Dataset Information

Identification of new and unusual rev and nef transcripts expressed by an HIV type 1 primary isolate.

ABSTRACT: We analyzed RNA splice site usage in three HIV-1 subtype B primary isolates through reverse transcriptase polymerase chain reaction (RT-PCR) amplification of spliced RNAs using a fluorescently labeled primer, with computerized size determination and quantification of PCR products, which were also identified by clone sequencing. In one isolate, P2149-3, unusual and unreported spliced transcripts were detected. This isolate preferentially used for rev RNA generation a 3' splice site (3'ss) located five nucleotides upstream of A4a, previously identified only in a T cell line-adapted virus and in a group O isolate, and designated A4d. P2149-3 also used an unreported 3'ss for rev RNA generation, designated A4h, located 20 nucleotides upstream of 3'ss A4c. Additionally, unusual nef RNAs using 3'ss A5a and A7a and with exon composition 1.3.7 were identified. The identification of several unusual and unreported spliced transcripts in an HIV-1 primary isolate suggests a greater diversity of splice site usage in HIV-1 than previously appreciated.

SUBMITTER: Vega Y

PROVIDER: S-EPMC3685689 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature

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Identification of new and unusual rev and nef transcripts expressed by an HIV type 1 primary isolate.

Vega Yolanda Y Delgado Elena E Carrera Cristina C Nebreda Paloma P Fernández-García Aurora A Cuevas María Teresa MT Pérez-Álvarez Lucía L Thomson Michael M MM

AIDS research and human retroviruses 20130508 7

We analyzed RNA splice site usage in three HIV-1 subtype B primary isolates through reverse transcriptase polymerase chain reaction (RT-PCR) amplification of spliced RNAs using a fluorescently labeled primer, with computerized size determination and quantification of PCR products, which were also identified by clone sequencing. In one isolate, P2149-3, unusual and unreported spliced transcripts were detected. This isolate preferentially used for rev RNA generation a 3' splice site (3'ss) located ...[more]

PMID: 23540799

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Dataset Information

Identification of new and unusual rev and nef transcripts expressed by an HIV type 1 primary isolate.

Publications

Identification of new and unusual rev and nef transcripts expressed by an HIV type 1 primary isolate.

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