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15 results for “pre-mRNA”

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  1. Dual-targeting snRNA gene therapy rescues STMN2 and UNC13A splicing in TDP-43 proteinopathies.

    bioRxiv : the preprint server for biology · 2025

    Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder caused by the selective deterioration of motor neurons in the central nervous system (CNS). A key driver of this pathogenesis is nuclear loss of ALS-associated protein TDP-43, leading to mis-splicing of TDP-43 …

    PMID 41573891 DOI ↗

  2. Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs.

    Nature chemical biology · 2025

    Endogenous uridine-rich small nuclear RNAs (U snRNAs) form RNA-protein complexes to process eukaryotic pre-mRNA into mRNA. Previous studies have demonstrated programmable U snRNA guide-targeted exon inclusion and exclusion. Here we investigated whether snRNAs can also enhance RNA base editing over …

    PMID 40968292 DOI ↗

  3. Small nuclear RNAs enhance protein-free RNA-programmable base conversion on mammalian coding transcripts.

    bioRxiv : the preprint server for biology · 2024

    Endogenous U small nuclear RNAs (U snRNAs) form RNA-protein complexes responsible for eukaryotic processing of pre-mRNA into mature mRNA. Previous studies have demonstrated the utility of guide-programmable U snRNAs in targeted exon inclusion and exclusion. We investigated whether snRNAs can …

    PMID 38915553 DOI ↗

  4. Engineered U1 snRNAs to modulate alternatively spliced exons.

    Methods (San Diego, Calif.) · 2022 · 205: 140-148

    Alternative splicing accounts for a considerable portion of transcriptomic diversity, as most protein-coding genes are spliced into multiple mRNA isoforms. However, errors in splicing patterns can give rise to mis-splicing with pathological consequences, such as the congenital diseases familial dysautonomia, …

    PMID 35764245 DOI ↗

  5. Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.

    Molecular cell · 2022 · 82(3): 645-659.e9

    Pseudouridine is a modified nucleotide that is prevalent in human mRNAs and is dynamically regulated. Here, we investigate when in their life cycle mRNAs become pseudouridylated to illuminate the potential regulatory functions of endogenous mRNA pseudouridylation. Using single-nucleotide resolution pseudouridine …

    PMID 35051350 DOI ↗

  6. Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS.

    Molecular cell · 2021 · 81(9): 1905-1919.e12

    Oxidative phosphorylation (OXPHOS) and glycolysis are the two major pathways for ATP production. The reliance on each varies across tissues and cell states, and can influence susceptibility to disease. At present, the full set of molecular mechanisms governing the relative …

    PMID 33852893 DOI ↗

  7. A role for alternative splicing in circadian control of exocytosis and glucose homeostasis.

    Genes & development · 2020 · 34(15-16): 1089-1105

    The circadian clock is encoded by a negative transcriptional feedback loop that coordinates physiology and behavior through molecular programs that remain incompletely understood. Here, we reveal rhythmic genome-wide alternative splicing (AS) of pre-mRNAs encoding regulators of peptidergic secretion within pancreatic …

    PMID 32616519 DOI ↗

  8. Tethered Function Assays as Tools to Elucidate the Molecular Roles of RNA-Binding Proteins.

    Advances in experimental medicine and biology · 2016 · 907: 61-88

    Dynamic regulation of RNA molecules is critical to the survival and development of cells. Messenger RNAs are transcribed in the nucleus as intron-containing pre-mRNAs and bound by RNA-binding proteins, which control their fate by regulating RNA stability, splicing, polyadenylation, translation, …

    PMID 27256382 DOI ↗

  9. The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion.

    Annual review of biochemistry · 2015 · 84: 325-54

    Throughout their lifetimes, messenger RNAs (mRNAs) associate with proteins to form ribonucleoproteins (mRNPs). Since the discovery of the first mRNP component more than 40 years ago, what is known as the mRNA interactome now comprises >1,000 proteins. These proteins bind …

    PMID 25784054 DOI ↗

  10. Misregulated RNA processing in amyotrophic lateral sclerosis.

    Brain research · 2012 · 1462: 3-15

    Amyotrophic lateral sclerosis (ALS) research is undergoing an era of unprecedented discoveries with the identification of new genes as major genetic causes of this disease. These discoveries reinforce the genetic, clinical and pathological overlap between ALS and frontotemporal lobar degeneration …

    PMID 22444279 DOI ↗

  11. 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 ↗

  12. 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 ↗

  13. 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 ↗

  14. 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 ↗

  15. 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 19

GSE114922 GSE · GEO

RNA sequencing of bone marrow CD34+ hematopoietic stem and progenitor cells from patients with myelodysplastic syndrome and healthy controls

Homo sapiens · GPL20301

GSE122069 GSE · GEO

Premature polyadenylation-mediated loss of stathmin-2 is a hallmark of TDP-43-dependent neurodegeneration

Homo sapiens · GPL20301

GSE50178 GSE · GEO

Identification of FUS RNA targets in HeLa cells

Homo sapiens · GPL9115

GSE34992 GSE · GEO

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splicing arrays)

Homo sapiens · GPL15106

GSE123613 GSE · GEO

Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect splicingÂ

Homo sapiens · GPL11154

GSE34993 GSE · GEO

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (CLIP-Seq)

Homo sapiens · GPL9052

GSE40652 GSE · GEO

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (RNA-Seq)

Mus musculus · GPL9250

GSE66696 GSE · GEO

Whole brain RNA from congenic littermates does not support a general effect of Nxf1 CAST alleles on alternative pre-mRNA processing

Mus musculus · GPL13185

GSE27371 GSE · GEO

Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (Affymetrix)

Mus musculus · GPL13185

GSE34995 GSE · GEO

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (RNA-Seq)

Homo sapiens · GPL9115

GSE40649 GSE · GEO

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (microarray)

Mus musculus · GPL13185

GSE295421 GSE · GEO

Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs

Homo sapiens · GPL34284

GSE27201 GSE · GEO

Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (CLIP)

Mus musculus · GPL9250

GSE40651 GSE · GEO

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (CLIP-Seq)

Mus musculus · GPL11154

GSE157917 GSE · GEO

Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS

Homo sapiens · GPL16791

GSE27218 GSE · GEO

Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (RNA-seq)

Mus musculus · GPL9250

GSE40653 GSE · GEO

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs

Mus musculus · GPL9250

GSE27394 GSE · GEO

Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43

Mus musculus · GPL9250

GSE146916 GSE · GEO

A role for alternative splicing in circadian control of insulin secretion and glucose homeostasis

Mus musculus · GPL19057

Analyses 11

GSE123613 Processing Pipeline

GSE123613 · 9 steps · OTHER · code_examples

Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing. (2022)

GSE90963 Processing Pipeline

GSE90963 · 35 steps · RNA-Seq · code_examples

Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing. (2022)

GSE66696 Processing Pipeline

GSE66696 · 6 steps · GSE · code_examples

Nxf1 natural variant E610G is a semi-dominant suppressor of IAP-induced RNA processing defects. (2015)

GSE40649 Processing Pipeline

GSE40649 · 2 steps · GSE · code_examples

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs. (2012)

GSE40651 Processing Pipeline

GSE40651 · 1 step · RNA-Seq · code_examples

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs. (2012)

GSE40652 Processing Pipeline

GSE40652 · 1 step · RNA-Seq · code_examples

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs. (2012)

GSE40653 Processing Pipeline

GSE40653 · 2 steps · GSE · code_examples

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs. (2012)

GSE27201 Processing Pipeline

GSE27201 · 1 step · RNA-Seq · code_examples

Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43. (2011)

GSE27218 Processing Pipeline

GSE27218 · 1 step · RNA-Seq · code_examples

Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43. (2011)

GSE27371 Processing Pipeline

GSE27371 · 2 steps · GSE · code_examples

Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43. (2011)

GSE27394 Processing Pipeline

GSE27394 · 1 step · GSE · code_examples

Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43. (2011)