Polycomb Group (PcG) proteins form memory of transient transcriptional repression that is necessary for development. In Drosophila, DNA elements termed Polycomb Response Elements (PREs) recruit PcG proteins. How PcG activities are targeted to PREs to maintain repressed states only in appropriate developmental contexts has been difficult to elucidate. PcG complexes modify chromatin, but also interact with both RNA and DNA, and RNA is implicated in PcG targeting and function. Here we show that R-loops form at many PREs in Drosophila embryos, and correlate with repressive states. In vitro, both PRC1 and PRC2 can recognize R-loops and open DNA bubbles. Unexpectedly, we find that PRC2 drives formation of RNA-DNA hybrids, the key component of R-loops, from RNA and dsDNA. Our results identify R-loop formation as a feature of Drosophila PREs that can be recognized by PcG complexes, and RNA-DNA strand exchange as a PRC2 activity that could contribute to R-loop formation.

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Neurodevelopment is accompanied by a precise change in the expression of the translation elongation factor 1A variants from eEF1A1 to eEF1A2. These are paralogue genes that encode 92% identical proteins in mammals. The switch in the expression of eEF1A variants has been well studied in mouse motor neurons, which solely express eEF1A2 by four weeks of postnatal development. However, changes in the subcellular localization of eEF1A variants during neurodevelopment have not been studied in detail in other neuronal types because antibodies lack perfect specificity, and immunofluorescence has a low sensitivity. In hippocampal neurons, eEF1A is related to synaptic plasticity and memory consolidation, and decreased eEF1A expression is observed in the hippocampus of Alzheimer’s patients. However, the specific variant involved in these functions is unknown. To distinguish eEF1A1 from eEF1A2 expression, we have designed single-molecule fluorescence in-situ hybridization probes to detect either eEF1A1 or eEF1A2 mRNAs in cultured primary hippocampal neurons and brain tissues. We have developed a computational framework, ARLIN (analysis of RNA localization in neurons), to analyze and compare the subcellular distribution of eEF1A1 and eEF1A2 mRNAs at specific developmental stages and in mature neurons. We found that eEF1A1 and eEF1A2 mRNAs differ in expression and subcellular localization over neurodevelopment, and eEF1A1 mRNAs localize in dendrites and synapses during dendritogenesis and synaptogenesis. Interestingly, mature hippocampal neurons coexpress both variant mRNAs, and eEF1A1 remains the predominant variant in dendrites.

Epigenetic regulation is conveyed through information encoded by specific chromatin 20 features. Non-canonical nucleic acid structures could in principle also convey biological 21 information but their role(s) in epigenetic regulation is not known. Polycomb Group (PcG) 22 proteins form memory of transient transcriptional repression events that is necessary for 23 development. In Drosophila, PcG proteins are recruited to specific DNA sequences, Polycomb 24 Response Elements (PREs). PREs are switchable memory elements that can exist in repressed, 25 active, or unengaged states 1,2 . How PcG activities are targeted to PREs to maintain repressed 26 states only in appropriate developmental contexts has been difficult to elucidate. Biochemically, 27PcG protein complexes modify chromatin to maintain gene repression 1,3,4 . However, PcG 28 proteins also interact with both RNA and DNA, and RNA is implicated in the targeting of PcG 29 function. We find that R-loops, three-stranded nucleic acid structures formed when an RNA 30 hybridizes to its complementary DNA and displaces the other DNA strand 5 , form at many PREs 31 in Drosophila embryos, and correlate with the repressive state. R-loops are recognized by the 32 PcG complex PRC1 in vitro. Unexpectedly, we find that the PcG complex PRC2 has RNA strand 33 invasion activity, which can drive formation of RNA-DNA hybrids, the key component of R-34 loops. Our results suggest a new mechanism for targeting PcG function through R-loop 35 formation by PRC2 and recognition by PRC1. More generally, our findings suggest formation 36 and recognition 6 of non-canonical nucleic acid structures as an epigenetic mechanism.37 38 39 40 41 Main Text: 42 During Drosophila embryogenesis, transiently expressed transcription factors activate 43 homeotic (Hox) genes in certain regions of the embryo and repress them in others to dictate the 44 future body plan 7 . Polycomb Group (PcG) proteins form a memory of these early cues by 45 maintaining patterns of Hox gene repression for the rest of development 1,7,8 . This paradigm for 46 transcriptional memory is believed to be used by the PcG at many genes in Drosophila, and to 47 underlie the conserved and essential functions of PcG proteins in cell differentiation and 48 development from plants to mammals 9,10 . Polycomb Response Elements (PREs) are DNA 49 elements that can recruit PcG proteins, but they also recapitulate the memory function of the PcG-50 when combined with early acting, region-specific enhancers in transgenes, they maintain transgene 51 repression in a PcG-dependent manner only in regions where the early enhancer was not active 52 1,11,12 . PREs contain a high density of binding sites for transcription factors that can recruit PcG 53 proteins through physical interactions 12 . However, the widespread expression, binding pattern, 54 and properties of factors that bind PREs cannot explain how PREs can exist in alternate, 55 transcription-history dependent states to maintain restricted patterns of gene expression, or how 56