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Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing.

Molecular cell · 2013 · 50(2): 223-35

SR proteins are well-characterized RNA binding proteins that promote exon inclusion by binding to exonic splicing enhancers (ESEs). However, it has been unclear whether regulatory rules deduced on model genes apply generally to activities of SR proteins in the cell. …

PMID 23562324 DOI ↗

ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43.

Proceedings of the National Academy of Sciences of the United States of America · 2013 · 110(8): E736-45

Transactivating response region DNA binding protein (TDP-43) is the major protein component of ubiquitinated inclusions found in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) with ubiquitinated inclusions. Two ALS-causing mutants (TDP-43(Q331K) and TDP-43(M337V)), but not wild-type human TDP-43, …

PMID 23382207 DOI ↗

RNA-seq analysis of gene expression and alternative splicing by double-random priming strategy.

Methods in molecular biology (Clifton, N.J.) · 2011 · 729: 247-55

Transcriptome analysis by deep sequencing, more commonly known as RNA-seq is, becoming the method of choice for gene discovery and quantitative splicing detection. We published a double-random priming RNA-seq approach capable of generating strand-specific information [Li et al., Proc Natl …

PMID 21365495 DOI ↗

Alternative splicing in stem cell self-renewal and diferentiation.

Advances in experimental medicine and biology · 2010 · 695: 92-104

This chapter provides a review of recent advances in understanding the importance of alternative pre-messenger RNA splicing in stem cell biology. The majority of transcribed pre-mRNAs undergo RNA splicing where introns are excised and exons are juxtaposed to form mature …

PMID 21222201 DOI ↗

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans.

Nature structural & molecular biology · 2010 · 17(2): 173-9

MicroRNAs (miRNAs) regulate gene expression by guiding Argonaute proteins to specific target mRNA sequences. Identification of bona fide miRNA target sites in animals is challenging because of uncertainties regarding the base-pairing requirements between miRNA and target as well as the …

PMID 20062054 DOI ↗

An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells.

Nature structural & molecular biology · 2009 · 16(2): 130-7

The elucidation of a code for regulated splicing has been a long-standing goal in understanding the control of post-transcriptional gene expression events that are crucial for cell survival, differentiation and development. We decoded functional RNA elements in vivo by constructing …

PMID 19136955 DOI ↗

A regulator of Dscam mutually exclusive splicing fidelity.

Nature structural & molecular biology · 2007 · 14(12): 1134-40

The Down syndrome cell adhesion molecule (Dscam) gene has essential roles in neural wiring and pathogen recognition in Drosophila melanogaster. Dscam encodes 38,016 distinct isoforms via extensive alternative splicing. The 95 alternative exons in Dscam are organized into clusters that …

PMID 21188797 DOI ↗

Alternative splicing events identified in human embryonic stem cells and neural progenitors.

PLoS computational biology · 2007 · 3(10): 1951-67

Human embryonic stem cells (hESCs) and neural progenitor (NP) cells are excellent models for recapitulating early neuronal development in vitro, and are key to establishing strategies for the treatment of degenerative disorders. While much effort had been undertaken to analyze …

PMID 17967047 DOI ↗

The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression.

Cell · 2007 · 130(1): 179-91

Proper neuronal function and several forms of synaptic plasticity are highly dependent on precise control of mRNA translation, particularly in dendrites. We find that eIF4AIII, a core exon junction complex (EJC) component loaded onto mRNAs by pre-mRNA splicing, is associated …

PMID 17632064 DOI ↗

Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements.

PLoS genetics · 2007 · 3(5): e85

Knowledge of the functional cis-regulatory elements that regulate constitutive and alternative pre-mRNA splicing is fundamental for biology and medicine. Here we undertook a genome-wide comparative genomics approach using available mammalian genomes to identify conserved intronic splicing regulatory elements (ISREs). Our …

PMID 17530930 DOI ↗

Inference of splicing regulatory activities by sequence neighborhood analysis.

PLoS genetics · 2006 · 2(11): e191

Sequence-specific recognition of nucleic-acid motifs is critical to many cellular processes. We have developed a new and general method called Neighborhood Inference (NI) that predicts sequences with activity in regulating a biochemical process based on the local density of known …

PMID 17121466 DOI ↗

Identification and analysis of alternative splicing events conserved in human and mouse.

Proceedings of the National Academy of Sciences of the United States of America · 2005 · 102(8): 2850-5

Alternative pre-mRNA splicing affects a majority of human genes and plays important roles in development and disease. Alternative splicing (AS) events conserved since the divergence of human and mouse are likely of primary biological importance, but relatively few of such …

PMID 15708978 DOI ↗

RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons.

Nucleic acids research · 2004 · 32(Web Server issue): W187-90

A typical gene contains two levels of information: a sequence that encodes a particular protein and a host of other signals that are necessary for the correct expression of the transcript. While much attention has been focused on the effects …

PMID 15215377 DOI ↗

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