Complex epigenomes of endocycling ovaries vs. mitotic testis in the closest living relative of vertebrates
Abstract
The animal epigenome is composed of interconnected distinct functions, where the key is a chromatin structure and dynamics. Epigenetic information is highly specific for certain cell type and developmental stage and dynamically changes with the cell cycle. Here we present thorough analysis of epigenome components of maturing gonads of Oikopleura dioica. Use of ovary and testes samples enabled us to compare between mitotic male germline and endocycling female nurse cells. The urochordate Oikopleura is considered the closest relative to vertebrates with a great proportion of its extremely compact genome being splice-led and/or transcribed in operons. Genome-wide ChIP-chip profiles of numerous posttranslational histone modifications, along with RNA polymerase II, CTCF and p300 binding sites were generated from two homogeneous cell population samples. To capture the combinatorial action of the histone modifications we applied unsupervised learning method and annotated the genome with 15 distinct chromatin states and related those to numerous genomic features. Besides many conserved histone modification functions, we found some exceptions, which could be attributed to sex chromosomes, cell cycle mode or germ line-specificity. Interestingly, the nurse nuclei pattern is in agreement to what is known from other metazoan epigenomes, but testis epigenome revealed quite different histone code. In addition, to gain more insight into the cell cycle and developmental stage specificities of the histone modifications, we analyzed expression profiles of panel of histone modifier enzymes and address the complexity of the chromatin dynamics from this point of view. Overall, we provide a detailed structure of an early chordate epigenome.
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