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. 2017 Aug 28;37(18):e00154-17.
doi: 10.1128/MCB.00154-17. Print 2017 Sep 15.

Yeast RNA-Binding Protein Nab3 Regulates Genes Involved in Nitrogen Metabolism

Affiliations

Yeast RNA-Binding Protein Nab3 Regulates Genes Involved in Nitrogen Metabolism

Jonathan Merran et al. Mol Cell Biol. .

Abstract

Termination of Saccharomyces cerevisiae RNA polymerase II (Pol II) transcripts occurs through two alternative pathways. Termination of mRNAs is coupled to cleavage and polyadenylation while noncoding transcripts are terminated through the Nrd1-Nab3-Sen1 (NNS) pathway in a process that is linked to RNA degradation by the nuclear exosome. Some mRNA transcripts are also attenuated through premature termination directed by the NNS complex. In this paper we present the results of nuclear depletion of the NNS component Nab3. As expected, many noncoding RNAs fail to terminate properly. In addition, we observe that nitrogen catabolite-repressed genes are upregulated by Nab3 depletion.

Keywords: nitrogen metabolism; noncoding RNA; termination; transcription.

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Figures

FIG 1
FIG 1
Readthrough of ncRNA transcripts. (A) Pol II maps of mutant and control NAB3 strains on an snoRNA (SNR47) and the attenuated NRD1 gene. The gray track represents reads from the control strain, while the superimposed black track represents Pol II reads from the NAB3-FRB strain with (+rap) or without nuclear depletion. (B) Anchor plot (67) showing readthrough of snoRNA terminators. (C) Volcano plot showing readthrough of CUTs. (D) Pol II and Nab3 maps of mRNAs regulated by Nab3. rap, rapamycin.
FIG 2
FIG 2
Nab3 depletion changes expression of relatively few genes. (A) Rank order plot of changes in expression of protein coding genes after Nab3 depletion. Genes are ranked from left to right in order of increased expression upon Nab3 depletion. (B) Pol II map showing the increase in expression of GLT1 but no change in adjacent genes.
FIG 3
FIG 3
Increased expression of nitrogen catabolite-repressed genes. (A) The left panel is derived from the Nab3 anchor-away experiment, while the right panel is derived from the Nrd1 anchor-away experiment. Both panels show enrichment plots derived from GSEA analysis. In this analysis genes are rank ordered from left to right in order of their ratio of Pol II occupancy. The enrichment score is a running sum of enrichment of the NCR genes. (B) Venn diagram showing overlap of genes upregulated in response to either Nab3 or Nrd1 depletion.
FIG 4
FIG 4
Increased expression of nitrogen catabolite-repressed genes. Pol II and Nab3 binding maps showing examples of Nab3-regulated NCR genes.
FIG 5
FIG 5
Nab3 and Nrd1 binding regulates NCR gene expression. (A) Logos corresponding to known Nrd1 and Nab3 binding sites derived from sequences in the top Nab3 binding peaks identified on NCR transcripts. (B) Mapping Nrd1 and Nab3 binding sites in the GLT1 5′ UTR. (C) Reverse transcription-quantitative PCR of luciferase RNA driven by the Glt1 promoter as indicated in panel B. (D) Reverse transcription-quantitative PCR of the endogenous GLT1 gene in NAB3 and nab3-11 strains.
FIG 6
FIG 6
Growth of NAB3-FRB and control strain in the presence or absence of 0.5 mM MSX.

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