What Are The Significance Of Long Non-Coding Rnas In Development And Disease

The company ‘Invivogen’ made a transfectable and simple-to-use plasmid, called psiRNA™, that allows the production of siRNAs within the cells. To transfect means to introduce foreign material into eukaryotic cells. psiRNA is an RNA polymerase III-based plasmid that produces ‘short hairpin’ RNAs (shRNAs). shRNAs are more stable than synthetic siRNAs and since they are continuously expressed within the cells rather than having to be injected into the cytoplasm, this method permits long-lasting silencing of the BLG gene.

Methyl-seq was performed on genomic DNA isolated from lymphoblasts, providing DNA methylation patterns of the entire genome for each individual. Several loci displayed hypermethylation in both BPD patients compared to their unaffected siblings. When the lymphoblast cells were treated with a therapeutic dose of lithium (1mM), results showed hypomethylation at several loci. Among these, one locus had been hypermethylated in the BPD cells. This differentially methylated locus was where the novel lncRNA, LINC00486, was located. Sequencing data has indicated LINC00486 is found in human chromosome 2 and is flanked by genes TTC27 and LTBP1. A mouse homolog has yet to be discovered. Three distinct RNAs are predicted to be transcribed from the LINC00486 locus, each of different lengths and containing different exons.

Structurally, miRNAs are initially transcribed from the genome as a long primary transcript that are cleaved or undergoes sequential processing by the RNAse III endonucleases Drosha and Dicer to yield the 17-23 mature nucleotide species (Kim, 2005). Mature miRNAs enters the RNA-induced silencing complex (RISC), thus a multiprotein complex that separate the mature strand from passenger strand and assists the interaction of mRNAs with miRNA that contain complementary sequences (Bader, 2012). As a result, mRNAs targeted by miRNA loads are either degraded or silenced in order not to be translated into protein. In the genome, a given miRNA can regulate several hundred transcripts whose molecules function within various cellular pathways including cell proliferation and apoptosis. To date, more than 50% of the activities of all protein-coding genes in mammals are controlled by miRNAs and greatly contributes to cell-type specific profiles of protein expression

siRNA shows the potential to selectively silence the expression of a disease gene based on the gene’s sequence. By down regulating cancerous transcripts and restoring the wild type function of a gene, siRNA has the potential to play an important role in cancer

In this paper, the necessary RNA data set was generated by subcellular fractionation of the 15 cell lines considered to analyse the human transcriptome. Thus isolated RNAs were classified into two categories long (>200 nucleotides) and short (<200 nucleotides) and the long transcripts were further separated into polyadenylated and non-polyadenylated transcripts.

Studying the interactions of Runx2 and RNAPII with promoters, the experiment demonstrated that 9–10% of genes in the human genome may be regulated by Runx2 in osteosarcoma cells (van der Deen et al., 2012). Runx2 is bound to over 2,000 genes that are actively transcribed based on co-interactions with polymerase (van der Deen et al., 2012). Data also demonstrated that Runx2 interacts with inactive genes that lacked RNAPII (van der Deen et al., 2012). These results confirmed hypothesis that Runx2 is a bi-functional regulator, activating or repressing transcription (van der Deen et al., 2012). An interesting result of this study involved Runx2’s influence on genes involving cell adhesion and motility (van der Deen et al., 2012). Combining data from the immunprecipation and gene expression profiles with siRNA, researchers concluded target genes can be both up-regulated and down-regulated with Runx2 depletion (van der Deen et al., 2012). This result also supports Runx2’s role as a bi-functional regulator of expression in these cells. Depletion of Runx2 decreased motility of U2OS cells (van der Deen et al., 2012). After identifying Runx2 target genes involved in motility, one can concluded depletion of Runx2 lowers cell motility in osteosarcoma cells (van der Deen et al., 2012). All in all, Runx2

MiR-142-3p and mir-142-5p were depleted in Ago-IP profile, compared to total cellular profile, at least two-fold within each cell lines, separately.

The fourth exon of the MECP2 gene is the largest one; it contains a larger than 8.5 kb 3′-untranslated region, with numerous polyadenylation sites that enable the generation of multiple transcripts varying in size. Alternative polyadenylation in the 3′-untranslated region gives rise in a highly expressed 10.1-kb transcript in the foetal brain and a 5-kb transcript in the adult brain (Coy JF.,

Long non-coding RNAs (lncRNAs) are a class of RNAs that are more than 200 nucleotides long (2) and do not encode proteins. LncRNAs regulate a spectrum of biological functions and their misregulation or differential expression contribute to tumerogenesis. Exploiting this feature of lncRNAs make them excellent candidates for cancer therapy. An important indication of cancer is metabolic reprogramming which is indicated by increase in various pathways in cells such as glycolysis, glutaminolysis, Pentose Phosphate Pathway, synthesis of nucleotide and fatty acids, and formation of citrate through TCA cycle (4). Prostate Cancer Gene expression marker 1 (PCGEM1) (3), is a lncRNA that control the reprogramming of metabolic pathways in prostate

Hepatocellular carcinoma (HCC), a lethal liver cancer, has a very poor prognosis and is in dire need of novel targets to develop more effective treatments. The conventional treatment options of surgery and chemotherapy were limited to pre-metastatic HCC; however, a multi-kinase inhibitor, in addition to targeting other factors involved in development and progression of the disease showed promising results in advanced HCC [42]. LncRNAs such as HOTAIR, MALAT1, and H10 are dysregulated and have been suggested to play an essential role in HCC development whereas dysregulation affects proliferation, apoptosis, and metastasis. This is also true for gastric cancer, whereby dysregulation of lncRNAs- HOTAIR, HULC, and H19 are relatively linked to development, metastasis, and prognosis [43]. HCC is also characterized by aberrant expression of miRNAs. Respectively, upregulation and downregulation has been associated with invasion and metastasis, tumor progression, and drug resistance. Meng et al. proposed that aberrantly expressed miRNAs may regulate the expression of certain genes that control cell growth, migration, and invasion. In this study, the expression of miRNA in normal versus tumor tissue was investigated which led to the identification of overexpressed miR-21 in human HCC that could potentially serve as a target for regulating downstream events [44].

JAK2/STAT signaling pathway was one of the most significantly differentially expressed gene sets in BC compared with CP progenitors. This signaling pathway increases the ADAR1 expression in progenitor LSCs and promotes ADAR1-mediated A-to-I editing. Furthermore, ADAR1 impairs biogenesis of tumour suppressive miRNAs, thereby contributing to cancer progression. Since the let-7 miRNA family is also related to self renewal of LSC, it led the authors to investigate the correlation between JAK2/STAT pathway and LIN28B/let-7-axis, they hypothesized that the LIN28B/let-7self-renewal axis may also be disrupted by increased JAK2 signaling. This hypothesis was validated by a lentiviral transduction of BCR-ABL1 in normal progenitor, it shows an

Aim 1.3 – Determine and evaluate the oncogenic lncRNA landscape with validated activity in the neural tube.

Different approaches have been developed in order to understand the function of these genes. The first methods involved random integration of short hairpin RNAs (shRNAs) or short inhibitory RNAs (siRNAs) to inhibit the production of a protein or overexpress it to gain insights about its function. 1

This mechanism inhibits translation of the protein for which the target mRNA codes for and therefore silences that specific gene. RNAi can also involve the use of coded short hairpin RNAs (shRNAs), which are larger dsRNA molecules containing a loop section which folds back on itself to form a double stranded molecule contains a sense and antisense strain. The shRNAs are cleaved into siRNAs when they bind to RISC and can also found in examples of exogenous introduction such as viral or experimental insertion. The ability to post translational control of gene expression with a precise sequence specific manner has been exploited experimentally in researching gene knockdown and loss of function gene analysis.

Heterogeneous ribonucleic proteins (HNRNPs) are a family of RNA binding proteins that play a key role in various metabolic functions of RNA. There are roughly twenty major hnRNPs which are readily found in large quantities in the nucleus and in some cases in the cytoplasm. hnRNPs are expressed throughout all tissues at different levels depending on the hnRNP (Kamma et al. 1994). hnRNP metabolic roles include polyadanilation, shuttling mRNA out of the nuclear envelope, telomere biogenesis and localization. (Dreyfuss et al. 2002). In particular, hnRNP A1 can acts an an antagonist to the SF2/ASF protein, which allows A1 to inhibitor exon splicing and cytoplasm bound transport of mRNA. An example of localization is hnRNP A2, which confers the dendritic mRNA transport of various transcripts when induced by neuronal activity (Muslimov et al. 2002).