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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Xenopus Piwi protein associated transcripts indicate regulation beyond transposons

ABSTRACT: This study examines the population of transcripts associated with the Xenopus Piwi proteins, Xiwi and Xili, from X.laevis and X.tropicalis. RIP-seq, CLIP-seq, piRNA-seq, and mRNA-seq datasets were integrated to determine how the Xenopus Piwi proteins where using piRNAs and binding interactions to associate with transcripts in gonadal cells. We performed several replicates of a Piw CLIP-Seq experiment to isolate RNA fragments as CLIP-tags to discover which transcripts are preferentially bound by the Piwi protein. Then we performed several types of mRNA expression profiling experiments using several forms of mRNA-Seq library construction formats. Finally, we sequenced the piRNAs from the OSS cells

ORGANISM(S): Xenopus (Silurana) tropicalis

SUBMITTER: Nelson Lau

PROVIDER: E-GEOD-63228 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome and transposable element dynamics during PIWI regulation in Drosophila ovarian cell cultures

Project description:This study examines the regulatory capacity of the Piwi protein in the Drosophila OSS cell. Piwi CLIP-Seq, mRNA-Seq and nascent RNAseq datasets were integrated to determine how Piwi proteins where using piRNAs and binding interactions to regulate the expression of transcripts. We also sequenced the genomes of various OSS cell lines. We first performed several replicates of a Piw CLIP-Seq experiment to isolate RNA fragments as CLIP-tags to discover which transcripts are preferentially bound by the Piwi protein. Then we performed several types of mRNA expression profiling experiments using several forms of mRNA-Seq library construction formats. Finally, we sequenced the genomes from various OSS cell lines. The genomic sequencing component of the study is represented by BioProject PRJNA240323. The genomic sequencing raw data have been deposited at SRA (SRP039565).

2014-09-15 | E-GEOD-45112 | biostudies-arrayexpress

Somatic Primary piRNA Biogenesis Driven by Cis-Acting RNA Elements and Trans- Acting Yb

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Target RNA repertoire of mouse Mili and Miwi proteins reveals piRNA biogenesis and Miwi function in spermiogenesis [HITS-CLIP]

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HITS-CLIP analysis of Yb binding sites in Drosophila ovary cell line

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2014-06-24 | E-GEOD-54875 | biostudies-arrayexpress

FLX sequencing of Piwi-associated small RNAs extracted from Drosophila ovarian somatic cells (OSC)

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2009-10-01 | E-GEOD-15137 | biostudies-arrayexpress

High throughput sequencing of Piwi bound piRNAs from Drosophila ovaries in which key factors for primary piRNA biogenesis in somatic support cells were knocked down using RNAi

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2010-10-03 | E-GEOD-23560 | biostudies-arrayexpress

The binding specificity and regulatory effect of WT and redesigned Puf2p [CLIP-Seq]

Project description:PUF proteins have become a leading scaffold for designing RNA-binding proteins to contact and control RNAs at will. We analyze the effects of that reengineering across the transcriptome in vivo for the first time. We show, by HITS-CLIP and PAR-CLIP, that S. cerevisiae Puf2p, a non-canonical PUF protein, binds more than 1000 mRNA targets. Puf2p binds multiple UAAU elements, unlike canonical PUF proteins. We also perform CLIP-seq on truncations of the Puf2p, showing that its prion domain is dispensable for WT binding. We design a modified Puf2p to bind UAAG rather than UAAU, which allows us to align the protein with the binding site. In vivo, the redesigned protein binds UAAG sites. Its altered specificity redistributes the protein away from 3âUTRs, such that the protein tracks with its sites, binds throughout the mRNA. We use RNA-seq to determine that R1 SNE Puf2p represses a novel RNA network.Â CLIP-seq was performed in BY4742 S. cerevisiae grown in log phase, and using 2 replicates of TAP-tagged proteins.

2015-12-15 | E-GEOD-73273 | biostudies-arrayexpress

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2007-10-24 | E-GEOD-9138 | biostudies-arrayexpress

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