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QKI regulated splicing required for cell polarity

ABSTRACT: the RNA binding protein QKI is a post-transcriptional regulator of polarity proteins in muscle stem cells

ORGANISM(S): Mus musculus

PROVIDER: GSE193899 | GEO | 2022/01/25

REPOSITORIES: GEO

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QKI regulated splicing required for cell polarity

Project description:QKI regulated splicing required for cell polarity

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Genomewide analysis of QKI-dependent alternative splicing

Project description:To identify QKI targets, we performed QKI knockdown in BEAS2B cells and analyzed alternative splicing patterns by high-throughput RNA sequencing. The mRNA profiles of control- and QKI-knockdown BEAS2B cells were generated by deep sequencing using Illumina GAIIx sequencer.

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QKI dysregulation induces extensive splicing changes in T-Cell Acute Lymphoblastic Leukemia (T-ALL)

Project description:Understanding the molecular mechanisms underlying T-cell acute lymphoblastic leukemia (T-ALL) is essential for developing more effective therapeutic strategies. Despite therapeutic advances, the role of RNA-binding proteins in the pathogenesis of T-ALL remains poorly understood. Here, we investigate the RNA-binding protein Quaking (QKI), identifying it as a key regulator of splicing with tumor-suppressive properties in T-ALL. Through the analysis of two independent pediatric T-ALL cohorts, we demonstrate that QKI expression is frequently reduced in T-ALL, particularly within the HOXA subtype, and this reduction correlates with poor overall and event-free survival. Using T-ALL cell lines, we show that QKI depletion induces widespread splicing alterations, with numerous events corroborated in patient samples. Transcriptome profiling indicates that QKI downregulation leads to broad changes in gene expression, notably affecting pathways related to cell cycle progression, cholesterol homeostasis, and epithelial?mesenchymal transition. Functional assays demonstrate that QKI overexpression in T-ALL cells significantly reduces cell proliferation, induces G0/G1 cell cycle arrest, and limits leukemia progression and dissemination, ultimately improving survival in xenograft models. Together, these findings provide compelling evidence that QKI functions as a regulator of RNA splicing with tumor-suppressive activity in T-ALL.

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QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5’splice sites [eCLIP Hues6]

Project description:During organogenesis, the establishment of tissue architecture requires precise RNA processing. Many developmentally essential exons bear weak 5′ splice sites (5′SS) yet are spliced with high precision, implying unknown yet active splicing fidelity mechanisms. Combining transcriptome and alternative splicing profiling and with temporal eCLIP mapping of RNA interactions across development, we identify the RNA-binding protein QKI as an essential direct regulator of splicing fidelity in key cardiac transcripts. Although QKI is dispensable for cardiac lineage specification, its loss disrupts sarcomere assembly despite intact expression of sarcomere mRNAs through exon skipping and intron retention in key sarcomeric mRNAs. QKI-dependent exons in essential cardiac genes have weak 5′SS and frequently show poor complementarity with U6 snRNA; we show that QKI directly interacts with U6 snRNA using an overlapping interface to its traditional intronic binding activity, securing U4/U6·U5 tri-snRNP recruitment to ensure exon inclusion. Thus, QKI exemplifies how context-aware RBPs enforce splicing fidelity at structurally vulnerable splice sites by coupling local intronic cues to spliceosome engagement, thereby securing accurate exon inclusion during organogenesis.

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QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5’splice sites [RNA-Seq]

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QKI and miR-155 in inflammation and leukemogenesis

Project description:Transcription profiling by array of siRNA against Quaking (QKI) transcripts to identify transcripts that are modulated by QKI activity. MiR-155 is an oncogene and we report here that it targets QKI transcripts. Therefore, we believe that QKI acts as a tumor suppressor gene in different leukemias. We ablated the expression of QKI transcripts using siRNAs in order to further elucidate the effects of QKI in leukemogenesis, and how miR-155 and QKI functionally interact with each other.

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Circular Slc17a5 regulated by VLDLR/QKI pathway inhibits ocular neovascularization

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