The Development and Use of Scalable Systems for Studying Aberrant Splicing in SF3B1-Mutant CLL View Full Text


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Chapter Info

DATE

2018-10-23

AUTHORS

Tushar Murthy , Kiran V. Paul , Alexander C. Minella , Manoj M. Pillai

ABSTRACT

Mutational landscape of CLL is now known to include recurrent non-synonymous mutations in SF3B1, a core splicing factor. About 5-10% of newly diagnosed CLL harbor these mutations which are typically limited to HEAT domains in the carboxyl-terminus of the protein. Importantly, the mutations are not specific to CLL but also present in several unrelated clonal disorders. Analysis of patient samples and cell lines has shown the primary splicing aberration in SF3B1-mutant cells to the use of novel or "cryptic" 3' splice sites (3SS). Advances in genome-editing and next-generation sequencing (NGS) have allowed development of isogenic models and detailed analysis of changes to the transcriptome with relative ease. In this manuscript, we focus on two relevant methods to study splicing factor mutations in CLL: development of isogenic scalable cell lines and informatics analysis of RNA-Seq datasets. More... »

PAGES

83-99

References to SciGraph publications

  • 2015-05. The impact of SF3B1 mutations in CLL on the DNA-damage response in LEUKEMIA
  • 2011-09. Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36 in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2016-12. A survey of best practices for RNA-seq data analysis in GENOME BIOLOGY
  • 2011-10. Frequent pathway mutations of splicing machinery in myelodysplasia in NATURE
  • 2013-11. Genome engineering using the CRISPR-Cas9 system in NATURE PROTOCOLS
  • 2017-02. Cancer-associated SF3B1 mutants recognize otherwise inaccessible cryptic 3′ splice sites within RNA secondary structures in ONCOGENE
  • 2012-06. Whole-genome analysis informs breast cancer response to aromatase inhibition in NATURE
  • 2012-01. Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia in NATURE GENETICS
  • 2013-02. Recurrent mutations at codon 625 of the splicing factor SF3B1 in uveal melanoma in NATURE GENETICS
  • 2013-11. Distinct patterns of novel gene mutations in poor-prognostic stereotyped subsets of chronic lymphocytic leukemia: the case of SF3B1 and subset #2 in LEUKEMIA
  • 2017-09-27. Mechanistic insights into precursor messenger RNA splicing by the spliceosome in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2014-12. Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling in BMC GENOMICS
  • 2016-02-04. Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage in NATURE COMMUNICATIONS
  • 2017-10. Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2012-01. Spliceosome mutations in hematopoietic malignancies in NATURE GENETICS
  • 2006-09. Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2015-07. Applications of the CRISPR-Cas9 system in cancer biology in NATURE REVIEWS CANCER
  • 2012-11. Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes in NATURE
  • 2017-03. Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts in LEUKEMIA
  • 2014. Methods to Study Splicing from High-Throughput RNA Sequencing Data in SPLICEOSOMAL PRE-MRNA SPLICING
  • Book

    TITLE

    Chronic Lymphocytic Leukemia

    ISBN

    978-1-4939-8875-4
    978-1-4939-8876-1

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/978-1-4939-8876-1_7

    DOI

    http://dx.doi.org/10.1007/978-1-4939-8876-1_7

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1107766430

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30350199


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