Результаты поиска

Substrate-dependent differences in U2AF requirement for splicing in adenovirus-infected cell extracts.

U2AF has been characterized as an essential splicing factor required for efficient recruitment of U2 small nuclear ribonucleoprotein to the 3'-splice site in a pre-mRNA. The U2AF65 subunit binds to the pyrimidine tract of the pre-mRNA, whereas the U2AF(35) subunit contacts the 3'-splice site AG. Here we show that U2AF35 appears to be completely dispensable for splicing in nuclear extracts prepared from adenovirus late-infected cells (Ad-NE). As a consequence, the viral IIIa and cellular IgM introns, which both have suboptimal 3'-splice sites and require U2AF35 for splicing in nuclear extracts

Intron retention regulates STAT2 function and associates with immunotherapy response in lung cancer.

Immunotherapy with checkpoint inhibitors has revolutionized cancer therapy and enabled considerable therapeutic advances for treating various diseases, including lung cancer. However, the molecular determinants of variable patient outcomes remain unclear. Using long-read RNA sequencing, we mapped the landscape of alternative RNA splicing in human primary lung adenocarcinomas. We identified more than 149,000 full-length messenger RNA (mRNA) isoforms, more than half of which were unannotated and many that occurred in immune-related genes, particularly within the type I interferon response pathwa…

Влияние регулирования разбрызгивания на нервно-мышечные расстройства и текущую нейромускульную генетическую терапию.

Эукариотические гены содержат некодирующие сегменты, известные как интроны, которые прерывают последовательности кодирования. Таким образом, эукариотическая транскрипция производит прекурсор-прекурсор РНК (до-мРНК), который основывается на точной скрещивании для удаления весьма разнообразных интронов из генома и создания зрелого mRNA, необходимого для поддержания нормальной клеточной активности. Широкая неоднородность нейронов требует сложного регулирования сплетения, особенно альтернативного сплечения, для обеспечения точности генного выражения в нейрогенессе, трансдукции сигналов и синаптиче

Совпадение в аннотации оригинала
Eukaryotic genes contain non-coding segments known as introns, which interrupt coding sequences. Consequently, eukaryotic transcription prod … ing effective therapies. In this review, we introduce the intricate process and key factors of pre-mRNA splicing, with a focus on aberrant splicing and pathogenesis in several major neuromuscular disorders, providing an overview of the latest therapeutic strategies.

Arginine/serine-rich protein interaction domain-dependent modulation of a tau exon 10 splicing enhancer: altered interactions and mechanisms for functionally antagonistic FTDP-17 mutations Delta280K AND N279K.

Tau exon 10 splicing is altered by autosomal dominant mutations that cause frontotemporal dementia with parkinsonism chromosome 17-type and by unknown mechanisms in other related neurodegenerative disorders. Identifying cis- and trans-regulators of tau exon 10 splicing is therefore crucial for understanding disease mechanisms. We previously identified several splicing enhancers and silencers within exon 10 and intron 10. Here, we show that splicing factors SF2/ASF, Tra2beta, and a 50-kDa nuclear protein bind in vitro to the polypurine enhancer at the 5' end of exon 10. Disease splicing mutatio

Small Molecule Screening Discovers Compounds that Reduce FMRpolyG Protein Aggregates and Splicing Defect Toxicity in Fragile X-Associated Tremor/Ataxia Syndrome.

Expansion of CGG trinucleotide repeats in 5' untranslated region of the FMR1 gene is the causative mutation of neurological diseases such as fragile X syndrome (FXS), fragile X-associated tremor/ataxia syndrome (FXTAS), and ovarian disorder such as fragile X-associated primary ovarian insufficiency (FXPOI). CGG repeats containing FMR1 transcripts form the toxic ribonuclear aggregates, abrupt pre-mRNA splicing, and cause repeat-associated non-AUG translation, leading to the disease symptoms. Here, we utilized a small molecule library of ~ 250,000 members obtained from the National Cancer Instit…

Functional characterization of the AFF (AF4/FMR2) family of RNA-binding proteins: insights into the molecular pathology of FRAXE intellectual disability.

The AFF (AF4/FMR2) family of genes includes four members: AFF1/AF4, AFF2/FMR2, AFF3/LAF4 and AFF4/AF5q31. AFF2/FMR2 is silenced in FRAXE int … calizes to nuclear speckles, subnuclear structures considered as storage/modification sites of pre-mRNA splicing factors, and modulates alternative splicing via the interaction with the G-quadruplex RNA-forming structure. We show here that similarly to AFF2/FMR2, AFF3/LAF4 and AFF4/AF5q31 localize to nuclear speckles and are able to bind RNA, having a high app …

Characterization of the pathogenic mechanism of a novel BRCA2 variant in a Chinese family.

INTRODUCTION: Germline mutations of BRCA1 and BRCA2 account for the majority of hereditary breast cancers, many of which are classified as v … the blood of the proband and her family, and was used for BRCA gene mutation/deletion screening and RNA splicing analysis. RESULTS: BRCA2 c.7806-9T > G was identified in the proband, which was suggestive of a variant. This change was also found in two sisters of the proband with a history of breast cancer, as well as from the proband's maternal gastric cancer …

Transcriptomic profiling uncovers mis-splicing and gene fusions in amyotrophic lateral sclerosis.

Advances in transcriptomics have transformed our understanding of amyotrophic lateral sclerosis (ALS), a progressive neurodegenerative disease, revealing disrupted gene expression profiles and highlighting the multi-system biology of ALS. Despite major advances, transcriptomic studies have only begun to capture the complexity and the molecular hierarchy of transcriptomic alterations in ALS. To resolve and characterize the transcriptome in ALS, we performed a comprehensive reanalysis of bulk RNA sequencing from the New York Genome Center ALS Consortium cohort across five post-mortem tissues inc

PRMT1 Deficiency in Mouse Juvenile Heart Induces Dilated Cardiomyopathy and Reveals Cryptic Alternative Splicing Products.

Protein arginine methyltransferase 1 (PRMT1) catalyzes the asymmetric dimethylation of arginine residues in proteins and methylation of various RNA-binding proteins and is associated with alternative splicing in vitro. Although PRMT1 has essential in vivo roles in embryonic development, CNS development, and skeletal muscle regeneration, the functional importance of PRMT1 in the heart remains to be elucidated. Here, we report that juvenile cardiomyocyte-specific PRMT1-deficient mice develop severe dilated cardiomyopathy and exhibit aberrant cardiac alternative splicing. Furthermore, we identifi

Global Analysis of mRNA Alternative Splicing in the Trigeminal Ganglion at Different Stages of Trigeminal Neuropathic Pain in Mice.

INTRODUCTION: Trigeminal neuropathic pain (TNP) is a chronic pain disorder with incompletely understood molecular mechanisms. Alternative splicing (AS), a key post-transcriptional regulatory process, has emerged as an important modulator of neuronal excitability and synaptic plasticity. However, the temporal dynamics of AS in the trigeminal ganglion (TG) during TNP progression remain poorly defined. METHODS: Poly(A)-enriched RNA sequencing was performed on TG tissues from a partial infraorbital nerve transection (pIONT) mouse model at day 3 and day 10 after surgery, representing the onset and

Cryptic splicing in synaptic and membrane excitability genes links TDP-43 loss to neuronal dysfunction.

TAR DNA binding protein 43 (TDP-43) pathology is a defining pathological hallmark of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). A major feature of TDP-43 pathology is its nuclear depletion, leading to the aberrant inclusion of cryptic exons during RNA splicing. STMN2 and UNC13A have emerged as prominent TDP-43 splicing targets, but the broader impact of TDP-43-dependent cryptic splicing on neuronal function remains unclear. Here, we report previously unidentified TDP-43 splicing targets critical for membrane excitabilit…

Redirecting splicing with bifunctional oligonucleotides.

Ectopic modulators of alternative splicing are important tools to study the function of splice variants and for correcting mis-splicing events that cause human diseases. Such modulators can be bifunctional oligonucleotides made of an antisense portion that determines target specificity, and a non-hybridizing tail that recruits proteins or RNA/protein complexes that affect splice site selection (TOSS and TOES, respectively, for targeted oligonucleotide silencer of splicing and targeted oligonucleotide enhancer of splicing). The use of TOSS and TOES has been restricted to a handful of targets. T

Structural disruption of exonic stem-loops immediately upstream of the intron regulates mammalian splicing.

Recognition of highly degenerate mammalian splice sites by the core spliceosomal machinery is regulated by several protein factors that predominantly bind exonic splicing motifs. These are postulated to be single-stranded in order to be functional, yet knowledge of secondary structural features that regulate the exposure of exonic splicing motifs across the transcriptome is not currently available. Using transcriptome-wide RNA structural information we show that retained introns in mouse are commonly flanked by a short (≲70 nucleotide), highly base-paired segment upstream and a predominantly s

HIV DNA and transcription before and after ART in natural controllers compared to noncontrollers.

HIV-1 natural controllers can limit plasma HIV RNA levels in the absence of antiretroviral therapy (ART). Although controllers have less HIV DNA, it remains unclear how HIV transcription differs from noncontrollers, and whether ART further reduces HIV DNA or RNA in controllers. To address these questions, we quantified different HIV transcripts and HIV DNA regions/proviruses in longitudinal blood samples collected before ART and up to 3-5 years on suppressive ART from 10 controllers (5 "elite" and 5 viremic) and compared them to ART-suppressed noncontrollers. Compared to noncontrollers, contro

Hepatitis B virus serum RNA transcript isoform composition and proportion in chronic hepatitis B patients by nanopore long-read sequencing.

INTRODUCTION: Serum hepatitis B virus (HBV) RNA is a promising new biomarker to manage and predict clinical outcomes of chronic hepatitis B (CHB) infection. However, the HBV serum transcriptome within encapsidated particles, which is the biomarker analyte measured in serum, remains poorly characterized. This study aimed to evaluate serum HBV RNA transcript composition and proportionality by PCR-cDNA nanopore sequencing of samples from CHB patients having varied HBV genotype (gt, A to F) and HBeAg status. METHODS: Longitudinal specimens from 3 individuals during and following pregnancy (approx

SARS-CoV-2 N protein-induced Dicer, XPO5, SRSF3, and hnRNPA3 downregulation causes pneumonia.

Though RNAi and RNA-splicing machineries are involved in regulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication, their precise roles in coronavirus disease 2019 (COVID-19) pathogenesis remain unclear. Herein, we show that decreased RNAi component (Dicer and XPO5) and splicing factor (SRSF3 and hnRNPA3) expression correlate with increased COVID-19 severity. SARS-CoV-2 N protein induces the autophagic degradation of Dicer, XPO5, SRSF3, and hnRNPA3, inhibiting miRNA biogenesis and RNA splicing and triggering DNA damage, proteotoxic stress, and pneumonia. Dicer, XPO5, …

SF3B1 mutation and ATM deletion codrive leukemogenesis via centromeric R-loop dysregulation.

RNA splicing factor SF3B1 is recurrently mutated in various cancers, particularly in hematologic malignancies. We previously reported that coexpression of Sf3b1 mutation and Atm deletion in B cells, but not either lesion alone, leads to the onset of chronic lymphocytic leukemia (CLL) with CLL cells harboring chromosome amplification. However, the exact role of Sf3b1 mutation and Atm deletion in chromosomal instability (CIN) remains unclear. Here, we demonstrated that SF3B1 mutation promotes centromeric R-loop (cen-R-loop) accumulation, leading to increased chromosome oscillation, impaired chro…

Minigene-based splicing analysis uncovers pathogenic splice-altering effects of PAX2.

BACKGROUND: Missense variants in disease-associated genes cause aberrant pre-mRNA splicing, carrying profound implications for molecular diagnostics, pathogenic mechanism elucidation, and personalized therapy development. The distinct genotype-phenotype correlation observed in PAX2-related disorders underscores the need to evaluate how identified PAX2 gene variants impact pre-mRNA splicing. This study aimed to investigate the effects of PAX2 missense variants localized to the first or last nucleotides of an exon on pre-mRNA splicing. METHODS: Four PAX2 variants located at the last nucleotide o…

The pre-mRNA splicing modulator pladienolide B inhibits Cryptococcus neoformans germination and growth.

Cryptococcus neoformans is an opportunistic fungal pathogen responsible for life-threatening infections, particularly in immunocompromised individuals. The limitations of current antifungal therapies due to toxicity and the emergence of resistance highlight the need for novel treatment strategies and targets. C. neoformans has an intron-rich genome, and pre-mRNA splicing is required for expression of the vast majority of its genes. In this study, we investigated the efficacy of a human splicing inhibitor, pladienolide B (PladB), as an antifungal against C. neoformans. PladB inhibited the growt…

Characterization of BRCA1 and BRCA2 splicing variants: a collaborative report by ENIGMA consortium members.

Mutations in BRCA1 and BRCA2 predispose carriers to early onset breast and ovarian cancer. A common problem in clinical genetic testing is interpretation of variants with unknown clinical significance. The Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium was initiated to evaluate and implement strategies to characterize the clinical significance of BRCA1 and BRCA2 variants. As an initial project of the ENIGMA Splicing Working Group, we report splicing and multifactorial likelihood analysis of 25 BRCA1 and BRCA2 variants from seven different laborator