POSTAR

POST-trAnscriptional Regulation

POSTAR: POST-trAnscriptional Regulation

1. RBP Binding: 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

2. 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

  • 2020 - Nature Reviews - Roles and mechanisms of alternative splicing in cancer — implications for care

PDFs

3. 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

4. RNA Velocity

  • 2020 - Nature Biotech. - Generalizing RNA velocity to transient cell states through dynamical modeling

PDFs

5. 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

6. DNA mutation using RNA-seq

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

7. Translation: Ribo-seq

关于RNA翻译(Ribo-seq)

  • ORF finding

  • Difference of Translation Efficiency

    • RiboDiff: 2017 Bioinformatics

    • Xtail: 2016 Nature Communications

Preprocessing

ORF Iden.

Quantification TE

Translation elongation

Integrative & visualization

Rfoot

DeepRibo

scikit-ribo

diricore

Plastid

RiboWaltz

FLOSS

RiboDiff

Iχnos

Rfeet

RiboWave

ORF-RATER

riborex

PausePred

RiboGalaxy

PRICE

Xtail

ROSE

RiboProfiling

RiboCode

RiboMiner

riboSeqR

RiboHMM

RiboTools

RibORF

RIVIT

RiboTaper

Shoelaces

RP-BP

tRanslatome

SPECtre

POSTAR

TITER

PDFs and PPTs

7.1. RiboShape

  • ✨ 2018 Cell (e. coli, proposed a model) Pervasive regulatory functions of mRNA structure revealed by high-resolution SHAPE probing

  • 2014 NAR (proposed a model) - Deciphering the rules by which dynamics of mRNA secondary structure affect translation efficiency in Saccharomyces cerevisiae

  • 2018 Mol. Cell (e. coli)- A Stress Response that Monitors and Regulates mRNA Structure Is Central to Cold Shock Adaptation

  • 2020 Genome Biology (zebrafish) RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function

  • ✨ 2017 Nature - Global translational reprogramming is a fundamental layer of immune regulation in plants

2.1 Motif

  • 2015 Cell - polyU hairpin - EIN2-Directed Translational Regulation of Ethylene Signaling in Arabidopsis

  • 2021 PNAS - polyU internal loop - Structural analyses of an RNA stability element interacting with poly(A)