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Global analysis of uncapped mRNA changes under drought stress and microRNA-dependent endonucleolytic cleavages in foxtail millet.

Yi F, Chen J, Yu J - BMC Plant Biol. (2015)

Bottom Line: Beauv.).Finally, we found 11 C4 photosynthesis-related enzymes encoded by drought-responsive genes.In addition, PARE analysis identified many miRNA targets and revealed miRNA-precursor processing modes in foxtail millet.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. yifei56@cau.edu.cn.

ABSTRACT

Background: mRNA degradation plays an important role in the determination of mRNA abundance and can quickly regulate gene expression. The production of uncapped mRNAs, an important mechanism of mRNA degradation, can be initiated by decapping enzymes, endonucleases or small RNAs such as microRNAs (miRNAs). Little is known, however, about the role of uncapped mRNAs in plants under environmental stress.

Results: Using a novel approach called parallel analysis of RNA ends (PARE), we performed a global study of uncapped mRNAs under drought stress in foxtail millet (Setaria italica [L.] P. Beauv.). When both gene degradation (PARE) and gene transcription (RNA-sequencing) data were considered, four types of mRNA decay patterns were identified under drought stress. In addition, 385 miRNA-target interactions were identified in the PARE data using PAREsnip. The PARE analysis also suggested that two miRNA hairpin processing mechanisms--loop-last and loop-first processing--operate in foxtail millet, with both miR319 and miR156 gene families undergoing precise processing via the unusual loop-first mechanism. Finally, we found 11 C4 photosynthesis-related enzymes encoded by drought-responsive genes.

Conclusions: We performed a global analysis of mRNA degradation under drought stress and uncovered diverse drought-response mechanisms in foxtail millet. This information will deepen our understanding of mRNA expression under stressful environmental conditions in gramineous plants. In addition, PARE analysis identified many miRNA targets and revealed miRNA-precursor processing modes in foxtail millet.

No MeSH data available.


Related in: MedlinePlus

Gene transcript features and sequence motifs contributing to different mRNA decay patterns. a-d A display of mRNA length, 5′ UTR length, 3' UTR length and number of introns for different gene types. “I”, “II”, “IV”, “R” and “A” represent type-I, −II, −IV, randomly selected genes and all genes, respectively. “***” indicates statistically significant difference at P-value < 0.001 (Student’s wilcox-test). e-h Enriched motifs (E-value < 0.001) in the 5' UTRs of type-I (e), type-II (f and g) and type-IV (h) genes
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Fig2: Gene transcript features and sequence motifs contributing to different mRNA decay patterns. a-d A display of mRNA length, 5′ UTR length, 3' UTR length and number of introns for different gene types. “I”, “II”, “IV”, “R” and “A” represent type-I, −II, −IV, randomly selected genes and all genes, respectively. “***” indicates statistically significant difference at P-value < 0.001 (Student’s wilcox-test). e-h Enriched motifs (E-value < 0.001) in the 5' UTRs of type-I (e), type-II (f and g) and type-IV (h) genes

Mentions: Sequence characteristics have been reported to contribute to uncapped mRNA abundance [15, 16]. To reveal the characteristics of mRNAs with different decay patterns, we calculated the mRNA lengths, GC contents, minimal folding free energy indexes (MFEIs) [54] of secondary structures, untranslated region (UTR) lengths and intron numbers for type-I, −II and -IV genes (Fig. 2 and Additional file 6). The results showed that the mean lengths of 5′ UTRs, 3′ UTRs and mRNAs of type-I, −II and -IV genes were significantly greater (P < 0.001) than those of all genes and 898 (average number of I, II and IV genes) randomly selected genes (Fig. 2a–c). Moreover, the mean MFEI values of 5′ UTRs, 3′ UTRs and mRNAs of type-I, −II and -IV genes were significantly lower than those of all genes and randomly selected genes (Additional file 6). In contrast, no significant differences were found for the mean GC contents of 5′ UTRs and 3′ UTRs among these gene groups (Additional file 6). Overall, the lengths and MFEIs of UTRs and mRNAs correlated with the structural features of genes involved in the drought response.Fig. 2


Global analysis of uncapped mRNA changes under drought stress and microRNA-dependent endonucleolytic cleavages in foxtail millet.

Yi F, Chen J, Yu J - BMC Plant Biol. (2015)

Gene transcript features and sequence motifs contributing to different mRNA decay patterns. a-d A display of mRNA length, 5′ UTR length, 3' UTR length and number of introns for different gene types. “I”, “II”, “IV”, “R” and “A” represent type-I, −II, −IV, randomly selected genes and all genes, respectively. “***” indicates statistically significant difference at P-value < 0.001 (Student’s wilcox-test). e-h Enriched motifs (E-value < 0.001) in the 5' UTRs of type-I (e), type-II (f and g) and type-IV (h) genes
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4594888&req=5

Fig2: Gene transcript features and sequence motifs contributing to different mRNA decay patterns. a-d A display of mRNA length, 5′ UTR length, 3' UTR length and number of introns for different gene types. “I”, “II”, “IV”, “R” and “A” represent type-I, −II, −IV, randomly selected genes and all genes, respectively. “***” indicates statistically significant difference at P-value < 0.001 (Student’s wilcox-test). e-h Enriched motifs (E-value < 0.001) in the 5' UTRs of type-I (e), type-II (f and g) and type-IV (h) genes
Mentions: Sequence characteristics have been reported to contribute to uncapped mRNA abundance [15, 16]. To reveal the characteristics of mRNAs with different decay patterns, we calculated the mRNA lengths, GC contents, minimal folding free energy indexes (MFEIs) [54] of secondary structures, untranslated region (UTR) lengths and intron numbers for type-I, −II and -IV genes (Fig. 2 and Additional file 6). The results showed that the mean lengths of 5′ UTRs, 3′ UTRs and mRNAs of type-I, −II and -IV genes were significantly greater (P < 0.001) than those of all genes and 898 (average number of I, II and IV genes) randomly selected genes (Fig. 2a–c). Moreover, the mean MFEI values of 5′ UTRs, 3′ UTRs and mRNAs of type-I, −II and -IV genes were significantly lower than those of all genes and randomly selected genes (Additional file 6). In contrast, no significant differences were found for the mean GC contents of 5′ UTRs and 3′ UTRs among these gene groups (Additional file 6). Overall, the lengths and MFEIs of UTRs and mRNAs correlated with the structural features of genes involved in the drought response.Fig. 2

Bottom Line: Beauv.).Finally, we found 11 C4 photosynthesis-related enzymes encoded by drought-responsive genes.In addition, PARE analysis identified many miRNA targets and revealed miRNA-precursor processing modes in foxtail millet.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. yifei56@cau.edu.cn.

ABSTRACT

Background: mRNA degradation plays an important role in the determination of mRNA abundance and can quickly regulate gene expression. The production of uncapped mRNAs, an important mechanism of mRNA degradation, can be initiated by decapping enzymes, endonucleases or small RNAs such as microRNAs (miRNAs). Little is known, however, about the role of uncapped mRNAs in plants under environmental stress.

Results: Using a novel approach called parallel analysis of RNA ends (PARE), we performed a global study of uncapped mRNAs under drought stress in foxtail millet (Setaria italica [L.] P. Beauv.). When both gene degradation (PARE) and gene transcription (RNA-sequencing) data were considered, four types of mRNA decay patterns were identified under drought stress. In addition, 385 miRNA-target interactions were identified in the PARE data using PAREsnip. The PARE analysis also suggested that two miRNA hairpin processing mechanisms--loop-last and loop-first processing--operate in foxtail millet, with both miR319 and miR156 gene families undergoing precise processing via the unusual loop-first mechanism. Finally, we found 11 C4 photosynthesis-related enzymes encoded by drought-responsive genes.

Conclusions: We performed a global analysis of mRNA degradation under drought stress and uncovered diverse drought-response mechanisms in foxtail millet. This information will deepen our understanding of mRNA expression under stressful environmental conditions in gramineous plants. In addition, PARE analysis identified many miRNA targets and revealed miRNA-precursor processing modes in foxtail millet.

No MeSH data available.


Related in: MedlinePlus