Direct RNA Sequencing on Maragkakis Lab

Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress

Thu, 19 Dec 2024 00:00:00 +0000

Summary

Using full-length direct RNA sequencing, this study uncovers a previously unrecognized role for stress granules in promoting selective mRNA decay during cellular stress. The findings show that mRNAs recruited to stress granules undergo preferential degradation, linking stress granule biology to RNA homeostasis.

Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics

Sun, 29 Sep 2024 00:00:00 +0000

Summary

We developed RNAkinet, a neural network that identifies newly synthesized RNA molecules labeled with 5-ethynyl uridine (5EU) using nanopore direct RNA sequencing, processing raw electrical signals without requiring basecalling or sequence alignment. RNAkinet enables simultaneous analysis of RNA metabolism alongside poly(A) tail length and RNA modifications at single-molecule resolution.

Differential Poly(A) Tail Length Analysis Using Nanopore Sequencing

Fri, 13 Oct 2023 00:00:00 +0000

Summary

This methods chapter describes a protocol for transcriptome-wide measurement of differential poly(A) tail lengths using nanopore direct RNA sequencing, combined with linear mixed models for statistical analysis. The approach enables quantitative comparison of poly(A) tail dynamics across conditions and provides a framework for studying the role of deadenylation in post-transcriptional gene regulation.

TERA-Seq: True end-to-end sequencing of native RNA molecules for transcriptome characterization

Tue, 24 Aug 2021 00:00:00 +0000

Summary

TERA-Seq is a method that combines chemical ligation of adapters to both RNA ends with nanopore direct RNA sequencing to capture complete native RNA molecules from the 5’ cap to the 3’ poly(A) tail. This enables simultaneous characterization of RNA modifications, poly(A) tail length, and transcript boundaries at single-molecule resolution.