title: Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis.
abstract: BACKGROUND
  Increasing evidence demonstrates that stem cells maintain their identities by a unique transcription network and chromatin structure. Opposing epigenetic modifications H3K27 me3 and H3K4 me3 have been proposed to label differentiation-associated genes in stem cells, progenitor and precursor cells. In addition, many differentiation-associated genes are maintained at a poised status by recruitment of the initiative RNA Polymerase II (Pol II) at their promoter regions, in preparation for lineage-specific expression upon differentiation. Previous studies have been performed using cultured mammalian embryonic stem cells. To a lesser extent, chromatin structure has been delineated in other model organisms, such as Drosophila, to open new avenues for genetic analyses.
  
  
  RESULTS
  Here we use testes isolated from a Drosophila bag of marbles mutant strain, from which germ cells are in their undifferentiated status. We use these testes to study the endogenous chromatin structure of undifferentiated cells using ChIP-seq. We integrate the ChIP-seq with RNA-seq data, which measures the digital transcriptome. Our genome-wide analyses indicate that most differentiation-associated genes in undifferentiated cells lack an active chromatin mark and initiative Pol II; instead, they are associated with either the repressive H3K27 me3 mark or no detectable mark.
  
  
  CONCLUSIONS
  Our results reveal that most of the differentiation-associated genes in undifferentiated-cell-enriched Drosophila testes are associated with monovalent but not bivalent modifications, a chromatin signature that is distinct from the data reported in mammalian stem or precursor cells, which may reflect cell type specificity, species specificity, or both.
authors.affiliation: Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Gan
authors.forename: Dustin E
authors.initials: DE
authors.lastname: Schones
authors.forename: Suk
authors.initials: S
authors.lastname: Ho Eun
authors.forename: Gang
authors.initials: G
authors.lastname: Wei
authors.forename: Kairong
authors.initials: K
authors.lastname: Cui
authors.forename: Keji
authors.initials: K
authors.lastname: Zhao
authors.forename: Xin
authors.initials: X
authors.lastname: Chen
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000235:genetics; D002843:Chromatin / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D004330:Drosophila / Q000235:genetics*; D029721:Drosophila Proteins / Q000235:genetics; D020869:Gene Expression Profiling; D017344:Genes, Insect; D008297:Male; D013094:Spermatozoa / Q000166:cytology / Q000378:metabolism*; D013234:Stem Cells / Q000166:cytology / Q000378:metabolism*; D013737:Testis / Q000378:metabolism*
chemical_list: D002843:Chromatin; D029721:Drosophila Proteins
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