Identification of new splice sites used for generation of rev transcripts in human immunodeficiency virus type 1 subtype C primary isolates.
The HIV-1 primary transcript undergoes a complex splicing process by which more than 40 different spliced RNAs are generated. One of the factors contributing to HIV-1 splicing complexity is the multiplicity of 3' splice sites (3'ss) used for generation of rev RNAs, with two 3'ss, A4a...
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doaj-4deffcb05f724616ac36a38de0ec32732020-11-25T01:53:27ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0172e3057410.1371/journal.pone.0030574Identification of new splice sites used for generation of rev transcripts in human immunodeficiency virus type 1 subtype C primary isolates.Elena DelgadoCristina CarreraPaloma NebredaAurora Fernández-GarcíaMilagros PinillaValentina GarcíaLucía Pérez-ÁlvarezMichael M ThomsonThe HIV-1 primary transcript undergoes a complex splicing process by which more than 40 different spliced RNAs are generated. One of the factors contributing to HIV-1 splicing complexity is the multiplicity of 3' splice sites (3'ss) used for generation of rev RNAs, with two 3'ss, A4a and A4b, being most commonly used, a third site, A4c, used less frequently, and two additional sites, A4d and A4e, reported in only two and one isolates, respectively. HIV-1 splicing has been analyzed mostly in subtype B isolates, and data on other group M clades are lacking. Here we examine splice site usage in three primary isolates of subtype C, the most prevalent clade in the HIV-1 pandemic, by using an in vitro infection assay of peripheral blood mononuclear cells. Viral spliced RNAs were identified by RT-PCR amplification using a fluorescently-labeled primer and software analyses and by cloning and sequencing the amplified products. The results revealed that splice site usage for generation of rev transcripts in subtype C differs from that reported for subtype B, with most rev RNAs using two previously unreported 3'ss, one located 7 nucleotides upstream of 3'ss A4a, designated A4f, preferentially used by two isolates, and another located 14 nucleotides upstream of 3'ss A4c, designated A4g, preferentially used by the third isolate. A new 5' splice site, designated D2a, was also identified in one virus. Usage of the newly identified splice sites is consistent with sequence features commonly found in subtype C viruses. These results show that splice site usage may differ between HIV-1 subtypes.http://europepmc.org/articles/PMC3281843?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Elena Delgado Cristina Carrera Paloma Nebreda Aurora Fernández-García Milagros Pinilla Valentina García Lucía Pérez-Álvarez Michael M Thomson |
spellingShingle |
Elena Delgado Cristina Carrera Paloma Nebreda Aurora Fernández-García Milagros Pinilla Valentina García Lucía Pérez-Álvarez Michael M Thomson Identification of new splice sites used for generation of rev transcripts in human immunodeficiency virus type 1 subtype C primary isolates. PLoS ONE |
author_facet |
Elena Delgado Cristina Carrera Paloma Nebreda Aurora Fernández-García Milagros Pinilla Valentina García Lucía Pérez-Álvarez Michael M Thomson |
author_sort |
Elena Delgado |
title |
Identification of new splice sites used for generation of rev transcripts in human immunodeficiency virus type 1 subtype C primary isolates. |
title_short |
Identification of new splice sites used for generation of rev transcripts in human immunodeficiency virus type 1 subtype C primary isolates. |
title_full |
Identification of new splice sites used for generation of rev transcripts in human immunodeficiency virus type 1 subtype C primary isolates. |
title_fullStr |
Identification of new splice sites used for generation of rev transcripts in human immunodeficiency virus type 1 subtype C primary isolates. |
title_full_unstemmed |
Identification of new splice sites used for generation of rev transcripts in human immunodeficiency virus type 1 subtype C primary isolates. |
title_sort |
identification of new splice sites used for generation of rev transcripts in human immunodeficiency virus type 1 subtype c primary isolates. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2012-01-01 |
description |
The HIV-1 primary transcript undergoes a complex splicing process by which more than 40 different spliced RNAs are generated. One of the factors contributing to HIV-1 splicing complexity is the multiplicity of 3' splice sites (3'ss) used for generation of rev RNAs, with two 3'ss, A4a and A4b, being most commonly used, a third site, A4c, used less frequently, and two additional sites, A4d and A4e, reported in only two and one isolates, respectively. HIV-1 splicing has been analyzed mostly in subtype B isolates, and data on other group M clades are lacking. Here we examine splice site usage in three primary isolates of subtype C, the most prevalent clade in the HIV-1 pandemic, by using an in vitro infection assay of peripheral blood mononuclear cells. Viral spliced RNAs were identified by RT-PCR amplification using a fluorescently-labeled primer and software analyses and by cloning and sequencing the amplified products. The results revealed that splice site usage for generation of rev transcripts in subtype C differs from that reported for subtype B, with most rev RNAs using two previously unreported 3'ss, one located 7 nucleotides upstream of 3'ss A4a, designated A4f, preferentially used by two isolates, and another located 14 nucleotides upstream of 3'ss A4c, designated A4g, preferentially used by the third isolate. A new 5' splice site, designated D2a, was also identified in one virus. Usage of the newly identified splice sites is consistent with sequence features commonly found in subtype C viruses. These results show that splice site usage may differ between HIV-1 subtypes. |
url |
http://europepmc.org/articles/PMC3281843?pdf=render |
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