A compendium of human RNA structures and modifications | LC 25

Biography

Yasuhiro Murakawa graduated from Kyoto University School of Medicine in 2008. After completing his residency at Kyoto University Hospital, he moved to the Max Delbrück Center for Molecular Medicine in Berlin, Germany, where he obtained his PhD from Free University of Berlin in 2014 and has been leading a laboratory at RIKEN since 2016 (Team Leader of RIKEN Center for Integrative Medical Sciences, Group Leader of IFOM since 2018). In 2020, Yasuhiro became a full professor at Kyoto University.

Abstract

Gene expression is regulated by transcriptional and post-transcriptional processes, playing key roles in human development and disease. However, challenges remain in identifying full-length sequences of structurally diverse RNAs and their modifications, which occur in a cell-type-specific manner. To address this, we prepared hundreds of high-quality RNA samples across human cell lines and tissues, and performed cDNA and direct RNA nanopore sequencing. Conventional cDNA sequencing often fails to accurately retrieve full-length RNAs, making it difficult to determine complete sequences from transcription start to termination sites. Here, we developed an improved cDNA preparation method, achieving an average read length of >3,000 bases of full-length cDNA sequencing, applying this method to hundreds of human RNA samples. We identified tens of thousands of unannotated isoforms from known loci and thousands of cell-type-specific isoforms not found in intergenic regions, significantly expanding existing gene annotations. Many of these newly identified elements were specific to primates or humans.

Furthermore, we used direct RNA nanopore sequencing to comprehensively analyse RNA base modifications across human cell types. This technique enabled the direct, high-resolution detection of RNA modifications, including previously unknown modifications. The resulting transcriptome and epitranscriptome atlas across human cell types provides novel insights into human biology, evolution, and disease.