Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing

  1. Mariano A. Garcia-Blanco1,2,6
  1. 1Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
  2. 2Center for RNA Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
  3. 3Medical Scientist Training Program, Duke University Medical Center, Durham, North Carolina 27710, USA
  4. 4Program in Molecular Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
  5. 5Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
  6. 6Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
  • 7 Present address: Biotechnology Program and Department of Plant Biology, North Carolina State University, Raleigh, NC 27695, USA.

  • 8 Present address: Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.

Abstract

Tat specific factor 1 (Tat-SF1) interacts with components of both the transcription and splicing machineries and has been classified as a transcription-splicing factor. Although its function as an HIV-1 dependency factor has been investigated, relatively little is known about the cellular functions of Tat-SF1. To identify target genes of Tat-SF1, we utilized a combination of RNAi and exon-specific microarrays. These arrays, which survey genome-wide changes in transcript and individual exon levels, revealed 450 genes with transcript level changes upon Tat-SF1 depletion. Strikingly, 98% of these target genes were down-regulated upon depletion, indicating that Tat-SF1 generally activates gene expression. We also identified 89 genes that showed differential exon level changes after Tat-SF1 depletion. The 89 genes showed evidence of many different types of alternative exon use consistent with the regulation of transcription initiation sites and RNA processing. Minimal overlap between genes with transcript-level and exon-level changes suggests that Tat-SF1 does not functionally couple transcription and splicing. Biological processes significantly enriched with transcript- and exon-level targets include the cell cycle and nucleic acid metabolism; the insulin signaling pathway was enriched with Tat-SF1 transcript-level targets but not exon-level targets. Additionally, a hexamer, ATGCCG, was over-represented in the promoter region of genes showing changes in transcription initiation upon Tat-SF1 depletion. This may represent a novel motif that Tat-SF1 recognizes during transcription. Together, these findings suggest that Tat-SF1 functions independently in transcription and splicing of cellular genes.

Keywords

Footnotes

  • Reprint requests to: Mariano A. Garcia-Blanco, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; e-mail: garci001{at}mc.duke.edu; fax: (919) 613-8646.

  • Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.2462011.

  • Received September 11, 2010.
  • Accepted December 15, 2010.

Freely available online through the RNA Open Access option.

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