Search publications
38 results for “alternative splicing”
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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Multiple layers of molecular controls modulate self-renewal and neuronal lineage specification of embryonic stem cells.
Human molecular genetics · 2008 · 17(R1): R67-75
Elucidating the molecular changes that arise during neural differentiation and fate specification is crucial for building accurate in vitro models of neurodegenerative diseases using human embryonic stem cells (hESCs). Here we review the importance of hESCs and derived progenitors in …
PMID 18632700 DOI ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 25+
Single-cell and isoform-specific translational profiling of the mouse brain with long-read sequencing [scRNA-Seq, longread]
GPL34585
Single-cell and isoform-specific translational profiling of the mouse brain [scRNA-seq]
GPL34475
Loss of canonical splicing factor SRSF1 in hepatocytes results in acute liver injury and regeneration
Mus musculus · GPL21103
Exonuclease assisted mapping of protein-RNA interactions (ePRINT)
Homo sapiens · GPL30173
Exonuclease assisted mapping of protein-RNA interactions (ePRINT)
Homo sapiens · GPL24676
Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [RNA-seq]
Homo sapiens · GPL24676
Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [eCLIP-seq]
Mus musculus · GPL24676
Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [RNASeq, RiboSeq]
Homo sapiens · GPL24676
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splicing arrays)
Homo sapiens · GPL15106
Distinct and shared molecular targets and functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [CLIP-Seq]
Mus musculus · GPL13112
Distinct and shared functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [RNA-Seq_human]
Homo sapiens · GPL11154
HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_small_rnaseq]
Mus musculus · GPL15520
ALS-causative mutations in FUS/TLS confer gain- and loss-of-function by altered association with SMN and U1-snRNP
Homo sapiens · GPL11154
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (CLIP-Seq)
Homo sapiens · GPL9052
Systematic identification of RNA-binding proteins and tethered domains that activate exon splicing inclusion [eCLIP-seq]
Homo sapiens · GPL24676
Distinct and shared functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [RNA-Seq_mouse]
Mus musculus · GPL13112
Integrative RNA-omics discovers GNAS alternative splicing as a phenotypic driver of splicing factor mutant neoplasms
Homo sapiens · GPL20301
HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_Arrays_human_Fibs_2]
Homo sapiens · GPL15106
HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [iCLIP-seq]
Mus musculus · GPL13112
Systematic identification of RNA-binding proteins and tethered domains that activate exon splicing inclusion [RNA-seq]
Homo sapiens · GPL24676
HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_Arrays_human_Fibs_1]
Homo sapiens · GPL15106
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (RNA-Seq)
Homo sapiens · GPL9115
Distinct and shared functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [array]
Mus musculus · GPL13185
Showing first 25 dataset results.
Analyses 19
GSE114922 · 7 steps · RNA-Seq · code_examples
Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms. (2022)
GSE121569 · 12 steps · RNA-Seq · code_examples
Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis. (2022)
GSE122069 · 2 steps · RNA-Seq · code_examples
Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis. (2022)
GSE122649 · 3 steps · RNA-Seq · code_examples
Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis. (2022)
GSE124439 · 2 steps · RNA-Seq · code_examples
Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis. (2022)
GSE164666 · 4 steps · OTHER · code_examples
Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms. (2022)
GSE18920 · 4 steps · GSE · code_examples
Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis. (2022)
GSE56504 · 2 steps · GSE · code_examples
Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis. (2022)
GSE63816 · 6 steps · RNA-Seq · code_examples
Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms. (2022)
GSE65973 · 5 steps · RNA-Seq · code_examples
Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis. (2022)
GSE146916 · 4 steps · RNA-Seq · code_examples
A role for alternative splicing in circadian control of exocytosis and glucose homeostasis. (2020)
GSE69889 · 5 steps · RNA-Seq · code_examples
A role for alternative splicing in circadian control of exocytosis and glucose homeostasis. (2020)
GSE92602 · 5 steps · RNA-Seq · code_examples
A role for alternative splicing in circadian control of exocytosis and glucose homeostasis. (2020)
GSE95156 · 7 steps · RNA-Seq · code_examples
A role for alternative splicing in circadian control of exocytosis and glucose homeostasis. (2020)
GSE85908 · 11 steps · RNA-Seq · code_examples
Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation. (2017)
GSE34992 · 2 steps · GSE · code_examples
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. (2012)
GSE34993 · 2 steps · RNA-Seq · code_examples
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. (2012)
GSE34995 · 2 steps · RNA-Seq · code_examples
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. (2012)
GSE34996 · 2 steps · GSE · code_examples
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. (2012)