Identification of GLD-1 target mRNAs
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE33081 | GEO | 2012/06/18
SECONDARY ACCESSION(S): PRJNA155529
REPOSITORIES: GEO
Similar Datasets
Project description:To determine which mRNAs are bound by GLD-1 we performed GLD-1 and MYC (as a negative control) immunoprecipitation experiments on wildtype animals. A total of 6 samples was analyzed (triplicates of GLD-1 IPs and MYC IPs respectively)
2012-06-17 | E-GEOD-33081 | biostudies-arrayexpress
Project description:RNA-binding proteins (RBPs) are critical regulators of gene expression and elucidating the interactions of RBPs with their RNA targets is necessary to understand how combinations of RBPs control transcriptome expression. The Quaking-related (QR) sub-family of STAR domain RBPs includes developmental regulators and tumor suppressors such as C. elegans GLD-1, which functions as a master regulator of germ line development. To understand how GLD-1 interacts with the transcriptome, we identified GLD-1 associated mRNAs by a ribonomic approach. The scale of GLD-1 mRNA interactions allowed us to determine rules governing GLD-1 target selection and to derive a predictive model where GLD-1 association with mRNA is based on the number and strength of 7-mer GLD-1 binding elements (GBEs) within UTRs. GLD-1/mRNA interactions were quantified, and predictions were verified both in vitro and in live animals, including by M-bM-^@M-^XtransplantationM-bM-^@M-^Y experiments where M-bM-^@M-^XweakM-bM-^@M-^Y and M-bM-^@M-^XstrongM-bM-^@M-^Y GBEs imposed translational repression of increasing strength on a non-target mRNA.Importantly, this study provides a unique quantitative picture of how an RBP interacts with its mRNA targets. As combinatorial regulation by multiple RBPs is thought to regulate gene expression, quantification of RBP/mRNA interactions should be a way to predict and potentially modify biological outcomes of complex posttranscriptional regulatory networks, and our analysis suggests that such an approach is possible. Wild-type (N2) or gld-1(q485); ozIs2 [gld-1::gfp::flag] worms were synchronized and harvested as young adults. To identify GLD-1 associated transcripts, two independent IP strategies were performed: 1. Comparison of anti-FLAG IP to anti-MYC IP on the gld-1(q485); ozIs2 [gld-1::gfp::flag] worm extract, 2. Comparison of anti-FLAG IP on the gld-1(q485); ozIs2 [gld-1::gfp::flag] worm extract to anti-FLAG IP on wild type extract. All IPs were performed in triplicate (12 IPs).
2011-02-04 | E-GEOD-21591 | biostudies-arrayexpress
Project description:RNA-binding proteins (RBPs) are critical regulators of gene expression and elucidating the interactions of RBPs with their RNA targets is necessary to understand how combinations of RBPs control transcriptome expression. The Quaking-related (QR) sub-family of STAR domain RBPs includes developmental regulators and tumor suppressors such as C. elegans GLD-1, which functions as a master regulator of germ line development. To understand how GLD-1 interacts with the transcriptome, we identified GLD-1 associated mRNAs by a ribonomic approach. The scale of GLD-1 mRNA interactions allowed us to determine rules governing GLD-1 target selection and to derive a predictive model where GLD-1 association with mRNA is based on the number and strength of 7-mer GLD-1 binding elements (GBEs) within UTRs. GLD-1/mRNA interactions were quantified, and predictions were verified both in vitro and in live animals, including by ‘transplantation’ experiments where ‘weak’ and ‘strong’ GBEs imposed translational repression of increasing strength on a non-target mRNA.Importantly, this study provides a unique quantitative picture of how an RBP interacts with its mRNA targets. As combinatorial regulation by multiple RBPs is thought to regulate gene expression, quantification of RBP/mRNA interactions should be a way to predict and potentially modify biological outcomes of complex posttranscriptional regulatory networks, and our analysis suggests that such an approach is possible.
2011-02-04 | GSE21591 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE33081: Identification of GLD-1 target mRNAs GSE33082: mRNA expression analysis in wild-type, gld-1 and cgh-1 mutant animals GSE33083: Polysome profiling of wild-type and gld-1 mutant animals GSE36713: mRNA expression analysis in mock and cgh-1(RNAi) animals Refer to individual Series
2012-06-17 | E-GEOD-33084 | biostudies-arrayexpress
Project description:C. elegans GLD-2 forms an active PAP with multiple RNA-binding partners to regulate diverse aspects of germline and early embryonic development. One GLD-2 partner, RNP-8, was previously shown to influence oocyte fate specification. To identify transcripts selectively associated with both GLD-2 and RNP-8, we employ a genomic approach using the method of RNA immunoprecipitation followed by microarray analysis (RIP-chip). We used microarrays to identify mRNAs selectively associated with either GLD-2 or RNP-8.
2010-09-21 | GSE23843 | GEO
Project description:To determine the translational status of mRNAs in wild-type and gld-1 mutant animals, we analyzed total and polysomal RNA levels in both strains by tiling arrays A total of 16 samples was analyzed (quadruplicates of wild-type_total, wild-type_polysomal, gld-1_total, gld-1_polysomal RNA respectively)
2012-06-17 | E-GEOD-33083 | biostudies-arrayexpress
Project description:To determine the translational status of mRNAs in wild-type and gld-1 mutant animals, we analyzed total and polysomal RNA levels in both strains by tiling arrays
2012-06-18 | GSE33083 | GEO
Project description:Animal mRNAs are regulated by hundreds of RNA binding proteins (RBPs). The identification of RBP targets is crucial for understanding their function. A recent method, PAR-CLIP, uses photoreactive nucleosides to crosslink RBPs to target RNAs in cells prior to immunoprecipitation. Here, we establish iPAR-CLIP (in vivo PAR-CLIP) to determine, at nucleotide resolution, transcriptome-wide target sites of GLD-1, a conserved, germline-specific translational repressor in C. elegans. We identified 439 reproducible targets and demonstrate an excellent dynamic range of target detection by iPAR-CLIP. Upon GLD-1 knock-down, protein but not mRNA expression of the 439 targets was specifically and highly significantly upregulated, demonstrating functionality. Finally, we discovered strongly conserved GLD-1 binding sites nearby the start codon of target genes. We propose that GLD-1 interacts with the translation machinery nearby the start codon, a so far unknown mode of gene regulation in eukaryotes. PolyA mRNA was extracted from young adult wildtype (N2) worms and young adult germline less worms (glp-4(bn2) TS) to identify and quantify genes expressed in the young adult germline by sequencing. 2x100 paired end sequencing was performed according to the protocol on the Illumina HiSeq 2000.
2011-12-09 | E-GEOD-33573 | biostudies-arrayexpress
Project description:To determine mRNA expression levels in wild-type, gld-1 (q485) mutant and cgh-1(tn691) mutant animals, RNA was purified from dissected gonads of young adult worms, using the PicoPur Kit. A total of 9 samples was analyzed (triplicates of wild-type, gld-1 mutant and cgh-1 mutant animals respectively)
2012-06-17 | E-GEOD-33082 | biostudies-arrayexpress
Project description:To determine mRNA expression levels in wild-type, gld-1 (q485) mutant and cgh-1(tn691) mutant animals, RNA was purified from dissected gonads of young adult worms, using the PicoPur Kit.
2012-06-18 | GSE33082 | GEO