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Dynamic regulation of mRNA decay during neural development.

Burow DA, Umeh-Garcia MC, True MB, Bakhaj CD, Ardell DH, Cleary MD - Neural Dev (2015)

Bottom Line: A search for candidate cis-regulatory elements identified enrichment of the Pumilio recognition element (PRE) in mRNAs encoding regulators of neurogenesis.We found that decreased expression of the RNA-binding protein Pumilio stabilized predicted neural mRNA targets and that a PRE is necessary to trigger reporter-transcript decay in the nervous system.We found that Pumilio is one component of this network, revealing a novel function for this RNA-binding protein.

View Article: PubMed Central - PubMed

Affiliation: Quantitative and Systems Biology Graduate Program, University of California, 5200 N. Lake Rd, Merced, CA, USA. dburow@ucmerced.edu.

ABSTRACT

Background: Gene expression patterns are determined by rates of mRNA transcription and decay. While transcription is known to regulate many developmental processes, the role of mRNA decay is less extensively defined. A critical step toward defining the role of mRNA decay in neural development is to measure genome-wide mRNA decay rates in neural tissue. Such information should reveal the degree to which mRNA decay contributes to differential gene expression and provide a foundation for identifying regulatory mechanisms that affect neural mRNA decay.

Results: We developed a technique that allows genome-wide mRNA decay measurements in intact Drosophila embryos, across all tissues and specifically in the nervous system. Our approach revealed neural-specific decay kinetics, including stabilization of transcripts encoding regulators of axonogenesis and destabilization of transcripts encoding ribosomal proteins and histones. We also identified correlations between mRNA stability and physiologic properties of mRNAs; mRNAs that are predicted to be translated within axon growth cones or dendrites have long half-lives while mRNAs encoding transcription factors that regulate neurogenesis have short half-lives. A search for candidate cis-regulatory elements identified enrichment of the Pumilio recognition element (PRE) in mRNAs encoding regulators of neurogenesis. We found that decreased expression of the RNA-binding protein Pumilio stabilized predicted neural mRNA targets and that a PRE is necessary to trigger reporter-transcript decay in the nervous system.

Conclusions: We found that differential mRNA decay contributes to the relative abundance of transcripts involved in cell-fate decisions, axonogenesis, and other critical events during Drosophila neural development. Neural-specific decay kinetics and the functional specificity of mRNA decay suggest the existence of a dynamic neurodevelopmental mRNA decay network. We found that Pumilio is one component of this network, revealing a novel function for this RNA-binding protein.

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TU-decay measures genome-wide mRNA half-lives without transcription arrest. (A) Distribution of whole embryo mRNA half-lives based on uridine chase conditions (Uridine only) and uridine chase combined with actinomycin D to arrest transcription (Uridine + ActD). t1/2 = half-life. (B) Individual transcript decay curves based on the uridine-only and uridine + actD measurements. Chase times are plotted on the x-axis (0-hour = end of 1-hour pulse). Mean chase/pulse values are plotted at the 1-hour and 3-hour time points, and curves were fit using a single-order exponential decay equation. Error bars are standard deviation.
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Fig1: TU-decay measures genome-wide mRNA half-lives without transcription arrest. (A) Distribution of whole embryo mRNA half-lives based on uridine chase conditions (Uridine only) and uridine chase combined with actinomycin D to arrest transcription (Uridine + ActD). t1/2 = half-life. (B) Individual transcript decay curves based on the uridine-only and uridine + actD measurements. Chase times are plotted on the x-axis (0-hour = end of 1-hour pulse). Mean chase/pulse values are plotted at the 1-hour and 3-hour time points, and curves were fit using a single-order exponential decay equation. Error bars are standard deviation.

Mentions: The distribution of mRNA half-lives was similar for pulse-chase experiments performed with or without actD (Figure 1A), and decay kinetics for the majority of mRNAs were highly reproducible; only 11.6% of mRNAs had standard deviations in half-life ≥30% of the mean for that transcript. Many transcripts gave nearly identical results with or without actD in the chase media (Figure 1B), including orthologs of known mammalian high-stability mRNAs (for example, eIF4a [15]) and low-stability mRNAs (for example, Myc [16]). An additional indication of the reproducibility of these measurements is provided by gene ontology (GO) analysis of the UO and U + actD datasets. The top 1,000 most stable transcripts and the bottom 1,000 least stable transcripts from both datasets yielded very similar GO results (Additional file 3). Given the reproducibility and similarity of decay measurements obtained with or without actD, we conclude that TU-decay effectively measures mRNA decay without the need to use pharmacological inhibitors of RNA polymerase II or other methods of arresting transcription.Figure 1


Dynamic regulation of mRNA decay during neural development.

Burow DA, Umeh-Garcia MC, True MB, Bakhaj CD, Ardell DH, Cleary MD - Neural Dev (2015)

TU-decay measures genome-wide mRNA half-lives without transcription arrest. (A) Distribution of whole embryo mRNA half-lives based on uridine chase conditions (Uridine only) and uridine chase combined with actinomycin D to arrest transcription (Uridine + ActD). t1/2 = half-life. (B) Individual transcript decay curves based on the uridine-only and uridine + actD measurements. Chase times are plotted on the x-axis (0-hour = end of 1-hour pulse). Mean chase/pulse values are plotted at the 1-hour and 3-hour time points, and curves were fit using a single-order exponential decay equation. Error bars are standard deviation.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4413985&req=5

Fig1: TU-decay measures genome-wide mRNA half-lives without transcription arrest. (A) Distribution of whole embryo mRNA half-lives based on uridine chase conditions (Uridine only) and uridine chase combined with actinomycin D to arrest transcription (Uridine + ActD). t1/2 = half-life. (B) Individual transcript decay curves based on the uridine-only and uridine + actD measurements. Chase times are plotted on the x-axis (0-hour = end of 1-hour pulse). Mean chase/pulse values are plotted at the 1-hour and 3-hour time points, and curves were fit using a single-order exponential decay equation. Error bars are standard deviation.
Mentions: The distribution of mRNA half-lives was similar for pulse-chase experiments performed with or without actD (Figure 1A), and decay kinetics for the majority of mRNAs were highly reproducible; only 11.6% of mRNAs had standard deviations in half-life ≥30% of the mean for that transcript. Many transcripts gave nearly identical results with or without actD in the chase media (Figure 1B), including orthologs of known mammalian high-stability mRNAs (for example, eIF4a [15]) and low-stability mRNAs (for example, Myc [16]). An additional indication of the reproducibility of these measurements is provided by gene ontology (GO) analysis of the UO and U + actD datasets. The top 1,000 most stable transcripts and the bottom 1,000 least stable transcripts from both datasets yielded very similar GO results (Additional file 3). Given the reproducibility and similarity of decay measurements obtained with or without actD, we conclude that TU-decay effectively measures mRNA decay without the need to use pharmacological inhibitors of RNA polymerase II or other methods of arresting transcription.Figure 1

Bottom Line: A search for candidate cis-regulatory elements identified enrichment of the Pumilio recognition element (PRE) in mRNAs encoding regulators of neurogenesis.We found that decreased expression of the RNA-binding protein Pumilio stabilized predicted neural mRNA targets and that a PRE is necessary to trigger reporter-transcript decay in the nervous system.We found that Pumilio is one component of this network, revealing a novel function for this RNA-binding protein.

View Article: PubMed Central - PubMed

Affiliation: Quantitative and Systems Biology Graduate Program, University of California, 5200 N. Lake Rd, Merced, CA, USA. dburow@ucmerced.edu.

ABSTRACT

Background: Gene expression patterns are determined by rates of mRNA transcription and decay. While transcription is known to regulate many developmental processes, the role of mRNA decay is less extensively defined. A critical step toward defining the role of mRNA decay in neural development is to measure genome-wide mRNA decay rates in neural tissue. Such information should reveal the degree to which mRNA decay contributes to differential gene expression and provide a foundation for identifying regulatory mechanisms that affect neural mRNA decay.

Results: We developed a technique that allows genome-wide mRNA decay measurements in intact Drosophila embryos, across all tissues and specifically in the nervous system. Our approach revealed neural-specific decay kinetics, including stabilization of transcripts encoding regulators of axonogenesis and destabilization of transcripts encoding ribosomal proteins and histones. We also identified correlations between mRNA stability and physiologic properties of mRNAs; mRNAs that are predicted to be translated within axon growth cones or dendrites have long half-lives while mRNAs encoding transcription factors that regulate neurogenesis have short half-lives. A search for candidate cis-regulatory elements identified enrichment of the Pumilio recognition element (PRE) in mRNAs encoding regulators of neurogenesis. We found that decreased expression of the RNA-binding protein Pumilio stabilized predicted neural mRNA targets and that a PRE is necessary to trigger reporter-transcript decay in the nervous system.

Conclusions: We found that differential mRNA decay contributes to the relative abundance of transcripts involved in cell-fate decisions, axonogenesis, and other critical events during Drosophila neural development. Neural-specific decay kinetics and the functional specificity of mRNA decay suggest the existence of a dynamic neurodevelopmental mRNA decay network. We found that Pumilio is one component of this network, revealing a novel function for this RNA-binding protein.

Show MeSH
Related in: MedlinePlus