scholarly journals RUNX1/RUNX1T1 mediates alternative splicing and reorganises the transcriptional landscape in leukemia

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Vasily V. Grinev ◽  
Farnaz Barneh ◽  
Ilya M. Ilyushonak ◽  
Sirintra Nakjang ◽  
Job Smink ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Rna Splicing ◽  
Leukemic Cells ◽  
Splicing Factors ◽  
Domain Structures ◽  
Indirect Control ◽  
Expression Of Genes ◽  
Alternative Transcription ◽  
Genes Encoding ◽  
Alternative Structure

AbstractThe fusion oncogene RUNX1/RUNX1T1 encodes an aberrant transcription factor, which plays a key role in the initiation and maintenance of acute myeloid leukemia. Here we show that the RUNX1/RUNX1T1 oncogene is a regulator of alternative RNA splicing in leukemic cells. The comprehensive analysis of RUNX1/RUNX1T1-associated splicing events identifies two principal mechanisms that underlie the differential production of RNA isoforms: (i) RUNX1/RUNX1T1-mediated regulation of alternative transcription start site selection, and (ii) direct or indirect control of the expression of genes encoding splicing factors. The first mechanism leads to the expression of RNA isoforms with alternative structure of the 5’-UTR regions. The second mechanism generates alternative transcripts with new junctions between internal cassettes and constitutive exons. We also show that RUNX1/RUNX1T1-mediated differential splicing affects several functional groups of genes and produces proteins with unique conserved domain structures. In summary, this study reveals alternative splicing as an important component of transcriptome re-organization in leukemia by an aberrant transcriptional regulator.

scholarly journals ALG-1 Influences Accurate mRNA Splicing Patterns in the Caenorhabditis elegans Intestine and Body Muscle Tissues by Modulating Splicing Factor Activities

Genetics ◽  
2019 ◽  
Vol 212 (3) ◽  
pp. 931-951 ◽  
Author(s):  
Kasuen Kotagama ◽  
Anna L. Schorr ◽  
Hannah S. Steber ◽  
Marco Mangone
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Splicing ◽  
Specific Gene ◽  
Splicing Factors ◽  
Tissue Specific ◽  
Link Type ◽  
Body Muscle ◽  
Mirna Targets ◽  
Mirna Pathway

MicroRNAs (miRNAs) are known to modulate gene expression, but their activity at the tissue-specific level remains largely uncharacterized. To study their contribution to tissue-specific gene expression, we developed novel tools to profile putative miRNA targets in the Caenorhabditis elegans intestine and body muscle. We validated many previously described interactions and identified ∼3500 novel targets. Many of the candidate miRNA targets curated are known to modulate the functions of their respective tissues. Within our data sets we observed a disparity in the use of miRNA-based gene regulation between the intestine and body muscle. The intestine contained significantly more putative miRNA targets than the body muscle highlighting its transcriptional complexity. We detected an unexpected enrichment of RNA-binding proteins targeted by miRNA in both tissues, with a notable abundance of RNA splicing factors. We developed in vivo genetic tools to validate and further study three RNA splicing factors identified as putative miRNA targets in our study (asd-2, hrp-2, and smu-2), and show that these factors indeed contain functional miRNA regulatory elements in their 3′UTRs that are able to repress their expression in the intestine. In addition, the alternative splicing pattern of their respective downstream targets (unc-60, unc-52, lin-10, and ret-1) is dysregulated when the miRNA pathway is disrupted. A reannotation of the transcriptome data in C. elegans strains that are deficient in the miRNA pathway from past studies supports and expands on our results. This study highlights an unexpected role for miRNAs in modulating tissue-specific gene isoforms, where post-transcriptional regulation of RNA splicing factors associates with tissue-specific alternative splicing.

scholarly journals Splicing factor mutations in hematologic malignancies

Blood ◽  
2021 ◽  
Author(s):  
Sisi Chen ◽  
Salima Benbarche ◽  
Omar Abdel-Wahab
Keyword(s):  
Rna Splicing ◽  
Messenger Rna ◽  
Hematologic Malignancies ◽  
Splicing Factor ◽  
Splicing Factors ◽  
Loss Of Function ◽  
Genes Encoding ◽  
Precursor Rna ◽  
Early Phase Clinical Trials ◽  
Splicing Machinery

Mutations in genes encoding RNA splicing factors were discovered nearly ten years ago and are now understood to be amongst the most recurrent genetic abnormalities in patients with all forms of myeloid neoplasms and several types of lymphoproliferative disorders as well as subjects with clonal hematopoiesis. These discoveries implicate aberrant RNA splicing, the process by which precursor RNA is converted into mature messenger RNA, in the development of clonal hematopoietic conditions. Both the protein as well as the RNA components of the splicing machinery are affected by mutations at highly specific residues and a number of these mutations alter splicing in a manner distinct from loss of function. Importantly, cells bearing these mutations have now been shown to generate mRNA species with novel aberrant sequences, some of which may be critical to disease pathogenesis and/or novel targets for therapy. These findings have opened new avenues of research to understand biological pathways disrupted by altered splicing. In parallel, multiple studies have revealed that cells bearing change-of-function mutation in splicing factors are preferentially sensitized to any further genetic or chemical perturbations of the splicing machinery. These discoveries are now being pursued in several early phase clinical trials using molecules with diverse mechanisms of action. Here we review the molecular effects of splicing factor mutations on splicing, mechanisms by which these mutations drive clonal transformation of hematopoietic cells, and the development of new therapeutics targeting these genetic subsets of hematopoietic malignancies.

scholarly journals miRNA activity contributes to accurate RNA splicing inC. elegansintestine and body muscle tissues

2018 ◽  
Author(s):  
Kasuen Kotagama ◽  
Anna L Schorr ◽  
Hannah S Steber ◽  
Marco Mangone
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Splicing ◽  
Specific Gene ◽  
Splicing Factors ◽  
Tissue Specific ◽  
C Elegans ◽  
Body Muscle ◽  
Mirna Targets ◽  
Mirna Pathway

ABSTRACTMicroRNAs (miRNAs) are known to modulate gene expression, but their activity at the tissue-specific level remains largely uncharacterized. In order to study their contribution to tissue-specific gene expression, we developed novel tools to profile miRNA targets in theC. elegansintestine and body muscle.We validated many previously described interactions, and identified ~3,500 novel targets. Many of the miRNA targets curated are known to modulate the functions of their respective tissues. Within our datasets we observed a disparity in the use of miRNA-based gene regulation between the intestine and body muscle. The intestine contained significantly more miRNA targets than the body muscle highlighting its transcriptional complexity. We detected an unexpected enrichment of RNA binding proteins targeted by miRNA in both tissues, with a notable abundance of RNA splicing factors.We developedin vivogenetic tools to validate and further study three RNA splicing factors identified as miRNA targets in our study (asd-2,hrp-2andsmu-2), and show that these factors indeed contain functional miRNA regulatory elements in their 3’UTRs that are able to repress their expression in the intestine. In addition, the alternative splicing pattern of their respective downstream targets (unc-60,unc-52,lin-10andret-1) is dysregulated when the miRNA pathway is disrupted.A re-annotation of the transcriptome data inC. elegansstrains that are deficient in the miRNA pathway from past studies supports and expands on our results. This study highlights an unexpected role for miRNAs in modulating tissue-specific gene isoforms, where post-transcriptional regulation of RNA splicing factors associates with tissue-specific alternative splicing.

scholarly journals Comprehensive network analysis reveals alternative splicing-related lncRNAs in hepatocellular carcinoma

2019 ◽  
Author(s):  
Junqing Wang ◽  
Yixin Chen ◽  
Keli Xu ◽  
Yin-yuan Mo ◽  
Yunyun Zhou
Keyword(s):  
Hepatocellular Carcinoma ◽  
Alternative Splicing ◽  
Rna Splicing ◽  
Normal Liver ◽  
Splicing Factors ◽  
Primary Concern ◽  
Rna Seq ◽  
Genome Wide ◽  
Tumorigenesis And Progression ◽  
Extensive Collection

AbstractA number of recent studies have highlighted the findings that certain lncRNAs are associated with alternative splicing (AS) in tumorigenesis and progression. Although existing work showed the importance of linking certain misregulations of RNA splicing with lncRNAs, a primary concern is the lack of genome-wide comprehensive analysis for their associations.We analyzed an extensive collection of RNA-seq data, quantified 198,619 isoform expressions, and found systematic isoform usage changes between hepatocellular carcinoma (HCC) and normal liver tissue. We identified a total of 1375 splicing switched isoforms and further analyzed their biological functions.To predict which lncRNAs are associated with these AS genes, we integrated the co-expression networks and epigenetic interaction networks collected from text mining and database searching, linking lncRNA modulators such as splicing factors, transcript factors, and miRNAs with their targeted AS genes in HCC. To model the heterogeneous networks in a single framework, we developed a multi-graphic random walk (RWMG) network method to prioritize the lncRNAs associated with AS in HCC. RWMG showed a good performace evaluated by ROC curve based on cross-validation and bootstrapping strategy.As a summary, we identified 31 AS-related lncRNAs including MALAT1 and HOXA11-AS, which have been reported before, as well as some novel lncRNAs such as DNM1P35, HAND2-AS1, and DLX6-AS1. Survival analysis further confirmed the clinical significance of identified lncRNAs.

scholarly journals Modulation of Multidrug Resistance Gene Expression by Coumarin Derivatives in Human Leukemic Cells

2017 ◽  
Vol 2017 ◽  
pp. 1-13 ◽  
Author(s):  
Tomasz Kubrak ◽  
Anna Bogucka-Kocka ◽  
Łukasz Komsta ◽  
Daniel Załuski ◽  
Jacek Bogucki ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Cell Lines ◽  
Leukemic Cells ◽  
Coumarin Derivatives ◽  
Multidrug Resistance Gene ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Ic50 Values ◽  
Presence And Absence ◽  
Human Leukemic Cells

The presence of multidrug resistance (MDR) in tumor cells is considered as the major cause of failure of cancer chemotherapy. The mechanism responsible for the phenomenon of multidrug resistance is explained, among others, as overexpression of membrane transporters primarily from the ABC family which actively remove cytostatics from the tumor cell. The effect of 20 coumarin derivatives on the cytotoxicity and expression ofMDR1,MRP1,BCRP, andLRPgenes (encoding proteins responsible for multidrug resistance) in cancer cells was analyzed in the study. The aim of this research included determination of IC10 and IC50 values of selected coumarin derivatives in the presence and absence of mitoxantrone in leukemia cells and analysis of changes in the expression of genes involved in multidrug resistance:MDR1,MRP,LRP, andBCRPafter 24-hour exposure of the investigated cell lines to selected coumarins in the presence and absence of mitoxantrone in IC10 and IC50 concentrations. The designed research was conducted on 5 cell lines derived from the human hematopoietic system: CCRF/CEM, CEM/C1, HL-60, HL-60/MX1, and HL-60/MX2. Cell lines CEM/C1, HL-60/MX1, and HL-60/MX2 exhibit a multidrug resistance phenotype.

scholarly journals PTBP2-dependent alternative splicing regulates protein transport and mitochondria morphology in post-meiotic germ cells.

2018 ◽  
Author(s):  
Molly M Hannigan ◽  
Hisashi Fujioka ◽  
Adina Brett-Morris ◽  
Jason A Mears ◽  
Donny D Licatalosi
Keyword(s):  
Alternative Splicing ◽  
Germ Cells ◽  
Protein Trafficking ◽  
Rna Splicing ◽  
Protein Transport ◽  
Rna Binding ◽  
Binding Protein ◽  
Polypyrimidine Tract Binding Protein ◽  
Alternative Mrna Splicing ◽  
Genes Encoding

The RNA binding protein PTBP2 (polypyrimidine tract binding protein 2) is a key regulator of tissue-specific alternative RNA splicing. In the testis, PTBP2 is expressed in meiotic and post-meiotic germ cells (spermatocytes and spermatids, respectively). In these cells, PTBP2 is required for proper alternative mRNA splicing for over 200 genes, disproportionately affecting genes encoding proteins involved in protein trafficking via transport vesicles. In this study, we used electron microscopy to test the hypothesis that protein trafficking is impaired in the absence of PTBP2, and to further investigate why spermatogenesis abruptly halts in PTBP2-deficient spermatids. Ultrastructural analysis shows that protein trafficking in spermatids is aberrant in the absence of PTBP2. Unexpectedly, we also found that mitochondria morphology and number are significantly altered in PTBP2-deficient spermatids, consistent with increased mitochondria fission. Furthermore, we show that genes with key roles in mitochondria dynamics and function are post-transcriptionally regulated by PTBP2 and in different stages of spermatogenesis. Collectively, the data provide ultrastructural evidence that alternative splicing regulation by PTBP2 during spermatogenesis is critical for proper regulation of protein trafficking and mitochondria morphology.

scholarly journals Pathway-guided analysis identifies Myc-dependent alternative pre-mRNA splicing in aggressive prostate cancers

2020 ◽  
Vol 117 (10) ◽  
pp. 5269-5279 ◽  
Author(s):  
John W. Phillips ◽  
Yang Pan ◽  
Brandon L. Tsai ◽  
Zhijie Xie ◽  
Levon Demirdjian ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Rna Splicing ◽  
Large Scale ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Mrna Splicing ◽  
Cancer Driver ◽  
Genes Encoding ◽  
Prostate Cancers

We sought to define the landscape of alternative pre-mRNA splicing in prostate cancers and the relationship of exon choice to known cancer driver alterations. To do so, we compiled a metadataset composed of 876 RNA-sequencing (RNA-Seq) samples from five publicly available sources representing a range of prostate phenotypes from normal tissue to drug-resistant metastases. We subjected these samples to exon-level analysis with rMATS-turbo, purpose-built software designed for large-scale analyses of splicing, and identified 13,149 high-confidence cassette exon events with variable incorporation across samples. We then developed a computational framework, pathway enrichment-guided activity study of alternative splicing (PEGASAS), to correlate transcriptional signatures of 50 different cancer driver pathways with these alternative splicing events. We discovered that Myc signaling was correlated with incorporation of a set of 1,039 cassette exons enriched in genes encoding RNA binding proteins. Using a human prostate epithelial transformation assay, we confirmed the Myc regulation of 147 of these exons, many of which introduced frameshifts or encoded premature stop codons. Our results connect changes in alternative pre-mRNA splicing to oncogenic alterations common in prostate and many other cancers. We also establish a role for Myc in regulating RNA splicing by controlling the incorporation of nonsense-mediated decay-determinant exons in genes encoding RNA binding proteins.

scholarly journals Rare and private spliceosomal gene mutations drive partial, complete, and dual phenocopies of hotspot alterations

Blood ◽  
2020 ◽  
Author(s):  
Joseph Pangallo ◽  
Jean-Jacques Kiladjian ◽  
Bruno Cassinat ◽  
Aline Renneville ◽  
Justin Taylor ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Gene Mutations ◽  
Splicing Factors ◽  
Missense Mutations ◽  
Molecular Assays ◽  
Genes Encoding ◽  
Disease Relevance ◽  
Hotspot Mutations ◽  
Site Recognition

Genes encoding the RNA splicing factors SF3B1, SRSF2, and U2AF1 are subject to frequent missense mutations in clonal hematopoiesis and diverse neoplastic diseases. Most "spliceosomal" mutations affect specific hotspot residues, resulting in splicing changes that promote disease pathophysiology. However, a subset of patients carry spliceosomal mutations that affect non-hotspot residues, whose potential functional contributions to disease are unstudied. Here, we undertook a systematic characterization of diverse rare and private spliceosomal mutations to infer their likely disease relevance. We utilized isogenic cell lines and primary patient materials to discover that 11 of 14 studied rare and private mutations in SRSF2 and U2AF1 induced distinct splicing alterations, including partially or completely phenocopying the alterations in exon and splice site recognition induced by hotspot mutations or driving "dual" phenocopies that mimicked two co-occurring hotspot mutations. Our data suggest that many rare and private spliceosomal mutations contribute to disease pathogenesis and illustrate the utility of molecular assays to inform precision medicine by inferring the potential disease relevance of newly discovered mutations.

scholarly journals Secondary motifs enable concentration-dependent regulation by Rbfox family proteins

2019 ◽  
Author(s):  
Bridget E. Begg ◽  
Marvin Jens ◽  
Peter Y. Wang ◽  
Christopher B. Burge
Keyword(s):  
Alternative Splicing ◽  
Rna Splicing ◽  
Neuronal Development ◽  
Splicing Factors ◽  
Reporter Assay ◽  
Animal Development ◽  
High Affinity ◽  
Second Wave ◽  
Relevant Range

AbstractThe Rbfox family of splicing factors regulate alternative splicing during animal development and in disease, impacting thousands of exons in the maturing brain, heart, and muscle. Rbfox proteins have long been known to bind to the RNA sequence GCAUG with high affinity, but just half of Rbfox CLIP peaks contain a GCAUG motif. We incubated recombinant RBFOX2 with over 60,000 transcriptomic sequences to reveal significant binding to several moderate-affinity, non-GCAYG sites at a physiologically relevant range of RBFOX concentrations. We find that many of these “secondary motifs” bind Rbfox robustly in vivo and that several together can exert regulation comparable to a GCAUG in a trichromatic splicing reporter assay. Furthermore, secondary motifs regulate RNA splicing in neuronal development and in neuronal subtypes where cellular Rbfox concentrations are highest, enabling a second wave of splicing changes as Rbfox levels increase.

scholarly journals Hallmarks of Splicing Defects in Cancer: Clinical Applications in the Era of Personalized Medicine

Cancers ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1381 ◽  
Author(s):  
Mohammad Alinoor Rahman ◽  
Farhana Nasrin ◽  
Sonali Bhattacharjee ◽  
Saikat Nandi
Keyword(s):  
Alternative Splicing ◽  
Rna Splicing ◽  
Rna Binding ◽  
Control Point ◽  
Splicing Factors ◽  
Cancer Therapies ◽  
Cis Elements ◽  
Oncogenic Mutations ◽  
Splicing Defects ◽  
The Right

Alternative splicing promotes proteome diversity by using limited number of genes, a key control point of gene expression. Splicing is carried out by large macromolecular machineries, called spliceosome, composed of small RNAs and proteins. Alternative splicing is regulated by splicing regulatory cis-elements in RNA and trans-acting splicing factors that are often tightly regulated in a tissue-specific and developmental stage-specific manner. The biogenesis of ribonucleoprotein (RNP) complexes is strictly regulated to ensure that correct complements of RNA and proteins are coordinated in the right cell at the right time to support physiological functions. Any perturbations that impair formation of functional spliceosomes by disrupting the cis-elements, or by compromising RNA-binding or function of trans-factors can be deleterious to cells and result in pathological consequences. The recent discovery of oncogenic mutations in splicing factors, and growing evidence of the perturbed splicing in multiple types of cancer, underscores RNA processing defects as a critical driver of oncogenesis. These findings have resulted in a growing interest in targeting RNA splicing as a therapeutic approach for cancer treatment. This review summarizes our current understanding of splicing alterations in cancer, recent therapeutic efforts targeting splicing defects in cancer, and future potentials to develop novel cancer therapies.

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