Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice

Lacombe, Séverine; Nagasaki, Hiroshi; Santi, Carole; Duval, David Timothy; Piégu, Benoît; Bangratz, Martine; Breitler, Jean‐Christophe; Guiderdoni, Emmanuel; Brugidou, Christophe; Hirsch, Judith; Cao, Xiaofeng; Brice, Claire; Panaud, Olivier; Karłowski, Wojciech M.; Satō, Yutaka; Echeverrı́a, Manuel

doi:10.1186/1471-2229-8-123

Cited by 47 publications

(42 citation statements)

References 52 publications

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“…On the other hand, we obtained more than one precursor for the miRNAs 482, 159 etc. as reported in rice [34]. In addition, we observed single precursor gave rise to two distinct miRNAs.…”

Section: Discussionsupporting

confidence: 59%

Deciphering microRNAs and Their Associated Hairpin Precursors in a Non-Model Plant, <em>Abelmoschus esculentus</em>

Kumar

Srikakulam

Padbhanabhan

et al. 2017

Preprint

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MicroRNAs (miRNAs) are crucial regulatory RNAs, originated from hairpin precursors. For the past decade, researchers are focusing extensively on miRNA profiles in various plants. However studies on precursor miRNAs (pre-miRNAs) global profiling stay static even in model plants. Here, for the first time in a non-model plant, Abelmoschus esculentus with negligible genome information, we are reporting the global profiling to characterize the miRNAs and their associated pre-miRNAs by applying next generation sequencing approach. Preliminarily we performed sRNA (small RNA) sequencing with five biological replicates of leaf samples to attain 207,285,863 reads and data analysis using miRPlant keyed out 128 known and 845 novel miRNA candidates. With the objective to seize their associated hairpin precursors, we accomplished pre-miRNA sequencing to attain 83,269,844 reads. The paired end reads are merged, adaptor trimmed and the resulting 40-241 nt (nucleotide) sequences were picked out for analysis by using perl scripts from miRGrep tool and in-house built shell script for Minimum Fold Energy Index (MFEI) calculation. Applying stringent criteria of dicer cleavage pattern and perfect stem loop structure revealed precursors for 57 known miRNAs of 15 families and 18 novel miRNAs. Quantitative Real Time (qRT) PCR was performed to determine the expression of selected miRNAs.

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“…On the other hand, we obtained more than one precursor for the miRNAs 482, 159 etc. as reported in rice [34]. In addition, we observed single precursor gave rise to two distinct miRNAs.…”

Section: Discussionsupporting

confidence: 59%

Deciphering microRNAs and Their Associated Hairpin Precursors in a Non-Model Plant, <em>Abelmoschus esculentus</em>

Kumar

Srikakulam

Padbhanabhan

et al. 2017

Preprint

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“…antisense-miR444 loci were found in our data (see Supplemental Table 3 online). Precursors of the miR159/319 family are relatively long, and it has been proposed that miR159a generates an additional miRNA, miR159a.2, from same arm of a precursor (Lacombe et al, 2008). We found that miR159c, miR159f, miR319a, and miR319b loci also produce other miRNAs that are similar to miR159a.2 in sequence, and we designated them as miR159cf.2, miR319a.2, and miR319b.2.…”

Section: Evaluation Of Annotated Mirnasmentioning

confidence: 87%

Massive Analysis of Rice Small RNAs: Mechanistic Implications of Regulated MicroRNAs and Variants for Differential Target RNA Cleavage

et al. 2011

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Small RNAs have a variety of important roles in plant development, stress responses, and other processes. They exert their influence by guiding mRNA cleavage, translational repression, and chromatin modification. To identify previously unknown rice (Oryza sativa) microRNAs (miRNAs) and those regulated by environmental stress, 62 small RNA libraries were constructed from rice plants and used for deep sequencing with Illumina technology. The libraries represent several tissues from control plants and plants subjected to different environmental stress treatments. More than 94 million genomematched reads were obtained, resulting in more than 16 million distinct small RNA sequences. This allowed an evaluation of ;400 annotated miRNAs with current criteria and the finding that among these, ;150 had small interfering RNA-like characteristics. Seventy-six new miRNAs were found, and miRNAs regulated in response to water stress, nutrient stress, or temperature stress were identified. Among the new examples of miRNA regulation were members of the same miRNA family that were differentially regulated in different organs and had distinct sequences Some of these distinct family members result in differential target cleavage and provide new insight about how an agriculturally important rice phenotype could be regulated in the panicle. This high-resolution analysis of rice miRNAs should be relevant to plant miRNAs in general, particularly in the Poaceae.

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“…japonica) (Goff et al, 2002;Yu et al, 2002). Small RNAs have also been extensively discovered in rice Jones-Rhoades and Bartel, 2004;Sunkar and Zhu, 2004;Liu et al, 2005;Sunkar et al, 2005;Luo et al, 2006;Lacombe et al, 2008;Lu et al, 2008;Zhu et al, 2008;Johnson et al, 2009;Xue et al, 2009). However, rice small RNA targets were mainly predicted via computational approaches, and only a small proportion of targets have been validated experimentally (Sunkar and Zhu, 2004;Sunkar et al, 2005;Yang et al, 2006;Liu et al, 2007a;Lacombe et al, 2008;Lu et al, 2008;Zhu et al, 2008;Liu et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)

Zhou

et al. 2010

Front. Biol.

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159

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MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA (sRNA) targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). One hundred and seventy-seven transcripts targeted by a total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORs (ARFs) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligasemediated 5′ rapid amplification of cDNA ends (RLM 5′-RACE). Our degradome results present a detailed sRNAtarget interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice.

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Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice

Cited by 47 publications

References 52 publications

Deciphering microRNAs and Their Associated Hairpin Precursors in a Non-Model Plant, <em>Abelmoschus esculentus</em>

Deciphering microRNAs and Their Associated Hairpin Precursors in a Non-Model Plant, <em>Abelmoschus esculentus</em>

Massive Analysis of Rice Small RNAs: Mechanistic Implications of Regulated MicroRNAs and Variants for Differential Target RNA Cleavage

Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)

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