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TranscriptomicsRNAcompete: a method for rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins
Metazoan genomes encode hundreds of RNA binding proteins (RBPs) but relatively few have well-defined RNA-binding preferences. Current techniques for determining RNA targets, including those involving in vitro selection and RNA co-immunoprecipitation, require significant time and labour investment. H...
ORGANISM(S): synthetic construct 
2010-05-18 | E-GEOD-15769 | biostudies-arrayexpress
TranscriptomicsIdentifying mRNA Sequence Elements for Target Recognition by Human Argonaute Proteins
It is commonly known that mammalian microRNAs guide the RNA-induced silencing complex (RISC) to target mRNAs through the seed-pairing rule. However, recent experiments by co-immunoprecipitating the argonaute proteins (AGOs), the central catalytic component of RISC, have consistently revealed extensi...
ORGANISM(S): Homo sapiens 
2014-02-19 | E-GEOD-55122 | biostudies-arrayexpress
TranscriptomicsGenome-wide identification of BRAT- and PUM-associated mRNAs reveals PUM-independent functions for BRAT in translational repression and mRNA degradation during the Drosophila maternal-to-zygotic transition
Here, we analyze the RNA-binding preferences of the Drosophila melanogaster BRAT protein using RNAcompete. In the RNAcompete assay, purified GST-tagged BRAT is incubated with an excess of RNA pool and bound RNA from individual pulldown experiments are directly labeled and hybridized to a custom Agil...
ORGANISM(S): synthetic construct 
2015-03-30 | E-GEOD-60498 | biostudies-arrayexpress
TranscriptomicsRIP-Chip of BRAT and PUM from 0-3 hour Drosophila melanogaster embryos
BRAT-associated mRNAs and PUM-associated mRNAs were identified in early Drosophila embryos by RNA co-immunoprecipitation of the endogenous proteins using synthetic antibodies, followed by microarray analysis (RIP-Chip). Nine RNA co-immunoprecipitations were performed. This includes 3 biological repl...
ORGANISM(S): Drosophila melanogaster 
2015-03-28 | E-GEOD-60466 | biostudies-arrayexpress
TranscriptomicsConserved functional antagonism between CELF and MBNL proteins regulates stem cell-specific alternative splicing and regeneration in planarians
Understanding gene regulation in stem cells is key to understanding stem cell biology.Contrary to transcriptional regulation the function of alternative splicing (AS) in stem cells is poorly understood. Here we study function and mechanisms of AS in a powerful in vivo model for stem cell biology, th...
ORGANISM(S): Schmidtea mediterranea 
2016-08-01 | E-GEOD-75296 | biostudies-arrayexpress
TranscriptomicsConserved functional antagonism between CELF and MBNL proteins regulates stem cell-specific alternative splicing and regeneration in planarians
Here, we analyze the RNA-binding preferences of the planarian smed-mbnl-like-2, smed-mbnl-1 (isoform X1), smed-bruli, smed-mbnl-1 (isoform Xins), and smed-mbnl-like-1 protein using RNAcompete. In the RNAcompete assay, a purified GST-tagged protein is incubated with an excess of RNA pool and bound RN...
ORGANISM(S): synthetic construct 
2016-08-01 | E-GEOD-75554 | biostudies-arrayexpress
TranscriptomicsThe crystal structure of the NHL domain in complex with RNA reveals the molecular basis of Drosophila Brain tumor-mediated gene regulation
Here, we analyze the RNA-binding preferences of several NHL containing RNA-binding proteins (BRAT, NCL-1, TRIM71, WECH, LIN-41, TRIM56, and MEI-P26) using RNAcompete. In the RNAcompete assay, purified GST-tagged RNA-binding protein is incubated with an excess of RNA pool and bound RNA from individua...
ORGANISM(S): synthetic construct 
2015-09-14 | E-GEOD-73000 | biostudies-arrayexpress
TranscriptomicsA compendium of RNA-binding motifs for analysis of gene regulation
RNA binding proteins are key regulators of gene expression, yet only a small fraction of these proteins has been functionally characterized. Here, we report the first large-scale analysis of the RNA motifs recognised by RNA binding proteins, encompassing 205 distinct proteins from 24 diverse eukary...
ORGANISM(S): synthetic construct 
2013-05-10 | E-GEOD-41235 | biostudies-arrayexpress
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