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POSTAR: POST-trAnscriptional Regulation Analysis

POSTAR Database: (POST-trAnscriptional Regulation) http://POSTAR.ncRNAlab.org

0. POSTAR & Genetics

  • 2024 Nature Communications - Systematic identification of posttranscriptional regulatory modules

1. 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)

1.1 Splicing & Cancer

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

2. 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)

3. 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)

4. DNA mutation using RNA-seq

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

5. RNA modification

  • 2022 Nature Methods - Detection of m6A from direct RNA sequencing using a multiple instance learning framework

6. RNA Velocity

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

7. Translation: Ribo-seq

关于RNA翻译（Ribo-seq）

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

7.1. RiboShape

  • ✅ 2023 Nature - Pervasive downstream RNA hairpins dynamically dictate start-codon selection
  • 2021 Genome Biology Wheat in vivo RNA structure landscape reveals a prevalent role of RNA structure in modulating translational subgenome expression asymmetry
  • ✅ 2018 Cell (e. coli, proposed a model) Pervasive regulatory functions of mRNA structure revealed by high-resolution SHAPE probing
  • 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
  • 2014 NAR (proposed a model) - Deciphering the rules by which dynamics of mRNA secondary structure affect translation efficiency in Saccharomyces cerevisiae

7.2 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)

8. Quantum Biology

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