Loss of ISWI Function in Drosophila Nuclear Bodies Drives Cytoplasmic Redistribution of Drosophila TDP-43

Abstract

Over the past decade, evidence has identified a link between protein aggregation, RNA biology, and a subset of degenerative diseases. An important feature of these disorders is the cytoplasmic or nuclear aggregation of RNA-binding proteins (RBPs). Redistribution of RBPs, such as the human TAR DNA-binding 43 protein (TDP-43) from the nucleus to cytoplasmic inclusions is a pathological feature of several diseases. Indeed, sporadic and familial forms of amyotrophic lateral sclerosis (ALS) and fronto-temporal lobar degeneration share as hallmarks ubiquitin-positive inclusions. Recently, the wide spectrum of neurodegenerative diseases characterized by RBPs functions’ alteration and loss was collectively named proteinopathies. Here, we show that TBPH (TAR DNA-binding protein-43 homolog), the Drosophila ortholog of human TDP-43 TAR DNA-binding protein-43, interacts with the arcRNA hsrω and with hsrω-associated hnRNPs. Additionally, we found that the loss of the omega speckles remodeler ISWI (Imitation SWI) changes the TBPH sub-cellular localization to drive a TBPH cytoplasmic accumulation. Our results, hence, identify TBPH as a new component of omega speckles and highlight a role of chromatin remodelers in hnRNPs nuclear compartmentalization.

Altered levels ofhsromegalncRNAs further enhance Ras signaling during ectopically activated Ras induced R7 differentiation inDrosophila

“…Together, these results confirm that the similar end-result of down-or up-regulation of hsrω transcripts on Ras signaling in high activated Ras background reflects specific consequences of the complex interactions between ectopically expressed activated Ras and altered levels of hsrω lncRNAs. It may be mentioned that these same lines have been used in several earlier studies Mallik and Lakhotia, 2009;Mallik and Lakhotia, 2010;Mallik and Lakhotia, 2011;Onorati et al, 2011;Piccolo et al, 2018;Piccolo and Yamaguchi, 2017;Singh and Lakhotia, 2015) without any indication of nonspecific effects, although similar as well as dissimilar end-phenotypes were seen following down-or up-regulation of the hsrω gene expression.…”

“…Since the hsrω transcripts are not known to bind with gene promoters or other RNAs, the changes in activities of the above noted negative and positive modulators of Ras signaling appears to be related to changes in activities of the diverse proteins that associate with these lncRNAs. Of the multiple transcripts produced by hsrω gene (Lakhotia, 2011;Lakhotia, 2017b), the >10kb nucleus-limited transcripts are essential for biogenesis of the omega speckles and consequently for the dynamic movement of the omega speckle associated proteins like various hnRNPs, certain other RNA binding proteins and some nuclear matrix proteins etc (Lakhotia et al, 2012;Mallik and Lakhotia, 2011;Piccolo et al, 2018;Piccolo and Yamaguchi, 2017;Singh and Lakhotia, 2015). The GAL4 induced expression of hsrωRNAi transgene or of the EP3037 allele of hsrω is known to primarily lower and elevate, respectively, levels of the larger and nucleus-limited transcripts of hsrω gene (Mallik and Lakhotia, 2009) .…”

“…We also checked the status of known transcription factors (Rhee et al, 2014) and RNA binding proteins (RNA binding protein Database at http://rbpdb.ccbr.utoronto.ca) in Drosophila melanogaster as hsrω transcripts are known to bind to various RNA binding proteins regulating gene expression and RNA processing Piccolo et al, 2018;Piccolo and Yamaguchi, 2017;Prasanth et al, 2000;Singh and Lakhotia, 2015). Out of the nearly 1000 known transcription factors (Rhee et al, 2014), 91 were commonly down-regulated following down-or up-regulation of hsrω transcripts (Fig.…”

“…8A), all of the 16 RBPs, which showed significant down regulation in sev-GAL4>UAS-EP3037, also showed a downward trend in sev-GAL4>UAS-hsrωRNAi eye discs. These 16 RBPs included some of the hsrω lncRNAs interactors like Hrb87F, Caz/dFus, TDP-43 (dTBPH) Piccolo et al, 2018;Piccolo and Yamaguchi, 2017;Prasanth et al, 2000;Singh and Lakhotia, 2015). Surprisingly, none of the examined RBPs were up-regulated when hsrω transcripts were altered.…”

“…Consequently, the Ras activity increased in both cases. An over-or under-expression of the nuclear lncRNAs produced by the hsrω gene, affects dynamics of the omega speckle associated RNA binding proteins, including diverse hnRNPs Piccolo et al, 2018;Piccolo and Yamaguchi, 2017;Prasanth et al, 2000;Singh and Lakhotia, 2015). Bioinformatic analysis indicated that several of these known interactors of hsrω RNAs can bind to transcripts of modulators of Ras signaling, which may be responsible for the observed further elevation of Ras signaling following co-alteration in hsrω lncRNA levels in activated Ras expression background.…”