OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica

Danks, Gemma B.; Campsteijn, Coen; Parida, Mruyunjaya; Butcher, Stephen; Doddapaneni, Harshavardhan; Fu, Bolei; Petrin, Raul; Metpally, Raghu; Lenhard, Boris; Wincker, Patrick; Chourrout, Daniel; Thompson, Eric M.; Manak, J. Robert

doi:10.1093/nar/gks1159

Cited by 60 publications

(68 citation statements)

References 31 publications

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“…Sampled testes were in the mitotically dividing pre-meiotic (spermatogonia) stage, whereas ovaries were dominated by endocycling, transcriptionally active nurse nuclei. We focused on histone H3 and H4 PTMs and related these profiles to gene expression levels [32], trans -splicing status [28], chromosomal location, and GC content of promoters (Fig. 1; Additional file 1: Supplemental Results; Additional file 2: Fig.…”

Section: Resultsmentioning

confidence: 99%

“…These autonomous elements carry an env gene and are expressed in a variety of Oikopleura tissues including germline-associated cells [31]. A comprehensive developmental transcriptome for O. dioica has been assembled and includes ovary and testes samples [32]. The full histone complement and associated PTMs have also been characterized, showing conservation of histone variants and a histone modification repertoire comparable to vertebrates [33].…”

Section: Introductionmentioning

confidence: 99%

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Sex-specific chromatin landscapes in an ultra-compact chordate genome

Navrátilová

Danks

Long

et al. 2017

Epigenetics & Chromatin

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BackgroundIn 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.ResultsAcross the 70 MB Oikopleura dioica 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.ConclusionsCompacted 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-016-0110-4) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Sex-specific chromatin landscapes in an ultra-compact chordate genome

Navrátilová

Danks

Long

et al. 2017

Epigenetics & Chromatin

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“…The genome compaction in I. linei is reflected in both lower gene count and higher average gene density in comparison with other metazoan genomes. However, it is not the most gene dense among metazoans: the average gene density in the genome of I. linei is around 200 genes per Mb, on par with that of Caenorhabditis elegans [8] but noticeably lower than the gene density in the highly compact genome of a parasitic nematode Trichinella spiralis [9] or a pelagic tunicate Oikopleura dioica [10,11] (Figure S1). Despite its comparatively small size, the genome of I. linei carries a considerable amount of repetitive elementsmore than a quarter of the total assembly size, with the largest contribution to the repetitive element repertoire provided by unclassified repeats (Table S1).…”

Section: Resultsmentioning

confidence: 99%

The Genome of Intoshia linei Affirms Orthonectids as Highly Simplified Spiralians

et al. 2016

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Orthonectids are rare parasites of marine invertebrates [1] that are commonly treated in textbooks as a taxon of uncertain affinity [2]. Trophic forms of orthonectids reside in the tissues of their hosts as multinucleated plasmodia, generating short-lived, worm-like ciliated female and male organisms that exit into the environment for copulation [3]. These ephemeral males and females are composed of just several hundred somatic cells and are deprived of digestive, circulatory, or excretory systems. Since their discovery in the 19(th) century, the orthonectids were described as organisms with no differentiated cell types and considered as part of Mesozoa, a putative link between multicellular animals and their unicellular relatives. More recently, this view was challenged as the new data suggested that orthonectids are animals that became simplified due to their parasitic way of life [3, 4]. Here, we report the genomic sequence of Intoshia linei, one of about 20 known species of orthonectids. The genomic data confirm recent morphological analysis asserting that orthonectids are members of Spiralia and possess muscular and nervous systems [5]. The 43-Mbp genome of I. linei encodes about 9,000 genes and retains those essential for the development and activity of muscular and nervous systems. The simplification of orthonectid body plan is associated with considerable reduction of metazoan developmental genes, leaving what might be viewed as the minimal gene set necessary to retain critical bilaterian features.

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“…Similarly to TtAgo, Argonaute of O. dioica may mediate DNAi, inhibiting transcription and degrading mRNA. In a BLAST search of the O. dioica genome database (OikoBase) [17], we found nine Argonaute family protein homologues bearing both the PAZ and PIWI domains. For host defence, some of these homologues might mediate RNAi in response to dsRNA, whereas others might mediate DNAi in response to introduced DNA.…”

Section: Resultsmentioning

confidence: 99%

DNA interference: DNA-induced gene silencing in the appendicularian Oikopleura dioica

2015

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RNA interference is widely employed as a gene-silencing system in eukaryotes for host defence against invading nucleic acids. In response to invading double-stranded RNA (dsRNA), mRNA is degraded in sequence-specific manner. So far, however, DNA interference (DNAi) has been reported only in plants, ciliates and archaea, and has not been explored in Metazoa. Here, we demonstrate that linear double-stranded DNA promotes both sequencespecific transcription blocking and mRNA degradation in developing embryos of the appendicularian Oikopleura dioica. Introduced polymerase chain reaction (PCR) products or linearized plasmids encoding Brachyury induced tail malformation and mRNA degradation. This malformation was also promoted by DNA fragments of the putative 5 0 -flanking region and intron without the coding region. PCR products encoding Zic-like1 and acetylcholine esterase also induced loss of sensory organ and muscle acetylcholinesterase activity, respectively. Co-injection of mRNA encoding EGFP and mCherry, and PCR products encoding these fluorescent proteins, induced sequence-specific decrease in the green or red fluorescence, respectively. These results suggest that O. dioica possesses a defence system against exogenous DNA and RNA, and that DNA fragment-induced gene silencing would be mediated through transcription blocking as well as mRNA degradation. This is the first report of DNAi in Metazoa.

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OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica

Cited by 60 publications

References 31 publications

Sex-specific chromatin landscapes in an ultra-compact chordate genome

Sex-specific chromatin landscapes in an ultra-compact chordate genome

The Genome of Intoshia linei Affirms Orthonectids as Highly Simplified Spiralians

DNA interference: DNA-induced gene silencing in the appendicularian Oikopleura dioica

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