4.8 Article

Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect

Gongwang Yu et al.

Summary: The authors present eSPET-seq, a method to measure cotranscriptional RNA folding in eukaryotes. Further analysis reveals an antimutagenic effect of nascent RNA folding and contribution to the variability of local mutation rates across the yeast genome.

NATURE COMMUNICATIONS (2023)

Article Biochemical Research Methods

DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model

Stefan Badelt et al.

Summary: The folding of RNA during transcription plays a crucial role in its structure and function. A new algorithm has been developed to track and predict the changes in RNA secondary structure during transcription. This algorithm is deterministic, fast, and capable of folding long RNA sequences.

BIOINFORMATICS (2023)

Article Ecology

Expression level is a major modifier of the fitness landscape of a protein coding gene

Zhuoxing Wu et al.

Summary: This study found that the phenotypic effects of genetic mutations are related to gene expression levels, with at least 42% of single-nucleotide mutations showing fitness effects dependent on gene expression levels and influenced by stochastic molecular errors.

NATURE ECOLOGY & EVOLUTION (2022)

Article Biochemistry & Molecular Biology

Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing

Tassa Saldi et al.

Summary: The co-transcriptional folding of RNA plays a crucial role in splicing, A-I editing, and transcription speed. Slow transcription can lead to significant structural changes in RNA, affecting splicing and editing processes. More structured introns near the 30 splice site are excised more efficiently during co-transcriptional processing.

MOLECULAR CELL (2021)

Review Cell Biology

Transcription-Coupled DNA Repair: From Mechanism to Human Disorder

Diana van den Heuvel et al.

Summary: DNA lesions are a major obstacle during gene transcription by RNA polymerase II enzymes, but can be eliminated by the transcription-coupled DNA repair pathway. Recent advances suggest that RNAPII ubiquitylation activates TCR complex assembly during repair and promotes processing and degradation of RNAPII to prevent prolonged stalling, making the fate of stalled RNAPII a crucial link between TCR and associated human diseases.

TRENDS IN CELL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Higher Germline Mutagenesis of Genes with Stronger Testis Expressions Refutes the Transcriptional Scanning Hypothesis

Haoxuan Liu et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Biochemistry & Molecular Biology

RNA structure maps across mammalian cellular compartments

Lei Sun et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Yeast Spontaneous Mutation Rate and Spectrum Vary with Environment

Haoxuan Liu et al.

CURRENT BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing

Anthony M. Mustoe et al.

Article Biochemistry & Molecular Biology

Long-read sequencing of nascent RNA reveals coupling among RNA processing events

Lydia Herzel et al.

GENOME RESEARCH (2018)

Article Biochemical Research Methods

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

Meghan Zubradt et al.

NATURE METHODS (2017)

Article Biochemistry & Molecular Biology

Deciphering the Genic Basis of Yeast Fitness Variation by Simultaneous Forward and Reverse Genetics

Calum J. Maclean et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Biochemistry & Molecular Biology

In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding

Danny Incarnato et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

Nascent RNA folding mitigates transcription-associated mutagenesis

Xiaoshu Chen et al.

GENOME RESEARCH (2016)

Article Biochemistry & Molecular Biology

Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II

Fernando Carrillo Oesterreich et al.

Article Biochemistry & Molecular Biology

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

Zhipeng Lu et al.

Article Biochemical Research Methods

Predicting RNA secondary structures from sequence and probing data

Ronny Lorenz et al.

METHODS (2016)

Article Biochemical Research Methods

Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE

Ryan A. Flynn et al.

NATURE PROTOCOLS (2016)

Review Genetics & Heredity

Genetic drift, selection and the evolution of the mutation rate

Michael Lynch et al.

NATURE REVIEWS GENETICS (2016)

Article Multidisciplinary Sciences

Structural imprints in vivo decode RNA regulatory mechanisms

Robert C. Spitale et al.

NATURE (2015)

Article Biochemical Research Methods

Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq

Yiliang Ding et al.

NATURE PROTOCOLS (2015)

Review Genetics & Heredity

Determinants of the rate of protein sequence evolution

Jianzhi Zhang et al.

NATURE REVIEWS GENETICS (2015)

Review Genetics & Heredity

Transcription-Associated Mutagenesis

Sue Jinks-Robertson et al.

ANNUAL REVIEW OF GENETICS, VOL 48 (2014)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

deepTools: a flexible platform for exploring deep-sequencing data

Fidel Ramirez et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

Codon-by-Codon Modulation of Translational Speed and Accuracy Via mRNA Folding

Jian-Rong Yang et al.

PLOS BIOLOGY (2014)

Article Biotechnology & Applied Microbiology

Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome

Danny Incarnato et al.

GENOME BIOLOGY (2014)

Article Multidisciplinary Sciences

Agrobacterium tumefaciens recognizes its host environment using ChvE to bind diverse plant sugars as virulence signals

Xiaozhen Hu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biotechnology & Applied Microbiology

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

Mallory A. Freeberg et al.

GENOME BIOLOGY (2013)

Article Multidisciplinary Sciences

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases

Bradley Zamft et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Evolutionary Biology

The Lower Bound to the Evolution of Mutation Rates

Michael Lynch

GENOME BIOLOGY AND EVOLUTION (2011)

Article Multidisciplinary Sciences

Nascent transcript sequencing visualizes transcription at nucleotide resolution

L. Stirling Churchman et al.

NATURE (2011)

Review Biochemistry & Molecular Biology

New insights into RNA secondary structure in the alternative splicing of pre-mRNAs

Yongfeng Jin et al.

RNA BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Global Analysis of Nascent RNA Reveals Transcriptional Pausing in Terminal Exons

Fernando Carrillo Oesterreich et al.

MOLECULAR CELL (2010)

Article Multidisciplinary Sciences

Genome-wide measurement of RNA secondary structure in yeast

Michael Kertesz et al.

NATURE (2010)

Review Biochemistry & Molecular Biology

Role of RNA structure in regulating pre-mRNA splicing

M. Bryan Warf et al.

TRENDS IN BIOCHEMICAL SCIENCES (2010)

Article Biochemistry & Molecular Biology

Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines

Peter D. Keightley et al.

GENOME RESEARCH (2009)

Article Multidisciplinary Sciences

The transcriptional landscape of the yeast genome defined by RNA sequencing

Ugrappa Nagalakshmi et al.

SCIENCE (2008)

Article Genetics & Heredity

A Catalog of Neutral and Deleterious Polymorphism in Yeast

Scott W. Doniger et al.

PLOS GENETICS (2008)

Review Cell Biology

The highways and byways of mRNA decay

Nicole L. Garneau et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2007)

Article Cell Biology

Mutation rate variation in the mammalian genome

H Ellegren et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2003)

Article Genetics & Heredity

Human SNP variability and mutation rate are higher in regions of high recombination

MJ Lercher et al.

TRENDS IN GENETICS (2002)