Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Myelodysplastic syndromes: moving towards personalized management

(2020) Eva Hellström-Lindberg et al.   HAEMATOLOGICA

Clinical presentation and differential splicing of SRSF2, U2AF1 and SF3B1 mutations in patients with acute myeloid leukemia

(2020) Stefanos A. Bamopoulos et al.   LEUKEMIA

DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis

(2020) Yafeng Zhu et al.   MOLECULAR & CELLULAR PROTEOMICS

Roles and mechanisms of alternative splicing in cancer — implications for care

(2020) Sophie C. Bonnal et al.   Nature Reviews Clinical Oncology

A splice site-sensing conformational switch in U2AF2 is modulated by U2AF1 and its recurrent myelodysplasia-associated mutation

(2020) Chandani Warnasooriya et al.   NUCLEIC ACIDS RESEARCH

Elucidation of the aberrant 3′ splice site selection by cancer-associated mutations on the U2AF1

(2020) Hisashi Yoshida et al.   Nature Communications

Spatiotemporal Proteomic Analysis of Stress Granule Disassembly Using APEX Reveals Regulation by SUMOylation and Links to ALS Pathogenesis

(2020) Hagai Marmor-Kollet et al.   MOLECULAR CELL

ISRIB Blunts the Integrated Stress Response by Allosterically Antagonising the Inhibitory Effect of Phosphorylated eIF2 on eIF2B

(2020) Alisa F. Zyryanova et al.   MOLECULAR CELL

RNA partitioning into stress granules is based on the summation of multiple interactions

(2020) Tyler Matheny et al.   RNA

Small molecule ISRIB suppresses the integrated stress response within a defined window of activation

(2019) Huib H. Rabouw et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The splicing factor U2AF1 contributes to cancer progression through a noncanonical role in translation regulation

(2019) Murali Palangat et al.   GENES & DEVELOPMENT

Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia

(2019) Eric Wang et al.   CANCER CELL

Epidemiology of acute myeloid leukemia: Recent progress and enduring challenges

(2019) Rory M. Shallis et al.   BLOOD REVIEWS

Stress granule: a promising target for cancer treatment

(2019) Xiaomeng Gao et al.   BRITISH JOURNAL OF PHARMACOLOGY

Therapeutic Targeting of RNA Splicing Catalysis through Inhibition of Protein Arginine Methylation

(2019) Jia Yi Fong et al.   CANCER CELL

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Mutations in Splicing Factor Genes in Myeloid Malignancies: Significance and Impact on Clinical Features

(2019) Valeria Visconte et al.   Cancers

Functional significance of U2AF1 S34F mutations in lung adenocarcinomas

(2019) Mohammad S. Esfahani et al.   Nature Communications

Impact of spliceosome mutations on RNA splicing in myelodysplasia: dysregulated genes/pathways and clinical associations

(2018) Andrea Pellagatti et al.   BLOOD

Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules

(2018) Sebastian Markmiller et al.   CELL

High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies

(2018) Ji-Young Youn et al.   MOLECULAR CELL

TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding

(2018) Jeremy A Schofield et al.   NATURE METHODS

RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome

(2018) Briana Van Treeck et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spliceosome Mutations Induce R Loop-Associated Sensitivity to ATR Inhibition in Myelodysplastic Syndromes

(2018) Hai Dang Nguyen et al.   CANCER RESEARCH

Emerging Roles for Intermolecular RNA-RNA Interactions in RNP Assemblies

(2018) Briana Van Treeck et al.   CELL

Stress Granules and Processing Bodies in Translational Control

(2018) Pavel Ivanov et al.   Cold Spring Harbor Perspectives in Biology

The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes

(2017) Bon Ham Yip et al.   JOURNAL OF CLINICAL INVESTIGATION

Clinical Implications of Genetic Mutations in Myelodysplastic Syndrome

(2017) James A. Kennedy et al.   JOURNAL OF CLINICAL ONCOLOGY

CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins

(2017) Eric L. Van Nostrand et al.   METHODS

The Stress Granule Transcriptome Reveals Principles of mRNA Accumulation in Stress Granules

(2017) Anthony Khong et al.   MOLECULAR CELL

Mutant U2AF1-expressing cells are sensitive to pharmacological modulation of the spliceosome

(2017) Cara Lunn Shirai et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Splicing factor gene mutations in hematologic malignancies

(2016) Borja Saez et al.   BLOOD

Mutant KRAS Enhances Tumor Cell Fitness by Upregulating Stress Granules

(2016) Elda Grabocka et al.   CELL

ATPase-Modulated Stress Granules Contain a Diverse Proteome and Substructure

(2016) Saumya Jain et al.   CELL

Droplet organelles?

(2016) Edward M Courchaine et al.   EMBO JOURNAL

Modulation of splicing catalysis for therapeutic targeting of leukemia with mutations in genes encoding spliceosomal proteins

(2016) Stanley Chun-Wei Lee et al.   NATURE MEDICINE

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Splicing-factor alterations in cancers

(2016) Olga Anczuków et al.   RNA

Principles and Properties of Stress Granules

(2016) David S.W. Protter et al.   TRENDS IN CELL BIOLOGY

An extended U2AF65–RNA-binding domain recognizes the 3′ splice site signal

(2016) Anant A. Agrawal et al.   Nature Communications

Wild-Type U2AF1 Antagonizes the Splicing Program Characteristic of U2AF1-Mutant Tumors and Is Required for Cell Survival

(2016) Dennis Liang Fei et al.   PLoS Genetics

Stress granules, P-bodies and cancer

(2015) Paul Anderson et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo

(2015) Cara Lunn Shirai et al.   CANCER CELL

A novel 3′ splice site recognition by the two zinc fingers in the U2AF small subunit

(2015) Hisashi Yoshida et al.   GENES & DEVELOPMENT

Myelodysplastic Syndromes

(2015) David P. Steensma   MAYO CLINIC PROCEEDINGS

Acute Myeloid Leukemia

(2015) Hartmut Döhner et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2014) S. Anders et al.   BIOINFORMATICS

U2AF1mutations alter splice site recognition in hematological malignancies

(2014) Janine O. Ilagan et al.   GENOME RESEARCH

U2AF1 mutations alter sequence specificity of pre-mRNA binding and splicing

(2014) T Okeyo-Owuor et al.   LEUKEMIA

Mechanisms for U2AF to define 3′ splice sites and regulate alternative splicing in the human genome

(2014) Changwei Shao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Systematic integration of RNA-Seq statistical algorithms for accurate detection of differential gene expression patterns

(2014) Panagiotis Moulos et al.   NUCLEIC ACIDS RESEARCH

A Pan-Cancer Analysis of Transcriptome Changes Associated with Somatic Mutations in U2AF1 Reveals Commonly Altered Splicing Events

(2014) Angela N. Brooks et al.   PLoS One

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Patterns of missplicing due to somatic U2AF1 mutations in myeloid neoplasms

(2013) B. Przychodzen et al.   BLOOD

Clinical and biological implications of driver mutations in myelodysplastic syndromes

(2013) E. Papaemmanuil et al.   BLOOD

Pharmacological brake-release of mRNA translation enhances cognitive memory

(2013) Carmela Sidrauski et al.   eLife

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Development of an All-in-One Inducible Lentiviral Vector for Gene Specific Analysis of Reprogramming

(2012) Tomoyuki Yamaguchi et al.   PLoS One

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Frequent pathway mutations of splicing machinery in myelodysplasia

(2011) Kenichi Yoshida et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes

(2011) Timothy A Graubert et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Context-Dependent Regulatory Mechanism of the Splicing Factor hnRNP L

(2010) Laura B. Motta-Mena et al.   MOLECULAR CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS