RNA splicing articles within Nature Methods

Featured

• Research Briefing | 13 July 2023

  Circular RNA detection pipelines yield divergent sets of circular RNAs

  A decade ago, the first bioinformatics pipelines to detect circular RNA molecules based on short-read sequencing data were published. Here, we show that dozens of such circular RNA detection tools differ vastly in their sensitivity but not in their specificity.

• Analysis | 13 July 2023

  Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

  This study describes benchmarking and validation of computational tools for detecting circRNAs, finding most to be highly precise with variations in sensitivity and total detection. The study also finds over 315,000 putative human circRNAs.

  • Marieke Vromman
  • , Jasper Anckaert
  •  & Pieter-Jan Volders

• Comment | 12 January 2023

  The variables on RNA molecules: concert or cacophony? Answers in long-read sequencing

  Long-read sequencing has become a widely employed technology that enables a comprehensive view of RNA transcripts. Here, we discuss the importance of long-read sequencing in interpreting the variables along RNA molecules, such as polyadenylation sites, transcription start sites, splice sites and other RNA modifications. In addition, we highlight the history of short-read and long-read technologies and their advantages and disadvantages, as well as future directions in the field.

  • Careen Foord
  • , Justine Hsu
  •  & Hagen U. Tilgner

• Research Highlight | 08 April 2022

  Enhanced protein isoform characterization

  Long-read proteogenomics helps delineate isoform diversity in full-length proteins.

  • Arunima Singh

• Research Highlight | 30 August 2019

  Spatial RNA mapping

  Tagging and sequencing RNAs that are in close spatial proximity in the nucleus shows how the transcriptome is partitioned.

  • Nicole Rusk

• Brief Communication | 25 March 2019

  Deep-learning augmented RNA-seq analysis of transcript splicing

  DARTS first uses public domain data to train a deep neural network to predict differential alternative splicing; the predictions are then combined with observed RNA-seq data in a Bayesian framework to infer changes in alternative splicing between biological samples.

  • Zijun Zhang
  • , Zhicheng Pan
  •  & Yi Xing

• Brief Communication | 20 December 2018

  Detection of splice isoforms and rare intermediates using multiplexed primer extension sequencing

  MPE-seq uses pools of reverse-transcription primers to facilitate enrichment of splice isoforms and pre-mRNA splicing intermediates.

  • Hansen Xu
  • , Benjamin J. Fair
  •  & Jeffrey A. Pleiss

• In Brief | 30 October 2018

  Improving long-read accuracy

  • Lei Tang

• Research Highlight | 02 July 2018

  Transcripts from a spliceosome

  Two new methods provide high-resolution profiles of splicing events in yeast.

  • Tal Nawy

• Article | 15 January 2018

  Highly parallel direct RNA sequencing on an array of nanopores

  Direct sequencing of RNA molecules in real time using nanopores allows for the detection of splice variants and hold promises for profiling RNA modifications.

  • Daniel R Garalde
  • , Elizabeth A Snell
  •  & Daniel J Turner

• Article | 08 August 2016

  Spliced synthetic genes as internal controls in RNA sequencing experiments

  Synthetic spike-in standards (‘sequins’), representing spliced mRNA isoforms, provide internal controls for assessing transcript assembly and quantification within and between RNA sequencing libraries. Sequins representing fused genes can be used to determine the sensitivity limit for oncogenic fusions in cancer samples.

  • Simon A Hardwick
  • , Wendy Y Chen
  •  & Tim R Mercer

• Article | 04 July 2016

  m⁶A-LAIC-seq reveals the census and complexity of the m⁶A epitranscriptome

  m⁶A-LAIC-seq quantifies the levels of N⁶-methyladenosine in isoforms of the same gene in a cell-type-specific manner.

  • Benoit Molinie
  • , Jinkai Wang
  •  & Cosmas C Giallourakis

• Methods in Brief | 30 December 2015

  Synthetic data feed machine-learning predictors of splicing

• Brief Communication | 09 March 2015

  Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

  CaptureSeq was used to quantitatively profile transcripts with low expression, resulting in a catalog of long noncoding RNA expression in 20 human tissues.

  • Michael B Clark
  • , Tim R Mercer
  •  & Marcel E Dinger

• Tools in Brief | 30 October 2014

  Seeking genetic variants that affect splicing

• Methods in Brief | 29 May 2014

  Cellular imaging of single-splice variants

• Research Highlights | 30 January 2012

  Timing an intron's departure

  An in vitro RNA-labeling technique with single-molecule resolution offers a look into the kinetics and the location of splicing.

  • Nicole Rusk

• Article | 07 November 2010

  Analysis and design of RNA sequencing experiments for identifying isoform regulation

  The mixture of isoforms model (MISO) assesses the confidence in estimates of the abundance of spliced exons or isoforms from paired-end RNA-seq data and detects their differential expression.

  • Yarden Katz
  • , Eric T Wang
  •  & Christopher B Burge

• Article | 04 April 2010

  Conditional gene expression and RNAi using MEC-8–dependent splicing in C. elegans

  A conditional gene expression system in Caenorhabditis elegans is reported. It should permit the generation of temperature-sensitive alleles for most genes.

  • Andrea Calixto
  • , Charles Ma
  •  & Martin Chalfie