Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential

Most non-canonical proteins uniquely populate the proteome or immunopeptidome

(2021) Maria Virginia Ruiz Cuevas et al.   Cell Reports

Integrator enforces the fidelity of transcriptional termination at protein-coding genes

(2021) Lucas Ferreira Dasilva et al.   Science Advances

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

U1 snRNP regulates cancer cell migration and invasion in vitro

(2020) Jung-Min Oh et al.   Nature Communications

RASP: an atlas of transcriptome-wide RNA secondary structure probing data

(2020) Pan Li et al.   NUCLEIC ACIDS RESEARCH

Regulation of Intronic Polyadenylation by PCF11 Impacts mRNA Expression of Long Genes

(2019) Ruijia Wang et al.   Cell Reports

Alternative cleavage and polyadenylation in health and disease

(2019) Andreas J. Gruber et al.   NATURE REVIEWS GENETICS

A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes

(2019) Charlotte Soneson et al.   Nature Communications

RNA m6A methylation regulates the epithelial mesenchymal transition of cancer cells and translation of Snail

(2019) Xinyao Lin et al.   Nature Communications

The biogenesis, biology and characterization of circular RNAs

(2019) Lasse S. Kristensen et al.   NATURE REVIEWS GENETICS

The U1 spliceosomal RNA is recurrently mutated in multiple cancers

(2019) Shimin Shuai et al.   NATURE

Cap-Independent Translation: What’s in a Name?

(2018) Ivan N. Shatsky et al.   TRENDS IN BIOCHEMICAL SCIENCES

Widespread intronic polyadenylation diversifies immune cell transcriptomes

(2018) Irtisha Singh et al.   Nature Communications

A potentially abundant junctional RNA motif stabilized by m6A and Mg2+

(2018) Bei Liu et al.   Nature Communications

Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development

(2018) Seth D. Kasowitz et al.   PLoS Genetics

VIRMA mediates preferential m6A mRNA methylation in 3′UTR and near stop codon and associates with alternative polyadenylation

(2018) Yanan Yue et al.   Cell Discovery

Widespread intronic polyadenylation inactivates tumour suppressor genes in leukaemia

(2018) Shih-Han Lee et al.   NATURE

The Role of m6A/m-RNA Methylation in Stress Response Regulation

(2018) Mareen Engel et al.   NEURON

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

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

Translation of CircRNAs

(2017) Nagarjuna Reddy Pamudurti et al.   MOLECULAR CELL

m 6 A Facilitates eIF4F-Independent mRNA Translation

(2017) Ryan A. Coots et al.   MOLECULAR CELL

m6A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways

(2017) Hua-Bing Li et al.   NATURE

The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells

(2017) Ly P Vu et al.   NATURE MEDICINE

RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data

(2017) Jia-Jia Xuan et al.   NUCLEIC ACIDS RESEARCH

Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments

(2017) Yuval Malka et al.   Nature Communications

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

(2016) Zhipeng Lu et al.   CELL

Structured RNAs that evade or confound exonucleases: function follows form

(2016) Benjamin M Akiyama et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2016) Benoit Molinie et al.   NATURE METHODS

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

(2016) Meghan Zubradt et al.   NATURE METHODS

Genome-wide quantification of 5′-phosphorylated mRNA degradation intermediates for analysis of ribosome dynamics

(2016) Vicent Pelechano et al.   Nature Protocols

Signalling to eIF4E in cancer

(2015) N. Siddiqui et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

5′ UTR m6A Promotes Cap-Independent Translation

(2015) Kate D. Meyer et al.   CELL

Structure and Thermodynamics of N6-Methyladenosine in RNA: A Spring-Loaded Base Modification

(2015) Caroline Roost et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Dynamic m6A mRNA methylation directs translational control of heat shock response

(2015) Jun Zhou et al.   NATURE

Efficient and quantitative high-throughput tRNA sequencing

(2015) Guanqun Zheng et al.   NATURE METHODS

Rapid and efficient one-step generation of paired gRNA CRISPR-Cas9 libraries

(2015) Joana A. Vidigal et al.   Nature Communications

IL-21-mediated non-canonical pathway for IL-1β production in conventional dendritic cells

(2015) Chi-Keung Wan et al.   Nature Communications

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

(2014) S. Anders et al.   BIOINFORMATICS

Distinct Epigenetic Signatures Delineate Transcriptional Programs during Virus-Specific CD8+ T Cell Differentiation

(2014) Brendan E. Russ et al.   IMMUNITY

Acute myeloid leukemia cells harboring MLL fusion genes or with the acute promyelocytic leukemia phenotype are sensitive to the Bcl-2-selective inhibitor ABT-199

(2014) X Niu et al.   LEUKEMIA

Global Analyses of the Effect of Different Cellular Contexts on MicroRNA Targeting

(2014) Jin-Wu Nam et al.   MOLECULAR CELL

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

CFIm25 links alternative polyadenylation to glioblastoma tumour suppression

(2014) Chioniso P. Masamha et al.   NATURE

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA

(2014) Erich G Chapman et al.   eLife

CruzDB: software for annotation of genomic intervals with UCSC genome-browser database

(2013) Brent S. Pedersen et al.   BIOINFORMATICS

Alternative cleavage and polyadenylation: extent, regulation and function

(2013) Ran Elkon et al.   NATURE REVIEWS GENETICS

Selective BCL-2 Inhibition by ABT-199 Causes On-Target Cell Death in Acute Myeloid Leukemia

(2013) R. Pan et al.   Cancer Discovery

p53 induces transcriptional and translational programs to suppress cell proliferation and growth

(2013) Fabricio Loayza-Puch et al.   GENOME BIOLOGY

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

ViennaRNA Package 2.0

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

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome

(2010) T. R. Mercer et al.   GENOME RESEARCH

Diverse Endonucleolytic Cleavage Sites in the Mammalian Transcriptome Depend upon MicroRNAs, Drosha, and Additional Nucleases

(2010) Fedor V. Karginov et al.   MOLECULAR CELL

Translational Regulation of Gene Expression during Conditions of Cell Stress

(2010) Keith A. Spriggs et al.   MOLECULAR CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Expression of distinct RNAs from 3′ untranslated regions

(2010) Tim R. Mercer et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

PPAR gamma protects cardiomyocytes against oxidative stress and apoptosis via Bcl-2 upregulation

(2009) Yusheng Ren et al.   VASCULAR PHARMACOLOGY

Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1

(2008) I. Chernyakov et al.   GENES & DEVELOPMENT

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

The BCL-2 protein family: opposing activities that mediate cell death

(2007) Richard J. Youle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY