Over-representation of exonic splicing enhancers in human intronless genes suggests multiple functions in mRNA processing

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13 Citations (Scopus)

Abstract

The human transcriptome is constituted of a great majority of intron-containing and a minority of intron-lacking mRNAs; given the different processing these transcripts undergo, they are expected to carry, intermingled with coding properties, very different editing information. Here we applied a computational approach to compare intronless and intron-containing coding sequences. Hexamer composition comparison allowed the definition of over- and under-represented motifs in intronless genes; surprisingly, experimental testing revealed that intron-lacking coding sequences are enriched rather than depleted in elements with splicing enhancement ability. Similarly, we show evidence that intronless transcripts display a significantly higher frequency of both shuttling and non-shuttling SR protein binding sites compared to intron-containing sequences. These observations suggest that SR proteins (and possibly other splicing factors) play a role in cellular processes distinct from splicing.

Original languageEnglish
Pages (from-to)470-476
Number of pages7
JournalBiochemical and Biophysical Research Communications
Volume322
Issue number2
DOIs
Publication statusPublished - Sep 17 2004

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Introns
Genes
Messenger RNA
Processing
Transcriptome
Protein Binding
Binding Sites
Testing
Chemical analysis
Proteins

Keywords

  • Intronless genes
  • Nuclear export
  • Splicing enhancers
  • SR proteins

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology

Cite this

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abstract = "The human transcriptome is constituted of a great majority of intron-containing and a minority of intron-lacking mRNAs; given the different processing these transcripts undergo, they are expected to carry, intermingled with coding properties, very different editing information. Here we applied a computational approach to compare intronless and intron-containing coding sequences. Hexamer composition comparison allowed the definition of over- and under-represented motifs in intronless genes; surprisingly, experimental testing revealed that intron-lacking coding sequences are enriched rather than depleted in elements with splicing enhancement ability. Similarly, we show evidence that intronless transcripts display a significantly higher frequency of both shuttling and non-shuttling SR protein binding sites compared to intron-containing sequences. These observations suggest that SR proteins (and possibly other splicing factors) play a role in cellular processes distinct from splicing.",
keywords = "Intronless genes, Nuclear export, Splicing enhancers, SR proteins",
author = "Uberto Pozzoli and Laura Riva and Giorgia Menozzi and Rachele Cagliani and Comi, {Giacomo P.} and Nereo Bresolin and Roberto Giorda and Manuela Sironi",
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T1 - Over-representation of exonic splicing enhancers in human intronless genes suggests multiple functions in mRNA processing

AU - Pozzoli, Uberto

AU - Riva, Laura

AU - Menozzi, Giorgia

AU - Cagliani, Rachele

AU - Comi, Giacomo P.

AU - Bresolin, Nereo

AU - Giorda, Roberto

AU - Sironi, Manuela

PY - 2004/9/17

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N2 - The human transcriptome is constituted of a great majority of intron-containing and a minority of intron-lacking mRNAs; given the different processing these transcripts undergo, they are expected to carry, intermingled with coding properties, very different editing information. Here we applied a computational approach to compare intronless and intron-containing coding sequences. Hexamer composition comparison allowed the definition of over- and under-represented motifs in intronless genes; surprisingly, experimental testing revealed that intron-lacking coding sequences are enriched rather than depleted in elements with splicing enhancement ability. Similarly, we show evidence that intronless transcripts display a significantly higher frequency of both shuttling and non-shuttling SR protein binding sites compared to intron-containing sequences. These observations suggest that SR proteins (and possibly other splicing factors) play a role in cellular processes distinct from splicing.

AB - The human transcriptome is constituted of a great majority of intron-containing and a minority of intron-lacking mRNAs; given the different processing these transcripts undergo, they are expected to carry, intermingled with coding properties, very different editing information. Here we applied a computational approach to compare intronless and intron-containing coding sequences. Hexamer composition comparison allowed the definition of over- and under-represented motifs in intronless genes; surprisingly, experimental testing revealed that intron-lacking coding sequences are enriched rather than depleted in elements with splicing enhancement ability. Similarly, we show evidence that intronless transcripts display a significantly higher frequency of both shuttling and non-shuttling SR protein binding sites compared to intron-containing sequences. These observations suggest that SR proteins (and possibly other splicing factors) play a role in cellular processes distinct from splicing.

KW - Intronless genes

KW - Nuclear export

KW - Splicing enhancers

KW - SR proteins

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