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Profile of small RNA transcriptome during cortical development in the Rat

ABSTRACT: Small non-coding RNAs play important roles in regulating gene expression during development and disease. However, a comprehensive analysis of small RNAs in developing brain is largely lacking. By using next-generation sequencing technique, we carried out a systematic analysis of small RNA transcriptome of rat neocortex from early developmental stage till adult. Our results revealed an extraordinary degree of stage-specific profiling of miRNA, and other classes of small RNAs including snoRNA, rasRNA, scRNA and unexpectedly piRNA, which was considered to be solely expressed in germline tissues. Developmentally regulated miRNA editing was also observed. This study further showed the effectiveness of the high through-put sequencing in genome-wide analysis of small RNAs. The dataset described here will greatly contribute to our understanding of the divergence, variation, and function of small RNAs and may be a valuable resource in clarifying new regulatory mechanisms of cortical development.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE27576 | GEO | 2012/06/26

SECONDARY ACCESSION(S): PRJNA138383

REPOSITORIES: GEO

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Profile of small RNA transcriptome during cortical development in the Rat

Project description:Small non-coding RNAs play important roles in regulating gene expression during development and disease. However, a comprehensive analysis of small RNAs in developing brain is largely lacking. By using next-generation sequencing technique, we carried out a systematic analysis of small RNA transcriptome of rat neocortex from early developmental stage till adult. Our results revealed an extraordinary degree of stage-specific profiling of miRNA, and other classes of small RNAs including snoRNA, rasRNA, scRNA and unexpectedly piRNA, which was considered to be solely expressed in germline tissues. Developmentally regulated miRNA editing was also observed. This study further showed the effectiveness of the high through-put sequencing in genome-wide analysis of small RNAs. The dataset described here will greatly contribute to our understanding of the divergence, variation, and function of small RNAs and may be a valuable resource in clarifying new regulatory mechanisms of cortical development. Identification and quantification of small RNA: forebrain and cortex from E10 to P28

2012-06-25 | E-GEOD-27576 | biostudies-arrayexpress

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Project description:As the fetal heart develops, cardiomyocyte proliferation potential decreases while fatty acid oxidative capacity increases, a highly regulated transition known as cardiac maturation. Small noncoding RNAs, such as microRNAs (miRNAs), contribute to the establishment and control of tissue-specific transcriptional programs. However, small RNA expression dynamics and genome wide miRNA regulatory networks controlling maturation of the human fetal heart remain poorly understood. Transcriptome profiling of small RNAs revealed the temporal expression patterns of miRNA, piRNA, circRNA, snoRNA, snRNA and tRNA in the developing human heart between 8 and 19 weeks of gestation. Our analysis revealed that miRNAs were the most dynamically expressed small RNA species throughout mid-gestation. Cross-referencing differentially expressed miRNAs and mRNAs predicted 6,200 mRNA targets, 2134 of which were upregulated and 4066 downregulated as gestation progresses. Moreover, we found that downregulated targets of upregulated miRNAs predominantly control cell cycle progression, while upregulated targets of downregulated miRNAs are linked to energy sensing and oxidative metabolism. Furthermore, integration of miRNA and mRNA profiles with proteomes and reporter metabolites revealed that proteins encoded in mRNA targets, and their associated metabolites, mediate fatty acid oxidation and are enriched as the heart develops.This study revealed the small RNAome of the maturing human fetal heart. Furthermore, our findings suggest that coordinated activation and repression of miRNA expression throughout mid-gestation is essential to establish a dynamic miRNA-mRNA-protein network that decreases cardiomyocyte proliferation potential while increasing the oxidative capacity of the maturing human fetal heart.

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Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing

Project description:Background: In recent years, a variety of small RNAs derived from other RNAs with well-known functions such as tRNAs and snoRNAs, have been identified. The functional relevance of these RNAs is largely unknown. To gain insight into the complexity of snoRNA processing and the functional relevance of snoRNA-derived small RNAs, we sequenced long and short RNAs, small RNAs that co-precipitate with the Argonaute 2 protein and RNA fragments obtained in photoreactive nucleotide-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of core snoRNA-associated proteins. Results: Analysis of these data sets revealed that many loci in the human genome reproducibly give rise to C/D box-like snoRNAs, whose expression and evolutionary conservation are typically less pronounced relative to the snoRNAs that are currently catalogued. We further found that virtually all C/D box snoRNAs are specifically processed inside the regions of terminal complementarity, retaining in the mature form only 4-5 nucleotides upstream of the C box and 2-5 nucleotides downstream of the D box. Sequencing of the total and Argonaute 2-associated populations of small RNAs revealed that despite their cellular abundance, C/D box-derived small RNAs are not efficiently incorporated into the Ago2 protein. Conclusions: We conclude that the human genome encodes a large number of snoRNAs that are processed along the canonical pathway and expressed at relatively low levels. Generation of snoRNA-derived processing products with alternative, particularly miRNA-like, functions appears to be uncommon. PAR-CLIP profiling for snoRNP core proteins NOP56, NOP58, Fibrillarin, and Dyskerin in HEK293 cells. Small RNA profiling using RNA-seq in HEK293 and HeLa cells, small RNA profiling using IP-seq of Ago2 associated small RNAs.

2013-05-08 | E-GEOD-43666 | biostudies-arrayexpress

Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing

2013-05-08 | GSE43666 | GEO

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Project description:Small RNAs were deep sequenced from the liver and spleen of adult mice in an effort to identify somatic piRNAs. Following sequencing of all small RNAs, known non-coding RNAs were computationally removed from the dataset. The remaining RNAs were then mapped to the genome and analyzed for sequence characteristics (5' base, length) typical of known piRNAs. To determine if any of the identified small RNAs were MIWI2 dependent, we deep sequenced small RNAs from liver and spleen of MIWI2 KO mice and analyzed them as above. We deep sequenced small RNAs from the liver and spleen of one WT mouse and one MIWI2 knock-out mouse. We then trimmed sequencing adapters and removed known ncRNAs (rRNA, tRNA, snoRNA, snRNA, miRNA) from the dataset before aligning reads to the mm9 assembly of the mouse genome.

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Project description:small RNA seq form Hek 293 using IonTorrent Sequencing; To assess the general expression of snoRNA derived miRNA like fragments in Hek293. Three independent small RNA libraries were sequenced, aligned and subset for snoRNA (C/D, H/ACA, Small Cajal bodies); analysis of read-length for individual snoRNAs was used to define fragments, then to define coherent processing or degradation of the fragments the location of individual reads over the snoRNA annotation was define.

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Small Nucleolar RNAs in the Dlk1-Gtl2 Imprinting Locus Maintains LT-HSC Self-renewal by Regulation of rRNA Modification and Translation [ncRNA-seq]

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NOP10 predicts NSCLC prognosis and its associated small nucleolar RNAs drive proliferation and migration [ncRNA-seq]

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