Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine

Chemical modifications to mRNA nucleobases impact translation elongation and termination

(2022) Monika K. Franco et al.   BIOPHYSICAL CHEMISTRY

Site-Specific Synthesis of N4-Acetylcytidine in RNA Reveals Physiological Duplex Stabilization

(2022) David Bartee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Uncovering N4-Acetylcytidine-Related mRNA Modification Pattern and Landscape of Stemness and Immunity in Hepatocellular Carcinoma

(2022) Sicheng Liu et al.   Frontiers in Cell and Developmental Biology

Prognostic and Immunological Role of mRNA ac4C Regulator NAT10 in Pan-Cancer: New Territory for Cancer Research?

(2021) Chuanxi Yang et al.   Frontiers in Oncology

Structure of the translating Neurospora ribosome arrested by cycloheximide

(2021) Lunda Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Codon and amino acid content are associated with mRNA stability in mammalian cells

(2020) Megan E. Forrest et al.   PLoS One

Structural Insights into the Mammalian Late-Stage Initiation Complexes

(2020) Angelita Simonetti et al.   Cell Reports

Acetylation of Cytidine Residues Boosts HIV-1 Gene Expression by Increasing Viral RNA Stability

(2020) Kevin Tsai et al.   Cell Host & Microbe

Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping

(2020) Aldema Sas-Chen et al.   NATURE

Epitranscriptomic N4-Acetylcytidine Profiling in CD4+ T Cells of Systemic Lupus Erythematosus

(2020) Gangqiang Guo et al.   Frontiers in Cell and Developmental Biology

High Frequency of Either Altered Pre-Core Start Codon or Weakened Kozak Sequence in the Core Promoter Region in Hepatitis B Virus A1 Strains from Rwanda

(2019) Heléne Norder et al.   Genes

KDM4B: A Nail for Every Hammer?

(2019) Cailin Wilson et al.   Genes

Late steps in bacterial translation initiation visualized using time-resolved cryo-EM

(2019) Sandip Kaledhonkar et al.   NATURE

Identification and Quantification of Modified Nucleosides in Saccharomyces cerevisiae mRNAs

(2019) Mehmet Tardu et al.   ACS Chemical Biology

Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing

(2019) Christel Enroth et al.   NUCLEIC ACIDS RESEARCH

Suppression of Ribosomal Pausing by eIF5A Is Necessary to Maintain the Fidelity of Start Codon Selection

(2019) Hema Manjunath et al.   Cell Reports

Loss of nucleolar localization of NAT10 promotes cell migration and invasion in hepatocellular carcinoma

(2018) Yuqin Tan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection

(2018) Will McIntyre et al.   NUCLEIC ACIDS RESEARCH

A Chemical Signature for Cytidine Acetylation in RNA

(2018) Justin M. Thomas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis

(2018) Takaaki Taniguchi et al.   Nature Chemical Biology

Landscape of the complete RNA chemical modifications in the human 80S ribosome

(2018) Masato Taoka et al.   NUCLEIC ACIDS RESEARCH

Keratin 80 promotes migration and invasion of colorectal carcinoma by interacting with PRKDC via activating the AKT pathway

(2018) Changcan Li et al.   Cell Death & Disease

riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data

(2018) Fabio Lauria et al.   PLoS Computational Biology

A new sequence logo plot to highlight enrichment and depletion

(2018) Kushal K. Dey et al.   BMC BIOINFORMATICS

Acetylation of Cytidine in mRNA Promotes Translation Efficiency

(2018) Daniel Arango et al.   CELL

New tools for automated high-resolution cryo-EM structure determination in RELION-3

(2018) Jasenko Zivanov et al.   eLife

Structures of translationally inactive mammalian ribosomes

(2018) Alan Brown et al.   eLife

Non-AUG translation: a new start for protein synthesis in eukaryotes

(2017) Michael G. Kearse et al.   GENES & DEVELOPMENT

Paxillin: a crossroad in pathological cell migration

(2017) Ana María López-Colomé et al.   Journal of Hematology & Oncology

Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

(2017) Kathrin Leppek et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structural Insights into the Mechanism of Scanning and Start Codon Recognition in Eukaryotic Translation Initiation

(2017) Alan G. Hinnebusch   TRENDS IN BIOCHEMICAL SCIENCES

Genome-wide identification and differential analysis of translational initiation

(2017) Peng Zhang et al.   Nature Communications

tRNA modification profiles of the fast-proliferating cancer cells

(2016) Chao Dong et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Translational control by 5'-untranslated regions of eukaryotic mRNAs

(2016) A. G. Hinnebusch et al.   SCIENCE

Functional genetic variant in the Kozak sequence of WW domain-containing oxidoreductase (WWOX) gene is associated with oral cancer risk

(2016) Hsin-Lin Cheng et al.   Oncotarget

PreTIS: A Tool to Predict Non-canonical 5’ UTR Translational Initiation Sites in Human and Mouse

(2016) Kerstin Reuter et al.   PLoS Computational Biology

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

The regulation role of interferon regulatory factor-1 gene and clinical relevance

(2014) Lei Dou et al.   HUMAN IMMUNOLOGY

Structural basis for the inhibition of the eukaryotic ribosome

(2014) Nicolas Garreau de Loubresse et al.   NATURE

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Conformational Preferences of Modified Nucleoside N(4)-Acetylcytidine, ac4C Occur at “Wobble” 34th Position in the Anticodon Loop of tRNA

(2013) Bajarang V. Kumbhar et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Towards automated crystallographic structure refinement withphenix.refine

(2012) Pavel V. Afonine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution

(2012) S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Kinetic and thermodynamic analysis of the role of start codon/anticodon base pairing during eukaryotic translation initiation

(2008) S. E. Kolitz et al.   RNA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY