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Mir-125 in Normal and Malignant Hematopoiesis

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Mir-125 in Normal and Malignant Hematopoiesis Leukemia (2012) 26, 2011–2018 & 2012 Macmillan Publishers Limited All rights reserved 0887-6924/12 www.nature.com/leu SPOTLIGHT REVIEW MiR-125 in normal and malignant hematopoiesis L Shaham1,2, V Binder3,4,NGefen1,5, A Borkhardt3 and S Izraeli1,5 MiR-125 is a highly conserved microRNA throughout many different species from nematode to humans. In humans, there are three homologs (hsa-miR-125b-1, hsa-miR-125b-2 and hsa-miR-125a). Here we review a recent research on the role of miR-125 in normal and malignant hematopoietic cells. Its high expression in hematopoietic stem cells (HSCs) enhances self-renewal and survival. Its expression in specific subtypes of myeloid and lymphoid leukemias provides resistance to apoptosis and blocks further differentiation. A direct oncogenic role in the hematopoietic system has recently been demonstrated by several mouse models. Targets of miR-125b include key proteins regulating apoptosis, innate immunity, inflammation and hematopoietic differentiation. Leukemia (2012) 26, 2011–2018; doi:10.1038/leu.2012.90 Keywords: microRNA; hematopoiesis; hematological malignancies; acute myeloid leukemia; acute lymphoblastic leukemia MicroRNAs (miRNAs) are 21–23-nucleotide non-coding RNAs that nucleotides with the seed region of miR-125b (ebv-miR-BART21-5p, have crucial roles in fundamental biological processes by ebv-miR-BART8 and rlcv-miR-rL1-25). In humans, as in most of the regulating the levels of multiple proteins. They are transcribed genomes, there are two paralogs (hsa-miR-125b-1 on chromosome as primary miRNAs and processed in the nucleus by the RNase III 11 and hsa-miR-125b-2 on chromosome 21), coding for the same endonuclease DROSHA to liberate 70-nucleotide stem loops, the mature sequence. There is no obvious correlation between precursor miRNA. The precursor miRNAs are then exported from the number of paralogs and the complexity of the genome, as the nucleus to the cytoplasm by Exportin 5/RanGTP, where further the genome of the zebrafish (Danio rerio) contains three paralogs cleavage by the second RNase III enzyme DICER releases the of miR-125b, whereas there is only one copy in chimpanzees (Pan mature miRNAs.1–3 MiRNAs bind mainly to the 30untranslated paniscus), pufferfish (Tetraodon nigroviridis) or worms (Schistosoma region of mRNAs by direct base-pairing to the 50miRNA japonicum, Schmidtea mediterranea). seed region, resulting either in repression of gene translation1 In addition to paralogs that code for the same mature or induction of mRNA degradation.2 Recent data reveals, sequence, there are homologs that code for different mature however, that miRNA regulation entails a far more complex sequences, which contain the same seed region and therefore posttranscriptional control than initially anticipated.3 might have similar functions. In the human genome, the homolog Many miRNAs are genomically organized as clusters and are co- miR-125a is encoded on chromosome 19. In some other species transcribed from a single promoter as a single polycistronic (Danio rerio), there are three homologs encoded on different transcript, although inconsistent expression of members can be chromosomes (miR-125a, -125b and -125c), all sharing the same detected in some miRNA clusters.4,5 seed region (Figure 1a). Interestingly, miR-351, which is encoded Here, we review the role of miR-125 in normal and malignant only in the mouse and rat genome, has the same seed region as hematopoiesis. MiR-125, a highly conserved miRNA transcribed miR-125b. from three different clusters, has recently emerged as a key In humans, miR-125b-2 is organized in a cluster with miR-99a regulator of HSCs. It has been shown to be dysregulated in and let-7c. Hsa-miR-125b-2 is encoded B50 kb downstream of multiple malignancies and to affect cell survival, differentiation hsa-miR-99a and hsa-let-7c, which are located about 650 bp from SPOTLIGHT and proliferation through the suppression of multiple targets. each other. Although the distance of 50 kb is greater than the These fascinating recent discoveries raise many questions regard- standard distance for a cluster, analysis of various genomes shows ing its regulation, interactions with additional co-transcribed that this region is highly conserved in its organization, and miRNAs and mechanisms of activity. therefore this region is considered to be a cluster. A second cluster (on chromosome 11 in humans) contains the paralog miR-125b-1 with let-7a-2 and miR-100, which both differ in only one GENOMIC ORGANIZATION OF THE MIR-125B CLUSTER nucleotide outside of the seed region of their family members, MiR-125b is highly conserved among mammals, vertebrates let-7c and miR-99a, respectively. The genomic organization of and nematodes. Although the nomenclature sometimes differ this second cluster is similar to that of the first. A third cluster (for example cel-lin-4 in Caenorhabditis elegans), the seed region is (on chromosome 19 in humans) contains miR-99b, let-7e and the same throughout all species containing miR-125b (Figure 1a). miR-125a. Here, all three miRNAs are encoded close to each In viral genomes, there is a maximum concordance of only six other (o1 kb). 1Department of Pediatric Hemato-Oncology, Functional Genomics and Childhood Leukemia Research, Cancer Research Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel; 2The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel; 3Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University, Du¨sseldorf, Germany; 4Stem Cell Program and Division of Hematology/Oncology, Children’s Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA and 5Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel. Correspondence: Professor S Izraeli, Department of Pediatric Hemato-Oncology, Functional Genomics and Childhood Leukemia Research, Cancer Research Center, Sheba Medical Center, Tel Hashomer, Ramat Gan 52621, Israel. E-mail [email protected] The study is partial fulfillment of the requirements for completing a PhD degree (Lital Shaham) for Bar-Ilan University, Ramat Gan, Israel. Received 27 April 2011; revised 12 March 2012; accepted 13 March 2012; accepted article preview online 29 March 2012; advance online publication, 24 April 2012 Mir 125 in hematopoiesis and leukemia L Shaham et al 2012 Seed region Host gene‚ MiR-100-let-7a-2 cluster host gene‘ 1 2 [-] Chr 11 Hsa-miR-100 Hsa-let-7a-2 Hsa-miR-125b-1 50 kb 6 kb 47 kb Host gene‚ LINC00478‘ 3 4 [+] Chr 21 SPOTLIGHT Hsa-miR-99a Hsa-let-7c Hsa-miR-125b-2 470 kb <1 kb 50 kb 5 [+] Chr 19 Hsa-miR-99b Hsa1-let-7e Hsa-miR-125a <1 kb <1 kb Figure 1. (a) The seed region of homologs and orthologs of miR-125 is highly conserved throughout different species. (b) Genomic organization of the miR-cluster containing miR-125, shown together with their host genes and potential promoter regions. 1: A putative promoter predicted by Long et al.,7 Wang et al.,9 Ozsolak et al.8 and Corcoran et al.6 2: A putative promoter predicted by Long et al.,7 Wang et al.,9 and Corcoran et al. 6 3: A putative promoter predicted by Long et al.,7 Wang et al.,9 Ozsolak et al.,8 Corcoran et al.,6 and Montey et al.11 4: A putative promoter predicted by Corcoran et al.,6 and Ozsolak et al.8 5: A putative promoter predicted by Long et al.,7 Wang et al.,9 Ozsolak et al.,8 and Corcoran et al.6 Dashed lines indicate structures that were annotated only in a single study. This composition suggests that the cluster containing miR-125a the miR-125b clusters. Whereas most of the studies agree on probably has only one promoter and is transcribed as one hsa-miR-99a, hsa-let-7c and hsa-miR-125b-2 being intragenic transcript, whereas the cluster containing miR-125b may (host gene LINC00478, chr 21: 17.442.842–17.982.094; contain an alternative promoter, making it possible to transcribe NC_000021.8, NCBI build 37.2) and hsa-miR-100, hsa-let-7a-2, miR-125b solely (Figure 1b).6–9 This hypothesis is supported by hsa-miR-125b-1, hsa-miR-99b, hsa-let-7e and hsa-miR-125a being recent research predicting miRNA promoters by combining intergenic, Corcoran et al.6 claim that hsa-miR-100 and hsa-let-7a-2 bioinformatic analysis of nearby upstream DNA regulatory are also intragenic (host gene, non-protein coding, chr 11: elements (transcription start sites (TSS), conserved transcription 121.959.811–122.073.770; NC_000011.9, AK091713). Several factor-binding sites, TATA boxes, A/B boxes) and epigenetic independent putative promoters have been described modifications (CpG islands, histone modifications, nucleosome (Figure 1b). One that drives co-expression of hsa-miR-100 and positioning patterns) with chromatin immunopreciptiation hsa-let-7a-2 independent of their potential host gene,6–9 one that screens or reporter assays.6–11 drives co-expression of hsa-miR-99a and hsa-let-7c independent of It seems that about half of the miRNAs located in introns their host gene,6–9,11 and another that drives co-expression of protein-coding genes (B60%) contain putative promoters of hsa-miR-99b, hsa-let-7c and hsa-miR-125a.6–9 Hsa-miR-125b- regulating transcription independent of their host gene.7 This is 1(refs 6,7,9) and hsa-miR-125b-2(refs 6,8) are predicted to be expressed also supported by the observed discrepancy in expression of from an independent promoter. several miRNAs and their host genes.12,13 Ozsolak et al.8 showed In summary, all three human homologs of miR-125 are involved that intronic miRNAs having independent transcription initiation in a cluster containing members of the miR-99 and let-7 family.
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