Lab Activities

Laboratory for Transcriptome Technology

Research Activities

Piero Carninci portrait

Team Director

Piero Carninci

Our laboratory develops transcriptome technologies and investigates the functions of long non-coding RNAs in the human genome. Cap analysis of gene expression (CAGE) enables single-nucleotide–resolution identification of RNA 5’-ends, allowing precise mapping of transcription start sites and quantitative measurement of promoter and enhancer activities. We recently updated the CAGE protocol to support Illumina’s patterned flow cell system, improving data robustness, throughput, and scalability for applications from basic to clinical studies (Delobel et al., STAR Protocols, 6:103594, 2025).

We lead the FANTOM6 consortium, which focuses on elucidating the RNA–chromatin interactome using RADICL-seq, a technology developed to map RNA–chromatin interactions. This effort has generated key findings. Integration of high-resolution DNA–DNA contact maps with RNA–DNA interaction profiles demonstrated that RNA dynamically coordinates enhancer–promoter communication during neural differentiation (Sahlén et al., bioRxiv, doi.org/10.64898/2025.12.15.694370, 2025). Additionally, multi-omics framework combining 3D genome architecture, RNA–DNA interactions, and transcriptional dynamics elucidated that nuclear RNAs actively shape three-dimensional genome organization and transcriptional programs during neuronal differentiation (Kang et al., bioRxiv, doi.org/10.1101/2025.03.13.641826, 2025). Further, short tandem repeats (STRs), previously considered inert repetitive elements, showed function as regulatory units by acting as SNP-modulated transcription start sites (Grapotte et al., bioRxiv, doi.org/10.1101/2025.04.10.648102, 2025). Moreover, we established a framework to decode dynamic changes in cis-regulatory element (CRE) activity and the underlying cis-regulatory grammar during cellular differentiation (Cassan et al., bioRxiv, doi.org/10.1101/2025.05.14.653995, 2025).

Simultaneously, we contribute to the Human Cell Atlas (HCA), which aims to construct a comprehensive single-cell reference of the human body. Integration of multimodal single-cell datasets improved cell-type annotation and interpretation of cellular states in complex tissues, profiling approximately 120,000 nuclei and cells (Acera-Mateos et al., bioRxiv, doi.org/10.1101/2025.03.06.637075, 2025). Furthermore, the Asian Immune Diversity Atlas (AIDA) characterized immune system diversity across Asian populations using over 1.2 million cells (Kock et al., Cell, 188:2288, 2025).

Workflow of direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencing

Laboratory for Transcriptome Technology figure

Workflow of direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencing

Laboratory for Transcriptome Technology figure

Cap analysis of gene expression (CAGE) is a technique to identify the 5'-end of RNA transcript starting site (TSS) of both coding and non-coding genes. This protocol is for using CAGE on Illumina patterned flow cell technology, which was replaced from non-patterned flow cell, with dual indexes on mouse and human samples.

Cap analysis of gene expression (CAGE) is a technique to identify the 5'-end of RNA transcript starting site (TSS) of both coding and non-coding genes. This protocol is for using CAGE on Illumina patterned flow cell technology, which was replaced from non-patterned flow cell, with dual indexes on mouse and human samples.

Recent Major Publications

  1. Ikedo A, Aoki R, Sakai H, Saeki N, Yanagihara Y, Moody J, Kojima M, Kouno T, Ando Y, Hino K, Kinoshita T, Carninci P, Shin JW, Hon C, Uezumi A, Kamei Y, Imai Y. Estrogen signaling in PDGFRα+ cells positively regulates cortical bone metabolism via IGFBP5 in female mice. JBMR Plus 10, ziaf178 (2025)

  2. Ramirez P, Sun W, Dehkordi SK, Zare H, Pascarella G, Carninci P, Fongang B, Bieniek KF, Frost B. Long‐read sequencing reveals genomic and epigenomic variation in the dark genome of human Alzheimer's disease. Alzheimer's & Dementia 21, e70852 (2025)

  3. D’Agostino S, Tettey-Matey A, Volpe M, Pierattini B, D’Agostino M, Smělá D, Ansaloni F, Broglia L, Lau P, Peruzzo O, Braccia C, Armirotti A, Scarpato M, Damiani D, Ros G, Di Carlo V, Maniscalco F, Bechara E, Tartaglia GG, Carninci P, Santoro C, Persichetti F, Pandolfini L, Simonetti A, Espinoza S, Zucchelli S, Sanges R, Bon C, Gustincich S. Internal ribosome entry sites enhance translation in trans in antisense non-coding SINEUP and circular RNAs. Nucleic Acids Res 53, gkaf788 (2025)

  4. Patrinos GP, Reichardt JK, Carninci P, Hamosh A, Mitropoulou C, Vasiliou V. Bringing our genomes to medicine – the 2026 human genome meeting. Hum Genomics 19, 93 (2025)

  5. Kock K, Tan L, Han K, Ando Y, Jevapatarakul D, Chatterjee A, Lin Q, Buyamin E, Sonthalia R, Rajagopalan D, Tomofuji Y, Sankaran S, Park M, Abe M, Chantaraamporn J, Furukawa S, Ghosh S, Inoue G, Kojima M, Kouno T, Lim J, Myouzen K, Nguantad S, Oh J, Rayan N, Sarkar S, Suzuki A, Thungsatianpun N, Venkatesh P, Moody J, Nakano M, Chen Z, Tian C, Zhang Y, Tong Y, Tan C, Tizazu A, Loh M, Hwang Y, Ho RC, Larbi A, Ng T, Won H, Wright FA, Villani A, Park J, Choi M, Liu B, Maitra A, Pithukpakorn M, Suktitipat B, Ishigaki K, Okada Y, Yamamoto K, Carninci P, Chambers JC, Hon C, Matangkasombut P, Charoensawan V, Majumder PP, Shin JW, Park W, Prabhakar S. Asian diversity in human immune cells. Cell 188, 2288-2306.e24 (2025)

  6. Delobel D, Nishiyori-Sueki H, Nisoli I, Kawaji H, Robbe P, Carninci P, Takahashi H. Protocol for direct cDNA Cap Analysis of Gene Expression for paired-end patterned flow cell sequencing. STAR Protoc 6, 103594 (2025)

Invited Presentations

  • Carninci P. "Long non-coding RNA Functions in Genome Regulatio." RIKEN-Tubingen-Symposium, Tubingen, Germany, November 3–4 (2025)

  • Kato M. "Genome-wide Mapping of RNA–Chromatin Interactions by RADICL-seq: Application to NEAT1 and Paraspeckles." The 3rd Paraspeckle & Condensates Conference, Nara, Japan, October 31 (2025)

  • Carninci P. "Keynote Talk: Genomic regulation and functional aspects of long non-coding RNAs." Genomics India, Bengaluru, India, August 12–14 (2025)

  • Carninci P. "Elucidating genome regulation by non-coding transcription." RIKEN-McGill Workshop 2025, Montreal, Canada, July 7–8 (2025)

  • Takahashi H, Carninci P. "Potential RNA based medicine - SINEUPs that upregulate target mRNA translation in the disease models." Thai Symposium & Workshop on Genomic Medicine, Therapeutics and Health, Bangkok, Thailand, June 9–10 (2025)

  • Carninci P. "Long non-coding RNA functions in genome regulation." Key note lecture at Silvia Zucchelli Prize, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Trieste, Italy, May 23–23 (2025)

  • Carninci P. "Multiple roles of long non-coding RNAs in genome regulation." Seminar at Istituto di Genetica Molecolare del CNR in Pavia, Pavia, Italy, April 1–1 (2025)

  • CARNINCI P. "Impact of 25 years of the Functional Annotation of Mammalian (FANTOM) Project." RIKEN Symposia: OLSP Symposium 2025 – Present and Future Perspectives of Open Life Sciences –, Wako, Japan, January 27 (2025)

  • CARNINCI P. "Long non-coding RNAs functions in genomics regulation." 2nd Thailand Bioinformatics Research Network (TBRN) Conference, Chiang Mai, Thailand, January 22–24 (2025)

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