Transcriptome analyses of miRNA pathway mutants and injury response in developing and adult sciatic nerves
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE109075 | GEO | 2018/10/08
REPOSITORIES: GEO
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Project description:RNA sequencing was performed comparing sciatic nerves of Schwann cell specific DICER mutants with SC-specific DGCR8 and DROSHA mutants.
2018-10-08 | GSE64880 | GEO
Project description:We report RNA sequencing data from induced Schwann cell specific knockouts for DICER and DGCR8 as well as crush injured wild type animals. Induced deletion of DICER and DGCR8 results in expression of numerous injury response genes suggesting a requirement of those proteins in maintaining the myelinated Schwann cell fate.
2018-10-08 | GSE109074 | GEO
Project description:Canonical microRNAs (miRNAs) require two processing steps: the first by the Microprocessor, a complex of DGCR8 and Drosha, and the second by Dicer. dgcr8delta/delta mouse embryonic stem cells (mESCs) have less severe phenotypes than dicer1delta/delta mESCs, suggesting a physiological role for Microprocessor-independent, Dicer-dependent small RNAs. To identify these small RNAs with unusual biogenesis, we performed high-throughput sequencing from wild type, dgcr8delta/delta, and dicer1delta/delta mESCs. Several of the DGCR8-independent, Dicer-dependent RNAs were non-canonical miRNAs. These derived from mirtrons and a newly identified subclass of miRNA precursors, which appears to be the endogenous counterpart of short hairpin RNAs (shRNAs). Our analyses also revealed endogenous siRNAs resulting from Dicer cleavage of long hairpins, the vast majority of which originated from one genomic locus with tandem, inverted short interspersed nuclear elements (SINEs). Our results extend the known diversity of mammalian small-RNA generating pathways and show that mammalian siRNAs exist in tissues outside of oocytes. Small RNAs were sequenced from wt, dgcr8(-), and dicer(-) mouse ES cells and the frequencies of small RNA types compared between the three. This record includes Illumina-platform-generated datasets from all three samples and 454-platform-generated datasets from wt and dgcr8(-) samples. [raw data files are unavailable]
2008-09-09 | E-GEOD-12521 | biostudies-arrayexpress
Project description:Non-canonical microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) are distinct subclasses of small RNAs that bypass the DGCR8/Drosha Microprocessor but still require Dicer for their biogenesis. What, if any, role they have in mammals remains unknown. To identify potential roles for these Microprocessor-independent, Dicer-dependent small RNAs, we compared the phenotypes resulting from conditional deletion of dgcr8 versus dicer in post-mitotic neurons. Loss of dicer resulted in an earlier lethality, more severe structural abnormalities, and increased apoptosis relative to dgcr8 loss. Deep sequencing of small RNAs from the hippocampus and cortex of the conditional knockouts and control littermates identified multiple novel non-canonical microRNAs including new mirtrons H/ACA box snoRNA-derived small RNAs, and a previously unidentified mammalian subclass derived from C/D box snoRNAs. These non-canonical miRNAs were expressed at high levels in the brain relative to other tissues. In contrast, we found no evidence for endo-siRNAs in the brain. Taken together, our findings provide evidence for a diverse population of highly expressed non-canonical miRNAs that together play important functional roles in post-mitotic neurons. Examination of small RNA populations in the hippocampus and cortex of 2 conditional knockout and control littermates
2011-03-23 | E-GEOD-21090 | biostudies-arrayexpress
Project description:Canonical microRNAs (miRNAs) require two processing steps: the first by the Microprocessor, a complex of DGCR8 and Drosha, and the second by Dicer. dgcr8delta/delta mouse embryonic stem cells (mESCs) have less severe phenotypes than dicer1delta/delta mESCs, suggesting a physiological role for Microprocessor-independent, Dicer-dependent small RNAs. To identify these small RNAs with unusual biogenesis, we performed high-throughput sequencing from wild type, dgcr8delta/delta, and dicer1delta/delta mESCs. Several of the DGCR8-independent, Dicer-dependent RNAs were non-canonical miRNAs. These derived from mirtrons and a newly identified subclass of miRNA precursors, which appears to be the endogenous counterpart of short hairpin RNAs (shRNAs). Our analyses also revealed endogenous siRNAs resulting from Dicer cleavage of long hairpins, the vast majority of which originated from one genomic locus with tandem, inverted short interspersed nuclear elements (SINEs). Our results extend the known diversity of mammalian small-RNA generating pathways and show that mammalian siRNAs exist in tissues outside of oocytes.
2008-09-10 | GSE12521 | GEO
Project description:Non-canonical microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) are distinct subclasses of small RNAs that bypass the DGCR8/Drosha Microprocessor but still require Dicer for their biogenesis. What, if any, role they have in mammals remains unknown. To identify potential roles for these Microprocessor-independent, Dicer-dependent small RNAs, we compared the phenotypes resulting from conditional deletion of dgcr8 versus dicer in post-mitotic neurons. Loss of dicer resulted in an earlier lethality, more severe structural abnormalities, and increased apoptosis relative to dgcr8 loss. Deep sequencing of small RNAs from the hippocampus and cortex of the conditional knockouts and control littermates identified multiple novel non-canonical microRNAs including new mirtrons H/ACA box snoRNA-derived small RNAs, and a previously unidentified mammalian subclass derived from C/D box snoRNAs. These non-canonical miRNAs were expressed at high levels in the brain relative to other tissues. In contrast, we found no evidence for endo-siRNAs in the brain. Taken together, our findings provide evidence for a diverse population of highly expressed non-canonical miRNAs that together play important functional roles in post-mitotic neurons.
2011-03-23 | GSE21090 | GEO
Project description:The Drosha-DGCR8 complex (Microprocessor) is required for microRNA (miRNA) biogenesis. DGCR8 contains two double-stranded RNA binding motifs that recognize the RNA substrate, whereas Drosha functions as the endonuclease. We have used high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) to identify endogenous RNA targets of DGCR8 in mammalian cells. Unexpectedly, miRNAs were not the most abundant targets. DGCR8-bound RNAs comprised several hundred mRNAs as well as snoRNAs and long non-coding RNAs. We found that DGCR8 together with Drosha controls the abundance of several mRNAs, as well as long non-coding RNAs, such as MALAT-1. By contrast, the DGCR8-mediated cleavage of snoRNAs is independent of Drosha, suggesting the involvement of DGCR8 in cellular complexes with other endonucleases. Interestingly, binding of DGCR8 to cassette exons, acts as a novel mechanism to regulate the relative abundance of alternatively spliced isoforms. Collectively, these data provide new insights in the complex role of DGCR8 in controlling the fate of several classes of RNAs. Comparison of RNAs associated to both endogenous (D8) and overexpressed (T7) DGCR8 in HEK293T cells
2012-07-15 | E-GEOD-39086 | biostudies-arrayexpress
Project description:The Drosha-DGCR8 complex (Microprocessor) is required for microRNA (miRNA) biogenesis. DGCR8 contains two double-stranded RNA binding motifs that recognize the RNA substrate, whereas Drosha functions as the endonuclease. We have used high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) to identify endogenous RNA targets of DGCR8 in mammalian cells. Unexpectedly, miRNAs were not the most abundant targets. DGCR8-bound RNAs comprised several hundred mRNAs as well as snoRNAs and long non-coding RNAs. We found that DGCR8 together with Drosha controls the abundance of several mRNAs, as well as long non-coding RNAs, such as MALAT-1. By contrast, the DGCR8-mediated cleavage of snoRNAs is independent of Drosha, suggesting the involvement of DGCR8 in cellular complexes with other endonucleases. Interestingly, binding of DGCR8 to cassette exons, acts as a novel mechanism to regulate the relative abundance of alternatively spliced isoforms. Collectively, these data provide new insights in the complex role of DGCR8 in controlling the fate of several classes of RNAs.
2012-07-15 | GSE39086 | GEO
Project description:The Microprocessor, composed of Drosha and Pasha/DGCR8, is necessary for the biogenesis of canonical microRNAs (miRNAs), and required for animal embryogenesis. However, the cause for this requirement is largely unknown. The Microprocessor may be required to produce one or few essential miRNAs, or alternatively, many individually non-essential miRNAs. Additionally, Drosha and Pasha/DGCR8 may be required for processing non-miRNA substrates. To distinguish between these possibilities, we developed a system in C. elegans to stringently deplete embryos from the Microprocessor and miRNAs. We show that the early embryonic arrest upon loss of the Microprocessor is rescued by the addition of two individual miRNAs from the miR-35 and miR-51 families, resulting in morphologically normal larvae. Thus, just two canonical miRNAs are sufficient for morphogenesis and organogenesis in C. elegans, and indicate that miRNA processing explains the essential requirement for the Microprocessor during embryogenesis.
2020-11-21 | GSE153233 | GEO
Project description:The Microprocessor plays an essential role in canonical miRNA biogenesis by facilitating cleavage of stem-loop structures in primary transcripts to yield pre-miRNAs. Although miRNA biogenesis has been extensively studied through biochemical and molecular genetic approaches, it has yet to be addressed to what extent the current miRNA biogenesis models hold true in intact cells. To address the issues of in vivo recognition and cleavage by the Microprocessor, we investigate RNAs that are associated with DGCR8 and Drosha by using immunoprecipitation coupled with next-generation sequencing. Here, we present global protein-RNA interactions with unprecedented sensitivity and specificity. Our data indicate that precursors of canonical miRNAs and miRNA-like hairpins are the major substrates of the Microprocessor. As a result of specific enrichment of nascent cleavage products, we are able to pinpoint the Microprocessor-mediated cleavage sites per se at single-nucleotide resolution. Unexpectedly, a 2-nt 3M-bM-^@M-^Y overhang invariably exists at the ends of cleaved bases instead of nascent pre-miRNAs. Besides canonical miRNA precursors, we find that two novel miRNA-like structures embedded in mRNAs are cleaved to yield pre-miRNA-like hairpins, uncoupled from miRNA maturation. Our data provide a framework for in vivo Microprocessor-mediated cleavage and a foundation for experimental and computational studies on miRNA biogenesis in living cells. CLIP-seq for DGCR8 and Drosha, RIP-seq for DGCR8, sequencing of AGO2-assocated miRNA
2014-10-02 | E-GEOD-61979 | biostudies-arrayexpress