Analysis of transcription asymmetries along the tRNAE-COB operon: Evidence for transcription attenuation and rapid RNA degradation between coding sequences

Kirsten Krause, Carol L Dieckmann

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12 Citations (Scopus)

Abstract

Mitochondrial gene expression in yeast is believed to be regulated predominantly at the post-transcriptional level. However, the contribution of mitochondrial transcription and RNA-turnover rates to differential gene regulation is still largely unknown. Mitochondrial run-on transcription and hybrid selection assays showed that some of the multigenic transcription units of the mitochondrial genome are transcribed evenly, whereas others are transcribed asymmetrically, with higher transcription rates for promoter-proximal genes, than for promoter-distal genes. The tRNAE-cytochrome b (COB) operon was analyzed in detail to investigate the mechanisms underlying transcription rate asymmetries in yeast mitochondria. We showed that a drop in transcription rates occurs in a particular region between the coding sequences and is independent of the coding sequence of the downstream COB gene. Deletion of the region between tRNAE and COB coding sequences decreases the drop in transcription rates. Deletion of the nuclear gene encoding the Pet 127 protein, which is involved in mitochondrial RNA 5′ processing and degradation, also partially relieves transcriptional asymmetry. Therefore, asymmetry is probably due to a combination of attenuated transcription at specific sites between the coding sequences and very rapid RNA degradation.

Original languageEnglish (US)
Pages (from-to)6276-6283
Number of pages8
JournalNucleic Acids Research
Volume32
Issue number21
DOIs
StatePublished - 2004

Fingerprint

Cytochromes b
RNA Stability
Operon
Genes
Yeasts
Mitochondrial Genome
Mitochondrial Genes
Pets
Gene Deletion
Mitochondria
Gene Expression
Proteins
mitochondrial RNA

ASJC Scopus subject areas

  • Genetics

Cite this

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abstract = "Mitochondrial gene expression in yeast is believed to be regulated predominantly at the post-transcriptional level. However, the contribution of mitochondrial transcription and RNA-turnover rates to differential gene regulation is still largely unknown. Mitochondrial run-on transcription and hybrid selection assays showed that some of the multigenic transcription units of the mitochondrial genome are transcribed evenly, whereas others are transcribed asymmetrically, with higher transcription rates for promoter-proximal genes, than for promoter-distal genes. The tRNAE-cytochrome b (COB) operon was analyzed in detail to investigate the mechanisms underlying transcription rate asymmetries in yeast mitochondria. We showed that a drop in transcription rates occurs in a particular region between the coding sequences and is independent of the coding sequence of the downstream COB gene. Deletion of the region between tRNAE and COB coding sequences decreases the drop in transcription rates. Deletion of the nuclear gene encoding the Pet 127 protein, which is involved in mitochondrial RNA 5′ processing and degradation, also partially relieves transcriptional asymmetry. Therefore, asymmetry is probably due to a combination of attenuated transcription at specific sites between the coding sequences and very rapid RNA degradation.",
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AB - Mitochondrial gene expression in yeast is believed to be regulated predominantly at the post-transcriptional level. However, the contribution of mitochondrial transcription and RNA-turnover rates to differential gene regulation is still largely unknown. Mitochondrial run-on transcription and hybrid selection assays showed that some of the multigenic transcription units of the mitochondrial genome are transcribed evenly, whereas others are transcribed asymmetrically, with higher transcription rates for promoter-proximal genes, than for promoter-distal genes. The tRNAE-cytochrome b (COB) operon was analyzed in detail to investigate the mechanisms underlying transcription rate asymmetries in yeast mitochondria. We showed that a drop in transcription rates occurs in a particular region between the coding sequences and is independent of the coding sequence of the downstream COB gene. Deletion of the region between tRNAE and COB coding sequences decreases the drop in transcription rates. Deletion of the nuclear gene encoding the Pet 127 protein, which is involved in mitochondrial RNA 5′ processing and degradation, also partially relieves transcriptional asymmetry. Therefore, asymmetry is probably due to a combination of attenuated transcription at specific sites between the coding sequences and very rapid RNA degradation.

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