RNA structure papers

RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data

  • Yang Wu, Rihao Qu, Yiming Huang, Binbin Shi, Mengrong Liu, Yang Li, and Zhi John Lu*
  • April, 2016.
  • RNAex server to access structure probing data
  • in vivo and in vitro
  • in silico: MaxExpect, SeqFold, RNAstructure, and RNAfold
    • RNA editing, RNA modification, SNP sites
Species Method Sample
Homo sapiens DMS-seq PARS K562 trio
Arabi DMS-seq  
Mouse icSHAPE Frag-seq CIRS-seq  

A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer)

  • Nathan D. Berkowitz, Ian M. Silverman, Daniel M. Childress, Hilal Kazan, Li-San Wang, and Brian D. Gregory
  • May, 2016.
  • ds/ssRNA-seq (RNaseONE ss and RNase V1 ds)
\[S_i = \log_2 \frac{ONE_i + 1}{V_{1j}+1}\]
  • similar to PARS
\[S_i = \log_2 (\sum \frac{V_{1j}+5}{5} )- \log_2 (\sum \frac{S_{1j}+5}{5})\]
  • DMS-seq (in vivo)
\[R_i = \frac{D_i / D_{max}}{C_i / C_{max}}\]
  • icSHAPE (in vivo)
\[R_i = (D_i - C_i) / B\]

–

The RNA structurome: transcriptome-wide structure probing with next-generation sequencing.

  • Chun Kit Kwok, Yin Tang, Sarah M. Assmann, and Philip C. Bevilacqua.
  • April, 2015.
sample Name Probing method Features Paper
in vitro PARS RNase S1 & V1 cleavage – Kertesz, et al. 2010. Nature
– PARTE RNase V1 – Wan, et al. 2012. Mol. cell.
– FragSeq Nuclease P1 cleavage – Underwood, et al. 2010. Nat. Met.
– SHAPE 2’-hydroxyl acylation RT stops Lucks, et al. 2011. PNAS.
– ds/ssRNA-seq RNase ONE & V1 cleavage – Li, et al. 2012. Cell reports.
– Map-Seq DMS, CMCT, 1M7 – Smola, et al. 2014. Protocol RNA.
– HRF-Seq hydroxyl radicals break acc region Kielpinski, et al. 2014. NAR.
– ChemModSeq 2’-hydroxyl acylation – Hector, et al. 2014. NAR.
– RING-MaP DMS mutational profiling Homan, et al. 2014. PNAS.
– SHAPE-MaP 2M7, 1M6, NMIA mutational profiling Smola, et al. 2015. Nat. Prot.
in vivo DMS-seq DMS modification (+DMS-AC?) Rouskin, et al. 2014. Nature.
– Mod-seq – – Talkish, et al. 2014. RNA.
– Structure-seq – – Ding, et al. 2014. Nat. Prot.
– CIRS-seq CMCT, DMS G and AC Incarnato, et al. 2014. Genome Biol.
– icSHAPE NAI-N3 AU rich? Spittle, et al. 2015. Nature.