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A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver. | LitMetric

AI Article Synopsis

  • Research using ChIP-seq in human and mouse cells has shown that only about 40% of human tRNA genes are occupied by RNA polymerase III (RNAP-III), often found in regions with active RNAP-II transcription.
  • In the mouse liver, RNAP-III binding sites include a conserved repeat that may regulate RNAP-III subunit gene expression, linking tRNA gene occupancy to genomic variations and relationships between mouse and human genes.
  • Factors like A and B promoter box variations and terminator strength significantly influence RNAP-III occupancy, with findings indicating that 50% of annotated mouse tRNA genes are occupied, reflecting conserved genomic organization between different cell types.

Article Abstract

The genomic loci occupied by RNA polymerase (RNAP) III have been characterized in human culture cells by genome-wide chromatin immunoprecipitations, followed by deep sequencing (ChIP-seq). These studies have shown that only ∼40% of the annotated 622 human tRNA genes and pseudogenes are occupied by RNAP-III, and that these genes are often in open chromatin regions rich in active RNAP-II transcription units. We have used ChIP-seq to characterize RNAP-III-occupied loci in a differentiated tissue, the mouse liver. Our studies define the mouse liver RNAP-III-occupied loci including a conserved mammalian interspersed repeat (MIR) as a potential regulator of an RNAP-III subunit-encoding gene. They reveal that synteny relationships can be established between a number of human and mouse RNAP-III genes, and that the expression levels of these genes are significantly linked. They establish that variations within the A and B promoter boxes, as well as the strength of the terminator sequence, can strongly affect RNAP-III occupancy of tRNA genes. They reveal correlations with various genomic features that explain the observed variation of 81% of tRNA scores. In mouse liver, loci represented in the NCBI37/mm9 genome assembly that are clearly occupied by RNAP-III comprise 50 Rn5s (5S RNA) genes, 14 known non-tRNA RNAP-III genes, nine Rn4.5s (4.5S RNA) genes, and 29 SINEs. Moreover, out of the 433 annotated tRNA genes, half are occupied by RNAP-III. Transfer RNA gene expression levels reflect both an underlying genomic organization conserved in dividing human culture cells and resting mouse liver cells, and the particular promoter and terminator strengths of individual genes.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3317149PMC
http://dx.doi.org/10.1101/gr.130286.111DOI Listing

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