Project description:Purpose: Slam protein and RNA co-localize in early drosophila embryos. slam RNA specifically co-immunoprecipitates with its own protein from embryonic lysate as shown by RNA-IP and QRT-PCR. The goal of this study is to survey transcriptome wide (RNA-seq) targets of slam protein and validate the data from qRT–PCR analysis. Methods: RNA-ip was performed for staged embryos (1.5 – 3 h after egg laying) Using slam antibody or GFP binder. RNA profiles in immune-predicates were generated by deep sequencing. Results: Slam RNA specifically co-predicates with slam protein as shown by both next generation sequencing and RT-QPCR. No mRNA of other genes was detected in all independent experiments or showed the averaged enrichment in the same range.
Project description:RIN-associated mRNAs were identified in early Drosophila embryos by RNA co-immunoprecipitation of the endogenous protein using a synthetic antibody (anti-RIN D072), followed by microarray analysis (RIP-Chip).
Project description:Nucleus is a highly structured organelle and contains many functional compartments. While the structural basis for this complex spatial organization of compartments is unknown, a major component of this organization is likely to be the non-chromatin scaffolding called nuclear matrix (NuMat). Experimental evidence over the past decades indicates that most of the nuclear functions are at least transiently associated with the NuMat although the components of NuMat itself are poorly known. Here, we report NuMat proteome analysis from Drosophila melanogaster embryos and discuss its links with nuclear architecture and functions. In the NuMat proteome, we find structural proteins, chaperones related, DNA/RNA binding, chromatin remodeling and transcription factors. This complexity of NuMat proteome is an indicator of its structural and functional significance. Comparison of the 2D profile of NuMat proteome from different developmental stages of Drosophila embryos shows that less than half of the NuMat proteome is constant and rest of the proteins are stage specific dynamic components. This NuMat dynamics suggests a possible functional link between NuMat and the embryonic development. Finally, we also show that a subset of NuMat proteins remain associated with the mitotic chromosomes implicating their role in mitosis and possibly the epigenetic cellular memory. NuMat proteome analysis provides tools and opens up ways to understand nuclear organization and function.
