Limits...
Temporal small RNA transcriptome profiling unraveled partitioned miRNA expression in developing maize endosperms between reciprocal crosses.

Xin M, Yang G, Yao Y, Peng H, Hu Z, Sun Q, Wang X, Ni Z - Front Plant Sci (2015)

Bottom Line: In addition, we found a subset of distinct tandem miRNAs are generated from a single stem-loop structure in maize that might be conserved in monocots.Furthermore, a SNP variation of Zma-miR408-5p at 11th base position was characterized between B73 and Mo17 which might lead to completely different functions in repressing targets.Together, this study suggests that miRNA plays a crucial role in regulating endosperm development, and exhibited distinct expression patterns in developing endosperm between maize reciprocal crosses.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University Beijing, China.

ABSTRACT
In angiosperms, the endosperm nurtures the embryo and provides nutrients for seed germination. To identify the expression pattern of small interfering RNA in the developing maize endosperm, we have performed high-throughput small RNA transcriptome sequencing of kernels at 0, 3, and 5 days after pollination (DAP) and endosperms at 7, 10, and 15 DAP using B73 and Mo17 reciprocal crosses in previous study. Here, we further explored these small RNA-seq data to investigate the potential roles of miRNAs in regulating the gene expression process. In total, 57 conserved miRNAs and 18 novel miRNAs were observed highly expressed in maize endosperm. Temporal expression profiling indicated that these miRNAs exhibited dynamic and partitioned expression patterns at different developmental stages between maize reciprocal crosses, and quantitative RT-PCR results further confirmed our observation. In addition, we found a subset of distinct tandem miRNAs are generated from a single stem-loop structure in maize that might be conserved in monocots. Furthermore, a SNP variation of Zma-miR408-5p at 11th base position was characterized between B73 and Mo17 which might lead to completely different functions in repressing targets. More interestingly, Zma-miR408-5p exhibited B73-biased expression pattern in the B73 and Mo17 reciprocal hybrid endosperms at 7, 10, and 15 DAP according to the reads abundance with SNPs and CAPS experiment. Together, this study suggests that miRNA plays a crucial role in regulating endosperm development, and exhibited distinct expression patterns in developing endosperm between maize reciprocal crosses.

No MeSH data available.


Related in: MedlinePlus

Biosynthesis and dynamic expression patterns of tandem miRNAs. (A) Stem-loop structures of tandem miRNAs. Zma-miR169&Zma-miR169.1, Zma-miR319 and Zma-miR319.1, Zma-miR2001 and Zma-miR2001.1, Zma-miR2013 and Zma-miR2013.1 were generated from a single precursor. (B) Varied expression patterns of Zma-miR319 and Zma-miR319.1 during kernel and endosperm developmental stages. (C) Dynamically changed expression patterns of Zma-miR169 and Zma-miR169.1 during kernel and endosperm developmental stages. (D) Temporal expression patterns of Zma-miR169 and Zma-miR169.1 during kernel and endosperm developmental stages. (E) Development-dependent expression patterns of Zma-miR2001 and Zma-miR2001.1 during kernel and endosperm developmental stages.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4584948&req=5

Figure 5: Biosynthesis and dynamic expression patterns of tandem miRNAs. (A) Stem-loop structures of tandem miRNAs. Zma-miR169&Zma-miR169.1, Zma-miR319 and Zma-miR319.1, Zma-miR2001 and Zma-miR2001.1, Zma-miR2013 and Zma-miR2013.1 were generated from a single precursor. (B) Varied expression patterns of Zma-miR319 and Zma-miR319.1 during kernel and endosperm developmental stages. (C) Dynamically changed expression patterns of Zma-miR169 and Zma-miR169.1 during kernel and endosperm developmental stages. (D) Temporal expression patterns of Zma-miR169 and Zma-miR169.1 during kernel and endosperm developmental stages. (E) Development-dependent expression patterns of Zma-miR2001 and Zma-miR2001.1 during kernel and endosperm developmental stages.

Mentions: Recent analyses of massive amounts of data from high-throughput sequencing have identified subclasses of miRNA species derived from alternative biogenesis pathways except for the canonical miRNAs, including NAT-miRNA, miRtron, snoRNA-derived, and tRNA-derived miRNA (Miyoshi et al., 2010). In this study, we identified a group of miRNAs termed tandem miRNAs which were co-generated from a single hairpin locus. For example, in addition to Zma-miR319 and Zma-miR319*, their precursor also produces another pair of miRNA-like that were closer to the loop structure compared to Zma-miR319, these are defined as Zma-miR319.1 and Zma-miR319.1*, respectively (Figure 5A). Similarly, the precursor of Zma-miR169 also yields an accompanying miRNA (Zma-miR169.1), although its Zma-miR169.1* was not detected, possibly due to a relatively low expression level (Figure 5A). In addition, of the newly identified maize miRNAs, Zma-miR2001.1, and Zma-miR2013.1 were also detected during developing maize endosperm (Figure 5A). Interestingly, the precursors of five members of the miR159 family all exhibited this tandem miRNA expression pattern including Zma-miR159a, Zma-miR159b, Zma-miR159f, and Zma-miR159j/k (Figure S1A). Moreover, a previous study has reported that tandem miR159.1 and miR159.2 were co-produced in rice and its relatives (Lacombe et al., 2008), which raised an intriguing question of their evolution in plant species. Thus, we next examined the conservation of miR159 precursors among maize, rice, wheat, and barley, and surprisingly, that they all produced tandem miRNAs, although with several mismatches in miR159.1 among different species (Figure S1B). To summarize, tandem miRNA expression manner is evolutionarily conserved at least in monocots.


Temporal small RNA transcriptome profiling unraveled partitioned miRNA expression in developing maize endosperms between reciprocal crosses.

Xin M, Yang G, Yao Y, Peng H, Hu Z, Sun Q, Wang X, Ni Z - Front Plant Sci (2015)

Biosynthesis and dynamic expression patterns of tandem miRNAs. (A) Stem-loop structures of tandem miRNAs. Zma-miR169&Zma-miR169.1, Zma-miR319 and Zma-miR319.1, Zma-miR2001 and Zma-miR2001.1, Zma-miR2013 and Zma-miR2013.1 were generated from a single precursor. (B) Varied expression patterns of Zma-miR319 and Zma-miR319.1 during kernel and endosperm developmental stages. (C) Dynamically changed expression patterns of Zma-miR169 and Zma-miR169.1 during kernel and endosperm developmental stages. (D) Temporal expression patterns of Zma-miR169 and Zma-miR169.1 during kernel and endosperm developmental stages. (E) Development-dependent expression patterns of Zma-miR2001 and Zma-miR2001.1 during kernel and endosperm developmental stages.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4584948&req=5

Figure 5: Biosynthesis and dynamic expression patterns of tandem miRNAs. (A) Stem-loop structures of tandem miRNAs. Zma-miR169&Zma-miR169.1, Zma-miR319 and Zma-miR319.1, Zma-miR2001 and Zma-miR2001.1, Zma-miR2013 and Zma-miR2013.1 were generated from a single precursor. (B) Varied expression patterns of Zma-miR319 and Zma-miR319.1 during kernel and endosperm developmental stages. (C) Dynamically changed expression patterns of Zma-miR169 and Zma-miR169.1 during kernel and endosperm developmental stages. (D) Temporal expression patterns of Zma-miR169 and Zma-miR169.1 during kernel and endosperm developmental stages. (E) Development-dependent expression patterns of Zma-miR2001 and Zma-miR2001.1 during kernel and endosperm developmental stages.
Mentions: Recent analyses of massive amounts of data from high-throughput sequencing have identified subclasses of miRNA species derived from alternative biogenesis pathways except for the canonical miRNAs, including NAT-miRNA, miRtron, snoRNA-derived, and tRNA-derived miRNA (Miyoshi et al., 2010). In this study, we identified a group of miRNAs termed tandem miRNAs which were co-generated from a single hairpin locus. For example, in addition to Zma-miR319 and Zma-miR319*, their precursor also produces another pair of miRNA-like that were closer to the loop structure compared to Zma-miR319, these are defined as Zma-miR319.1 and Zma-miR319.1*, respectively (Figure 5A). Similarly, the precursor of Zma-miR169 also yields an accompanying miRNA (Zma-miR169.1), although its Zma-miR169.1* was not detected, possibly due to a relatively low expression level (Figure 5A). In addition, of the newly identified maize miRNAs, Zma-miR2001.1, and Zma-miR2013.1 were also detected during developing maize endosperm (Figure 5A). Interestingly, the precursors of five members of the miR159 family all exhibited this tandem miRNA expression pattern including Zma-miR159a, Zma-miR159b, Zma-miR159f, and Zma-miR159j/k (Figure S1A). Moreover, a previous study has reported that tandem miR159.1 and miR159.2 were co-produced in rice and its relatives (Lacombe et al., 2008), which raised an intriguing question of their evolution in plant species. Thus, we next examined the conservation of miR159 precursors among maize, rice, wheat, and barley, and surprisingly, that they all produced tandem miRNAs, although with several mismatches in miR159.1 among different species (Figure S1B). To summarize, tandem miRNA expression manner is evolutionarily conserved at least in monocots.

Bottom Line: In addition, we found a subset of distinct tandem miRNAs are generated from a single stem-loop structure in maize that might be conserved in monocots.Furthermore, a SNP variation of Zma-miR408-5p at 11th base position was characterized between B73 and Mo17 which might lead to completely different functions in repressing targets.Together, this study suggests that miRNA plays a crucial role in regulating endosperm development, and exhibited distinct expression patterns in developing endosperm between maize reciprocal crosses.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University Beijing, China.

ABSTRACT
In angiosperms, the endosperm nurtures the embryo and provides nutrients for seed germination. To identify the expression pattern of small interfering RNA in the developing maize endosperm, we have performed high-throughput small RNA transcriptome sequencing of kernels at 0, 3, and 5 days after pollination (DAP) and endosperms at 7, 10, and 15 DAP using B73 and Mo17 reciprocal crosses in previous study. Here, we further explored these small RNA-seq data to investigate the potential roles of miRNAs in regulating the gene expression process. In total, 57 conserved miRNAs and 18 novel miRNAs were observed highly expressed in maize endosperm. Temporal expression profiling indicated that these miRNAs exhibited dynamic and partitioned expression patterns at different developmental stages between maize reciprocal crosses, and quantitative RT-PCR results further confirmed our observation. In addition, we found a subset of distinct tandem miRNAs are generated from a single stem-loop structure in maize that might be conserved in monocots. Furthermore, a SNP variation of Zma-miR408-5p at 11th base position was characterized between B73 and Mo17 which might lead to completely different functions in repressing targets. More interestingly, Zma-miR408-5p exhibited B73-biased expression pattern in the B73 and Mo17 reciprocal hybrid endosperms at 7, 10, and 15 DAP according to the reads abundance with SNPs and CAPS experiment. Together, this study suggests that miRNA plays a crucial role in regulating endosperm development, and exhibited distinct expression patterns in developing endosperm between maize reciprocal crosses.

No MeSH data available.


Related in: MedlinePlus