Alternative splice acceptor utilization during human immunodeficiency virus type 1 infection of cultured cells

Guatelli, J. C., Gingeras, T. R., Richman, D. D. (1990) Alternative splice acceptor utilization during human immunodeficiency virus type 1 infection of cultured cells. Journal of Virology, 64 (9). pp. 4093-4098. ISSN 0022538X (ISSN)

URL: http://www.ncbi.nlm.nih.gov/pubmed/2384914

Abstract

The utilization of alternative splice acceptors for excision of the 5' major intron of human immunodeficiency virus type 1 RNA was observed after infection in vitro. Specific splice events were monitored by a cDNA-polymerase chain reaction. These splice events shared a common splice donor but utilized several alternative splice acceptors. In addition to identifying the previously documented splice acceptors for tat and nef (S.K. Arya, C.Guo, S.F. Josephs, and F. Wong-Staal, Science 229: 69-73, 1985), nucleotide sequence analysis of cDNA-polymerase chain reaction fragments also revealed the following: (i) two splice acceptors 15 and 9 nucleotides upstream from the rev start codon, which are utilized to create transcripts suitable for specific rev expression; and (ii) use of the splice acceptor previously attributed to nef to generate a singly spliced, env-encoding transcript. Hybridization signals representing the nef/env, tat, and rev splice events increased in intensity between 6 and 12 h after infection of CEM cells with the LAV-1(BRU) strain of human immunodeficiency virus type 1. In contrast, the signal for utilization of the nef/env splice acceptor for the singly spliced env transcript appeared first at 12 h and increased to maximum intensity by 24 h. The nef/env splice acceptor was dominant at all time points examined. We propose that this dominance ensures efficient downstream splicing proximal to the env initiation codon in singly spliced transcripts. However, early after infection, the dominance of the nef/env splice acceptor appears to divert primary transcripts away from tat- and rev-specific processing paths. The relative proportions of hybridization signals representing these alternative splice events remained constant throughout the viral replicative cycle. This result suggests that trans-acting factors that might influence splice choices are not induced during infection, but rather that cis-acting, sequence-specific splice preferences determine the relative efficiency of alternative acceptor utilization.

Item Type: Paper
Uncontrolled Keywords: article human immunodeficiency virus 1 human immunodeficiency virus infection in vitro study nonhuman priority journal transactivation virus cell interaction virus culture Base Sequence Cell Line Cell Transformation, Viral DNA, Viral HIV-1 Human Introns Kinetics Molecular Sequence Data Oligonucleotide Probes Polymerase Chain Reaction RNA Splicing RNA Viral
Subjects: diseases & disorders > viral diseases > HIV
Investigative techniques and equipment > cloning > PCR
Investigative techniques and equipment > assays > cloning > PCR

bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > splice site
CSHL Authors:
Communities: CSHL labs > Gingeras lab
Depositing User: CSHL Librarian
Date: 1990
Date Deposited: 13 Mar 2012 16:52
Last Modified: 28 Mar 2014 20:48
PMCID: PMC247871
Related URLs:
URI: http://repository.cshl.edu/id/eprint/25249

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