PMID- 30071678
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20230928
IS  - 2073-4425 (Print)
IS  - 2073-4425 (Electronic)
IS  - 2073-4425 (Linking)
VI  - 9
IP  - 8
DP  - 2018 Aug 1
TI  - RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates.
LID - 10.3390/genes9080392 [doi]
LID - 392
AB  - In this work, we present a computational screen conducted for functional RNA 
      structures, resulting in over 100,000 conserved RNA structure elements found in 
      alignments of mouse (mm10) against 59 other vertebrates. We explicitly included 
      masked repeat regions to explore the potential of transposable elements and 
      low-complexity regions to give rise to regulatory RNA elements. In our analysis 
      pipeline, we implemented a four-step procedure: (i) we screened genome-wide 
      alignments for potential structure elements using RNAz-2, (ii) realigned and 
      refined candidate loci with LocARNA-P, (iii) scored candidates again with RNAz-2 
      in structure alignment mode, and (iv) searched for additional homologous loci in 
      mouse genome that were not covered by genome alignments. The 3'-untranslated 
      regions (3'-UTRs) of protein-coding genes and small noncoding RNAs are enriched 
      for structures, while coding sequences are depleted. Repeat-associated loci make 
      up about 95% of the homologous loci identified and are, as expected, 
      predominantly found in intronic and intergenic regions. Nevertheless, we report 
      the structure elements enriched in specific genome elements, such as 3'-UTRs and 
      long noncoding RNAs (lncRNAs). We provide full access to our results via a custom 
      UCSC genome browser trackhub freely available on our website 
      (http://rna.tbi.univie.ac.at/trackhubs/#RNAz).
FAU - Thiel, Bernhard C
AU  - Thiel BC
AD  - Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, 
      Wahringerstrasse 17, 1090 Wien, Austria. thiel@tbi.univie.ac.at.
FAU - Ochsenreiter, Roman
AU  - Ochsenreiter R
AD  - Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, 
      Wahringerstrasse 17, 1090 Wien, Austria. romanoch@tbi.univie.ac.at.
FAU - Gadekar, Veerendra P
AU  - Gadekar VP
AD  - Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, 
      Wahringerstrasse 17, 1090 Wien, Austria. veerendra@tbi.univie.ac.at.
FAU - Tanzer, Andrea
AU  - Tanzer A
AUID- ORCID: 0000-0003-2873-4236
AD  - Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, 
      Wahringerstrasse 17, 1090 Wien, Austria. at@tbi.univie.ac.at.
FAU - Hofacker, Ivo L
AU  - Hofacker IL
AUID- ORCID: 0000-0001-7132-0800
AD  - Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, 
      Wahringerstrasse 17, 1090 Wien, Austria. ivo@tbi.univie.ac.at.
AD  - Research Group Bioinformatics and Computational Biology, Faculty of Computer 
      Science, University of Vienna, Wahringerstrasse 29, 1090 Wien, Austria. 
      ivo@tbi.univie.ac.at.
LA  - eng
GR  - I 1804/FWF_/Austrian Science Fund FWF/Austria
PT  - Journal Article
DEP - 20180801
PL  - Switzerland
TA  - Genes (Basel)
JT  - Genes
JID - 101551097
PMC - PMC6116022
OTO - NOTNLM
OT  - RNA regulation
OT  - RNA secondary structure
OT  - RNAz
OT  - conserved RNA structure elements
OT  - structural alignment
COIS- The authors declare no conflict of interest.
EDAT- 2018/08/04 06:00
MHDA- 2018/08/04 06:01
PMCR- 2018/08/01
CRDT- 2018/08/04 06:00
PHST- 2018/05/15 00:00 [received]
PHST- 2018/07/25 00:00 [revised]
PHST- 2018/07/27 00:00 [accepted]
PHST- 2018/08/04 06:00 [entrez]
PHST- 2018/08/04 06:00 [pubmed]
PHST- 2018/08/04 06:01 [medline]
PHST- 2018/08/01 00:00 [pmc-release]
AID - genes9080392 [pii]
AID - genes-09-00392 [pii]
AID - 10.3390/genes9080392 [doi]
PST - epublish
SO  - Genes (Basel). 2018 Aug 1;9(8):392. doi: 10.3390/genes9080392.