The Piwi-piRNA pathway is active in animal germ cells where its functions are required for germ cell maintenance and gamete differentiation. Piwi proteins and piRNAs have been detected outside germline tissue in multiple phyla, but activity of the pathway in mammalian somatic cells has been little explored. In particular, Piwi expression has been observed in cancer cells, but nothing is known about the piRNA partners or the function of the system in these cells. We have surveyed the expression of the three human Piwi genes, Hiwi, Hili and Hiwi2, in multiple normal tissues and cancer cell lines. We find that Hiwi2 is ubiquitously expressed; in cancer cells the protein is largely restricted to the cytoplasm and is associated with translating ribosomes. Immunoprecipitation of Hiwi2 from MDAMB231 cancer cells enriches for piRNAs that are predominantly derived from processed tRNAs and expressed genes, species which can also be found in adult human testis. Our studies indicate that a Piwi-piRNA pathway is present in human somatic cells, with an uncharacterised function linked to translation. Taking this evidence together with evidence from primitive organisms, we propose that this somatic function of the pathway predates the germline functions of the pathway in modern animals.

In the post‐genomic era, thousands of putative noncoding regulatory regions have been identified, such as enhancers, promoters, long noncoding RNAs (lncRNAs), and a cadre of small peptides. These ever‐growing catalogs require high‐throughput assays to test their functionality at scale. Massively parallel reporter assays have greatly enhanced the understanding of noncoding DNA elements en masse. Here, we present a massively parallel RNA assay (MPRNA) that can assay 10,000 or more RNA segments for RNA‐based functionality. We applied MPRNA to identify RNA‐based nuclear localization domains harbored in lncRNAs. We examined a pool of 11,969 oligos densely tiling 38 human lncRNAs that were fused to a cytosolic transcript. After cell fractionation and barcode sequencing, we identified 109 unique RNA regions that significantly enriched this cytosolic transcript in the nucleus including a cytosine‐rich motif. These nuclear enrichment sequences are highly conserved and over‐represented in global nuclear fractionation sequencing. Importantly, many of these regions were independently validated by single‐molecule RNA fluorescence in situ hybridization. Overall, we demonstrate the utility of MPRNA for future investigation of RNA‐based functionalities.

Summary 27One of the biggest surprises since the sequencing of the human genome has been the discovery 28 of thousands of long noncoding RNAs (lncRNAs) [1][2][3][4][5][6] . Although lncRNAs and mRNAs are similar 29 in many ways, they differ with lncRNAs being more nuclear-enriched and in several cases 30 exclusively nuclear 7,8 . Yet, the RNA-based sequences that determine nuclear localization remain 31 poorly understood [9][10][11] . Towards the goal of systematically dissecting the lncRNA sequences that 32 impart nuclear localization, we developed a massively parallel reporter assay (MPRA). Unlike 33 previous MPRAs 12-15 that determine motifs important for transcriptional regulation, we have 34 modified this approach to identify sequences sufficient for RNA nuclear enrichment for 38 human 35 lncRNAs. Using this approach, we identified 109 unique, conserved nuclear enrichment regions, 36originating from 29 distinct lncRNAs. We also discovered two shorter motifs within our nuclear 37 enrichment regions. We further validated the sufficiency of several regions to impart nuclear 44RNA subcellular localization provides a fundamental mechanism through which cells modulate 45 and utilize the functions encoded in their transcriptomes 16 . This spatial layer of gene regulation is 46 known to be critical in a variety of contexts, including asymmetric cell divisions 17 , embryonic 47 development [18][19][20] , and signal transduction 21 . Previous work has identified a small number of cis-48 acting mRNA localization elements, using genetic approaches or hybrid reporter constructs to 49 decipher sequences required for localization to different parts of the cell 16,18 . These elements are 50. CC-BY-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/189654 doi: bioRxiv preprint first posted online Sep. 15, 2017; often located in 3´ untranslated regions (UTRs), and range from five to several hundred 51 nucleotides in length [9][10][11]18 . Yet, the sequences and structures responsible for RNA localization 52 remain inchoate. In contrast to mRNAs that are mostly localized outside the nucleus, lncRNAs 53 are enriched or retained in the nucleus. Increasing evidence suggests that many lncRNAs may 54 reside in the nucleus for the purpose of regulating nuclear processes, including formation of 55 paraspeckles, topological organization of the nucleus, and regulation of gene expression 1,3,4,22 . 56However, while it is now evident that lncRNAs have important functions in the nucleus 22 , very little 57 is known about specific sequence elements driving their nuclear enrichment 9-11 . 59To elucidate which sequences drive lncRNA nuclear enrichment, we developed a high-throughput 60 approach for identifying nuclear enrichment elements. Our approach, derived from a massively 61 parallel reporter assay (MPRA) [12][13][14][15] 23 , is based on a previous assay demonstrating that the native 62 cytosolic loc...

Keywords Drosophila melanogaster; embryogenesis; lncRNA; spatiotemporal transcriptome; neurogenesis McCorkindale et al. "lncRNAs in Drosophila neurogenesis" 2 Summary statementWe present a spatiotemporal transcriptome during early Drosophila embryonic nervous system development, revealing a complex cell type-specific network of mRNAs and lncRNAs. AbstractCell type specification during early nervous system development in Drosophila melanogaster requires precise regulation of gene expression in time and space. Resolving the programs driving neurogenesis has been a major challenge owing to the complexity and rapidity with which distinct cell populations arise. To resolve the cell type-specific gene expression dynamics in early nervous system development, we have sequenced the transcriptomes of purified neurogenic cell types across consecutive time points covering critical events in neurogenesis.The resulting gene expression atlas comprises a detailed resource of global transcriptome dynamics that permits systematic analysis of how cells in the nervous system acquire distinct fates. We resolve known gene expression dynamics and uncover novel expression signatures for hundreds of genes among diverse neurogenic cell types, most of which remain unstudied.We also identified a set of conserved and processed long-noncoding RNAs (lncRNAs) that exhibit spatiotemporal expression during neurogenesis with exquisite specificity. LncRNA expression is highly dynamic and demarcates specific subpopulations within neurogenic cell types. Our spatiotemporal transcriptome atlas provides a comprehensive resource to investigate the function of coding genes and noncoding RNAs during critical stages of early neurogenesis.