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

Heather B. Miller, Timothy J. Robinson, Raluca Gordân, Alexander J. Hartemink, Mariano Garcia-Blanco

Research output: Contribution to journalArticle

12 Citations (Scopus)

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 overrepresented 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.

Original languageEnglish (US)
Pages (from-to)665-674
Number of pages10
JournalRNA
Volume17
Issue number4
DOIs
StatePublished - Apr 2011
Externally publishedYes

Fingerprint

Exons
Genes
tat Genes
Biological Phenomena
Transcription Initiation Site
RNA Interference
Genetic Promoter Regions
Nucleic Acids
HIV-1
Cell Cycle
Transcription Factors
Genome
RNA
Insulin
Gene Expression

Keywords

  • Alternative RNA processing
  • Exon array
  • RNA splicing
  • Tat-SF1
  • Transcription

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing. / Miller, Heather B.; Robinson, Timothy J.; Gordân, Raluca; Hartemink, Alexander J.; Garcia-Blanco, Mariano.

In: RNA, Vol. 17, No. 4, 04.2011, p. 665-674.

Research output: Contribution to journalArticle

Miller, Heather B. ; Robinson, Timothy J. ; Gordân, Raluca ; Hartemink, Alexander J. ; Garcia-Blanco, Mariano. / Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing. In: RNA. 2011 ; Vol. 17, No. 4. pp. 665-674.
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