Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS

Genetic mutations in RNA-binding proteins and their roles in ALS

(2017) Katannya Kapeli et al.   HUMAN GENETICS

Differential analysis of RNA-seq incorporating quantification uncertainty

(2017) Harold Pimentel et al.   NATURE METHODS

Non-nuclear Pool of Splicing Factor SFPQ Regulates Axonal Transcripts Required for Normal Motor Development

(2017) Swapna Thomas-Jinu et al.   NEURON

Progressive Motor Neuron Pathology and the Role of Astrocytes in a Human Stem Cell Model of VCP-Related ALS

(2017) Claire E. Hall et al.   Cell Reports

Altered Tau Isoform Ratio Caused by Loss of FUS and SFPQ Function Leads to FTLD-like Phenotypes

(2017) Shinsuke Ishigaki et al.   Cell Reports

Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex

(2016) Xiaochang Zhang et al.   CELL

A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation

(2016) Andreas J. Gruber et al.   GENOME RESEARCH

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

The RNA-binding protein SFPQ orchestrates an RNA regulon to promote axon viability

(2016) Katharina E Cosker et al.   NATURE NEUROSCIENCE

ALS disrupts spinal motor neuron maturation and aging pathways within gene co-expression networks

(2016) Ritchie Ho et al.   NATURE NEUROSCIENCE

Alternative polyadenylation of mRNA precursors

(2016) Bin Tian et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Targeted Intron Retention and Excision for Rapid Gene Regulation in Response to Neuronal Activity

(2016) Oriane Mauger et al.   NEURON

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses

(2016) Katannya Kapeli et al.   Nature Communications

Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling

(2016) Susanne Nichterwitz et al.   Nature Communications

Polarizing the Neuron through Sustained Co-expression of Alternatively Spliced Isoforms

(2016) Karen Yap et al.   Cell Reports

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators

(2015) Qinghong Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PSF: nuclear busy-body or nuclear facilitator?

(2015) Christopher A. Yarosh et al.   Wiley Interdisciplinary Reviews-RNA

Introns and gene expression: Cellular constraints, transcriptional regulation, and evolutionary consequences

(2014) Patricia Heyn et al.   BIOESSAYS

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

(2014) S. Anders et al.   BIOINFORMATICS

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

(2014) Manuel Irimia et al.   CELL

Pathways Disrupted in Human ALS Motor Neurons Identified through Genetic Correction of Mutant SOD1

(2014) Evangelos Kiskinis et al.   Cell Stem Cell

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

ALS-associated mutation FUS-R521C causes DNA damage and RNA splicing defects

(2014) Haiyan Qiu et al.   JOURNAL OF CLINICAL INVESTIGATION

Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions

(2014) I. Gupta et al.   Molecular Systems Biology

Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion

(2014) Raphaëlle Luisier et al.   NUCLEIC ACIDS RESEARCH

Widespread and extensive lengthening of 3' UTRs in the mammalian brain

(2013) P. Miura et al.   GENOME RESEARCH

NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies

(2013) Tetsuro Hirose et al.   MOLECULAR BIOLOGY OF THE CELL

mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex

(2013) Allissa A Dillman et al.   NATURE NEUROSCIENCE

Deep Sequencing and High-Resolution Imaging Reveal Compartment-Specific Localization of Bdnf mRNA in Hippocampal Neurons

(2013) T. J. Will et al.   Science Signaling

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention

(2012) K. Yap et al.   GENES & DEVELOPMENT

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Tau-Mediated Nuclear Depletion and Cytoplasmic Accumulation of SFPQ in Alzheimer's and Pick's Disease

(2012) Yazi Ke et al.   PLoS One

A more efficient method to generate integration-free human iPS cells

(2011) Keisuke Okita et al.   NATURE METHODS

Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43

(2011) Magdalini Polymenidou et al.   NATURE NEUROSCIENCE

Characterizing the RNA targets and position-dependent splicing regulation by TDP-43

(2011) James R Tollervey et al.   NATURE NEUROSCIENCE

Cytoplasmic Intron Sequence-Retaining Transcripts Can Be Dendritically Targeted via ID Element Retrotransposons

(2011) Peter T. Buckley et al.   NEURON

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

TDP-43 regulates its mRNA levels through a negative feedback loop

(2010) Youhna M Ayala et al.   EMBO JOURNAL

Transgenic mice expressing mutant forms VCP/p97 recapitulate the full spectrum of IBMPFD including degeneration in muscle, brain and bone

(2010) Sara K. Custer et al.   HUMAN MOLECULAR GENETICS

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

Exome Sequencing Reveals VCP Mutations as a Cause of Familial ALS

(2010) Janel O. Johnson et al.   NEURON

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing

(2010) J. Q. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sporadic ALS has compartment-specific aberrant exon splicing and altered cell–matrix adhesion biology

(2009) Stuart J. Rabin et al.   HUMAN MOLECULAR GENETICS

Paraspeckles: nuclear bodies built on long noncoding RNA

(2009) Charles S. Bond et al.   JOURNAL OF CELL BIOLOGY

Altered Nuclear Retention of mRNAs Containing Inverted Repeats in Human Embryonic Stem Cells: Functional Role of a Nuclear Noncoding RNA

(2009) Ling-Ling Chen et al.   MOLECULAR CELL

Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development

(2009) Z. Ji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SnapShot: The Splicing Regulatory Machinery

(2008) Mathieu Gabut et al.   CELL

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE