The RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner

Abstract

Chromatin insulators are DNA-protein complexes that are situated throughout the genome that are proposed to contribute to higherorder organization and demarcation into distinct transcriptional domains. Mounting evidence in different species implicates RNA and RNA-binding proteins as regulators of chromatin insulator activities. Here, we identify the Drosophila hnRNP M homolog Rumpelstiltskin (Rump) as an antagonist of gypsy chromatin insulator enhancer-blocking and barrier activities. Despite ubiquitous expression of Rump, decreasing Rump levels leads to improvement of barrier activity only in tissues outside of the central nervous system (CNS). Furthermore, rump mutants restore insulator body localization in an insulator mutant background only in non-CNS tissues. Rump associates physically with core gypsy insulator proteins, and chromatin immunoprecipitation and sequencing analysis of Rump demonstrates extensive colocalization with a subset of insulator sites across the genome. The genome-wide binding profile and tissue specificity of Rump contrast with that of Shep, a recently identified RNA-binding protein that antagonizes gypsy insulator activity primarily in the CNS. Our findings indicate parallel roles for RNA-binding proteins in mediating tissue-specific regulation of chromatin insulator activity.

Restraint of the G2/M Transition by the SR/RRM Family mRNA Shuttling Binding Protein SNXAHRB1 in Aspergillus nidulans

“…A recent study of Rumplestiltskin (Rump), the Drosophila melanogaster homolog of snxA and hnRNP-M, provides evidence for direct involvement in an epigenetic mechanism affecting higher-order chromatin structure through modulation of insulator function (King et al 2014). Rump associates physically with Drosophila core insulator proteins, colocalizing to a subset of insulator binding sites.…”

“…Given its newly discovered and poorly understood role in promoting mitosis, and the apparent role of snxA in restraining nuclear division, it will be of interest to determine what kind of functional relationship may exist between Set1c and snxA. A recent study of Rumplestiltskin (Rump), the Drosophila melanogaster homolog of snxA and hnRNP-M, provides evidence for direct involvement in an epigenetic mechanism affecting higher-order chromatin structure through modulation of insulator function (King et al 2014). Rump associates physically with Drosophila core insulator proteins, colocalizing to a subset of insulator binding sites.…”

“…Depletion of Rump improved the enhancer-blocking and barrier function of a gypsy transposable element, suggesting that Rump acts normally to inhibit insulator activity, possibly by competing with insulatorinsulator interactions. In addition to this newly discovered role in chromatin dynamics, Rump also autoregulates its own expression (King et al 2014). These findings suggest a possible mechanisn for snxA in regulating the expression of G2-M regulators in A. nidulans.…”

Maintenance of a <em>Drosophila melanogaster</em> Population Cage

“…For example, collected embryos from population cages have been used very successfully in immunoprecipitation assays [6][7][8] , mass collection of larval tissues from dissociated larvae has demonstrated to be a very good source for 3C experiments 4 and RNA preparations 15 , and heads from adult flies have been utilized for ChIP experiments 16 . In addition, adults are often needed to make fly extracts for tissue culture 17 .…”

“…These studies often require large amounts of biological material, not only from adult flies, but also from larvae 4 , pupae 5 and embryos [6][7][8] .…”