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dMi-2 and RNA

Ikram Ullah, Mara John

In cells, DNA is maintained in the form of chromatin, a multiprotein-DNA complex that allows super-folding of long stretches of DNA such that it fits into the tiny nuclear space. However, this super-folding obstructs the gene expression machinery in binding to its target sites. Therefore, nature devised chromatin regulating enzymes that change the conformation of the chromatin to either compressed or relaxed states – allowing the genes to be expressed in the relaxed state while maintaining those not needed at a certain point of time, in a repressed state (Rando and Ahmad, 2007; Lai and Wade, 2011). Apart from their canonical modes of gene expression regulation, recent studies have revealed a new mode of action and that is through the interaction of chromatin regulating enzymes with RNA. Interaction with RNA has been proposed to both- recruit a chromatin regulator to its target sites, for example, Mof binding to roX2 RNA leads to its recruitment to the male X chromosome, or expulsion from the chromatin, for example, PRC2 interaction with nascent RNA leads to its expulsion from actively transcribing genes (Akhtar et al., 2000; Beltran et al., 2016). 

We study an ATP-dependent chromatin remodeler called dMi-2 that has been shown to be critical for proper gene expression. It uses the energy derived from the hydrolysis of ATP to change the chromatin conformation. dMi-2 can both promote or repress the transcription. For examples, during heat shock it is recruited to, and promotes efficient transcription, of heat shock genes (Mathieu et al., 2012; Murawska et al., 2011). Conversely, dMi-2 recruitment at hormone regulated genes causes their transcriptional repression (Kreher et al., 2017). We tested the RNA binding ability of dMi-2 and our in vitro and in vivo experiments suggest that dMi-2 is an RNA binding protein and it binds RNA with higher affinity than DNA. We suspect the RNA to play a major role in the recruitment and/or expulsion of dMi-2 from the chromatin and therefore, we tested its capability to bind RNAs on a whole genome scale. The data from our genome wide binding analysis, iCLIP (individual-nucleotide resolution Crosslinking and Immunoprecipitation), reveals that dMi-2 binds a wide range of RNAs and prefers to bind the 3’-end of the RNAs. Our biochemical and imaging experiments suggest RNA to play opposing roles depending upon the context: at certain genes, for example, at heat shock genes, RNA recruits dMi-2 while at other genes, RNA prevents dMi-2 from associating with chromatin, thereby regulating gene expression.