Selected Publications

Sharma H, Valentine MNZ, Toki N, Nishiyori Sueki H, Gustincich S, Takahashi H, Carninci P (2024). Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation.

DOI Link

Amaral P, Carbonell-Sala S, De La Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, Ulitsky I, Varabyou A, Wells CA, Yandell M, Carninci P, Salzberg SL (2023). The status of the human gene catalogue.

DOI Link

Miyajima Y, Noguchi S, Tanaka Y, Li JR, Nishimura H, Kishima M, Lim J, Furuhata E, Suzuki T, Kasukawa T, Suzuki H (2022). Prediction of transcription factors associated with DNA demethylation during human cellular development..

DOI Link

Yoshino T, Suzuki T, Nagamatsu G, Yabukami H, Ikegaya M, Kishima M, Kita H, Imamura T, Nakashima K, Nishinakamura R, Tachibana M, Inoue M, Shima Y, Morohashi K, Hayashi K (2021). Generation of ovarian follicles from mouse pluripotent stem cells.

DOI Link

Toki N, Takahashi H, Sharma H, Valentine NZ M, Rhaman M F, Zucchelli S, Gustincich S, Carninci P (2020). SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assemblies.

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Abe T, Nishimura H, Sato T, Suzuki H, Ogawa T, Suzuki T (2020). Time-course microarray transcriptome data of in vitro cultured testes and age-matched in vivo testes.

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Toki N, Takahashi H, Zucchelli S, Gustincich S, Carninci P (2020). Synthetic in vitro transcribed lncRNAs (SINEUPs) with chemical modifications enhance target mRNA translation.

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Abe T, Nishimura H, Sato T, Suzuki H, Ogawa T, Suzuki T (2020). Transcriptome analysis reveals inadequate spermatogenesis and immediate radical immune reactions during organ culture in vitro spermatogenesis.

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Ramilowski JA, Yap CW, [...], Carninci P (2020). Functional annotation of human long noncoding RNAs via molecular phenotyping.

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Ohyama T, Takahashi H, Sharma H, Yamazaki T, Gustincich S, Ishii Y, Carninci P (2020). An NMR-based approach reveals the core structure of the functional domain of SINEUP lncRNAs.

DOI Link

Bonetti A, Agostini F, Suzuki AM, Hashimoto K, Pascarella G, Gimenez J, Roos L, Nash AJ, Ghilotti M, [...], Carninci P (2020). RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions.

プロジェクト Link

Hashimoto K, Kouno T, Ikawa T, Hayatsu N, Miyajima N, Yabukami H, Terooatea T, Sasaki T, Suzuki T, [...], Carninci P (2019). Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians.

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Takahashi H, Sharma H, Carninci P (2017). Cell Based Assays of SINEUP Non-coding RNAｓThat Can Specifically Enhance mRNA Translation.

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Suzuki T, Maeda S, Furuhata E, Shimizu Y, Nishimura H, Kishima M, Suzuki H (2017). A screening system to identify transcription factors that induce binding site-directed DNA demethylation.

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Suzuki T, Shimizu Y, Furuhata E, Maeda S, Kishima M, Nishimura H, Enomoto S, Hayashizaki Y, Suzuki H (2017). RUNX1 regulates site specificity of DNA demethylation by recruitment of DNA demethylation machineries in hematopoietic cells.

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Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J, Lizio M, Kawaji H, [...], Carninci P, Forrest ARR (2017). An atlas of human long non-coding RNAs with accurate 5' ends.

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Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, [...], Carninci P, Hayashizaki Y (2015). Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

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Kashi K, Henderson L, Bonetti A, Carninci P (0001). Discovery and functional analysis of lncRNAs: Methodologies to investigate an uncharacterized transcriptome.

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