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H19X-Encoded Mir-424(322)/-503 Cluster

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H19X-Encoded Mir-424(322)/-503 Cluster Cellular and Molecular Life Sciences https://doi.org/10.1007/s00018-018-2971-0 Cellular andMolecular Life Sciences REVIEW H19X‑encoded miR‑424(322)/‑503 cluster: emerging roles in cell diferentiation, proliferation, plasticity and metabolism Fan Wang1,2 · Rui Liang2 · Neha Tandon2 · Elizabeth R. Matthews2 · Shreesti Shrestha2 · Jiao Yang1,2 · Benjamin Soibam3 · Jin Yang1 · Yu Liu2 Received: 15 September 2018 / Revised: 5 November 2018 / Accepted: 13 November 2018 © The Author(s) 2018 Abstract miR-424(322)/-503 are mammal-specifc members of the extended miR-15/107 microRNA family. They form a co-expression network with the imprinted lncRNA H19 in tetrapods. miR-424(322)/-503 regulate fundamental cellular processes includ- ing cell cycle, epithelial-to-mesenchymal transition, hypoxia and other stress response. They control tissue diferentiation (cardiomyocyte, skeletal muscle, monocyte) and remodeling (mammary gland involution), and paradoxically participate in tumor initiation and progression. Expression of miR-424(322)/-503 is governed by unique mechanisms involving sex hormones. Here, we summarize current literature and provide a primer for future endeavors. Keywords H19X · miR-424 · miR-322 · miR-503 · Tumor suppressor gene · EMT · Hypoxia Introduction The miR-15/107 family of microRNAs shares the “AGC​ AGC​” sequence within the “seed” region, starting at either MicroRNAs (miRNAs) are small non-coding RNAs 18–24 the frst or the second nucleotide from the 5′ end [2]. They nucleotides (nt) in length that regulate posttranscrip- are critical regulators of cell division, apoptosis, stress tional gene expression [1]. miRNA genes are transcribed response and metabolism, and involved in cancer, cardiovas- by RNA polymerase II to produce pri-miRNA, which is cular and neurodegenerative disorders. miR-424 (ortholog cleaved by Drosha to give rise to hairpin-structured pre- of rodent miR-322) and miR-503 are mammal-specific miRNA, ~ 60–100 nt in length. Exportin transports pre- members of the miR-15/107 family. They are encoded as miRNA into the cytoplasm, where it is processed by Dicer one cluster by H19X, located in human Xq26.3 [3]. Their to produce a ~ 22 nt double-stranded intermediate compris- expression is more dynamic and tissue restrictive than other ing the mature miRNA strand and its complementary strand. miR-15/107 family members. miR-424(322)/-503 regulate The mature miRNA is loaded into the RNA-induced silenc- fundamental processes such as cell cycle, epithelial-to-mes- ing complex (RISC) where it binds to the 3′ UTR of tar- enchymal transition and hypoxia, drive tissue diferentia- get mRNAs by partial sequence complement in the “seed” tion and remodeling, and paradoxically participate in tumor region, causing degradation of the mRNA transcript or inhi- initiation and progression. Here, we summarize a decade bition of its translation. of literature and provide a primer for future investigation concerning miR-424(322)/-503. * Jin Yang [email protected] miR‑424(322)/‑503 are unique members * Yu Liu [email protected] of the miR‑15/107 miRNA family 1 Department of Oncology, The First Afliated Hospital The miR‑15/107 family of miRNAs of Xian Jiaotong University, Xi’an 710061, Shaanxi, China 2 Department of Biology and Biochemistry, University The miR-15/107 family includes ten miRNAs based on the of Houston, Houston, TX 77204, USA presence of “AGC​AGC​” in the “seed” region situated at 3 Computer Science and Engineering Technology, University positions 2–7 from the 5′ end of mature microRNAs [2]. of Houston-Downtown, Houston, TX 77002, USA Vol.:(0123456789)1 3 F. Wang et al. 1 3 H19X‑encoded miR‑424(322)/‑503 cluster: emerging roles in cell diferentiation,… ◂Fig. 1 Members of the miR-15/107 microRNA family. a 10 micro- Association with the imprinted paradigm lncRNA, RNAs sharing “AGC AGC ” within the “seed” region. b A phyloge- H19 netic tree of miR-15/107 family members from Homo sapiens (hsa), Monodelphis domestica (mdo), Macaca mulatta (mml), Mus mus- culus (mmu), Ornithorhynchus anatinus (oan), Gallus gallus (gga) Necsulea et al. surveyed eight organs in 11 tetrapod spe- and Xenopus tropicalis (xtr). miR-103 and -107 are the least closely cies for the expression profles of ncRNAs [3]. They have related, and omitted in the plot. miR-424(322) is most closely related identifed approximately 400 lncRNA genes that are at least to miR-15c in mdo, oan, gga and xtr, while miR-503 is most closely related to miR-16c in gga, oan and xtr 300 million years old. These lncRNAs evolve rapidly in terms of sequence and expression levels, but conserve tis- sue specifcity. One evolutionarily conserved co-expression However, there is no consensus regarding the criteria of network is predicted to regulate placenta development. This miRNA family classifcation; distinct classifcations were network comprises H19 and the lncRNA that encodes the proposed for these ten miRNAs [4–9]. We have adopted miR-424(322)/-503 cluster, which was hence named H19X. the classifcation by Finnerty et al. [2], but this is likely H19 is best known as the imprinting paradigm [24–29]: to change with new functional data accumulated and new except under rare pathological conditions, the H19 gene miRNAs identifed (Fig. 1a). is only expressed from the maternal allele, while the adja- miR-15/107 family members are only expressed in cent IGF2 gene is only expressed from the paternal allele. chordates, with several being mammal specifc (miR-195, Imprinting provides an important mechanism of gene dose -497, -503, -424 and -646) [2]. Genes of miR-15/107 fam- control, allowing expression from only one allele, while the ily members are genomically associated with protein-cod- other is epigenetically silenced. Many imprinted genes are ing genes or lncRNAs. They also show conserved tandem involved in placenta development; H19 regulates placenta organization: miR-15 with miR-16, miR-424(322) with growth in late gestation, via its “spinof” miR-675 [30]. miR-503, and miR-497 with miR-195. To explore the Overexpression of H19 causes embryonic and perinatal evolutionary relation of miR-424(322)/-503 to others, we lethality [31]. H19 is quickly downregulated in most tissues have updated a phylogenetic tree originally built by Necsu- except skeletal muscles after birth [32, 33]. lea et al. [3], using “stem-loop” pre-miRNA sequences in H19X resembles H19 in several ways. First, H19X may Homo sapiens, Monodelphis domestica, Macaca mulatta, be imprinted (see following section). Second, miR-424 is Mus musculus, Ornithorhynchus anatinus, Gallus gallus downregulated by hypoxia in trophoblasts, and higher miR- and Xenopus tropicalis extracted from miRBase. miR- 424 levels are associated with fetal growth restriction, indi- 424 (together with miR-322 and miR-15c) and miR-503 cating a role in placenta growth regulation [34, 35]. Third, (together with miR-16c) represent two distinct subfamilies expression of H19X is striated muscle restricted during related to miR-15 and miR-16, respectively (Fig. 1b). embryogenesis. In addition to these suggestive evidences, Supporting a common phylogenetic origin, miR-15/107 it will be important to know if H19 and H19X are mutually family members have similar expression patterns and func- regulatory, and if they cooperate with or compensate for tions. miR-15a, -15b, -16, -322 and -503 are dynamically each other in genetic models. Addressing these questions upregulated during serum starvation and contact inhi- may provide insights into the intricate mechanisms of gene bition, with miR-503 showing the highest fold change dose control and coordination in embryonic development. [10]. miR-15a, -15b, -16 and -497 are essential for the switch from expansion to diferentiation in precursor B Structure of the H19X locus lymphocytes [11]. On the other side, loss of either miR- 15a/-16-1 or miR-15b/-16-2 by genomic deletion causes The human H19X locus encodes seven non-coding RNAs, B cell chronic lymphocytic leukemia [12–14]. miR-15/- including a number of microRNAs (miR-424, 503, 542, 16 family members also drive NK cell maturation, by 450-1, 450-2, and 450b) and a long non-coding RNA targeting Myb [15]. miR-15/107 family members inhibit (miR503HG), spanning a region of ~ 7 kb pairs on Xq26.3 cell proliferation in many tissue types. They are broadly (Fig. 2). The microRNAs are highly conserved in mam- upregulated after birth and cause cardiomyocyte mitotic mals. The lncRNA has similar expression patterns as miR- arrest in rodents [16, 17]. Additionally, miR-15/107 fam- 424(322)/-503, agreeing with being the host gene of the ily members respond to cellular stresses such as hypoxia, miRNA cluster. The ENCODE project has identifed clus- ischemia, ultraviolet, environmental toxin, etc., and induce tered H3K27Ac and DNAse I signals, while the GeneHancer adaptive changes in angiogenesis and cellular metabolism project has identifed a high-confdence cluster of regulatory [18–23]. As will be detailed in the rest of this essay, the elements in the upstream regulatory region and gene bod- function of miR-424(322)/-503 overlaps with other family ies of miR-424 [36], miR-503 and miR503HG, suggesting members, but is under unique temporal and spatial regula- that the H19X locus is actively transcribed and intricately tions and works in distinct processes. regulated. 1 3 F. Wang et al. Fig. 2 Schematic diagram of the H19X locus. miR-424, -503, -542, regulatory regions as well as gene bodies, active epigenetic marks -450b, -450a1 and -450a1, and at least one lncRNA, miR503HG, are including H3K27Ac and DNAse I-hypersensitive clusters were encoded in the H19X locus. H19X spans approximately 7 k nucleo- identifed by the ENCODE project; a high-confdence enhancer/pro- tides on the minus strand of Xq26.3. It is unknown if other adjacent moter cluster was identifed by the GeneHancer project. Information ncRNAs, such as linc00629, are related to H19X.
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