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Zhang J, et al.  (2008) Characteristic differences between the promoters of intron-containing and intronless ribosomal protein genes in yeast. BMC Res Notes 1(1):109

Abstract: ABSTRACT: BACKGROUND: More than two thirds of the highly expressed ribosomal protein (RP) genes in Saccharomyces cerevisiae contain introns, which is in sharp contrast to the genome-wide five percent intron-containing genes. It is well established that introns carry regulatory sequences and that the transcription of RP genes is extensively and coordinately regulated. Here we test the hypotheses that introns are innately associated with heavily transcribed genes and that introns of RP genes contribute regulatory TF binding sequences. Moreover, we investigate whether promoter features are significantly different between intron-containing and intronless RP genes. FINDINGS: We find that directly measured transcription rates tend to be lower for intron-containing compared to intronless RP genes. We do not observe any specifically enriched sequence motifs in the introns of RP genes other than those of the branch point and the two splice sites. Comparing the promoters of intron-containing and intronless RP genes, we detect differences in number and position of Rap1-binding and IFHL motifs. Moreover, the analysis of the length distribution and the folding free energies suggest that, at least in a sub-population of RP genes, the 5' untranslated sequences are optimized for regulatory function. CONCLUSION: Our results argue against the direct involvement of introns in the regulation of transcription of highly expressed genes. Moreover, systematic differences in motif distributions suggest that RP transcription factors may act differently on intron-containing and intronless gene promoters. Thus, our findings contribute to the decoding of the RP promoter architecture and may fuel the discussion on the evolution of introns.

Status: Published Type: Journal Article PubMed ID: 18959800

Topics addressed in this paper

Number of different genes curated to this paper: 124

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Topics Genes linked to topics (#1 - 10 )
RAP1 RPL10 RPL11A RPL11B RPL12A RPL12B RPL13A RPL13B RPL14A RPL15A
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DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#11 - 20 )
RPL16A RPL16B RPL17A RPL17B RPL18A RPL19A RPL19B RPL1A RPL1B RPL20A
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Topics Genes linked to topics (#21 - 30 )
RPL20B RPL21B RPL22A RPL22B RPL23A RPL23B RPL24A RPL24B RPL25 RPL26A
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Topics Genes linked to topics (#31 - 40 )
RPL26B RPL27A RPL27B RPL28 RPL2A RPL2B RPL3 RPL30 RPL31A RPL31B
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#41 - 50 )
RPL32 RPL33A RPL33B RPL34A RPL34B RPL35A RPL35B RPL36A RPL36B RPL37A
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#51 - 60 )
RPL38 RPL39 RPL40A RPL41A RPL41B RPL42A RPL42B RPL43A RPL43B RPL4A
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Transcription blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#61 - 70 )
RPL4B RPL5 RPL6A RPL7A RPL7B RPL8B RPL9A RPL9B RPP0 RPP1A
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#71 - 80 )
RPP1B RPP2A RPP2B RPS0A RPS0B RPS10A RPS10B RPS11B RPS12 RPS13
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Transcription blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#81 - 90 )
RPS14A RPS14B RPS15 RPS16A RPS16B RPS17A RPS17B RPS18A RPS18B RPS19A
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Transcription blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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    The topic is addressed in these papers but does not describe a specific gene or chromosomal feature.
  • To go to the Locus page for a gene, click on the gene name.

Topics Genes linked to topics (#91 - 100 )
RPS19B RPS1A RPS1B RPS20 RPS21A RPS21B RPS22A RPS22B RPS23A RPS23B
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Transcription blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#101 - 110 )
RPS24A RPS24B RPS25A RPS25B RPS26B RPS27A RPS27B RPS28A RPS28B RPS29B
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Transcription blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#111 - 120 )
RPS3 RPS30A RPS30B RPS31 RPS4A RPS4B RPS5 RPS6A RPS6B RPS7A
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Transcription blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#121 - 124 )
RPS7B RPS8B RPS9A RPS9B
Additional Literature blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball
Transcription blue ball blue ball blue ball blue ball

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