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标题:Circular RNAs are a large class of animal RNAs with regulatory potency
时间:2020-10-28 16:30:06
DOI:10.1038/nature11928
PMID:23446348
大小:1193 kb
页数:11 PAGES
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目录:
  • Title
  • Authors
  • Abstract
  • circRNAs have complex expression patterns
  • Characterization of 50 predicted circRNAs
  • circRNA CDR1as is densely bound by AGO
  • Co-expression of miR-7 and CDR1as in brain
  • Effects of miR-7 and CDR1as in zebrafish
  • Discussion
  • Methods Summary
    • Computational pipeline for predicting circRNAs from ribominus sequencing data
    • Cell culture and treatments
    • Single-molecule RNA fluorescence in situ hybridization (smRNA FISH)
    • Mouse strains and in situ hybridization
    • Zebrafish methods
  • References
  • Methods
    • Computational pipeline for predicting circRNAs from ribominus sequencing data
    • Permutation testing
    • HEK293 RNA-seq after rRNA depletion (RibominusSeq)
    • C. elegans oocyte isolation
    • C. elegans sperm isolation
    • C. elegans isolation of 1-cell- and 2-cell-stage embryos
    • Ribominus RNA preparation from C. elegans samples
    • Cluster generation and sequencing of C. elegans libraries
    • Human gene models
    • Intersection of circRNAs with known transcripts
    • Finding circRNAs conserved between human and mouse
    • Conserved element counting
    • Overlap of identified circRNAs with published circular RNAs
    • Cell culture and treatments
    • Quantitative PCR
    • PCR amplification and Sanger sequencing
    • Primer design
    • RNase R treatment
    • RNA nicking assay
    • Northern blotting
    • Genome alignments for detecting miRNA seed complementary sites
    • C. elegans human and mouse miRNAs
    • Detecting putative miRNA seed matches
    • AGO PAR-CLIP
    • Human Argonaute PAR-CLIP analysis
    • AGO binding sites in C. elegans
    • Analysis of sequence conservation in CDR1as
    • Analysis of miR-7 base-pairing within CDR1as
    • Single-molecule RNA fluorescence in situ hybridization (smRNA FISH)
    • Mouse strains and in situ hybridizations
    • siRNA- and shRNA-mediated knock down
    • Zebrafish methods
  • Methods References
  • Figure 1 Detection, classification and evolutionary conservation of circRNAs.
  • Figure 2 CircRNAs are stable transcripts with robust expression.
  • Figure 3 The circRNA CDR1as is bound by the miRNA effector protein AGO, and is cytoplasmic.
  • Figure 4 CDR1as and miR-7 have overlapping and specific expression in neuronal tissues.
  • Figure 5 In zebrafish, knockdown of miR-7 or expression of CDR1as causes midbrain defects.
  • Table 1 Summary of the validation experiments

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