MicroRNAs (miRNAs) interact with 3′ untranslated region (UTR) elements of target genes to regulate mRNA stability or translation and thus play a role in regulating many different biological processes, including circadian rhythms. However, specific miRNAs mediating the regulation of essential clock genes remain largely unknown. Because vesicles containing membrane-bound miRNAs are present in the circulatory system, we examined miRNAs predicted to target the clock gene, Bmal1, for evidence of rhythmic fluctuations in circulating levels and modulatory effects on the 3′ UTR activity of Bmal1. A number of miRNAs with Bmal1 as a predicted target were expressed in the serum of mice exposed to LD 12∶12 and of these miRNAs, miR-152 and miR-494 but not miR-142-3p were marked by diurnal oscillations with bimodal peaks in expression occurring near the middle of the day and 8 or 12 hr later during the night. Co-transfection of pre-miR over-expression constructs for miR-494 and miR-142-3p in HEK293 cells had significant effects in repressing luciferase-reported Bmal1 3′ UTR activity by as much as 60%, suggesting that these miRNAs may function as post-transcriptional modulators of Bmal1. In conjunction with previous studies implicating miRNAs as extracellular regulatory signals, our results suggest that circulating miRNAs may play a role in the regulation of the molecular clockworks in peripheral circadian oscillators.

MicroRNA (miRNA) dysregulation frequently occurs in cancer. Analysis of whole blood miRNA in tumor models has not been widely reported, but could potentially lead to novel assays for early detection and monitoring of cancer. To determine whether miRNAs associated with malignancy could be detected in the peripheral blood, we used real-time reverse transcriptase-PCR to determine miRNA profiles in whole blood obtained from transgenic mice with c-MYC-induced lymphoma, hepatocellular carcinoma and osteosarcoma. The PCR-based assays used in our studies require only 10 nanograms of total RNA, allowing serial mini-profiles (20 -30 miRNAs) to be carried out on individual animals over time. Blood miRNAs were measured from mice at different stages of MYC-induced lymphomagenesis and regression. Unsupervised hierarchical clustering of the data identified specific miRNA expression profiles that correlated with tumor type and stage. The miRNAs found to be altered in the blood of mice with tumors frequently reverted to normal levels upon tumor regression. Our results suggest that specific changes in blood miRNA can be detected during tumorigenesis and tumor regression. FindingsDistinct miRNA profiles have been described for many cancers including hematologic and solid malignancies [1][2][3][4][5][6][7][8][9][10][11][12]. Many reports have shown that patterns of miRNA expression differ between normal and cancerous tissues [1][2][3][4][5][6][7][8][9][10][12][13][14][15][16][17][18][19][20]. Gene expression profiling of traditional mRNA targets in whole blood or fractionated leukocytes has also shown correlations with many types of both neoplastic and non-neoplastic human disease, for example renal cancer and Crohn's disease [21][22][23][24][25][26][27][28][29][30]. To investigate whether miRNA patterns in blood correlated with tumorigenesis, we measured by qRT-PCR a panel of miRNAs in MYC-induced transgenic models of tumorigenesis.First, we developed a protocol optimized for collection, storage and shipping of whole mouse blood, RNA extraction from a small volume of stored sample, and qRT-PCR assays for mouse blood miRNA profiling. To enable blood to be collected from mice at different time points and stored so that total RNA extraction and miRNA quantitation could be batch analyzed, mouse blood was mixed with an RNA stabilizing reagent (RNAlater ® Tissue Collec-

Two phenotypic markers of mouse immuno- 2 for review). In several instances, the expression of strainspecific idiotypes has been shown to be due to differences among strains in the structure or repertoire of particular VH gene segments (3-5). A number of immunoglobulin K L-chain polymorphisms have been described (6-12), and in several instances Southern hybridization analyses have provided evidence that mice exhibit restriction enzyme polymorphisms involving VK gene segments (13-15).The present study explores the molecular genetic basis for two mouse VK polymorphisms, the IB-peptide marker (16) and the Efl isoelectric focusing marker (17). Both have been shown to be manifestations of the production of a characteristic group of K-chain V regions (called VKSer) by several strains of mice (C58/J, AKR/J, PL/J, and RF/J) but not by BALB/c and most other strains (18). Expression of these and other K polymorphisms maps to the K locus, which is closely linked to the Lyt-2 and Lyt-3 genes on chromosome 6 (19). Gottlieb et al. (18) have identified myeloma tumors producing K chains corresponding to the IB-peptide marker and Efl1 polymorphism in the C.C58 and C.AKR strains, which differ from BALB/c only in the region of the K and Lyt-2/Lyt-3 loci (20). These myelomas permitted isolation of a cDNA probe specific for the VKSer group, and Southern hybridizations with this probe provided evidence for a single strongly hybridizing VKSer-related gene in liver DNA of all strains tested (13). Restriction enzyme polymorphisms were observed among the strains tested, which correlated completely with expression or nonexpression of the IB-peptide and Efl1 phenotypic markers. Expressor strains contained the IgkVSera allele and nonexpressor strains contained the IgkVSerb allele (13,21).In the present studies, the VKSer-related genes of the expressor strain, C.C58, and the nonexpressor strain, BALB/c, have been cloned from phage libraries of liver DNA. Comparison of their nucleotide sequences demonstrates differences in their coding and 5' flanking regions, which explain the differences observed in expression of the IB-peptide and Efla phenotypic markers. Findings also bear generally upon the nature and origins of polymorphisms in mouse VK genes. MATERIALS AND METHODSCloning of C.C58 and BALB/c V,,Ser Genes. Liver DNA from C.C58 (20) and BALB/cAn mice raised in our colony was extracted according to a modification of the method of Maniatis et al. (22). DNA was subjected to partial digestion with Mbo I (New England Biolabs), and fragments 10-20 kilobases long were cloned into the BamHI site of the X phage vector EMBL3 (Promega Biotec, Madison, WI) according to Abbreviations: V and J, variable and joining regions of immunoglobulin; H chain and L chain, heavy chain and light chain. 9134The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.

The development of simple and rapid methods for the detection of the common genetic mutations associated with cystic fibrosis (CF) requires access to positive-control samples including the 5/7/9T variants of intron 8. We used PCR and a simple multiplex bead-array assay to identify 5/7/9T control samples from 29 commercially available DNA samples. Unpurified PCR products were directly hybridized to color-coded beads containing allele-specific capture probes for 5/7/9T detection. The performance of the assay was investigated using reverse-complement oligonucleotides, individual PCR products, and multiplex PCR products for 5/7/9T detection within a complex CFTR screening assay. Samples were genotyped by grouping the relative signal intensities from each capture probe. Of 29 commercially available DNA samples analyzed, 2 5T/7T, 2 5T/9T, 9 7T/9T, 11 7T/7T, and 5 9T/9T genotypes were identified. The genotype within each sample group was confirmed by DNA sequencing. The assay was compatible with the analysis of 10 to 1000 ng of genomic DNA isolated from whole blood and allowed for the separate identification of primary CFTR mutations from reflex variants. The correct identification of positive controls demonstrated the utility of a simple bead-array assay and provided accessible samples for assay optimization and for routine quality control in the clinical laboratory.

Mutation detection based on ribonuclease cleavage of basepair mismatches in single-stranded RNA probes hybridized to DNA targets was first described over 15 years ago. The original methods relied on RNase A for mismatch cleavage; however, this enzyme fails to cleave many mismatches and has other drawbacks. More recently, a new method for RNase-cleavage-based mutation scanning has been developed, which takes advantage of the ability of RNase 1 and RNase T1 to cleave mismatches in duplex RNA targets, when these enzymes are used in conjunction with nucleic acid intercalating dyes. The method, called NIRCA, is relatively low-cost in terms of materials and equipment required. It is being used to detect mutations and SNPs in a wide variety of genes involved in human genetic disease and cancer, as well as in disease-related viral and bacterial genes. This review describes historical and recently developed RNase cleavage-based methods for mutation/SNP scanning.