{{Infobox rfam | Name = R2 RNA element | image = RF00524.jpg | width = | caption = Predicted secondary structure and sequence conservation of R2_retro_el | Symbol = R2_retro_el | AltSymbols = | Rfam = RF00524 | miRBase = | miRBase_family = | RNA_type = Cis-reg | Tax_domain = Eukaryota | GO = | SO = {{SO|0000233}} | CAS_number = | EntrezGene = | HGNCid = | OMIM = | PDB = | RefSeq = | Chromosome = | Arm = | Band = | LocusSupplementaryData = }}
The '''R2 RNA element''' is a non-long terminal repeat (non-LTR) retrotransposable element that inserts at a specific site in the 28S ribosomal RNA (rRNA) genes of most insect genomes.<ref name="pmid7679954">{{cite journal |vauthors=Luan DD, Korman MH, Jakubczak JL, Eickbush TH | title = Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition | journal = Cell | volume = 72 | issue = 4 | pages = 595–605 | year = 1993 | pmid = 7679954 | doi = 10.1016/0092-8674(93)90078-5 | s2cid = 42587840 }}</ref> In order to insert itself into the genome, retrotransposon encoded protein (R2) protein makes a specific nick in one of the DNA strands at the insertion site and uses the 3′ hydroxyl group exposed by this nick to prime the reverse transcription process termed target primed reverse transcription (TPRT), where the RNA genome is transcribed into DNA.<ref>{{cite journal|last=Christensen|first=SM|author2=Ye, J |author3=Eickbush, TH |title=RNA from the 5′ end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site|journal=Proceedings of the National Academy of Sciences of the United States of America|year=2006|volume=103|issue=47|pages=17602–17607|pmid=17105809|doi=10.1073/pnas.0605476103|pmc=1693793|bibcode=2006PNAS..10317602C|doi-access=free}}</ref>
==3' UTR element== The R2 element 3' UTR RNA is a cis-acting element identified in R2 retrotransposons which is involved in priming the reverse transcription process (an essential part of retrotransposon insertion into the host genome).<ref name="pmid15146081">{{cite journal | author = Ruschak AM | title = Secondary structure models of the 3′ untranslated regions of diverse R2 RNAs | journal = RNA | volume = 10 | issue = 6 | pages = 978–987 | year = 2004 | pmid = 15146081 | doi = 10.1261/rna.5216204| pmc = 1370589 |name-list-style=vanc| author2 = Mathews DH | author3 = Bibillo A | display-authors = 3 | last4 = Spinelli | first4 = SL | last5 = Childs | first5 = JL | last6 = Eickbush | first6 = TH | last7 = Turner | first7 = DH }}</ref> An RNA fragment found in the R2 3' untranslated region (3'UTR), has been shown to interact with one copy of R2 protein during TPRT. This fragment has been shown to possess conserved secondary structure within ''Drosophila'' and silk moths, and also between the two groups.<ref name="pmid15146081" />
==5' UTR ribozyme== The R2 element is co-transcribed with host organism 28S ribosomal RNA (rRNA). To become a fully mature R2 messenger RNA (mRNA), requires that the initial R2 transcript be processed to remove the 28S rRNA. This processing occurs via a self-cleaving ribozyme that forms at the 5' junction of the R2 RNA.<ref name="Eic10">{{cite journal|last=Eickbush|first=DG|author2=Eickbush, TH |title=R2 Retrotransposons Encode a Self-Cleaving Ribozyme for Processing from an rRNA Cotranscript|journal=Molecular and Cellular Biology|date=Jul 2010|volume=30|issue=13|pages=3142–3150|pmid=20421411|doi=10.1128/MCB.00300-10|pmc=2897577}}</ref> This ribozyme has been found to have high structural similarity to the HDV ribozyme but they are not homologous; the two sequences are thought to have undergone convergent evolution.<ref name="Eic10" />
==The 5′ R2 protein binding site== The 5′ R2 protein binding site occurs in a region that spans part of the 5' UTR and the start of the R2 ORF. This region also has a conserved secondary structure, which has been deduced from binding to oligonucleotide microarrays, structure probing, and free energy minimization.<ref>{{cite journal|author1=Kierzek, E.|author2=Kierzek, R.|author3=Moss, W.N.|author4=Christensen, S.M.|author5=Eickbush, T.H.|author6=Turner, D.H.|year=2008|title=Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function|journal=Nucleic Acids Research|volume=36|pages=1770-1782|issue=6|doi=10.1093/nar/gkm1085|pmid=18252773|pmc=2346776|doi-access=free}}</ref> To date, conservation of structure has only been described in five moth species: ''Bombyx mori'' (R2Bm), ''Samia cynthia'' (R2Sc), ''Coscinocera hercules'' (R2Ch), ''Callosamia promethea'' (R2Cpr) and ''Saturnia pyri'' (R2Spy).
thumb|Structural Comparison of 5' R2 Pseudoknot RNAs Within this 5' protein binding site an RNA pseudoknot structure occurs.<ref>{{cite journal|author1=Kierzek, E.|author2=Christensen, S.M.|author3=Eickbush, T.H.|author4=Kierzek, R.|author5=Turner, D.H.|author6=Moss, W.N.|year=2009|title=Secondary structures for 5’ regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints|journal=Journal of Molecular Biology|volume=390|pages=428–442|issue=3|doi=10.1016/j.jmb.2009.04.048|pmid=19397915|pmc=2728621}}</ref> The pseudoknot is highly conserved between the five silk moth species. Sequence comparisons show evidence for compensatory mutations within the helical regions indicating the secondary structure of the RNA is of biological importance. In particular, this pseudoknot is proposed to have implications for initiation of translation.<ref>{{cite journal|author1=Moss, W.N.|author2=Eickbush, D.G.|author3=Lopez, M.J.|author4=Eickbush, T.H.|author5=Turner, D.H.|year=2011|title=The R2 retrotransposon RNA families|journal=RNA Biology|volume=8|issue=5|pages=714–718|doi=10.4161/rna.8.5.16033|doi-access=free|pmid=21734471|pmc=3256348}}</ref>
==References== {{reflist}}
==External links== * {{Rfam|id=RF00524|name=R2 RNA element}}
Category:Cis-regulatory RNA elements