Results 11 to 20 of about 721,346 (281)

Sequencing accuracy and systematic errors of nanopore direct RNA sequencing [PDF]

BMC Genomics, 2023
Background Direct RNA sequencing (dRNA-seq) on the Oxford Nanopore Technologies (ONT) platforms can produce reads covering up to full-length gene transcripts, while containing decipherable information about RNA base modifications and poly-A tail lengths.
Wang Liu-Wei, Wiep van der Toorn, Patrick Bohn, Martin Hölzer, Redmond P. Smyth, Max von Kleist   +5 more
doaj   +6 more sources

Detecting RNA modification using direct RNA sequencing: A systematic review

Computational and Structural Biotechnology Journal, 2022
Post-transcriptional RNA modifications are involved in a range of important cellular processes, including the regulation of gene expression and fine-tuning of the functions of RNA molecules.
Xichen Zhao, Yuxin Zhang, Daiyun Hang, Jia Meng, Zhen Wei   +4 more
doaj   +3 more sources

RNA Editing Detection by Direct Sequencing

Bio-Protocol, 2015
RNA editing is a widespread post-transcriptional phenomenon through which primary RNA sequences are altered by nucleotide insertion/deletion or base conversion.
Mehdi Jabnoune, David Secco, Cécile Lecampion, Christophe Robaglia, Qingyao Shu, Yves Poirier   +5 more
doaj   +2 more sources

Advances in Detecting RNA Modifications Using Direct RNA Nanopore Sequencing

Advanced Genetics
RNA modifications add a dynamic and versatile regulatory layer to gene expression, influencing RNA stability, splicing, translation, and cellular responses.
Yaran Liu, Yang Li, Qiang Sun
doaj   +4 more sources

Utilization of nanopore direct RNA sequencing to analyze viral RNA modifications

mSystems
Modifications on viral RNAs (vRNAs), either genomic RNAs or RNA transcripts, have complex effects on the viral life cycle and cellular responses to viral infection.
Lu Tan, Zhihao Guo, Xiaoming Wang, Dal Young Kim, Runsheng Li   +4 more
doaj   +3 more sources

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

eLife
Cells react to stress by triggering response pathways, leading to extensive alterations in the transcriptome to restore cellular homeostasis. The role of RNA metabolism in shaping the cellular response to stress is vital, yet the global changes in RNA ...
Showkat Ahmad Dar, Sulochan Malla, Vlastimil Martinek, Matthew John Payea, Christopher Tai-Yi Lee, Jessica Martin, Aditya Jignesh Khandeshi, Jennifer L Martindale, Cedric Belair, Manolis Maragkakis   +9 more
doaj   +2 more sources

Characterizing transcripts of HIV-1 different substrains using direct RNA sequencing [PDF]

Heliyon
Post-transcriptional processing and modification of viral RNA, including alternative splicing, polyadenylation, and methylation, play crucial roles in regulating viral gene expression, enhancing genomic stability, and increasing replication efficiency ...
Weizhen Li, Yong Huang, Haowen Yuan, Jingwan Han, Zhengyang Li, Aiping Tong, Yating Li, Hanping Li, Yongjian Liu, Lei Jia, Xiaolin Wang, Jingyun Li, Bohan Zhang, Lin Li   +13 more
doaj   +2 more sources

Unraveling C-to-U RNA editing events from direct RNA sequencing

RNA Biology, 2023
In mammals, RNA editing events involve the conversion of adenosine (A) in inosine (I) by ADAR enzymes or the hydrolytic deamination of cytosine (C) in uracil (U) by the APOBEC family of enzymes, mostly APOBEC1.
Adriano Fonzino, Caterina Manzari, Paola Spadavecchia, Uday Munagala, Serena Torrini, Silvestro Conticello, Graziano Pesole, Ernesto Picardi   +7 more
doaj   +5 more sources

DirectRM: integrated detection of landscape and crosstalk between multiple RNA modifications using direct RNA sequencing [PDF]

Nature Communications
Profiling RNA modifications is essential to understand their functions and interactions. By taking the advantages of nanopore direct RNA sequencing, we present DirectRM, enabling simultaneous detection of six abundant modifications (N4-acetylcytidine, 1 ...
Yuxin Zhang, Yuecheng Wu, Jiongming Ma, Yiyu Wu, Liying Li, Haozhe Wang, Guifang Jia, Daniel J. Rigden, Jia Meng, Daiyun Huang, Kunqi Chen   +10 more
doaj   +2 more sources

Probing the epitranscriptome and RNA damage with nanopore direct RNA sequencing. [PDF]

RNA
Nanopore direct RNA sequencing (DRS) is revolutionizing our ability to analyze the epitranscriptome to evaluate nucleoside modifications in both cellular and synthetic RNA. The process involves minimal handling of fragile RNA strands, one round of reverse transcription to provide a DNA:RNA duplex, and library preparation to directly read nucleotides ...
Fleming AM, Burrows CJ.
europepmc   +3 more sources