Search publications
69 results for “RNA splicing”
-
Nxf1 natural variant E610G is a semi-dominant suppressor of IAP-induced RNA processing defects.
PLoS genetics · 2015 · 11(4): e1005123
Endogenous retroviruses and retrotransposons contribute functional genetic variation in animal genomes. In mice, Intracisternal A Particles (IAPs) are a frequent source of both new mutations and polymorphism across laboratory strains. Intronic IAPs can induce alternative RNA processing choices, including alternative …
PMID 25835743 DOI ↗
-
ALS-causative mutations in FUS/TLS confer gain and loss of function by altered association with SMN and U1-snRNP.
Nature communications · 2015 · 6: 6171
The RNA-binding protein FUS/TLS, mutation in which is causative of the fatal motor neuron disease amyotrophic lateral sclerosis (ALS), is demonstrated to directly bind to the U1-snRNP and SMN complexes. ALS-causative mutations in FUS/TLS are shown to abnormally enhance their …
PMID 25625564 DOI ↗
-
Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges.
Nature structural & molecular biology · 2013 · 20(12): 1434-42
Alternative splicing (AS) enables programmed diversity of gene expression across tissues and development. We show here that binding in distal intronic regions (>500 nucleotides (nt) from any exon) by Rbfox splicing factors important in development is extensive and is an …
PMID 24213538 DOI ↗
-
Reactivation of fetal splicing programs in diabetic hearts is mediated by protein kinase C signaling.
The Journal of biological chemistry · 2013 · 288(49): 35372-86
Diabetic cardiomyopathy is one of the complications of diabetes that eventually leads to heart failure and death. Aberrant activation of PKC signaling contributes to diabetic cardiomyopathy by mechanisms that are poorly understood. Previous reports indicate that PKC is implicated in …
PMID 24151077 DOI ↗
-
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 ↗
-
LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance.
Molecular cell · 2012 · 48(2): 195-206
LIN28 is a conserved RNA-binding protein implicated in pluripotency, reprogramming, and oncogenesis. It was previously shown to act primarily by blocking let-7 microRNA (miRNA) biogenesis, but here we elucidate distinct roles of LIN28 regulation via its direct messenger RNA (mRNA) …
PMID 22959275 DOI ↗
-
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins.
Cell reports · 2012 · 1(2): 167-78
Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here, we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate …
PMID 22574288 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 ↗
-
Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43.
Nature neuroscience · 2011 · 14(4): 459-68
We used cross-linking and immunoprecipitation coupled with high-throughput sequencing to identify binding sites in 6,304 genes as the brain RNA targets for TDP-43, an RNA binding protein that, when mutated, causes amyotrophic lateral sclerosis. Massively parallel sequencing and splicing-sensitive junction …
PMID 21358643 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 ↗
-
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 ↗
-
Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model.
Proceedings of the National Academy of Sciences of the United States of America · 2008 · 105(51): 20179-84
High-throughput sequencing has rapidly gained popularity for transcriptome analysis in mammalian cells because of its ability to generate digital and quantitative information on annotated genes and to detect transcripts and mRNA isoforms. Here, we described a double-random priming method for …
PMID 19088194 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 ↗
-
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 ↗
-
Splicing regulators: targets and drugs.
Genome biology · 2005 · 6(12): 240
Silencing of splicing regulators by RNA interference, combined with splicing-specific microarrays, has revealed a complex network of distinct alternative splicing events in Drosophila, while a high-throughput screen of more than 6,000 compounds has identified drugs that interfere specifically and directly …
PMID 16356274 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 ↗
Datasets 21
Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (eCLIP).
Homo sapiens · GPL24676
Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS
Homo sapiens · GPL24676
Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (RNA-Seq).
Homo sapiens · Illumina
RNA sequencing of bone marrow CD34+ hematopoietic stem and progenitor cells from patients with myelodysplastic syndrome and healthy controls
Homo sapiens · GPL20301
Aberrant splicing of U12-type introns is the hallmark of ZRSR2 mutant myelodysplastic syndrome
Homo sapiens · GPL11154
Loss of nuclear TDP-43 in ALS causes altered expression of splicing machinery and widespread dysregulation of RNA splicing in motor neurons
Mus musculus · GPL5188
In vivo CRISPR screening unveils RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a potential therapeutic target [eCLIPseq]
Mus musculus · GPL21103
In vivo CRISPR screening unveils RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a potential therapeutic target [RNA-seq]
Mus musculus · GPL18480
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splicing arrays)
Homo sapiens · GPL15106
Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [RNA-seq]
Homo sapiens · GPL24676
ALS-causative mutations in FUS/TLS confer gain- and loss-of-function by altered association with SMN and U1-snRNP
Homo sapiens · GPL11154
Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [RBNS]
synthetic construct · GPL34014
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (CLIP-Seq)
Homo sapiens · GPL9052
Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [SLAM-Seq]
Homo sapiens · GPL24676
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (RNA-Seq)
Homo sapiens · GPL9115
Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [Cut&Run]
Homo sapiens · GPL24676
Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS
Homo sapiens · GPL16791
Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [eCLIP]
Homo sapiens · GPL24676
A two-step in vivo CRISPR screen unveils pervasive RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a therapeutic target
Homo sapiens · GPL18460
A role for alternative splicing in circadian control of insulin secretion and glucose homeostasis
Mus musculus · GPL19057
Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [Ribo-STAMP cell lines]
Homo sapiens · GPL24676
Analyses 2
GSE25421 · 1 step · GSE · code_examples
Inhibition of RNA splicing triggers CHMP7 nuclear entry, impacting TDP-43 function and leading to the onset of ALS cellular phenotypes. (2024)
GSE56504 · 2 steps · GSE · code_examples
Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis. (2022)