Identification of regulatory links between transcription and RNA processing 
with long-read sequencing

Alfonso-Gonzalez, Carlos; Arrigoni, Laura; Ozbulut, Hasan Can; Falk, Stefanie; Bönisch, Ulrike; Hilgers, Valérie

doi:10.1016/j.xpro.2023.102505

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Journal Article

Identification of regulatory links between transcription and RNA processing with long-read sequencing

MPS-Authors

Alfonso-Gonzalez, Carlos
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Arrigoni, Laura
Deep Sequencing Facility, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Ozbulut, Hasan Can
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Falk, Stefanie
Deep Sequencing Facility, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Bönisch, Ulrike
Deep Sequencing Facility, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

/persons/resource/persons201444

Hilgers, Valérie
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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https://www.sciencedirect.com/science/article/pii/S2666166723004720?via%3Dihub
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Citation

Alfonso-Gonzalez, C., Arrigoni, L., Ozbulut, H. C., Falk, S., Bönisch, U., & Hilgers, V. (2023). Identification of regulatory links between transcription and RNA processing with long-read sequencing. STAR Protocols, 4: 102505. doi:10.1016/j.xpro.2023.102505.

Cite as: https://hdl.handle.net/21.11116/0000-000D-BAEB-9

Abstract

We present a detailed protocol for sequencing full-length mRNA isoforms using the Oxford nanopore long-read sequencing technology. We describe steps for poly(A) RNA isolation, library preparation, and cDNA size selection. We then detail procedures for sequencing and processing and a computational framework to identify exon couplings and assign mRNA 5' ends and 3' ends to each other. Our approach enables the identification of links between transcription initiation and co-transcriptional RNA processing events. For complete details on the use and execution of this protocol, please refer to Alfonso-Gonzalez et al.¹.