an ultra-compact chordate genome
Epigenetics & chromatin, Vol.10(1), pp.3-3
2017
DOI: 10.1186/s13072-016-0110-4
PMCID: PMC5240408
PMID: 28115992
Abstract
In multicellular organisms, epigenome dynamics are associated with transitions in the cell cycle, development, germline specification, gametogenesis and inheritance. Evolutionarily, regulatory space has increased in complex metazoans to accommodate these functions. In tunicates, the sister lineage to vertebrates, we examine epigenome adaptations to strong secondary genome compaction, sex chromosome evolution and cell cycle modes.
Across the 70 MB
genome, we profiled 19 histone modifications, and RNA polymerase II, CTCF and p300 occupancies, to define chromatin states within two homogeneous tissues with distinct cell cycle modes: ovarian endocycling nurse nuclei and mitotically proliferating germ nuclei in testes. Nurse nuclei had active chromatin states similar to other metazoan epigenomes, with large domains of operon-associated transcription, a general lack of heterochromatin, and a possible role of Polycomb PRC2 in dosage compensation. Testis chromatin states reflected transcriptional activity linked to spermatogenesis and epigenetic marks that have been associated with establishment of transgenerational inheritance in other organisms. We also uncovered an unusual chromatin state specific to the Y-chromosome, which combined active and heterochromatic histone modifications on specific transposable elements classes, perhaps involved in regulating their activity.
Compacted regulatory space in this tunicate genome is accompanied by reduced heterochromatin and chromatin state domain widths. Enhancers, promoters and protein-coding genes have conserved epigenomic features, with adaptations to the organization of a proportion of genes in operon units. We further identified features specific to sex chromosomes, cell cycle modes, germline identity and dosage compensation, and unusual combinations of histone PTMs with opposing consensus functions.
Details
- Title: Subtitle
- Sex-specific chromatin landscapes in an ultra-compact chordate genome
- Creators
- Pavla Navratilova - Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, NorwayGemma Barbara Danks - Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, NorwayAbby Long - Departments of Biology and Pediatrics and the Roy J. Carver Center for Genomics, 459 Biology Building, University of Iowa, Iowa City, IA 52242 USAStephen Butcher - Departments of Biology and Pediatrics and the Roy J. Carver Center for Genomics, 459 Biology Building, University of Iowa, Iowa City, IA 52242 USAJohn Robert Manak - Departments of Biology and Pediatrics and the Roy J. Carver Center for Genomics, 459 Biology Building, University of Iowa, Iowa City, IA 52242 USAEric M Thompson - Department of Biology, University of Bergen, 5020 Bergen, Norway
- Resource Type
- Journal article
- Publication Details
- Epigenetics & chromatin, Vol.10(1), pp.3-3
- DOI
- 10.1186/s13072-016-0110-4
- PMID
- 28115992
- PMCID
- PMC5240408
- NLM abbreviation
- Epigenetics Chromatin
- ISSN
- 1756-8935
- eISSN
- 1756-8935
- Publisher
- England
- Grant note
- DOI: 10.13039/501100005416, name: Norges Forskningsråd, award: 204891, 133335/V40
- Language
- English
- Date published
- 2017
- Academic Unit
- Stead Family Department of Pediatrics; Biology; Craniofacial Anomalies Research Center
- Record Identifier
- 9983992060602771
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