Target-Enrichment Sequencing for Detailed Characterization of Small RNAs
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE102845 | GEO | 2017/08/22
SECONDARY ACCESSION(S): PRJNA399091
REPOSITORIES: GEO
Similar Datasets
Project description:Small RNAs (sRNAs) play important roles in plants encountering stress environments. However, limited research has been conducted on the sRNAs involved in plant wound responses. To identify potential roles for the wounding-related sRNAs, sRNA deep sequencing was used. After leaves were wounded for 0.5 hour, total RNAs from unwounded and wounded leaves were isolated for sRNA library construction. The Illumina platform was used to sequence sRNA libraries. About 12 million sequence reads were obtained for each sample.
2016-04-26 | GSE46457 | GEO
Project description:RNA silencing is a mechanism for regulating gene expression at the transcriptional and post-transcriptional levels. Its functions include regulating endogenous gene expression and protecting the cell against viruses and invading transposable elements (TEs). A key component of the mechanism is small RNAs (sRNAs) of 21-24 nucleotides (nt) in length, which direct the silencing machinery in a sequence specific manner to target nucleic acids. sRNAs of 24 nt are involved in methylation of cytosine residues of target loci in three sequence contexts (CG, CHG and CHH), referred to as RNA-directed DNA methylation (RdDM). We previously demonstrated that 24 nt sRNAs are mobile from shoot to root in Arabidopsis thaliana. In this study we demonstrated that methylation of thousands of loci in root tissues is dependent upon mobile sRNAs from the shoot. Furthermore, we found that mobile sRNA-dependent DNA methylation occurs predominantly in non-CG contexts. These findings were made using base-resolution next generation sequencing approaches and genome wide analyses. Specific classes of short TEs are the predominant targets of mobile sRNA-dependent DNA methylation; classes typically found in gene-rich euchromatic regions. Mobile sRNA-regulated genes were also identified. Mechanistically, we demonstrate that mobile sRNA-dependent non-CG methylation is largely independent of the CMT2/3 RdDM pathway but dependent upon the DRM1/DRM2 RdDM pathway. This is in contrast to non-mobile sRNA-dependent DNA methylation, which predominantly depends upon the CMT2/3 RdDM pathway. These data are complementary to the small RNA sequencing data from Arabidopsis root grafts described in Molnar et al (Science, 2010 May 14;328(5980):872-5).
2016-01-04 | E-MTAB-3473 | biostudies-arrayexpress
Project description:In Oxytricha, the somatic genome is responsible for vegetative growth, while the germline contributes DNA to the next sexual generation. Somatic nuclear development eliminates all transposons and other so-called "junk DNA", which constitute ~95% of the germline. We demonstrate that Piwi-interacting small RNAs (piRNAs) from the maternal nucleus can specify genomic regions for retention in this process. Oxytricha piRNAs map primarily to the somatic genome, representing the ~5% of the germline that is retained. Furthermore, injection of synthetic piRNAs corresponding to normally-deleted regions leads to their retention in subsequent generations. Our findings highlight small RNAs (sRNAs) as powerful transgenerational carriers of epigenetic information for genome programming. The backcross study here shows that the mating between an IES+ strain with the wild-type stain produces corresponding IES-containing sRNAs at 19 hr, and we provided the mapping to and the sequences of the specific loci of interest in the submission. As a control, wild-type cells do not produce such IES-containing sRNAs, and this analysis can be pulled out from the GSE35018 study since we provided mapping to the whole genome. The purpose of the 20 hr total sRNA sequencing study here is to show that the class of 27 nt sRNA is the major species of total sRNAs in Oxytricha at 20 hr, which we sequenced previously from Otiwi1-associated sRNAs at 12, 19, 23, and 30 hr (GSE35018). In addition, there is a less abundant class of small RNAs of 21-22 nt. These two classes are obvious by simply plotting the length distribution of the sRNA sequences. We sequenced sRNAs from Contig22226.0 IES1+ strain backcrossed to wild-type parental strain at 19hr post-mixing, and found corresponding IES-containing sRNAs. As a control, wild-type cells do not produce such IES-containing sRNAs (see GSE35018). Total RNA from the backcrossing at 19hr were isolated with mirVana small RNA extraction kit (Ambion), and directly used for making Illumina sRNA libraries. Oxytricha total small RNA (sRNA) sequencing at 20 hr post conjugation shows that a class of 27 nt, 5'-U sRNAs dominates the sRNA population at 20 hr, and this class of sRNAs associate with Otiwi1 (see GSE35018 for Otiwi1-interacting sRNAs in Oxytricha). In addition, a much less abundant class of 21-22 nt sRNAs is present according to the length distribution.
2012-09-01 | E-GEOD-40081 | biostudies-arrayexpress
Project description:To investigate the roles of sRNAs in keeping embryo dormancy or germination in Larix leptolepis, we deciphered the endogenous "sRNAome" in dormant and germinated embryos. High-throughput sequencing of the sRNA libraries showed that dormant embryos exhibited a length bias towards 24-nt, while germinated embryos showed a bias towards a 21-nt and/or 22-nt length. Both of proportions for miRNAs to the non-redundant and redundant sRNAs were higher in germinated embryos than those in dormant embryos, while the ratio of unknown sRNAs was higher in dormant embryos than in germinated embryos. The proportion of 21-nt and 22-nt sRNAs increased in germinated embryos, which might attribute to the higher expression level of miRNAs. We identified a total of 160 conserved miRNAs from 39 families, 16 novel miRNAs, and 14 plausible miRNA candidates, of which novel and non-conserved known miRNAs might be the main contributors. These findings indicate that larch and possibly other gymnosperms have complex mechanisms of gene regulation involving sRNAs and miRNAs operating transcriptionally and post-transcriptionally during embryo dormancy and germination. One embryogenic cell line of Japanese larch (Larix leptolepis), designated as D878, with a high embryo maturation capacity was used in this study. Embryogenic callus were induced from immature embryos of larch on induction medium, followed by sub-culture, and culture on ABA-containing mature medium in a dark environment at 25 2 C. After cultured 45 days in mature medium, embryogenic calli developed into mature somatic embryos. In our study, the samples were harvested at day 57, one sample was collected after mature embryos continued to stay for 12 days on ABA-containing medium, and the other one was harvested after cultured for 12 days on ABA-removing medium. All samples were snap-frozen in liquid nitrogen, and stored in liquid nitrogen until RNA extraction.
2014-07-19 | E-GEOD-49059 | biostudies-arrayexpress
Project description:PAZ/PIWI-domain (PPD) proteins carrying small RNAs (sRNAs) function in gene and genome regulation. The ciliate Tetrahymena thermophila encodes numerous PPD proteins exclusively of the Piwi clade. We show that the three Tetrahymena Piwi-family proteins (Twis) preferentially expressed in growing cells differ in their genetic essentiality and subcellular localization. Affinity purification of all eight distinct Twi proteins revealed unique properties of their bound sRNAs. Deep sequencing of Twi-bound and total sRNAs in strains disrupted for various silencing machinery uncovered an unanticipated diversity of 23-24 nt sRNA classes in growing cells, each with distinct genetic requirements for accumulation. Altogether Twis distinguish sRNAs derived from loci of pseudogene families, three types of DNA repeats, structured RNAs, and EST-supported loci with convergent or paralogous transcripts. Most surprisingly, Twi7 binds complementary strands of unequal length while Twi10 binds a specific permutation of the guanosine-rich telomeric repeat. These studies greatly expand the structural and functional repertoire of endogenous sRNAs and RNPs. 11 libraries were analyzed. 5 are total sRNA (from knockout strains or WT background strains), and 6 are Argonaute-bound sRNA
2009-11-23 | E-GEOD-17006 | biostudies-arrayexpress
Project description:Motivation: Most computational tools for small non-coding RNAs (sRNA) sequencing data analysis focus in microRNAs (miRNAs), overlooking other types of sRNAs that show multi-mapping hits. Here, we have developed a pipeline to non-redundantly quantify all types of sRNAs, and extract patterns of expression in biologically defined groups. We have used our tool to characterize and profile sRNAs in post-mortem brain samples of control individuals and Parkinson’s disease (PD) cases at early-premotor and late-symptomatic stages.Results: Clusters of co-expressed sRNAs mapping onto tRNAs significantly separated premotor and motor cases from controls. A similar result was obtained using a matrix of miRNAs slightly varying in sequence (isomiRs). The present framework revealed sRNA alterations at premotor stages of PD, which might reflect initial pathogenic perturbations. This tool may be useful to discover sRNA expression patterns linked to different biological conditions.
2017-04-01 | GSE97285 | GEO
Project description:We identified twin small non-coding RNAs regulating tricarboxylic acid (TCA) cycle activity in Neisseria meningitidis. Expression of TCA cycle enzymes was elevated in sRNA deletion mutants. Direct interaction between sRNAs and the ribosomal entry sites on target mRNAs was demonstrated. Expression of the sRNAs was down-regulated in cells grown in poor medium with glucose as the sole carbon source but not without lrp, indicating that sRNA expression is controlled by the stringent response. N. meningitidis, over-expressing the sRNAs replicated in blood, but not in human cerebrospinal fluid. In addition, Lrp synthesis was inhibited by direct interaction between the sRNA and the 5’ UTR of lrp. sRNAs control adaptation of N. meningitidis to variation in nutrient supply in different niches of its host.
2017-03-22 | PXD000891 | Pride
Project description:Next-generation Illumina sequencing technology was used to analyze small RNA associated with post-transcriptional gene silencing induced by intron-spliced hairpin RNA (ihpRNA) in Arabidopsis. The experimental induction of RNA silencing in plants often involves expression of transgenes encoding inverted repeat (IR) sequences to produce abundant dsRNAs that are processed into small RNAs (sRNAs). These sRNAs are key mediators of post-transcriptional gene silencing (PTGS) and determine the specificity of the inhibition of gene expression. Despite its broad utility as a research tool, IR-PTGS is only a partially understood mechanism of RNA silencing in plants. We generated four sets of 60 Arabidopsis plants, each containing IR transgenes expressing different configurations of uidA and CHALCONE SYNTHASE (CHS) gene fragments. The levels of PTGS were dependent on the orientation and position of the fragment in the IR construct. To investigate these differences, we characterized the sRNA profiles by Illumina sequencing of seven libraries generated from transgenic families showing different levels of IR-PTGS. Mapping of sRNA sequences to their corresponding transgene-derived and endogenous transcripts identified distinctive patterns of differential sRNA accumulation. Analyses of these patterns and peaks revealed similarities among sRNAs associated with IR-PTGS and endogenous sRNAs linked to uncapped mRNA decay. We also found unexpected associations between sRNA accumulation and the presence of predicted open reading frames in the trigger sequence. Our observations provide new guidelines for designing constructs to increase the efficiency of IR-PTGS. In addition, strong IR-PTGS affected the prevalence of endogenous sRNAs, which has implications for the use of PTGS for experimental or applied purposes. Sequencing of small RNA from Arabidopsis plants transformed with ihpRNA constructs. Seven small RNA libraries were sequenced: Lib 0, made from non-transgenic Arabidopsis plants, and Libs 1-6, made from plants transformed with different configurations of ihpRNA.
2012-06-26 | E-GEOD-38922 | biostudies-arrayexpress
Project description:Methicillin resistant Staphylococcus aureus (MRSA) is an infectious pathogen that poses a significant threat to human health. MRSA is renowned for its ability to adapt to and even thrive in hostile environment within its host. By expressing a battery of virulence factors and toxins, MRSA is able to scavenge effectively essential nutrients and evade the immune system within the host. Post-transcriptional regulation by sRNAs contributes significantly to regulating the expression of virulence factors and toxins. However, the roles of the vast majority of sRNAs during host adaptation remain unknown. To challenge this gap, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) in S. aureus to unravel sRNA-RNA interactions with the double stranded ribonuclease III (RNase III) as a bait under conditions that mimic the host environment. Here we report a global analysis of RNA-RNA interactions in MRSA in vivo, which uncovered hundreds of novel sRNA-RNA pairs. Strikingly, our results indicate that the production of small membrane-permeabilizing toxins is under extensive sRNA-mediated regulation and that their expression is intimately connected to metabolism. We show that at least two sRNAs, RNAIII and RsaE, enhance the production of five clinically relevant cytolytic toxins that are important for survival within the host. Taken together, our data greatly expands the repertoire of sRNA-target interactions in S. aureus and provide detail on how these contribute to adjusting virulence in response to changes in metabolism.
2022-06-16 | PXD025122 | Pride
Project description:Emerging evidence indicates that extracellular vesicles, particularly exosomes, play a role in several biological processes and actively contribute to cancer development and progression, by carrying and delivering proteins, transcripts and small RNAs (sRNAs). We profiled by RNA-seq the sRNA content of circulating exosomes of 20 pediatric patients with Anaplastic Large Cell Lymphoma (ALCL), 5 healthy controls and of 5 ALCL cell lines. Our analysis disclosed that non-miRNA derived sRNAs constitute the prominent fraction of sRNA loaded in exosomes. A fragment of RNY4 was the most abundant of 180 sRNAs significantly enriched in exosomes of ALCL patients compared to controls. Further investigation by qRT-PCR of RNY4 fragments and full-length sequence disclosed that the latter is massively loaded into exosomes of ALCL patients with more advanced and aggressive disease. Since recent findings supported a role of RNY4 in the modulation of tumor microenvironment, our data open new possibilities to understand how tumor derived exosomes can facilitate disease spread in ALCL patients.
2020-02-21 | GSE144781 | GEO