Role of NF-KB1 in Regulation of Micro RNA

INTRODUCTION

NF-KB is is an complex formed by five NF-KB-Rel family members namely NF-KB1(p50), NF-KB2(p52), Rel-A(p65), Rel-B, and c-rel (1). NF-KBs family regulates the expression of many genes involved in various physiological processes viz. cell proliferation, survival, inflammation, apoptosis and immunity (2). All these dimeric subunits retained in cytoplasm in a complex with inhibitory peptide (Ikbs) (1). Upon stimulation by various pathogens and their products, mitogens, stress, cytokines they migrate to nucleus with their interacting partner in either homodimer or heterodimer form to perform target gene expression. Unlike the other subunits, p50 doesn‘t have transactivation domain (TAD) and hence cannot regulate target gene expression of its own. Transcription factors (TFs) usually control gene expression by binding with either promoter or enhancer region of respective genes encoding either protein or encoding microRNAs (miRNA) precursors. microRNAs are genes encoding ~22 bp long, small non-coding RNAs, also known as miRs. TFs can regulate the expression of specific miRNAs and in turn miRNAs can also target respective TF mRNAs. Multiple miRNAs have been shown to alter NF-KB activity targeting either IKK complex or NF-KB individual subunits (3-5). NF-KB is known to have a major role in regulation of various miRNAs viz mir-9, mir-16, however, in this review we demonstrate for the first time, the regulation of set of miRNAs as well as their targets by NF-KB1partner protein. The NF-KB-miRNA network has been shown to regulate various physiological and pathological conditions such as inflammation, immune, and stress-like responses (6). Aberrant miRNAs expressions have been detected during inflammation and cancer.

NF-KB1 subunits have both positive as well as negative regulation of its wide range of target gene expression (1). NF-KB1 homodimers are known to suppress target genes (7) where-as NF-KB1 biding with other NF-KB subunit can activate various gene expressions. Here, we have shown that NF-KB1 is regulating 29 microRNAs in human (table 1). The genomic location of total 29 miRNA regulated by NF-KB1 is provided in table 2. The NF-KB1 targeting these microRNAs were retrieved using TransmiR v2.0 (8) database. Here, we consider only the literature-curated TF-miRNA regulation and repression. From human microRNA disease database (HMDD) (9), we found many of these miRNAs are associated with cancer. There is also feedback regulation by various miRNA which is a new emerging concept of its regulation. Two of these 29 microRNAs (miR-9 and miR-16) acts as feedback loop mechanism (Figure 1). These two and other miRs regulating NF-KB1 is also provided in table 3. Both these miRNAs bind to the 3‘ UTR of NF-KB1 gene and regulates its expression. It is also known that miR-16 significantly inhibits myoblast proliferation and promotes apoptosis (10). Another miRNA (miR-9) inhibits the growth of the gastric adenocarcinoma cell line MGC803 in vitro and in vivo (10). We predicted miR-340 have two binding sites in the 3‘UTR of the NF-KB1 gene which could be a potential miRNA to inhibit the 279 protein coding gene expressions. From computational and functional analysis, we found that most of these genes were positively regulating the immune system process and there carried out molecular functions like cytokine receptor binding.

Figure1. The combinatorial NF-KB1 regulatory network. The nodes in the network represent the NF-KB1 (red), mRNAs (cyan) and miRNAs (yellow). The edges denote the physical interaction and direction of regulation.

In order to identify the disease association of microRNA genes which are regulated by NF-KB1, we subjected these microRNAs to miRNet tool. It is a user-friendly, integrated tool suite designed for comprehensive analysis and functional interpretation of miRNAs. We found majority of these microRNAs are associated with lung cancer, prostate cancer, breast cancer, hematological disease, pancreatic cancer, squamous cell carcinoma, head and neck, muscular disorder, ovarian cancer, colorectal cancer and gastrointestinal cancer. In order to understand the functional role of these microRNA, its targets were identified using four standard and widely used miRNA target prediction programs: miRanda, TargetScan, PITA and PICTAR. We included the experimentally validated miRNA targets from miRTarBase and miRecords databases. We consider the genes which are predicted by all the four prediction programs. A total 2808 genes are regulated by 29 microRNAs.

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School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India shilpi5.biotech@gmail.com