TOHOKU UNIVERSITY Researchers

Research History 5

2024/06 - Present

Ochanomizu University　Marine and Coastal Research Center　Assistant Professor (Cross-appointment)
2024/04 - Present

Yamagata University　Faculty of Education, Art and Science
2021/10 - Present

Tohoku University　Graduate School of Life Sciences, Research Center for Marine Biology　Assistant Professor
2019/05 - 2021/09

Brown University　Molecular Biology, Cell Biology and Biochemistry (MCB)　Postdoctoral Fellow
2018/09 - 2019/05

University of Tsukuba　Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance　Researcher

Education 3

University of Tsukuba　Graduate School of Life and Environmental Sciences　Doctoral Program in Biological Science

2015/04 - 2018/09
The Graduate University for Advanced Studies　School of Life Science　Department of Basic Biology

2013/04 - 2015/03
Kyoto Institute of Technology　School of Science and Technology　Undergraduate Program of Applied Biology

2009/04 - 2013/03

Professional Memberships 2

日本動物学会

2026/04 - Present
日本比較内分泌学会

2024/09 - Present

Research Interests 3

Single-cell RNA-seq analysis
Developmental Biology
Germline cell

Awards 1

New England Biolabs Japan サイエンスグラント特別賞

2024/08　New England Biolabs Japan　生体内において体細胞から生殖細胞を再生するメカニズムの解明

Papers 12

Somatic gene repression ensures physical segregation of germline and soma in Drosophila embryos. Peer-reviewed

Miho Asaoka, Mizuki Kayama, Tomoki Kawagoe, Makoto Hayashi, Shumpei Morita, Satoru Kobayashi

EMBO Reports　in press　2026/02
Publisher: Cold Spring Harbor Laboratory
DOI： 10.1101/2025.06.13.659480 　

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Abstract In many animals, primordial germ cells are transiently segregated outside the somatic-cell cluster that forms the embryo’s body during early embryogenesis. This physical segregation of germline from the soma has been long believed to be crucial for germline development, but the mechanisms controlling this segregation and its developmental significance remain unclear. Here, inDrosophila, we show that somatic gene silencing in the germline is essential for maintaining this segregation. We showed that primordial germ cells (pole cells) lacking the Nanos- and Polar granule component (Pgc)-dependent dual repression mechanism caused misexpression of widespread somatic genes. They formed abnormal cellular protrusions, invaded adjacent somatic epithelium, and intermingled with somatic cells. These mislocalized pole cells ultimately underwent cell death, whereas properly segregated cells survived. Notably, the knockdown ofmiranda(mira), one of the somatic genes expressed ectopically in the pole cells lacking this repression mechanism, rescued these phenotypes. Our findings provide the first evidence that somatic gene silencing in germline is essential for preserving the physical segregation between germline and soma, highlighting its role in ensuring germline viability during early development.
Conservation and contrast in cell states of echinoderm ovaries Peer-reviewed

Nathalie Oulhen, Shumpei Morita, Cosmo Pieplow, Thomas M. Onorato, Stephany Foster, Gary Wessel

Molecular Reproduction and Development　91　(8)　2024/08/19
Publisher: Wiley
DOI： 10.1002/mrd.23721 　

ISSN： 1040-452X

eISSN： 1098-2795

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Abstract Echinoderms produce functional gametes throughout their lifespan, in some cases exceeding 200 years. The histology and ultrastructure of echinoderm ovaries has been described but how these ovaries function and maintain the production of high‐quality gametes remains a mystery. Here, we present the first single cell RNA sequencing data sets of mature ovaries from two sea urchin species (Strongylocentrotus purpuratus [Sp] and Lytechinus variegatus [Lv]), and one sea star species (Patiria miniata [Pm]). We find 14 cell states in the Sp ovary, 16 cell states in the Lv ovary and 13 cell states in the ovary of the sea star. This resource is essential to understand the structure and functional biology of the ovary in echinoderms, and better informs decisions in the utilization of in situ RNA hybridization probes selective for various cell types. We link key genes with cell clusters in validation of this approach. This resource also aids in the identification of the stem cells for prolonged and continuous gamete production, is a foundation for testing changes in the annual reproductive cycle, and is essential for understanding the evolution of reproduction of this important phylum.
Elements of divergence in germline determination in closely related species Peer-reviewed

Shumpei Morita, Nathalie Oulhen, Stephany Foster, Gary M. Wessel

iScience　26　(4)　106402-106402　2023/04
Publisher: Elsevier BV
DOI： 10.1016/j.isci.2023.106402 　

ISSN： 2589-0042
CRISPR/Cas9 knockin methodology for the sea urchin embryo Peer-reviewed

Nathalie Oulhen, Shumpei Morita, Jacob F. Warner, Gary Wessel

Molecular Reproduction and Development　90　(2)　69-72　2023/01/31
Publisher: Wiley
DOI： 10.1002/mrd.23672 　

ISSN： 1040-452X

eISSN： 1098-2795
Elements of divergence in germline determination in closely related species

Shumpei Morita, Nathalie Oulhen, Stephany Foster, Gary M. Wessel

bioRxiv　2022/08/14
Publisher: Cold Spring Harbor Laboratory
DOI： 10.1101/2022.08.12.503758 　

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Abstract Evolutionary transitions enable the wide diversity in life histories of plants and animals. This is particularly germane in the development of the germ line in which fitness is a direct readout of evolutionary change. Here, we focused on the gem line of two distinct sea urchin species who shared a common ancestor 50 million years ago. Even though they both rely on inherited mechanisms to specify their germ line, the integration of stage-matched single cell RNA-seq (scRNA-seq) datasets from these two sea urchins revealed a variety of differences in gene expression, including a broader expression of the germ line factor Nanos2 in Lytechinus variegatus (Lv) compared to Strongylocentrotus purpuratus (Sp). In Sp, Nanos2 mRNA expression is highly restricted to the primordial germ cells (PGCs) by a lability element in its 3’UTR. This element is lacking in the mRNA of Lv Nanos2, explaining how this mRNA more broadly accumulates in the Lv embryos. We discovered that the Lv Nanos2 3’UTR instead leads to a germline specific translation of the protein. The results emphasize that regulatory mechanisms resulting in germline diversity rely less on transcriptional regulation and more on post-transcriptional and post-translational restrictions of key gene products, such as Nanos2. Highlights -The first integration of scRNA-seq datasets comparing two echinoderm species. -We find Nanos2 positive cells in the embryonic soma of Lytechinus variegatus, an unusual occurrence, but not in Strongylocentrous purpuratus. -We discovered that this somatic Nanos2 mRNA is lacking an important regulatory element (GNARLE) in its 3’UTR -Instead, in Lv, the 3’UTR of Nanos2 leads to its specific translation in the germ cells.
A single-cell RNA-seq analysis of Brachyury-expressing cell clusters suggests a morphogenesis-associated signal center of oral ectoderm in sea urchin embryos International-journal

Noriyuki Satoh, Kanako Hisata, Stephany Foster, Shumpei Morita, Koki Nishitsuji, Nathalie Oulhen, Hitoshi Tominaga, Gary M. Wessel

Developmental Biology　483　128-142　2022/03
Publisher: Elsevier BV
DOI： 10.1016/j.ydbio.2022.01.005 　

ISSN： 0012-1606

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Brachyury is a T-box family transcription factor and plays pivotal roles in morphogenesis. In sea urchin embryos, Brachyury is expressed in the invaginating endoderm, and in the oral ectoderm of the invaginating mouth opening. The oral ectoderm is hypothesized to serve as a signaling center for oral (ventral)-aboral (dorsal) axis formation and to function as a ventral organizer. Our previous results of a single-cell RNA-seq (scRNA-seq) atlas of early Strongylocentrotus purpuratus embryos categorized the constituent cells into 22 clusters, in which the endoderm consists of three clusters and the oral ectoderm four clusters (Foster et al., 2020). Here we examined which clusters of cells expressed Brachyury in relation to the morphogenesis and the identity of the ventral organizer. Our results showed that cells of all three endoderm clusters expressed Brachyury in blastulae. Based on expression profiles of genes involved in the gene regulatory networks (GRNs) of sea urchin embryos, the three clusters are distinguishable, two likely derived from the Veg2 tier and one from the Veg1 tier. On the other hand, of the four oral-ectoderm clusters, cells of two clusters expressed Brachyury at the gastrula stage and genes that are responsible for the ventral organizer at the late blastula stage, but the other two clusters did not. At a single-cell level, most cells of the two oral-ectoderm clusters expressed organizer-related genes, nearly a half of which coincidently expressed Brachyury. This suggests that the ventral organizer contains Brachyury-positive cells which invaginate to form the stomodeum. This scRNA-seq study therefore highlights significant roles of Brachyury-expressing cells in body-plan formation of early sea urchin embryos, though cellular and molecular mechanisms for how Brachyury functions in these processes remain to be elucidated in future studies.
Post-transcriptional regulation of factors important for the germ line Invited Peer-reviewed

Nathalie Oulhen, Shumpei Morita, Gary M. Wessel

Current Topics in Developmental Biology　49-78　2022
Publisher: Elsevier
DOI： 10.1016/bs.ctdb.2021.10.003 　

ISSN： 0070-2153
Absence of X-chromosome dosage compensation in the primordial germ cells of Drosophila embryos

Ryoma Ota, Makoto Hayashi, Shumpei Morita, Hiroki Miura, Satoru Kobayashi

Scientific Reports　11　(1)　2021/12
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41598-021-84402-7 　

eISSN： 2045-2322

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<title>Abstract</title>Dosage compensation is a mechanism that equalizes sex chromosome gene expression between the sexes. In<italic>Drosophila</italic>, individuals with two X chromosomes (XX) become female, whereas males have one X chromosome (XY). In males, dosage compensation of the X chromosome in the soma is achieved by five proteins and two non-coding RNAs, which assemble into the male-specific lethal (MSL) complex to upregulate X-linked genes twofold. By contrast, it remains unclear whether dosage compensation occurs in the germline. To address this issue, we performed transcriptome analysis of male and female primordial germ cells (PGCs). We found that the expression levels of X-linked genes were approximately twofold higher in female PGCs than in male PGCs. Acetylation of lysine residue 16 on histone H4 (H4K16ac), which is catalyzed by the MSL complex, was undetectable in these cells. In male PGCs, hyperactivation of X-linked genes and H4K16ac were induced by overexpression of the essential components of the MSL complex, which were expressed at very low levels in PGCs. Together, these findings indicate that failure of MSL complex formation results in the absence of X-chromosome dosage compensation in male PGCs.
Somatic cell conversion to a germ cell lineage: A violation or a revelation?

Gary M. Wessel, Shumpei Morita, Nathalie Oulhen

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution　2020/05/23
Publisher: Wiley
DOI： 10.1002/jez.b.22952 　

ISSN： 1552-5007

eISSN： 1552-5015
Repression of G1/S Transition by Transient Inhibition of miR-10404 Expression in Drosophila Primordial Germ Cells

Shumpei Morita, Ryoma Ota, Makoto Hayashi, Satoru Kobayashi

iScience　23　(3)　100950-100950　2020/03
Publisher: Elsevier BV
DOI： 10.1016/j.isci.2020.100950 　

ISSN： 2589-0042
Downregulation of NHP2 promotes proper cyst formation in Drosophila ovary

Shumpei Morita, Ryoma Ota, Satoru Kobayashi

Development, Growth & Differentiation　60　(5)　248-259　2018/06
Publisher: Wiley
DOI： 10.1111/dgd.12539 　

ISSN： 0012-1592
Transcripts immunoprecipitated with Sxl protein in primordial germ cells ofDrosophilaembryos

Ryoma Ota, Shumpei Morita, Masanao Sato, Shuji Shigenobu, Makoto Hayashi, Satoru Kobayashi

Development, Growth & Differentiation　59　(9)　713-723　2017/12
Publisher: Wiley
DOI： 10.1111/dgd.12408 　

ISSN： 0012-1592

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Presentations 7

Antenna cells of ascidian larvae are neurons that sense gravity

Chokki, A., Tanimoto, M., Higashijima, S., Sasakura, Y., Morita, S., Kusakabe, T. G., Horie, T., Satou, Y.

13th International Tunicate Meeting　2026/07/20
GERMLINE REGENERATION IN MARINE INVERTEBRATES Invited

Shumpei Morita

HFSP SCIENCE SUMMIT 2025　2025/10/01
Mechanisms of an asexual to sexual reproduction conversion in the female Hydrozoa Proboscidactyla cf. ornata.

Miyazawa, Y., Fukumori, H., Morita, S., Kumano, G.

International Workshop “From Conservation to Innovation – adaptation insights from basal metazoans”　2025/09/24
GERMLINE REGENERATION MECHANISM IN AN ASCIDIAN, CIONA ROBUSTA

Shumpei Morita, Kenji Kobayashi, Gaku Kumano

19th International Congress of Comparative Endocrinology　2025/07/11
海産無脊椎動物における生殖系列の再生 Invited

森田俊平

日本比較内分泌学会　2024/08/30
Elements of divergence in germline determination in closely related species Invited

Shumpei Morita

2023/06/30
NOVEL MECHANISM ESTABLISHING TRANSCRIPTIONAL QUIESCENCE IN THE PRIMORDIAL GERM CELLS OF DROSOPHILA EMBRYOS

Shumpei Morita, Satoru Kobayashi

Cold Spring Harbor Laboratory Meeting; GERM CELLS　2016/10/06

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Research Projects 5

体細胞系列から生殖系列を再生する分子メカニズムの解明

Offer Organization: 日本学術振興会

System: 科学研究費助成事業若手研究

Institution: 東北大学

2026/04 - 2029/03
体細胞から始原生殖細胞への分化制御メカニズムの解明

Offer Organization: 日本学術振興会

System: 科学研究費助成事業若手研究

Institution: 東北大学

2023/04 - 2026/03
カタユウレイボヤにおける生殖系列再生メカニズムの解明

Offer Organization: 東北大学大学院生命科学研究科

System: 生命科学研究科研究奨励賞

Institution: 東北大学

2021/10 - 2022/03
アメリカムラサキウニにおける生殖系列補償機構の解明

Offer Organization: 東洋紡バイオテクノロジー研究財団

System: 長期研究助成

Institution: Brown University

2019/04 - 2020/03
ショウジョウバエにおけるＳｘｌｌｅｔｈａｌ下流候補遺伝子：ＮＨＰ２の機能解析

森田俊平

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 特別研究員奨励費

Institution: 筑波大学

2016/04 - 2018/03

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ショウジョウバエ卵巣における生殖幹細胞は、細胞分裂により2つの娘細胞を生み出す。娘細胞の一方は生殖幹細胞として維持され、もう一方は4回の同調した不完全分裂によって、2細胞シスト、4細胞シスト、8細胞シストを経て、16細胞シストと呼ばれる合胞体を形成する。本研究では、rRNAに修飾塩基を付与する複合体の構成要素をコードするNHP2のシスト形成過程における役割に着目して解析を行った。 NHP2タンパク質はシスト形成過程を通じて核小体に局在し、4細胞シストおよび8細胞シストにおける核小体のサイズ減少と並行して、NHP2タンパク質の発現が減少すること、16細胞シストにおいてNHP2タンパク質の発現が再び上昇することを明らかにした。次にNHP2の生殖系列特異的ノックダウン実験 (NHP2 GS-KD)を行った。NHP2 GS-KDによって4細胞および8細胞シストが増加し、8細胞シストまでの正常なシスト形成過程の進行が促進されることを明らかにした。これまでにSex lethal遺伝子(Sxl)の機能阻害によってシスト形成過程が2細胞シストで停止する腫瘍様の表現型を示すことが知られている。Sxl GS-KDによる腫瘍様の表現型はNHP2 GS-KDを導入(NHP2-Sxl GS-KD)することで救済され、8細胞シストまでシスト形成過程が進行することを明らかにした。この結果はNHP2タンパク質の発現が４細胞および8細胞シストで減少することと一致している。 NHP2 mRNAは、3´ UTRにSxl結合モチーフを有し、Sxlタンパク質と直接結合することを明らかにした。Sxlは、標的mRNAの3´ UTRへ直接結合することで翻訳を抑制する。以上の結果を総合すると、4細胞および8細胞シストにおいてSxlがNHP2を翻訳抑制することで、シスト形成過程が正常に進行していると考えることができる。

Teaching Experience 2

先端生態発生適応科学特論Ⅲ　東北大学大学院生命科学研究科
生態・進化生物学特選科目 I　東北大学理学部

Social Activities 4

青森南高校海洋実習

2026/07/25 - 2026/07/26
八戸工業大学第二高等学校臨海実習

2026/07/11 - 2026/07/11
海と日本プロジェクト「Sea Train〜青い森鉄道沿線の海の魅力を学ぶ～」

2025/08/24 - 2025/08/31
海と日本プロジェクト「あおもり・あきた海山調査団～県魚の秘密を探る～」

あおもり・あきた海山調査団～県魚の秘密を探る～

2022/07/19 -