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. |