1
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Yokomori R, Kusakabe TG, Nakai K. Characterization of trans-spliced chimeric RNAs: insights into the mechanism of trans-splicing. NAR Genom Bioinform 2024; 6:lqae067. [PMID: 38846348 PMCID: PMC11155486 DOI: 10.1093/nargab/lqae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 05/13/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
Trans-splicing is a post-transcriptional processing event that joins exons from separate RNAs to produce a chimeric RNA. However, the detailed mechanism of trans-splicing remains poorly understood. Here, we characterize trans-spliced genes and provide insights into the mechanism of trans-splicing in the tunicate Ciona. Tunicates are the closest invertebrates to humans, and their genes frequently undergo trans-splicing. Our analysis revealed that, in genes that give rise to both trans-spliced and non-trans-spliced messenger RNAs, trans-splice acceptor sites were preferentially located at the first functional acceptor site, and their paired donor sites were weak in both Ciona and humans. Additionally, we found that Ciona trans-spliced genes had GU- and AU-rich 5' transcribed regions. Our data and findings not only are useful for Ciona research community, but may also aid in a better understanding of the trans-splicing mechanism, potentially advancing the development of gene therapy based on trans-splicing.
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Affiliation(s)
- Rui Yokomori
- Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Takehiro G Kusakabe
- Institute for Integrative Neurobiology, Graduate School of Natural Science, Konan University, Kobe 658-8501, Japan
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan
| | - Kenta Nakai
- Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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2
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Satou Y, Tokuoka M, Oda-Ishii I, Tokuhiro S, Ishida T, Liu B, Iwamura Y. A Manually Curated Gene Model Set for an Ascidian, Ciona robusta (Ciona intestinalis Type A). Zoolog Sci 2022; 39:253-260. [DOI: 10.2108/zs210102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/15/2022] [Indexed: 11/17/2022]
Affiliation(s)
- Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Miki Tokuoka
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Izumi Oda-Ishii
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Sinichi Tokuhiro
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Tasuku Ishida
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Boqi Liu
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yuri Iwamura
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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3
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Oonuma K, Yamamoto M, Moritsugu N, Okawa N, Mukai M, Sotani M, Tsunemi S, Sugimoto H, Nakagome E, Hasegawa Y, Shimai K, Horie T, Kusakabe TG. Evolution of Developmental Programs for the Midline Structures in Chordates: Insights From Gene Regulation in the Floor Plate and Hypochord Homologues of Ciona Embryos. Front Cell Dev Biol 2021; 9:704367. [PMID: 34235159 PMCID: PMC8256262 DOI: 10.3389/fcell.2021.704367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 05/25/2021] [Indexed: 11/24/2022] Open
Abstract
In vertebrate embryos, dorsal midline tissues, including the notochord, the prechordal plate, and the floor plate, play important roles in patterning of the central nervous system, somites, and endodermal tissues by producing extracellular signaling molecules, such as Sonic hedgehog (Shh). In Ciona, hedgehog.b, one of the two hedgehog genes, is expressed in the floor plate of the embryonic neural tube, while none of the hedgehog genes are expressed in the notochord. We have identified a cis-regulatory region of hedgehog.b that was sufficient to drive a reporter gene expression in the floor plate. The hedgehog.b cis-regulatory region also drove ectopic expression of the reporter gene in the endodermal strand, suggesting that the floor plate and the endodermal strand share a part of their gene regulatory programs. The endodermal strand occupies the same topographic position of the embryo as does the vertebrate hypochord, which consists of a row of single cells lined up immediately ventral to the notochord. The hypochord shares expression of several genes with the floor plate, including Shh and FoxA, and play a role in dorsal aorta development. Whole-embryo single-cell transcriptome analysis identified a number of genes specifically expressed in both the floor plate and the endodermal strand in Ciona tailbud embryos. A Ciona FoxA ortholog FoxA.a is shown to be a candidate transcriptional activator for the midline gene battery. The present findings suggest an ancient evolutionary origin of a common developmental program for the midline structures in Olfactores.
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Affiliation(s)
- Kouhei Oonuma
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan.,Institute for Integrative Neurobiology, Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Maho Yamamoto
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan
| | - Naho Moritsugu
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan
| | - Nanako Okawa
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan.,Institute for Integrative Neurobiology, Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Megumi Mukai
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan.,Institute for Integrative Neurobiology, Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Miku Sotani
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan.,Institute for Integrative Neurobiology, Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Shuto Tsunemi
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan.,Institute for Integrative Neurobiology, Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Haruka Sugimoto
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan
| | - Eri Nakagome
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan
| | - Yuichi Hasegawa
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan.,Institute for Integrative Neurobiology, Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Kotaro Shimai
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan.,Institute for Integrative Neurobiology, Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Takeo Horie
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Japan
| | - Takehiro G Kusakabe
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan.,Institute for Integrative Neurobiology, Graduate School of Natural Science, Konan University, Kobe, Japan
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4
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Liu Q, Jiang F, Zhang J, Li X, Kang L. Transcription initiation of distant core promoters in a large-sized genome of an insect. BMC Biol 2021; 19:62. [PMID: 33785021 PMCID: PMC8011201 DOI: 10.1186/s12915-021-01004-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 03/16/2021] [Indexed: 12/30/2022] Open
Abstract
Background Core promoters have a substantial influence on various steps of transcription, including initiation, elongation, termination, polyadenylation, and finally, translation. The characterization of core promoters is crucial for exploring the regulatory code of transcription initiation. However, the current understanding of insect core promoters is focused on those of Diptera (especially Drosophila) species with small genome sizes. Results Here, we present an analysis of the transcription start sites (TSSs) in the migratory locust, Locusta migratoria, which has a genome size of 6.5 Gb. The genomic differences, including lower precision of transcription initiation and fewer constraints on the distance from transcription factor binding sites or regulatory elements to TSSs, were revealed in locusts compared with Drosophila insects. Furthermore, we found a distinct bimodal log distribution of the distances from the start codons to the core promoters of locust genes. We found stricter constraints on the exon length of mRNA leaders and widespread expression activity of the distant core promoters in locusts compared with fruit flies. We further compared core promoters in seven arthropod species across a broad range of genome sizes to reinforce our results on the emergence of distant core promoters in large-sized genomes. Conclusions In summary, our results provide novel insights into the effects of genome size expansion on distant transcription initiation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01004-5.
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Affiliation(s)
- Qing Liu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Feng Jiang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Jie Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xiao Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Kang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China. .,State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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5
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Satou Y, Nakamura R, Yu D, Yoshida R, Hamada M, Fujie M, Hisata K, Takeda H, Satoh N. A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona. Genome Biol Evol 2020; 11:3144-3157. [PMID: 31621849 PMCID: PMC6836712 DOI: 10.1093/gbe/evz228] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2019] [Indexed: 02/07/2023] Open
Abstract
Since its initial publication in 2002, the genome of Ciona intestinalis type A (Ciona robusta), the first genome sequence of an invertebrate chordate, has provided a valuable resource for a wide range of biological studies, including developmental biology, evolutionary biology, and neuroscience. The genome assembly was updated in 2008, and it included 68% of the sequence information in 14 pairs of chromosomes. However, a more contiguous genome is required for analyses of higher order genomic structure and of chromosomal evolution. Here, we provide a new genome assembly for an inbred line of this animal, constructed with short and long sequencing reads and Hi-C data. In this latest assembly, over 95% of the 123 Mb of sequence data was included in the chromosomes. Short sequencing reads predicted a genome size of 114-120 Mb; therefore, it is likely that the current assembly contains almost the entire genome, although this estimate of genome size was smaller than previous estimates. Remapping of the Hi-C data onto the new assembly revealed a large inversion in the genome of the inbred line. Moreover, a comparison of this genome assembly with that of Ciona savignyi, a different species in the same genus, revealed many chromosomal inversions between these two Ciona species, suggesting that such inversions have occurred frequently and have contributed to chromosomal evolution of Ciona species. Thus, the present assembly greatly improves an essential resource for genome-wide studies of ascidians.
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Affiliation(s)
- Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Japan
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan
| | - Deli Yu
- Department of Zoology, Graduate School of Science, Kyoto University, Japan
| | - Reiko Yoshida
- Department of Zoology, Graduate School of Science, Kyoto University, Japan
| | - Mayuko Hamada
- Ushimado Marine Institute, Faculty of Science, Okayama University, Setouchi, Japan
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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6
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Danks GB, Galbiati H, Raasholm M, Torres Cleuren YN, Valen E, Navratilova P, Thompson EM. Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR. BMC Genomics 2019; 20:908. [PMID: 31783727 PMCID: PMC6883708 DOI: 10.1186/s12864-019-6277-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 11/13/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND In phylogenetically diverse organisms, the 5' ends of a subset of mRNAs are trans-spliced with a spliced leader (SL) RNA. The functions of SL trans-splicing, however, remain largely enigmatic. RESULTS We quantified translation genome-wide in the marine chordate, Oikopleura dioica, under inhibition of mTOR, a central growth regulator. Translation of trans-spliced TOP mRNAs was suppressed, consistent with a role of the SL sequence in nutrient-dependent translational control of growth-related mRNAs. Under crowded, nutrient-limiting conditions, O. dioica continued to filter-feed, but arrested growth until favorable conditions returned. Upon release from unfavorable conditions, initial recovery was independent of nutrient-responsive, trans-spliced genes, suggesting animal density sensing as a first trigger for resumption of development. CONCLUSION Our results are consistent with a proposed role of trans-splicing in the coordinated translational down-regulation of nutrient-responsive genes under growth-limiting conditions.
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Affiliation(s)
- Gemma B Danks
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway.
| | - Heloisa Galbiati
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Martina Raasholm
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway.,University of Ulm, Ulm, Germany
| | - Yamila N Torres Cleuren
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway.,Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Eivind Valen
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway.,Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Pavla Navratilova
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway.,Inst Expt Bot, Czech Acad Sci, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Eric M Thompson
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway. .,Department of Biological Sciences, University of Bergen, Bergen, Norway.
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7
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Racioppi C, Wiechecki KA, Christiaen L. Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices. eLife 2019; 8:49921. [PMID: 31746740 PMCID: PMC6952182 DOI: 10.7554/elife.49921] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/18/2019] [Indexed: 12/22/2022] Open
Abstract
During embryogenesis, chromatin accessibility profiles control lineage-specific gene expression by modulating transcription, thus impacting multipotent progenitor states and subsequent fate choices. Subsets of cardiac and pharyngeal/head muscles share a common origin in the cardiopharyngeal mesoderm, but the chromatin landscapes that govern multipotent progenitors competence and early fate choices remain largely elusive. Here, we leveraged the simplicity of the chordate model Ciona to profile chromatin accessibility through stereotyped transitions from naive Mesp+ mesoderm to distinct fate-restricted heart and pharyngeal muscle precursors. An FGF-Foxf pathway acts in multipotent progenitors to establish cardiopharyngeal-specific patterns of accessibility, which govern later heart vs. pharyngeal muscle-specific expression profiles, demonstrating extensive spatiotemporal decoupling between early cardiopharyngeal enhancer accessibility and late cell-type-specific activity. We found that multiple cis-regulatory elements, with distinct chromatin accessibility profiles and motif compositions, are required to activate Ebf and Tbx1/10, two key determinants of cardiopharyngeal fate choices. We propose that these 'combined enhancers' foster spatially and temporally accurate fate choices, by increasing the repertoire of regulatory inputs that control gene expression, through either accessibility and/or activity.
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Affiliation(s)
- Claudia Racioppi
- Center for Developmental Genetics, Department of Biology, New York University, New York, United States
| | - Keira A Wiechecki
- Center for Developmental Genetics, Department of Biology, New York University, New York, United States
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, United States
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8
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Yu D, Oda-Ishii I, Kubo A, Satou Y. The regulatory pathway from genes directly activated by maternal factors to muscle structural genes in ascidian embryos. Development 2019; 146:dev.173104. [PMID: 30674480 DOI: 10.1242/dev.173104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/14/2019] [Indexed: 10/27/2022]
Abstract
Striated muscle cells in the tail of ascidian tadpole larvae differentiate cell-autonomously. Although several key regulatory factors have been identified, the genetic regulatory pathway is not fully understood; comprehensive understanding of the regulatory pathway is essential for accurate modeling in order to deduce principles for gene regulatory network dynamics, and for comparative analysis on how ascidians have evolved the cell-autonomous gene regulatory mechanism. Here, we reveal regulatory interactions among three key regulatory factors, Zic-r.b, Tbx6-r.b and Mrf, and elucidate the mechanism by which these factors activate muscle structural genes. We reveal a cross-regulatory circuit among these regulatory factors, which maintains the expression of Tbx6-r.b and Mrf during gastrulation. Although these two factors combinatorially activate muscle structural genes in late-stage embryos, muscle structural genes are activated mainly by Tbx6-r.b before gastrulation. Time points when expression of muscle structural genes become first detectable are strongly correlated with the degree of Tbx6-r.b occupancy. Thus, the genetic pathway, starting with Tbx6-r.b and Zic-r.b, which are activated by maternal factors, and ending with expression of muscle structural genes, has been revealed.
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Affiliation(s)
- Deli Yu
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Izumi Oda-Ishii
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Atsushi Kubo
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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9
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Oonuma K, Kusakabe TG. Spatio-temporal regulation of Rx and mitotic patterns shape the eye-cup of the photoreceptor cells in Ciona. Dev Biol 2018; 445:245-255. [PMID: 30502325 DOI: 10.1016/j.ydbio.2018.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/18/2018] [Accepted: 11/18/2018] [Indexed: 10/27/2022]
Abstract
The ascidian larva has a pigmented ocellus comprised of a cup-shaped array of approximately 30 photoreceptor cells, a pigment cell, and three lens cells. Morphological, physiological and molecular evidence has suggested evolutionary kinship between the ascidian larval photoreceptors and vertebrate retinal and/or pineal photoreceptors. Rx, an essential factor for vertebrate photoreceptor development, has also been suggested to be involved in the development of the ascidian photoreceptor cells, but a recent revision of the photoreceptor cell lineage raised a crucial discrepancy between the reported expression patterns of Rx and the cell lineage. Here, we report spatio-temporal expression patterns of Rx at single-cell resolution along with mitotic patterns up to the final division of the photoreceptor-lineage cells in Ciona. The expression of Rx commences in non-photoreceptor a-lineage cells on the right side of the anterior sensory vesicle at the early tailbud stage. At the mid tailbud stage, Rx begins to be expressed in the A-lineage photoreceptor cell progenitors located on the right side of the posterior sensory vesicle. Thus, Rx is specifically but not exclusively expressed in the photoreceptor-lineage cells in the ascidian embryo. Two cis-regulatory modules are shown to be important for the photoreceptor-lineage expression of Rx. The cell division patterns of the photoreceptor-lineage cells rationally explain the generation of the cup-shaped structure of the pigmented ocellus. The present findings demonstrate the complete cell lineage of the ocellus photoreceptor cells and provide a framework elucidating the molecular and cellular mechanisms of photoreceptor development in Ciona.
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Affiliation(s)
- Kouhei Oonuma
- Institute for Integrative Neurobiology and Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan.
| | - Takehiro G Kusakabe
- Institute for Integrative Neurobiology and Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan.
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10
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Danks GB, Navratilova P, Lenhard B, Thompson EM. Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate. BMC Genomics 2018; 19:164. [PMID: 29482522 PMCID: PMC6389100 DOI: 10.1186/s12864-018-4504-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/28/2018] [Indexed: 01/28/2023] Open
Abstract
Background Development is largely driven by transitions between transcriptional programs. The initiation of transcription at appropriate sites in the genome is a key component of this and yet few rules governing selection are known. Here, we used cap analysis of gene expression (CAGE) to generate bp-resolution maps of transcription start sites (TSSs) across the genome of Oikopleura dioica, a member of the closest living relatives to vertebrates. Results Our TSS maps revealed promoter features in common with vertebrates, as well as striking differences, and uncovered key roles for core promoter elements in the regulation of development. During spermatogenesis there is a genome-wide shift in mode of transcription initiation characterized by a novel core promoter element. This element was associated with > 70% of male-specific transcription, including the use of cryptic internal promoters within operons. In many cases this led to the exclusion of trans-splice sites, revealing a novel mechanism for regulating which mRNAs receive the spliced leader. Binding of the cell cycle regulator, E2F1, is enriched at the TSS of maternal genes in endocycling nurse nuclei. In addition, maternal promoters lack the TATA-like element found in zebrafish and have broad, rather than sharp, architectures with ordered nucleosomes. Promoters of ribosomal protein genes lack the highly conserved TCT initiator. We also report an association between DNA methylation on transcribed gene bodies and the TATA-box. Conclusions Our results reveal that distinct functional promoter classes and overlapping promoter codes are present in protochordates like in vertebrates, but show extraordinary lineage-specific innovations. Furthermore, we uncover a genome-wide, developmental stage-specific shift in the mode of TSS selection. Our results provide a rich resource for the study of promoter structure and evolution in Metazoa. Electronic supplementary material The online version of this article (10.1186/s12864-018-4504-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gemma B Danks
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5006, Norway.
| | - Pavla Navratilova
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5006, Norway
| | - Boris Lenhard
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5006, Norway.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, W12 0NN, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Eric M Thompson
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5006, Norway. .,Department of Biology, University of Bergen, Bergen, N-5006, Norway.
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11
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Brozovic M, Dantec C, Dardaillon J, Dauga D, Faure E, Gineste M, Louis A, Naville M, Nitta KR, Piette J, Reeves W, Scornavacca C, Simion P, Vincentelli R, Bellec M, Aicha SB, Fagotto M, Guéroult-Bellone M, Haeussler M, Jacox E, Lowe EK, Mendez M, Roberge A, Stolfi A, Yokomori R, Brown C, Cambillau C, Christiaen L, Delsuc F, Douzery E, Dumollard R, Kusakabe T, Nakai K, Nishida H, Satou Y, Swalla B, Veeman M, Volff JN, Lemaire P. ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucleic Acids Res 2018; 46:D718-D725. [PMID: 29149270 PMCID: PMC5753386 DOI: 10.1093/nar/gkx1108] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/22/2017] [Accepted: 11/09/2017] [Indexed: 12/14/2022] Open
Abstract
ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.
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Affiliation(s)
| | | | | | - Delphine Dauga
- Bioself Communication; 28 rue de la Bibliothèque, F-13001 Marseille, France
| | - Emmanuel Faure
- Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
- Team VORTEX, Institut de Recherche en Informatique de Toulouse, Universities Toulouse I and III, CNRS, INPT, ENSEEIHT; 2 rue Camichel, BP 7122, F-31071 Toulouse Cedex 7, France
| | | | - Alexandra Louis
- DYOGEN, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005, Paris, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
| | - Kazuhiro R Nitta
- IBDM, Aix-Marseille Université, CNRS, Campus de Luminy, Case 907; 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | - Jacques Piette
- CRBM, Université de Montpellier, CNRS, Montpellier, France
| | - Wendy Reeves
- Division of Biology, Kansas State University, Manhattan, Kansas
| | | | - Paul Simion
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Renaud Vincentelli
- AFMB, Aix-Marseille Université, CNRS, Campus de Luminy, Case 932, 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | | | - Sameh Ben Aicha
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
| | | | | | - Maximilian Haeussler
- Santa Cruz Genomics Institute, MS CBSE, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Edwin Jacox
- CRBM, Université de Montpellier, CNRS, Montpellier, France
| | - Elijah K Lowe
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA
| | - Mickael Mendez
- IBDM, Aix-Marseille Université, CNRS, Campus de Luminy, Case 907; 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | | | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Rui Yokomori
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo 108-8639, Japan
| | - C Titus Brown
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Christian Cambillau
- AFMB, Aix-Marseille Université, CNRS, Campus de Luminy, Case 932, 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | - Lionel Christiaen
- New York University, Center for Developmental Genetics, Department of Biology, 1009 Silver Center, 100 Washington Square East, New York City, NY10003, USA
| | - Frédéric Delsuc
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Emmanuel Douzery
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Rémi Dumollard
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
| | - Takehiro Kusakabe
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan
| | - Kenta Nakai
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo 108-8639, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Billie Swalla
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA
- Friday Harbor Laboratories, 620 University Road, Friday Harbor, WA 98250-9299, USA
| | - Michael Veeman
- Division of Biology, Kansas State University, Manhattan, Kansas
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
| | - Patrick Lemaire
- CRBM, Université de Montpellier, CNRS, Montpellier, France
- Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
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