4.8 Article

A cap 0-dependent mRNA capture method to analyze the yeast transcriptome

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Chemical capping improves template switching and enhances sequencing of small RNAs

Madalee G. Wulf et al.

Summary: Template-switching reverse transcription using CapTS-seq, which combines chemical capping and template switching, shows improved efficiency and reduced bias in sequencing small RNAs. The study provides evidence that the 5' cap acts as a template for the first nucleotide in reverse transcriptase-mediated post-templated addition, crucial for template switching efficiency. Deploying CapTS-seq for sequencing small RNAs consistently improves library quality compared to traditional methods.

NUCLEIC ACIDS RESEARCH (2022)

Article Multidisciplinary Sciences

Selectivity of mRNA degradation by autophagy in yeast

Shiho Makino et al.

Summary: The study demonstrates selective mRNA degradation by autophagy induced by rapamycin in yeast, with certain subsets of mRNAs encoding amino acid biosynthesis and ribosomal proteins being preferentially delivered to vacuoles for degradation. Autophagy-mediated mRNA degradation is closely linked with ribosomal translation, as suggested by genome-wide ribosome profiling, indicating a previously unappreciated role of autophagy in post-transcriptional gene regulation.

NATURE COMMUNICATIONS (2021)

Article Biochemistry & Molecular Biology

capCLIP: a new tool to probe translational control in human cells through capture and identification of the eIF4E-mRNA interactome

Kirk B. Jensen et al.

Summary: This study introduces a novel method, capCLIP, to comprehensively capture and quantify the eIF4E 'cap-ome' and investigate the biological consequences of eIF4E-cap binding in different cellular contexts. The results from analyzing human cells with mTORC1 inhibitor rapamycin and examining phosphorylation of eIF4E demonstrate that capCLIP is a valuable tool for studying the function of eIF4E and other cap-binding proteins.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

Global view on the metabolism of RNA poly(A) tails in yeast Saccharomyces cerevisiae

Agnieszka Tudek et al.

Summary: RNA polyadenosine tails, crucial for mRNA stability and translation, vary in length depending on mutations in yeast exonuclease, deadenylase, and poly(A) polymerase. The study demonstrates the impact of poly(A) tails on mRNA and ncRNA functions, highlighting their responses to growth conditions.

NATURE COMMUNICATIONS (2021)

Article Chemistry, Multidisciplinary

Selective Enrichment of A-to-I Edited Transcripts from Cellular RNA Using Endonuclease V

Steve D. Knutson et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

Article Biochemistry & Molecular Biology

Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads

Gianluca Prezza et al.

Article Biochemistry & Molecular Biology

High resolution biosensor to test the capping level and integrity of mRNAs

Ignacio Moya-Ramirez et al.

NUCLEIC ACIDS RESEARCH (2020)

Review Genetics & Heredity

Small Nucleolar RNAs Tell a Different Tale

Joanna Kufel et al.

TRENDS IN GENETICS (2019)

Article Biotechnology & Applied Microbiology

Efficient depletion of ribosomal RNA for RNA sequencing in planarians

Iana Kim et al.

BMC GENOMICS (2019)

Article Biochemistry & Molecular Biology

IFIT3 and IFIT2/3 promote IFIT1-mediated translation inhibition by enhancing binding to non-self RNA

Renata C. Fleith et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Cell Biology

Brr6 plays a role in gene recruitment and transcriptional regulation at the nuclear envelope

Anne de Bruyn Kops et al.

MOLECULAR BIOLOGY OF THE CELL (2018)

Article Biochemistry & Molecular Biology

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

Rene Dreos et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Multidisciplinary Sciences

Structure of human IFIT1 with capped RNA reveals adaptable mRNA binding and mechanisms for sensing N1 and N2 ribose 2′-O methylations

Yazan M. Abbas et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Biochemical Research Methods

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

Henry Heberle et al.

BMC BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics

Vicent Pelechano et al.

Review Multidisciplinary Sciences

Discovery of m7G-cap in eukaryotic mRNAs

Yasuhiro Furuichi

PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES (2015)

Review Virology

Interferon-Induced Ifit Proteins: Their Role in Viral Pathogenesis

Volker Fensterl et al.

JOURNAL OF VIROLOGY (2015)

Review Immunology

IFITs: emerging roles as key anti-viral proteins

Gregory I. Vladimer et al.

FRONTIERS IN IMMUNOLOGY (2014)

Article Genetics & Heredity

Ribogenomics: the Science and Knowledge of RNA

Jiayan Wu et al.

GENOMICS PROTEOMICS & BIOINFORMATICS (2014)

Article Multidisciplinary Sciences

Structural basis for viral 5′-PPP-RNA recognition by human IFIT proteins

Yazan M. Abbas et al.

NATURE (2013)

Article Multidisciplinary Sciences

Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae

Yuriko Harigaya et al.

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

Article Immunology

IFIT1 is an antiviral protein that recognizes 5′-triphosphate RNA

Andreas Pichlmair et al.

NATURE IMMUNOLOGY (2011)

Article Biotechnology & Applied Microbiology

Genomewide characterization of non-polyadenylated RNAs

Li Yang et al.

GENOME BIOLOGY (2011)

Article Biotechnology & Applied Microbiology

A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing

Peng Cui et al.

GENOMICS (2010)

Article Biochemistry & Molecular Biology

WebLogo: A sequence logo generator

GE Crooks et al.

GENOME RESEARCH (2004)

Article Multidisciplinary Sciences

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

T Shiraki et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

Article Multidisciplinary Sciences

Purifying mRNAs with a high-affinity eIF4E mutant identifies the short 3′ poly(A) end phenotype

YH Choi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)