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The Roles of Arabidopsis CDF2 in Transcriptional and Posttranscriptional Regulation of Primary MicroRNAs.

Sun Z, Guo T, Liu Y, Liu Q, Fang Y - PLoS Genet. (2015)

Bottom Line: CDF2 binds directly to the promoters of some miRNAs and works as a transcription activator or repressor for these miRNA genes.CDF2 binds preferentially to the pri-miRNAs regulated by itself and affects DCL1-mediated processing of these pri-miRNAs.We conclude that CDF2 regulates a group of pri-miRNAs at both the transcriptional and posttranscriptional levels to maintain proper levels of their mature miRNAs to control plant development.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

ABSTRACT
The precise regulation of microRNA (miRNA) transcription and processing is important for eukaryotic development. Plant miRNAs are first transcribed as stem-loop primary miRNAs (pri-miRNAs) by RNA polymerase II,then cleaved in the nucleus into mature miRNAs by Dicer-like 1 (DCL1). We identified a cycling DOF transcription factor, CDF2, which interacts with DCL1 and regulates the accumulation of a population of miRNAs. CDF2 binds directly to the promoters of some miRNAs and works as a transcription activator or repressor for these miRNA genes. CDF2 binds preferentially to the pri-miRNAs regulated by itself and affects DCL1-mediated processing of these pri-miRNAs. Genetically, CDF2 works in the same pathway as miR156 or miR172 to control flowering. We conclude that CDF2 regulates a group of pri-miRNAs at both the transcriptional and posttranscriptional levels to maintain proper levels of their mature miRNAs to control plant development.

No MeSH data available.


CDF2 is required for the accumulation of a group of miRNAs.(A) Comparision of miRNAs that are differently expressed in 22-day-old plant of Col and cdf2 mutant. (B) Northern blots show the levels of miRNAs in seedlings of Col and cdf2 mutant. U6 serves as a loading control.
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pgen.1005598.g002: CDF2 is required for the accumulation of a group of miRNAs.(A) Comparision of miRNAs that are differently expressed in 22-day-old plant of Col and cdf2 mutant. (B) Northern blots show the levels of miRNAs in seedlings of Col and cdf2 mutant. U6 serves as a loading control.

Mentions: As CDF2 interacts with the microprocessor DCL1/HYL1, we then investigated if miRNAs are regulated by CDF2. To this end, we applied high-throughput sequencing to analyze the global miRNAs in 22-day-old plants of Col and cdf2, using dcl1-9 mutant as a control. Totally, 114,892,98, 123,492,11 and 130,812,02 reads were obtained from WT, cdf2 and dcl1-9, and 13,233,29 (54.98%), 24,975,74 (75.97%) and 11,882,21 (53.42%) reads, representing 7,275,87, 18,973,61 and 6,346,98 distinct sequences, respectively, matched the Arabidopsis genome. The sequencing data for all known miRNAs were subjected to hierarchical clustering in an unsupervised manner to analyze the extent of differential miRNAs [27] (Figs 2A and S4, S1 and S2 Tables). At least 1.5-fold changes in the levels were observed for 72 of 195 miRNAs detected in both Col and the cdf2 mutant. Among these, 52 (72%) were significantly downregulated, whereas 20 (28%) were upregulated. The small RNA-seq results were validated by northern blotting of miR156, miR319, miR167, miR172, miR160, miR165, miR170, and miR171 repressed or activated by CDF2, respectively (Figs 2B and S5A). In contrast, almost all of the miRNAs are downregulated in dcl1-9 mutant (S4 Fig, S2 Table). To minimize the potential effect of different developmental stages between Col and cdf2 mutant on the interpretation of our data, we performed northern blots using inflorescences of Col, cdf2 and pCDF2::CDF2-HA/cdf2, which was generated by crossing of cdf2 mutant with the pCDF2::CDF2-HA/Col line. We found that the expressional levels of these miRNAs are similar to those in 22-day-old seedlings. In addition, the pCDF2::CDF2-HA/cdf2 line restored the phenotypes and miRNAs levels of cdf2 mutant (S2B and S5B Figs), Taking together, we concluded that CDF2 regulates biogenesis of a population of miRNAs.


The Roles of Arabidopsis CDF2 in Transcriptional and Posttranscriptional Regulation of Primary MicroRNAs.

Sun Z, Guo T, Liu Y, Liu Q, Fang Y - PLoS Genet. (2015)

CDF2 is required for the accumulation of a group of miRNAs.(A) Comparision of miRNAs that are differently expressed in 22-day-old plant of Col and cdf2 mutant. (B) Northern blots show the levels of miRNAs in seedlings of Col and cdf2 mutant. U6 serves as a loading control.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4608766&req=5

pgen.1005598.g002: CDF2 is required for the accumulation of a group of miRNAs.(A) Comparision of miRNAs that are differently expressed in 22-day-old plant of Col and cdf2 mutant. (B) Northern blots show the levels of miRNAs in seedlings of Col and cdf2 mutant. U6 serves as a loading control.
Mentions: As CDF2 interacts with the microprocessor DCL1/HYL1, we then investigated if miRNAs are regulated by CDF2. To this end, we applied high-throughput sequencing to analyze the global miRNAs in 22-day-old plants of Col and cdf2, using dcl1-9 mutant as a control. Totally, 114,892,98, 123,492,11 and 130,812,02 reads were obtained from WT, cdf2 and dcl1-9, and 13,233,29 (54.98%), 24,975,74 (75.97%) and 11,882,21 (53.42%) reads, representing 7,275,87, 18,973,61 and 6,346,98 distinct sequences, respectively, matched the Arabidopsis genome. The sequencing data for all known miRNAs were subjected to hierarchical clustering in an unsupervised manner to analyze the extent of differential miRNAs [27] (Figs 2A and S4, S1 and S2 Tables). At least 1.5-fold changes in the levels were observed for 72 of 195 miRNAs detected in both Col and the cdf2 mutant. Among these, 52 (72%) were significantly downregulated, whereas 20 (28%) were upregulated. The small RNA-seq results were validated by northern blotting of miR156, miR319, miR167, miR172, miR160, miR165, miR170, and miR171 repressed or activated by CDF2, respectively (Figs 2B and S5A). In contrast, almost all of the miRNAs are downregulated in dcl1-9 mutant (S4 Fig, S2 Table). To minimize the potential effect of different developmental stages between Col and cdf2 mutant on the interpretation of our data, we performed northern blots using inflorescences of Col, cdf2 and pCDF2::CDF2-HA/cdf2, which was generated by crossing of cdf2 mutant with the pCDF2::CDF2-HA/Col line. We found that the expressional levels of these miRNAs are similar to those in 22-day-old seedlings. In addition, the pCDF2::CDF2-HA/cdf2 line restored the phenotypes and miRNAs levels of cdf2 mutant (S2B and S5B Figs), Taking together, we concluded that CDF2 regulates biogenesis of a population of miRNAs.

Bottom Line: CDF2 binds directly to the promoters of some miRNAs and works as a transcription activator or repressor for these miRNA genes.CDF2 binds preferentially to the pri-miRNAs regulated by itself and affects DCL1-mediated processing of these pri-miRNAs.We conclude that CDF2 regulates a group of pri-miRNAs at both the transcriptional and posttranscriptional levels to maintain proper levels of their mature miRNAs to control plant development.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

ABSTRACT
The precise regulation of microRNA (miRNA) transcription and processing is important for eukaryotic development. Plant miRNAs are first transcribed as stem-loop primary miRNAs (pri-miRNAs) by RNA polymerase II,then cleaved in the nucleus into mature miRNAs by Dicer-like 1 (DCL1). We identified a cycling DOF transcription factor, CDF2, which interacts with DCL1 and regulates the accumulation of a population of miRNAs. CDF2 binds directly to the promoters of some miRNAs and works as a transcription activator or repressor for these miRNA genes. CDF2 binds preferentially to the pri-miRNAs regulated by itself and affects DCL1-mediated processing of these pri-miRNAs. Genetically, CDF2 works in the same pathway as miR156 or miR172 to control flowering. We conclude that CDF2 regulates a group of pri-miRNAs at both the transcriptional and posttranscriptional levels to maintain proper levels of their mature miRNAs to control plant development.

No MeSH data available.