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Genome-wide analysis for rice small RNAs by MPSS

ABSTRACT: Small RNAs (21-24 nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently ~240 miRNAs have been annotated. We sequenced more than four million small RNAs from rice and identified another 24 miRNA genes. Among these, we found a novel class of miRNAs that derive from natural cis-antisense transcript pairs. This configuration generates miRNAs that can perfectly match their targets. We provide evidence that the miRNAs function by inducing mRNA cleavage in the middle of their complementary site. Their production requires DCL1 activity, which is essential for canonical miRNA biogenesis. All of the nat-miRNAs identified in this study have large introns in their precursors that appear critical for nat-miRNA evolution and for the formation of functional miRNA loci. These findings suggest that other natural cis-antisense loci with similar exon-intron arrangements could be another source of miRNA genes Keywords: small RNA sequencing by MPSS

ORGANISM(S): Oryza sativa

PROVIDER: GSE10523 | GEO | 2008/02/15

SECONDARY ACCESSION(S): PRJNA107871

REPOSITORIES: GEO

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Genome-wide analysis for rice small RNAs by MPSS

Project description:Small RNAs (21-24 nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently ~240 miRNAs have been annotated. We sequenced more than four million small RNAs from rice and identified another 24 miRNA genes. Among these, we found a novel class of miRNAs that derive from natural cis-antisense transcript pairs. This configuration generates miRNAs that can perfectly match their targets. We provide evidence that the miRNAs function by inducing mRNA cleavage in the middle of their complementary site. Their production requires DCL1 activity, which is essential for canonical miRNA biogenesis. All of the nat-miRNAs identified in this study have large introns in their precursors that appear critical for nat-miRNA evolution and for the formation of functional miRNA loci. These findings suggest that other natural cis-antisense loci with similar exon-intron arrangements could be another source of miRNA genes Six rice samples are included in this study. They are 1) immature panicles, 2) germinating seedlings (control for Magnaporthe treatment), 3) germinating seedlings infected with Magnaporthe grisea,4)stems, 5) three-week-old seedlings (control for ABA treatment), 6) three-week-old seedlings treated with ABA.

2008-02-14 | E-GEOD-10523 | biostudies-arrayexpress

A quantitative map of human primary microRNA processing sites

Project description:Maturation of canonical microRNA (miRNA) is initiated by DROSHA that cleaves the primary transcript (pri-miRNA). Over 1,800 miRNA loci are annotated in humans, but it remains largely unknown if and at which sites the pri-miRNAs are cleaved by DROSHA. Here we performed in vitro processing on a full set of human pri-miRNAs (miRBase v21) followed by sequencing. This comprehensive profiling enabled us to classify miRNAs based on DROSHA-dependence and map their cleavage sites with respective processing efficiency measures. Only 758 pri-miRNAs are confidently processed by DROSHA, while the majority may be non-canonical or false entries. Analyses of the DROSHA-dependent pri-miRNAs show key cis-elements for processing. We observe widespread alternative processing as well as unproductive cleavage events such as “nick” or “inverse” processing. SRSF3 is a broad-acting auxiliary factor modulating alternative processing and suppressing unproductive processing. The profiling data and methods developed in this study will allow systematic analyses of miRNA regulation.

2021-07-28 | PXD025767 | Pride

Small RNA identification in Arabidopsis thaliana using modified MPSS

Project description:Small RNAs play important regulatory roles in most eukaryotes but only a small proportion of these molecules have been identified. We sequenced more than two million small RNAs from seedlings and the inflorescence of the model plant Arabidopsis thaliana. Known and new miRNAs were among the most abundant of the non-redundant set of more than 75,000 sequences, whereas more than half represented lower abundance small-interfering RNAs (siRNAs) that match repetitive sequences, intergenic regions, and genes. Individual or clusters of highly-regulated small RNAs were readily observed. Targets of antisense RNA or miRNA did not appear to be preferentially associated with siRNAs. Many genomic regions previously considered featureless were found to be sites of numerous small RNAs. Keywords: small RNA identification , modified MPSS

2005-09-02 | GSE3008 | GEO

Small RNA identification in Arabidopsis thaliana using modified MPSS

2005-09-02 | E-GEOD-3008 | biostudies-arrayexpress

Massive analysis of rice small RNAs: Mechanistic implications of regulated miRNAs and variants for differential target RNA cleavage

Project description:Small RNAs have 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 novel and regulated rice miRNAs, 62 small RNA libraries were constructed from rice plants and deeply sequenced with Illumina technology. The libraries represent several tissues from control plants and plants subjected to different environmental stress treatments. More than 94 million genome-matched reads were obtained resulting in more than 16 million distinct small RNA sequences. This allowed an evaluation with current criteria of about 400 annotated miRNAs and the finding that among these, about 150 had siRNA-like characteristics. Seventy nine new miRNAs were identified and miRNAs were distinguished that are regulated in response to water stress, nutrient stress, or temperature stress. 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 controlled in the panicle. This high resolution analysis of rice miRNAs should be relevant to plant miRNAs in general, particularly in the Poaceae. Examination of different tissue types and tissues treated with various environmental and nutrient stresses in rice by high throughput sequencing for small RNA profiling

2011-12-12 | E-GEOD-32973 | biostudies-arrayexpress

Small RNAs from 4-week old seedling of Oryza sativa

Project description:In order to identify new miRNAs, NAT-siRNAs and possibly abiotic-stress regulated small RNAs in rice, three small RNA libraries were constructed from control rice seedlings and seedlings exposed to drought or salt stress, and then subjected to pyrosequencing.

2008-12-08 | GSE12317 | GEO

rice ssRNA-seq

Project description:We took advantage of ssRNA-seq technology to deeply sequence mRNAs of the model plant species Oryza sativa ssp.japonica cv Nipponbare with clear transcriptional orientations for assessing rice cis-NATs at the best possible resolution. We also deeply sequenced rice small RNAs from the same tissues as that for preparing mRNAs to investigate rice cis-NAT pairs that potentially give rise to endogenous short interfering RNAs from their overlapping regions under normal and stress conditions.

2011-12-28 | E-MTAB-721 | biostudies-arrayexpress

Massive analysis of rice small RNAs: Mechanistic implications of regulated miRNAs and variants for differential target RNA cleavage

2011-12-12 | GSE32973 | GEO

Genome-wide profiling of small RNAs in rice under abiotic stresses

Project description:To identify novel miRNA and NAT-siRNAs that are associated with abiotic stresses in rice, we generated small RNA sequences from inflorescences from rice under control and under dought, salt, and cold stress treatments. Over 30 million reads were generated.

2012-03-12 | GSE26357 | GEO

A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains

Project description:Endogenous small RNAs, including microRNAs (miRNAs) and short-interfering RNAs (siRNAs), function as posttranscriptional or transcriptional regulators in plants. miRNA function is essential for normal development and therefore likely to be important in the growth of the rice grain. To investigate the likely roles of miRNAs in rice grain development we carried out deep sequencing of the small RNA populations of rice grains. A total of 96,091 (including 23,867 reads from vegetative tissues) and 5,379,724 small RNA sequences that are longer than 17nt were generated. Approximately 94% of these small RNAs were 20-24nt in length. The majority of the small RNAs were singletons, indicating that rice genome has a very complex small RNA population, which is harder to be saturated. From these smal RNA sequences we found representatives of all 20 conserved plant miRNA families and evidence for changes in expression of miRNAs during rice grain development. Using an approach based on the presence of the miRNA and miRNA* sequences, we identified 51 novel, non-conserved rice miRNA families expressed in grains with functionally diverse predicted target genes. miRNA-guided cleavage was confirmed for a number of targets genes including ones with roles in sugar signalling and restoration of cytoplasmic male sterility. We identified a likely mirtron, indicating that plants can also use spliced introns as a source of miRNAs. Our sequencing results revealed four TAS3 loci; these all contain dual miR390 sites of which only the 3? site is cleaved. We also found a miRNA-like long hairpin generating phased 21nt small RNAs, strongly expressed in developing grains and show that these small RNAs act in trans to cleave target mRNAs. Keywords: high throughput pyrosequencing, small RNA, microRNA, grain development, rice

2008-08-21 | GSE11014 | GEO

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