Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-Direct Regulation of pri-miRNA Processing by a Long Noncoding RNA Transcribed from an Ultraconserved Region

ABSTRACT: We investigate the role of a long ncRNA transcribed from an ultraconserved region (T-UCR) in the control of post-transcriptional pri-miRNA processing. The regulation is based on complementarity between the lower stem region in pri-miR-195 transcript and the ultraconserved sequence in Uc.283+A, which prevents pri-miRNA cleavage by Drosha. Mutation of the site in either RNA molecule uncouples regulation in vivo and in vitro. We propose a model in which lower-stem strand invasion by Uc.283+A impairs microprocessor recognition and efficient pri-miRNA cropping. In this work, we characterize a new role for Uc.283+A as a direct interactor and regulator of pri-miRNA-195 maturation at the level of Drosha processing. We combine cellular assays with in vitro biochemical analyses to reveal the first case of RNA-directed downregulation of miRNA biogenesis by a T-UCR In the study presented here, a colorrectal cancer cell line (HCT-116) was transiently transfected with Uc.283+A in order to identify putative miRNA targets for Uc.283+A. Variant 1 represents a SNP variant (8x(T) repeat in the sequence). Variant 2 represents a SNP variant (9x(T) repeat in the sequence).

ORGANISM(S): Homo sapiens

SUBMITTER: Antonio Gómez

PROVIDER: E-GEOD-56841 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-Direct Regulation of pri-miRNA Processing by a Long Noncoding RNA Transcribed from an Ultraconserved Region

Project description:We investigate the role of a long ncRNA transcribed from an ultraconserved region (T-UCR) in the control of post-transcriptional pri-miRNA processing. The regulation is based on complementarity between the lower stem region in pri-miR-195 transcript and the ultraconserved sequence in Uc.283+A, which prevents pri-miRNA cleavage by Drosha. Mutation of the site in either RNA molecule uncouples regulation in vivo and in vitro. We propose a model in which lower-stem strand invasion by Uc.283+A impairs microprocessor recognition and efficient pri-miRNA cropping. In this work, we characterize a new role for Uc.283+A as a direct interactor and regulator of pri-miRNA-195 maturation at the level of Drosha processing. We combine cellular assays with in vitro biochemical analyses to reveal the first case of RNA-directed downregulation of miRNA biogenesis by a T-UCR

2014-05-01 | GSE56841 | GEO

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

MicroRNA-seq of cell lines expressing pri-miR-9 paralog constructs II

Project description:MicroRNA (miRNA) biogenesis begins with Drosha cleavage, the fidelity of which is critical for downstream processing and mature miRNA target specificity. To understand how pri-miRNA sequence and structure influence Drosha cleavage, we studied the processing of pri-miR-9-1 sequence variants, which encode the same mature miRNA but differ in the surrounding scaffold. We show that, in addition to previously known features, the overall structural flexibility of pri-miRNA impacts Drosha cleavage fidelity. Internal loops and nearby G·U wobble pairs on the pri-miRNA stem induce the use of non-canonical cleavage sites by Drosha, resulting in 5’ isomiR production. Here, we report the the miRNA-seq data of HEK293T cell lines transfected with different pri-miR-9 constructs.

2022-01-27 | GSE172446 | GEO

MicroRNA-seq of cell lines expressing pri-miR-9 paralog constructs

Project description:MicroRNA (miRNA) biogenesis begins with Drosha cleavage, the fidelity of which is critical for downstream processing and mature miRNA target specificity. To understand how pri-miRNA sequence and structure influence Drosha cleavage, we studied the processing of three pri-miR-9 paralogs (pri-miR-9-1, pri-miR-9-2 and pri-miR-9-3), which encode the same miRNA but differ in the surrounding scaffold. We show that pri-miR-9-1 has a unique Drosha cleavage profile due to its kinked tertiary structure. Cleavage of pri-miR-9-1, but not pri-miR-9-2 or pri-miR-9-3, generates an alternative-miR-9 with a shifted seed sequence that expands the scope of its target RNAs. Here, we report the the miRNA-seq data of HEK293T and HeLa cell lines transfected with different pri-miR-9 constructs.

2018-12-10 | GSE108893 | GEO

A quantitative map of human primary microRNA processing sites [2]

2021-07-27 | GSE174222 | GEO

A quantitative map of human primary microRNA processing sites [1]

2021-07-27 | GSE174143 | GEO

Genome wide identification of targets of the drosha-pasha/DGCR8 complex

Project description:Drosha is a type III RNAse, which plays a critical role in miRNA biogenesis. Drosha and its double-stranded RNA-binding partner protein Pasha/DGCR8 likely recognize and cleave miRNA precursor RNAs or pri-miRNA hairpins co-transcriptionally. To identify RNAs processed by Drosha, we used tiling microarrays to examine transcripts after depletion of drosha mRNA with dsRNA in Drosophila Schneider S2 cells. This strategy identified 137 Drosha-regulated RNAs, including 11 putative pri-miRNAs comprising 15 annotated miRNAs. Most of the identified pri-miRNAs seem extremely large, >10 kilobases as revealed by both the Drosha knock down strategy and by RNA PolII chromatin IP followed by Drosophila tiling microarrays. Surprisingly, more than a hundred additional RNAs not annotated as miRNAs are under Drosha control and are likely to be direct targets of Drosha action. This is because many of them encode annotated genes, and unlike bona fide pri-miRNAs, they are not affected by depletion of the miRNA processing factor, dicer-1. Moreover, application of the evofold analysis software indicates that at least 25 of the Drosha-regulated RNAs contain evolutionarily conserved hairpins similar to those recognized by the Drosha-Pasha/DGCR8 complex in pri-miRNAs. One of these hairpins is located in the 5′ UTR of both pasha and mammalian DGCR8. These observations suggest that a negative feedback loop acting on pasha mRNA may regulate the miRNA-biogenesis pathway: i.e., excess Drosha cleaves pasha/DGCR8 primary transcripts and leads to a reduction in pasha/DGCR8 mRNA levels and Pasha/DGCR8 synthesis. Keywords: time course, ChIP-chip

2008-12-25 | GSE14215 | GEO

DROSHA complementation experiments using small RNA sequencing

Project description:DROSHA complementation experiments were performed to check whether dsRBD of DROSHA recognizes the lower stem of pri-miRNAs and affects miRNA biogenesis.

2018-12-13 | GSE117603 | GEO

Single cut products of Microprocessor on pri-miRNAs

Project description:The human Microprocessor complex cleaves primary microRNA (miRNA) transcripts (pri-miRNAs) to initiate miRNA synthesis. Microprocessor consists of DROSHA (an RNase III enzyme), and DGCR8. DROSHA has two conserved RNase III domains, which make double cuts on each of pri-miRNA strands. In this study, we show that Microprocessor has an unexpected single-cut activity, which creates a single cut on just one of the pri-miRNA strands using one of the two RNase III domains of DROSHA. This cleavage does not lead to the production of miRNA but instead it downregulates miRNA expression. We also demonstrate that certain RNA elements facilitate the single-cut activity of Microprocessor, and by manipulating these elements, we can regulate the ratio of single-cut to double-cut activities, thus controlling miRNA production both in vitro and in vivo.

2020-01-24 | GSE138950 | GEO

Genome-wide mapping of DROSHA cleavage sites on primary microRNAs and novel substrates [fCLIP-seq]

Project description:MicroRNA (miRNA) maturation is initiated by DROSHA, a double-stranded RNA (dsRNA)-specific RNase III enzyme. By cleaving primary miRNAs (pri-miRNAs) at specific positions, DROSHA serves as a main determinant of miRNA sequences and a highly selective gate-keeper for the canonical miRNA pathway. However, the sites of DROSHA-mediated processing have not been annotated on a genomic scale, and it remains unclear to what extent DROSHA functions outside the miRNA pathway. Here we establish a protocol termed ‘formaldehyde crosslinking and immunoprecipitation followed by sequencing (fCLIP-seq)’ that allows identification of DROSHA cleavage sites at single nucleotide resolution. fCLIP identifies numerous cleavage sites that do not match the ends of annotated mature miRNAs, particularly at the 3′ termini, suggesting widespread end modifications during miRNA maturation such as trimming and tailing. fCLIP also finds many pri-miRNAs undergoing alternative processing, yielding multiple miRNA isoforms. Moreover, we discover dozens of novel substrates that are bound and cleaved by DROSHA. These substrates are processed less efficiently than canonical pri-miRNAs, and produce only minute amounts of small RNAs. Depletion of DROSHA results in an increase of the hairpin-containing transcripts. Thus, the hairpins may serve mainly as cis-elements for DROSHA-mediated gene regulation rather than as miRNA genes. fCLIP-seq not only accurately maps the cleavage sites of DROSHA and suggests noncanonical functions of DROSHA, but also could be a general tool for investigating interactions between dsRNA binding proteins and structured RNAs.

2017-04-23 | GSE93651 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data