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Identification of novel post-transcriptional features in olfactory receptor family mRNAs.

Shum EY, Espinoza JL, Ramaiah M, Wilkinson MF - Nucleic Acids Res. (2015)

Bottom Line: Using RNA-seq analysis coupled with analysis of pre-existing databases, we found that Olfr mRNAs have several atypical features suggesting that post-transcriptional regulation impacts their expression.All of these novel properties correlated with higher Olfr expression.Together, our results suggest that the Olfr gene family has encountered unusual selective forces in neural cells that have driven them to acquire unique post-transcriptional regulatory features.

View Article: PubMed Central - PubMed

Affiliation: Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA.

No MeSH data available.


Related in: MedlinePlus

Olfr mRNAs are ARE-rich. (A) ARE pentamer density measured in silico. (B) Density distribution plot of the number of AUUUA ARE pentamers, assessed as in panel (A). (C) Scatterplots and linear regression analysis of expression level versus AUUUA pentamer density, assessed as in panel A. (D) Schematic of luciferase and renilla reporters used. (E,F) Two Olfr 3′ UTRs influence mRNA steady-state level and mRNA half-life in response to CCR4B depletion (using a siRNA targeting CCR4B [siCcr4b]) and CCR4B overexpression (using a CCR4B expression vector). Panel E is measurement of relative mRNA levels (RQ) and panel (F) is measurement of relative luciferase values (RLU). *P < 0.05; n.s. not significant.
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Figure 5: Olfr mRNAs are ARE-rich. (A) ARE pentamer density measured in silico. (B) Density distribution plot of the number of AUUUA ARE pentamers, assessed as in panel (A). (C) Scatterplots and linear regression analysis of expression level versus AUUUA pentamer density, assessed as in panel A. (D) Schematic of luciferase and renilla reporters used. (E,F) Two Olfr 3′ UTRs influence mRNA steady-state level and mRNA half-life in response to CCR4B depletion (using a siRNA targeting CCR4B [siCcr4b]) and CCR4B overexpression (using a CCR4B expression vector). Panel E is measurement of relative mRNA levels (RQ) and panel (F) is measurement of relative luciferase values (RLU). *P < 0.05; n.s. not significant.

Mentions: AREs have been computationally defined in mammalian transcriptomes and deposited in several databases, including ARED and AREsite (32,67). However, these databases do not contain most Olfr mRNAs, including those annotated recently (28). Our annotation of Olfr genes expressed in the mouse OE together with another data set provided an opportunity to fill this gap. We analyzed the average ARE density in Olfr mRNAs and found it is twice as high as in the Gpcr and Ctrl mRNA groups (Figure 5A, Supplementary Table S6). We found this to also be the case when we analyzed the recently defined Olfr mRNA data set from Ibarra-Soria et al. (28) (‘Olfr-B’ in Figure 5A). Given that Olfr mRNAs have much shorter average 3′ UTR length than these other groups (see below), this is consistent with the possibility that there has been strong selection pressure for enrichment of AREs to maintain regulation by ARE-binding proteins. The net result is that AREs are as prevalent in Olfr mRNAs as in the other gene groups (Figure 5B).


Identification of novel post-transcriptional features in olfactory receptor family mRNAs.

Shum EY, Espinoza JL, Ramaiah M, Wilkinson MF - Nucleic Acids Res. (2015)

Olfr mRNAs are ARE-rich. (A) ARE pentamer density measured in silico. (B) Density distribution plot of the number of AUUUA ARE pentamers, assessed as in panel (A). (C) Scatterplots and linear regression analysis of expression level versus AUUUA pentamer density, assessed as in panel A. (D) Schematic of luciferase and renilla reporters used. (E,F) Two Olfr 3′ UTRs influence mRNA steady-state level and mRNA half-life in response to CCR4B depletion (using a siRNA targeting CCR4B [siCcr4b]) and CCR4B overexpression (using a CCR4B expression vector). Panel E is measurement of relative mRNA levels (RQ) and panel (F) is measurement of relative luciferase values (RLU). *P < 0.05; n.s. not significant.
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Figure 5: Olfr mRNAs are ARE-rich. (A) ARE pentamer density measured in silico. (B) Density distribution plot of the number of AUUUA ARE pentamers, assessed as in panel (A). (C) Scatterplots and linear regression analysis of expression level versus AUUUA pentamer density, assessed as in panel A. (D) Schematic of luciferase and renilla reporters used. (E,F) Two Olfr 3′ UTRs influence mRNA steady-state level and mRNA half-life in response to CCR4B depletion (using a siRNA targeting CCR4B [siCcr4b]) and CCR4B overexpression (using a CCR4B expression vector). Panel E is measurement of relative mRNA levels (RQ) and panel (F) is measurement of relative luciferase values (RLU). *P < 0.05; n.s. not significant.
Mentions: AREs have been computationally defined in mammalian transcriptomes and deposited in several databases, including ARED and AREsite (32,67). However, these databases do not contain most Olfr mRNAs, including those annotated recently (28). Our annotation of Olfr genes expressed in the mouse OE together with another data set provided an opportunity to fill this gap. We analyzed the average ARE density in Olfr mRNAs and found it is twice as high as in the Gpcr and Ctrl mRNA groups (Figure 5A, Supplementary Table S6). We found this to also be the case when we analyzed the recently defined Olfr mRNA data set from Ibarra-Soria et al. (28) (‘Olfr-B’ in Figure 5A). Given that Olfr mRNAs have much shorter average 3′ UTR length than these other groups (see below), this is consistent with the possibility that there has been strong selection pressure for enrichment of AREs to maintain regulation by ARE-binding proteins. The net result is that AREs are as prevalent in Olfr mRNAs as in the other gene groups (Figure 5B).

Bottom Line: Using RNA-seq analysis coupled with analysis of pre-existing databases, we found that Olfr mRNAs have several atypical features suggesting that post-transcriptional regulation impacts their expression.All of these novel properties correlated with higher Olfr expression.Together, our results suggest that the Olfr gene family has encountered unusual selective forces in neural cells that have driven them to acquire unique post-transcriptional regulatory features.

View Article: PubMed Central - PubMed

Affiliation: Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA.

No MeSH data available.


Related in: MedlinePlus