The HnRNP A1 Protein Regulates HIV-1 Tat Splicing Via a Novel Intron Silencer Element

Overview

Journal EMBO J

Specialties Biotechnology
Molecular Biology

Date 2001 Oct 13

PMID 11598017

Citations 76

Authors

T O Tange

C K Damgaard

S Guth

J Valcarcel

J Kjems

Affiliations

Soon will be listed here.

Abstract

The generation of >30 different HIV-1 mRNAs is achieved by alternative splicing of one primary transcript. The removal of the second tat intron is regulated by a combination of a suboptimal 3' splice site and cis-acting splicing enhancers and silencers. Here we show that hnRNP A1 inhibits splicing of this intron via a novel heterogeneous nuclear ribonucleoprotein (hnRNP) A1-responsive intron splicing silencer (ISS) that can function independently of the previously characterized exon splicing silencer (ESS3). Surprisingly, depletion of hnRNP A1 from the nuclear extract (NE) enables splicing to proceed in NE that contains 100-fold reduced concentrations of U2AF and normal levels of SR proteins, conditions that do not support processing of other efficiently spliced pre-mRNAs. Reconstituting the extract with recombinant hnRNP A1 protein restores splicing inhibition at a step subsequent to U2AF binding, mainly at the time of U2 snRNP association. hnRNP A1 interacts specifically with the ISS sequence, which overlaps with one of three alternative branch point sequences, pointing to a model where the entry of U2 snRNP is physically blocked by hnRNP A1 binding.

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References

Zamore P, Green M . Identification, purification, and biochemical characterization of U2 small nuclear ribonucleoprotein auxiliary factor. Proc Natl Acad Sci U S A. 1989; 86(23):9243-7. PMC: 298470. DOI: 10.1073/pnas.86.23.9243. View

McNally M, Beemon K . Intronic sequences and 3' splice sites control Rous sarcoma virus RNA splicing. J Virol. 1992; 66(1):6-11. PMC: 238253. DOI: 10.1128/JVI.66.1.6-11.1992. View

Ge H, Zuo P, Manley J . Primary structure of the human splicing factor ASF reveals similarities with Drosophila regulators. Cell. 1991; 66(2):373-82. DOI: 10.1016/0092-8674(91)90626-a. View

Moore M . Intron recognition comes of AGe. Nat Struct Biol. 2000; 7(1):14-6. DOI: 10.1038/71207. View

Jamison S, Crow A, Garcia-Blanco M . The spliceosome assembly pathway in mammalian extracts. Mol Cell Biol. 1992; 12(10):4279-87. PMC: 360351. DOI: 10.1128/mcb.12.10.4279-4287.1992. View

Fu X, Mayeda A, Maniatis T, Krainer A . General splicing factors SF2 and SC35 have equivalent activities in vitro, and both affect alternative 5' and 3' splice site selection. Proc Natl Acad Sci U S A. 1992; 89(23):11224-8. PMC: 50522. DOI: 10.1073/pnas.89.23.11224. View

Watakabe A, Tanaka K, Shimura Y . The role of exon sequences in splice site selection. Genes Dev. 1993; 7(3):407-18. DOI: 10.1101/gad.7.3.407. View

Valcarcel J, Singh R, Zamore P, Green M . The protein Sex-lethal antagonizes the splicing factor U2AF to regulate alternative splicing of transformer pre-mRNA. Nature. 1993; 362(6416):171-5. DOI: 10.1038/362171a0. View

Mayeda A, Helfman D, Krainer A . Modulation of exon skipping and inclusion by heterogeneous nuclear ribonucleoprotein A1 and pre-mRNA splicing factor SF2/ASF. Mol Cell Biol. 1993; 13(5):2993-3001. PMC: 359692. DOI: 10.1128/mcb.13.5.2993-3001.1993. View

10.

Fu X . Specific commitment of different pre-mRNAs to splicing by single SR proteins. Nature. 1993; 365(6441):82-5. DOI: 10.1038/365082a0. View

11.

Gontarek R, McNally M, Beemon K . Mutation of an RSV intronic element abolishes both U11/U12 snRNP binding and negative regulation of splicing. Genes Dev. 1993; 7(10):1926-36. DOI: 10.1101/gad.7.10.1926. View

12.

Wu J, Maniatis T . Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell. 1993; 75(6):1061-70. DOI: 10.1016/0092-8674(93)90316-i. View

13.

Sun Q, Mayeda A, Hampson R, Krainer A, ROTTMAN F . General splicing factor SF2/ASF promotes alternative splicing by binding to an exonic splicing enhancer. Genes Dev. 1993; 7(12B):2598-608. DOI: 10.1101/gad.7.12b.2598. View

14.

Burd C, Dreyfuss G . RNA binding specificity of hnRNP A1: significance of hnRNP A1 high-affinity binding sites in pre-mRNA splicing. EMBO J. 1994; 13(5):1197-204. PMC: 394929. DOI: 10.1002/j.1460-2075.1994.tb06369.x. View

15.

Staffa A, Cochrane A . The tat/rev intron of human immunodeficiency virus type 1 is inefficiently spliced because of suboptimal signals in the 3' splice site. J Virol. 1994; 68(5):3071-9. PMC: 236797. DOI: 10.1128/JVI.68.5.3071-3079.1994. View

16.

Amendt B, Hesslein D, Chang L, Stoltzfus C . Presence of negative and positive cis-acting RNA splicing elements within and flanking the first tat coding exon of human immunodeficiency virus type 1. Mol Cell Biol. 1994; 14(6):3960-70. PMC: 358762. DOI: 10.1128/mcb.14.6.3960-3970.1994. View

17.

Lynch K, Maniatis T . Synergistic interactions between two distinct elements of a regulated splicing enhancer. Genes Dev. 1995; 9(3):284-93. DOI: 10.1101/gad.9.3.284. View

18.

Staffa A, Cochrane A . Identification of positive and negative splicing regulatory elements within the terminal tat-rev exon of human immunodeficiency virus type 1. Mol Cell Biol. 1995; 15(8):4597-605. PMC: 230700. DOI: 10.1128/MCB.15.8.4597. View

19.

Amendt B, Si Z, Stoltzfus C . Presence of exon splicing silencers within human immunodeficiency virus type 1 tat exon 2 and tat-rev exon 3: evidence for inhibition mediated by cellular factors. Mol Cell Biol. 1995; 15(8):4606-15. PMC: 230701. DOI: 10.1128/MCB.15.8.4606. View

20.

Del Gatto F, Breathnach R . Exon and intron sequences, respectively, repress and activate splicing of a fibroblast growth factor receptor 2 alternative exon. Mol Cell Biol. 1995; 15(9):4825-34. PMC: 230727. DOI: 10.1128/MCB.15.9.4825. View