Genome-wide chromatin regulatory signatures in an ultra-compact chordate genome

Chromatin is the template interface through which genetically encoded information is read out to orchestrate a wide diversity of cell and organismal functions. Histone H3 variants have a key role in chromatin: they dictate modes of chromatin assembly, and their post-transcriptional modifications (PTMs) are most clearly characterized in defining transcriptional states and propagating epigenetic memory. We assessed paradigms about how epigenetic coding along expansive vertebrate regulatory and coding regions apply to that in the sister urochordate, Oikopleura, where following strong secondary genome compaction to 70 Mb, gene regulatory regions are compressed to near maximal limits compatible with sophisticated gene regulation. We have developed a robust ChIP protocol on tissue-specific Oikopleura ovary and testes samples and have assessed the results on high resolution whole genome Oikopleura tiling arrays. 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. The epigenome of the male germline reflected a shift from tissue-specific gene expression towards establishment of transgenerational inheritance and showed features related to the mitotic proliferation ongoing in this tissue. Our data support the involvement of a modified Polycomb complex in sex chromosome dosage compensation in homogametic females. We also uncovered an unusual chromatin state specific to the Y-chromosome, that combined active and heterochromatic histone modifications on specific transposable element classes, perhaps involved in regulating their activity. Enhancers, promoters and protein-coding genes have conserved epigenomic features, with adaptations to the organization of a proportion of genes in operon units. Strong secondary genome compaction and disruption of evolutionarily conserved linear genome architecture in O. dioica have been epigenetically accompanied by reduced chromatin state domain widths and a general reduction of heterochromatin. This work provides the first comprehensive view of a protochordate epigenome, providing insight into its organization in two sex-specific tissue samples.

Gene regulation, a prevalent theme in modern molecular biology and medicine, is central to coordination of an organism?s development and response to its environment. Histone H3 variants have a key role in chromatin: they dictate modes of chromatin assembl y, and their post-transcriptional modifications (PTMs) are most clearly characterized in defining transcriptional states and propagating epigenetic memory. Examples indicate that H3 variant complements and combinatorial codes of their PTMs can be modified in different organisms. The limited set of biological model systems employed in these studies leaves provocative research challenges to understand how codes might be altered on different genome architectures, in different cell cycle variants, and in diff erent evolutionary lineages. Urochordates are the sister group to vertebrates and they share a sophisticated chordate developmental program. In carrying out these elaborate programs the urochordate Oikopleura genome has been secondarily compacted to 1/50t h of the human genome size. How do paradigms about epigenetic coding along expansive vertebrate regulatory and coding regions play out on a genome where regulatory regions are compressed to near maximal limits compatible with sophisticated gene regulation ? Genome-wide chromatin cartography has essentially been restricted to diploid, somatic, mitotically proliferating cells. Patterns in transcriptionally active germ cells or those in meiosis remain unknown. What happens to codes in cells that exit mitotic and enter endo- cycles? This step often precedes gene mis-regulation and tumorogensis in humans but in Oikopleura it is a main growth strategy and gene expression in cells with 1500 gene copies is as precisely temporally and spatially regulated as in huma n cells with a mere 2. Experiments in this proposal will address these questions and be of direct relevance to the wide community of biology and biomedical researchers studying epigenetic control of gene regulation.