Project description:We have used RIp-chip to identify mRNAs that coprecipitae with specific proteins, and later used the protein RNA interactions to predict protein-protein associations. To test whether some of the interactions we see require intact polysomes (that is, ribosomes translating mRNAs) we treated the extracts (and, in some cases, also the cells) with different compounds. In this case, we have a standard protocol, one in which the buffers contain EDTA, and one in which it includes puromycin.

2014-05-05 | E-MTAB-1856 | biostudies-arrayexpress

RIp-chip experiments with proteins that do not contain RNA-binding domains

Project description:In order to assess the prevalence of cotranslational assembly of protein complexes we performed RIp-chip experiments with many proteins that do not conatin RNA-binding motifs

2012-05-20 | E-TABM-1158 | biostudies-arrayexpress

Ribonucleoprotein immunoprecipitation of Schizosaccharomyces pombe cells using the RNA-binding protein Meu5

Project description:Ribonucleoprotein immunoprecipitation microarray (RIp-chip) study using the RNA-binding protein Meu5 from the fission Schizosaccaromyces pombe

2011-01-01 | E-TABM-932 | biostudies-arrayexpress

RNP immunoprecipitation of fission yeast using Rng3p myosin-specific chaperones to investigate if the association of Rng3p with RNAs occurs on ribosomes

Project description:Ribonucleoprotein immunoprecipitation microarray (RIp-chip) study using the Rng3p myosin-specific chaperones from the fission Schizosaccaromyces pombe. Rng3p associates with RNAs encoding myosins. To investigate if the association of Rng3p with these RNAs occurs on ribosomes, Rng3-purified fractions were immunoprecipitated with antibodies against a ribosomal RNA or an unrelated antibody. The RNAs present in the second immunoprecipitate were analysed using DNA microarrays

2008-12-23 | E-TABM-564 | biostudies-arrayexpress

Ribonucleoprotein immunoprecipitation of fission yeast to study myosin proteins and myosin-specific chaperones

Project description:Ribonucleoprotein immunoprecipitation microarray (RIp-chip) study using various myosin proteins and myosin-specific chaperones from the fission Schizosaccaromyces pombe. Two strains were used. In rng3TAP the rng3 protein has been tagged with TAP to allow its detection and immunoprecipitation. The TAP strain expresses the TAP sequence alone (without being attached to an other protein)

2008-12-23 | E-TABM-516 | biostudies-arrayexpress

Chromatin immunoprecipitation of human cells after lipopolysaccharide stimulation, to identify binding of NF-KappaB family members

Project description:The NF-KappaB family of transcription factors plays a critical role in numerous cellular processes, particularly the immune response. Our understanding of how the different NF-kappaB subunits act coordinately to regulate gene expression is based on a limited set of genes. We used genome-scale location analysis to identify targets of all five NF-kappaB proteins before and after stimulation of monocytic cells with bacterial lipopolysaccharide (LPS). In unstimulated cells, p50 and p52 bound to a significant number of gene promoters. p50 occupied genes together with RNA polymerase II and defined a set of genes to which other NF-kappaB proteins bound after LPS induction. In stimulated cells, genes bound by multiple NF-kappaB subunits exhibited the greatest increases in RNA polymerase II occupancy and gene expression. This study identifies novel NF-kappaB target genes, reveals how the different NF-kappaB proteins coordinate their activity and maps transcriptional regulatory networks that underlie the host response to infection.

2006-05-09 | E-WMIT-6 | biostudies-arrayexpress

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