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Conserved stem-loop structures in the HIV-1 RNA region containing the A3 3' splice site and its cis-regulatory element: possible involvement in RNA splicing.
Nucleic Acids Res. 2001 Jan 15; 29(2):464-78.NA

Abstract

The HIV-1 transcript is alternatively spliced to over 30 different mRNAs. Whether RNA secondary structure can influence HIV-1 RNA alternative splicing has not previously been examined. Here we have determined the secondary structure of the HIV-1/BRU RNA segment, containing the alternative A3, A4a, A4b, A4c and A5 3' splice sites. Site A3, required for tat mRNA production, is contained in the terminal loop of a stem-loop structure (SLS2), which is highly conserved in HIV-1 and related SIVcpz strains. The exon splicing silencer (ESS2) acting on site A3 is located in a long irregular stem-loop structure (SLS3). Two SLS3 domains were protected by nuclear components under splicing condition assays. One contains the A4c branch points and a putative SR protein binding site. The other one is adjacent to ESS2. Unexpectedly, only the 3' A residue of ESS2 was protected. The suboptimal A3 polypyrimidine tract (PPT) is base paired. Using site-directed mutagenesis and transfection of a mini-HIV-1 cDNA into HeLa cells, we found that, in a wild-type PPT context, a mutation of the A3 downstream sequence that reinforced SLS2 stability decreased site A3 utilization. This was not the case with an optimized PPT. Hence, sequence and secondary structure of the PPT may cooperate in limiting site A3 utilization.

Authors+Show Affiliations

Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 UHP-CNRS, France.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

11139617

Citation

Jacquenet, S, et al. "Conserved Stem-loop Structures in the HIV-1 RNA Region Containing the A3 3' Splice Site and Its Cis-regulatory Element: Possible Involvement in RNA Splicing." Nucleic Acids Research, vol. 29, no. 2, 2001, pp. 464-78.
Jacquenet S, Ropers D, Bilodeau PS, et al. Conserved stem-loop structures in the HIV-1 RNA region containing the A3 3' splice site and its cis-regulatory element: possible involvement in RNA splicing. Nucleic Acids Res. 2001;29(2):464-78.
Jacquenet, S., Ropers, D., Bilodeau, P. S., Damier, L., Mougin, A., Stoltzfus, C. M., & Branlant, C. (2001). Conserved stem-loop structures in the HIV-1 RNA region containing the A3 3' splice site and its cis-regulatory element: possible involvement in RNA splicing. Nucleic Acids Research, 29(2), 464-78.
Jacquenet S, et al. Conserved Stem-loop Structures in the HIV-1 RNA Region Containing the A3 3' Splice Site and Its Cis-regulatory Element: Possible Involvement in RNA Splicing. Nucleic Acids Res. 2001 Jan 15;29(2):464-78. PubMed PMID: 11139617.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Conserved stem-loop structures in the HIV-1 RNA region containing the A3 3' splice site and its cis-regulatory element: possible involvement in RNA splicing. AU - Jacquenet,S, AU - Ropers,D, AU - Bilodeau,P S, AU - Damier,L, AU - Mougin,A, AU - Stoltzfus,C M, AU - Branlant,C, PY - 2001/1/5/pubmed PY - 2001/2/28/medline PY - 2001/1/5/entrez SP - 464 EP - 78 JF - Nucleic acids research JO - Nucleic Acids Res VL - 29 IS - 2 N2 - The HIV-1 transcript is alternatively spliced to over 30 different mRNAs. Whether RNA secondary structure can influence HIV-1 RNA alternative splicing has not previously been examined. Here we have determined the secondary structure of the HIV-1/BRU RNA segment, containing the alternative A3, A4a, A4b, A4c and A5 3' splice sites. Site A3, required for tat mRNA production, is contained in the terminal loop of a stem-loop structure (SLS2), which is highly conserved in HIV-1 and related SIVcpz strains. The exon splicing silencer (ESS2) acting on site A3 is located in a long irregular stem-loop structure (SLS3). Two SLS3 domains were protected by nuclear components under splicing condition assays. One contains the A4c branch points and a putative SR protein binding site. The other one is adjacent to ESS2. Unexpectedly, only the 3' A residue of ESS2 was protected. The suboptimal A3 polypyrimidine tract (PPT) is base paired. Using site-directed mutagenesis and transfection of a mini-HIV-1 cDNA into HeLa cells, we found that, in a wild-type PPT context, a mutation of the A3 downstream sequence that reinforced SLS2 stability decreased site A3 utilization. This was not the case with an optimized PPT. Hence, sequence and secondary structure of the PPT may cooperate in limiting site A3 utilization. SN - 1362-4962 UR - https://www.unboundmedicine.com/medline/citation/11139617/Conserved_stem_loop_structures_in_the_HIV_1_RNA_region_containing_the_A3_3'_splice_site_and_its_cis_regulatory_element:_possible_involvement_in_RNA_splicing_ L2 - https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/29.2.464 DB - PRIME DP - Unbound Medicine ER -