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The human genome contains some thousands of long non coding RNAs

The human genome contains some thousands of long non coding RNAs (lncRNAs). coding RNAs are 99755-59-6 manufacture coordinately induced during neuronal differentiation, and that their expression is usually regulated by different mechanisms. While the production of miR-125b-1 relies on transcriptional regulation, linc-NeD125 is controlled at the post-transcriptional level, through modulation of its stability. We also demonstrate that linc-NeD125 functions independently of the hosted microRNA, by reducing cell proliferation and activating the antiapoptotic factor BCL-2. neuronal differentiation of NB and MB cells. We identify the minimal promoter driving its constitutive expression in proliferating conditions and unveil a post-transcriptional regulatory mechanism responsible for its induction upon the differentiation stimulus. We also demonstrate here that linc-NeD125 may act autonomously from the hosted miRNA by negatively regulating cell proliferation and apoptosis. Results Identification of a novel, neuronal-induced lincRNA as the host gene for miR-125b-1 UCSC genome browser (assembly 2009)25 shows that miR-125b-1 is located on chromosome 11q23 and embedded inside the third intron of a RefSeq26 annotated non-protein coding RNA, named MIR100HG (hereafter, RefSeq MIR100HG; NCBI Reference Sequence: “type”:”entrez-nucleotide”,”attrs”:”text”:”NR_024430.1″,”term_id”:”212549571″,”term_text”:”NR_024430.1″NR_024430.1). In the same intron, at a distance of about 45?kb from miR-125b-1, miR-100 and let-7a-2 are also positioned (Fig.?1A upper scheme). Physique 1. Structure and expression profile of miR-125b-1 made up of transcripts. (A) Genomic business of MIR125B1 locus, according to UCSC genome browser. RefSeq (upper panel) and Non RefSeq (lower panel) genes are depicted. The arrow points to non RefSeq MIR100HG … To correlate pri-miR-125b-1 expression with that of its putative host gene MIR100HG, we profiled their expression in proliferating differentiating cells by qRT-PCR. As model system, we used 99755-59-6 manufacture the BE(2)-C cell line deriving from human Neuroblastoma, a pediatric tumor of the sympathetic nervous system. Treatment of BE(2)-C cells with Retinoic Acid (RA) inhibits proliferation and triggers neuronal differentiation.12 The main advantage of this model system is the production in 6 days of a homogeneous populace of cells, displaying neuronal morphology (Fig.?S1A) and showing modulation of several neuronal differentiation markers.27 We treated BE(2)-C cells with RA for specific time points (0, 3 and 6?days) and verified by qRT-PCR: i) the increased expression of neuronal differentiation markers, as the neuropeptide (Inhibitor of DNA binding-2) and the pro-proliferative factor (Fig.?S1B). In parallel, the expression of the putative miR-125b-1 host gene, RefSeq MIR100HG, was analyzed. Its expression was evaluated using specific combinations of oligonucleotides designed to amplify the exonic sequences of interest (Fig.?1B and Fig.?S2A). We found that RefSeq MIR100HG was not significantly expressed either in proliferating (0?days) or in differentiating (3 and 6?days) cells (Fig.?1C, left panel and Fig.?S2B). Differently, pri-miR-125b-1 was induced upon RA treatment, reaching a peak of expression at 6 days (Fig.?1C). These results indicate that RefSeq 99755-59-6 manufacture MIR100HG is not the host gene for miR-125b-1 in NB cell lines induced to neuronal differentiation. We also analyzed the expression profile of lncRNA_N2 (AK0191713 transcript), previously reported in a human transcriptome analysis28 and described as the miR-125b-1, miR-100 and let-7a-2 host gene with a crucial function in neuronal differentiation of human neural stem cells.29 We found that this transcript was almost undetectable both in undifferentiated and in RA-treated BE(2)-C cells (Fig.?2SC). Other predicted RNA species that might host miR-125b-1 were then searched in the UCSC genome browser. The non RefSeq annotated genes, depicted in the lower scheme of Fig.?1A, were analyzed. Only one of them, also named MIR100HG (pointed by an arrow in Fig.?1A lower scheme), was found to be expressed and upregulated during neuronal differentiation (Fig.?S2D). This transcript showed the same expression profile as pri-miR-125b-1, indicating it may be the miR-125b-1 host gene in our cellular system (Fig.?1B lower Rabbit Polyclonal to SLC25A12 scheme 99755-59-6 manufacture andFig.?1C left panel). Therefore, it was renamed linc-NeD125 (Neuronal Differentiation lincRNA hosting miR-125). Non RefSeq MIR100HG, here renamed linc-NeD125, was reported in UCSC genome browser as a non coding RNA, since it does not harbour putative Open Reading Frames (ORFs) encoding polypeptides longer than 100 amino acids.30 To further verify its non coding nature, we analyzed the occurrence of small ORFs by the sORF finder program (http://evolver.psc.riken.jp/). We found that linc-NeD125 could potentially encode three short peptides of 16, 17 and 27 amino acids (Fig.?S3A). However, transcription/translation assay of the mature transcript indicated that it does not display any coding capacity (Fig.?S3B), and can therefore be referred to as a long non coding RNA. To verify whether linc-NeD125 is usually a neuronal-induced transcript, we profiled its expression in other differentiation models. As an additional neural system, we used the D283 Med cell line, that can also be induced toward neuronal differentiation by RA-treatment31. However, differently from BE(2)-C cells, the D283 Med cell line originates from human Medulloblastoma, a tumor of the CNS. Moreover, we used two human Acute Promyelocytic Leukemia (APL) cell lines, the NB4 and HL-60 cells, induced to granulocytic differentiation by RA-treatment32. Further, we tested linc-NeD125 expression in human primary.