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Homo sapiens

ABSTRACT: RNA sequencing identifies specific PIWI-interacting small non-coding RNA expression patterns in breast cancer

PROVIDER: PRJNA242528 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1202350.fastq.gz	Fastqsanger.gz
	SRR1202360.fastq.gz	Fastqsanger.gz
	SRR1202351.fastq.gz	Fastqsanger.gz
	SRR1202361.fastq.gz	Fastqsanger.gz
	SRR1202352.fastq.gz	Fastqsanger.gz

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Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members

Project description:In germ cells, Piwi proteins interact with a specific class of small non-coding RNAs, piwi-interacting RNAs (piRNAs). Together, these form a pathway that represses transposable elements, thus safeguarding germ cell genomes. While basic models describe the operation of piRNA pathways, neither the protein compositions of Piwi complexes, the critical protein-protein interactions that drive small RNA production and target recognition, or the precise molecular consequences of conserved localization to germline structures, call nuage, is well understood. We purified the three murine Piwi family proteins, Mili, Miwi, and Miwi2, from mouse germ cells and characterized their interacting protein partners. Piwi proteins were found in complex with Prmt5/Wdr77, an enzyme that di-methylates arginine residues. By immunoprecipitation with specific antibodies and by mass spectrometry, we found that Piwi proteins are arginine methylated at conserved positions in their amino termini. These modifications are essential to direct complex formation with specific Tudor-domain proteins, whose interactions with Piwis can be required for localization of RNP complexes in cytoplasmic nuage, proper piRNA expression, and transposon silencing. Considered together, our findings indicate that arginine methylation drives the assembly of multi-protein machines whose integrity and specific sub-cellular localization is necessary for efficient function of the piRNA pathway. Keywords: gene regulation study Total small RNA in embryonic and post-birth mouse testes of tdrd1 and tdrd6 mutants

2009-07-25 | E-GEOD-17319 | biostudies-arrayexpress

Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos

Project description:Here we report on genome-wide small RNA and transcriptome profiling of blastula, gastrula and neurula-stage Xenopus tropicalis embryos using deep sequencing. By combining bioinformatic analysis of the small RNA-seq dataset with experimental validation, we identify novel microRNAs and Piwi-interacting RNAs. We show that microRNA expression is highly dynamic and spatially localized in early embryos in contrast to Piwi-interacting RNAs, and we validate a novel microRNA prediction pipeline. We go on to identify a new class of small intronic non-coding RNAs, that we name sincRNAs. On a genome-wide scale we find that genes containing sincRNA clusters are transcriptionally repressed. Our data suggest a novel mechanism of sincRNA-mediated gene silencing in vertebrates. Examination of small RNAs and mRNA at 3 stages of Xenopus embryonic development.

2013-09-23 | E-GEOD-38605 | biostudies-arrayexpress

Development of omic biomarkers for Fathead minnow larva (Pimephales promelas) exposed to ethinyl estradiol [non-coding small RNA]

Project description:This work aimed to expand the panel of gene expression-based biomarkers to include estrogens, to identify training strategies that maximize the range of applicable concentrations, and to evaluate the potential for two classes of small non-coding RNAs (sncRNAs), microRNA (miRNA) and piwi-interacting RNA (piRNA), as biomarkers.

2021-03-12 | GSE158857 | GEO

The evolution of genic piRNA cluster loci expression patterns

Project description:This study examines the conservation of Piwi-interacting RNA (piRNA) clusters that come from protein coding gene transcripts. By sequencing small RNA libraries from gonad tissues of Drosophilids and Glires we discover a diverse set of genic piRNA clusters conserved across animals. This dataset reveals new expression patterns for genic piRNA clusters and examines whether changing piRNA expression patterns correlates with sequence changes in piRNA cluster genomic sequence across a variety of animal species.

2015-11-01 | GSE62556 | GEO

Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos

2013-09-23 | GSE38605 | GEO

Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members

2009-07-25 | GSE17319 | GEO

Development of omic biomarkers for Fathead minnow larva (Pimephales promelas) exposed to ethinyl estradiol [mRNA]

Project description:This work aimed to expand the panel of gene expression-based biomarkers to include estrogens, to identify training strategies that maximize the range of applicable concentrations, and to evaluate the potential for mRNA and two classes of small non-coding RNAs (sncRNAs), microRNA (miRNA) and piwi-interacting RNA (piRNA), as biomarkers.

2021-03-12 | GSE160520 | GEO

Specific patterns of PIWI-interacting small noncoding RNA expression changes in dysplastic liver nodules and hepatocellular carcinoma

Project description:Specific patterns of PIWI-interacting small noncoding RNA expression changes in dysplastic liver nodules and hepatocellular carcinoma

| PRJEB11462 | ENA

The MID-PIWI module of Piwi proteins specifies nucleotide- and strand-biases of piRNAs

Project description:Piwi-interacting RNAs (piRNAs) guide Piwi Argonautes to suppress transposon activity in animal gonads. Known piRNA populations are extremely complex, with millions of individual sequences present in a single organism. Despite this complexity, specific Piwi proteins incorporate piRNAs with distinct nucleotide- and transposon strand-biases (antisense or sense) of unknown origin. Here we examined the contribution of structural domains in Piwi proteins towards defining these biases. We report the first crystal structure of the MID domain from a Piwi Argonaute and use docking experiments to show its ability to specify recognition of 5M-bM-^@M-2 uridine (1U-bias) of piRNAs. Mutational analyses reveal the importance of 5M-bM-^@M-^Y end-recognition within the MID domain for piRNA biogenesis in vivo. Finally, domain-swapping experiments uncover an unexpected role for the MID-PIWI module of a Piwi protein in dictating the strand-orientation of its bound piRNAs. Our work identifies structural features that allow distinguishing individual Piwi members during piRNA biogenesis Immunoprecipitated small RNA were purified from Bmn4 cells for preparation of high-throughput sequencing libraries.

2014-07-01 | E-GEOD-55451 | biostudies-arrayexpress

Piwi interacts with chromatin at nuclear pores and promiscuously binds nuclear transcripts in Drosophila ovarian somatic cells

Project description:Piwi in a complex with Piwi-interacting RNAs (piRNAs) triggers transcriptional silencing of Transposable Elements (TEs) in Drosophila ovaries, thus ensuring genome stability. To do this, Piwi must scan the nascent transcripts of genes and TEs for complementarity to piRNAs. The mechanism of this scanning is currently unknown. Here we report the DamID-seq mapping of multiple Piwi-interacting chromosomal domains in somatic cells of Drosophila ovaries. These domains significantly overlap with genomic regions tethered to Nuclear Pore Complexes (NPCs). Accordingly, Piwi was coimmunoprecipitated with the component of NPCs Elys and with the Xmas-2 subunit of RNA transcription and export complex, known to interact with NPCs. However, only a small Piwi fraction has transient access to DNA at nuclear pores. Importantly, although 36%of protein-coding genes overlap with Piwi-interacting domains and RNA-immunoprecipitation results demonstrate promiscuous Piwi binding to numerous genic and TE nuclear transcripts, according to available data Piwi does not silence these genes, likely due to the absence of perfect base-pairing between piRNAs and their transcripts.

2017-04-19 | GSE87346 | GEO

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