RNA Regulation

Literature Recommendations

Noncoding RNA & Cancer

  • 2020 Nature - PCAWG - Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

PDFs

Quantum Biology

  • 2014 Nature Physics - Quantum coherence in photosynthesis for efficient solar-energy conversion

PDFs

AS: Alternative splicing

Reviews

  • Alternative splicing as a regulator of development and tissue identity. (Nature Reviews, 2017)

  • RNA mis-splicing in disease. (Nature Reviews, 2015)

Research

  • Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder. (Science, 2018)

  • An Arabidopsis PWI and RRM motif-containing protein is critical for pre-mRNA splicing and ABA responses. (Nature communications, 2015)

Splicing & Cancer

PDFs

APA: Alternative polyadenylation

Reviews

  • Alternative polyadenylation of mRNA precursors. (Nature Reviews, 2017)

  • Alternative cleavage and polyadenylation: extent, regulation and function. (Nature Reviews, 2013)

Research

  • Dynamic analysis of alternative polyadenylation from RNA-seq reveal a 30-UTR landscape across seven tumour types. (Nature communications, 2014)

  • Cellular stress alters 3′UTR landscape through alternative polyadenylation and isoform-specific degradation. (Nature communications, 2018)

PDFs

RNA editing

Review

  • A-to-I RNA editing — immune protector and transcriptome diversifier. (Nature Reviews, 2018)

  • RNA editing-dependent epitranscriptome diversity in cancer stem cells. (Nature Reviews, 2017)

Research

  • Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers. (Genome Research, 2017)

  • The Genomic Landscape and Clinical Relevance of A-to-I RNA Editing in Human Cancers. (Cancer cell, 2015)

PDFs

Call DNA mutation from RNA-seq data

  • RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues (Science, 2019)

CLIP-seq etc

Data about RBP-RNA interaction

Reviews

  • 2018 Nature Reviews - A brave new world of RNA-binding proteins

  • 2018 Mol Cell - Advances in CLIP Technologies for Studies of Protein-RNA Interactions.pdf

  • 2018 Annual Reviews - Data Science Issues in Studying Protein–RNA Interactions with CLIP Technologies

Research

  • Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. (Nature structural & molecular biology, 2013)

  • Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites. (Genome Biology, 2017)

PDFs

Ribo-seq

关于RNA翻译(Ribo-seq)

PDFs and PPTs

Structure-seq

关于RNA 二级结构高通量测序方法

PDFs

See computational models and algorithms for RNA secondary structure in RNA Structure.

RiboShape

  • 2018 Zhang, Yan, et al. “A Stress Response that Monitors and Regulates mRNA Structure Is Central to Cold Shock Adaptation.” Molecular cell 70.2 (2018): 274-286.

  • 2018 Mustoe, Anthony M., et al. "Pervasive regulatory functions of mRNA structure revealed by high-resolution SHAPE probing." Cell 173.1 (2018): 181-195.

PDFs