Mouse microRNA profiles determined with a new and sensitive cloning method

Abstract

MicroRNAs (miRNAs) are noncoding RNA molecules of 21 to 24 nt that regulate the expression of target genes in a post-transcriptional manner. Although evidence indicates that miRNAs play essential roles in embryogenesis, cell differentiation and pathogenesis of human diseases, extensive miRNA profiling in cells or tissues has been hampered by the lack of sensitive cloning methods. Here we describe a highly efficient profiling method, termed miRNA amplification profiling (mRAP), as well as its application both to mouse embryos at various developmental stages and to adult mouse organs. A total of 77 436 Small-RNA species was sequenced, with 11 776 of these sequences found to match previously described miRNAs. With the use of a newly developed computational prediction algorithm, we further identified 229 independent candidates for previously unknown miRNAs. The expression of some of these candidate miRNAs was confirmed by northern blot analysis and whole-mount in situ hybridization. Our data thus indicate that the total number of miRNAs in vertebrates is larger than previously appreciated and that the expression of these molecules is tightly controlled in a tissue- and developmental stage-specific manner.

Small RNAs analysis in CLL reveals a deregulation of miRNA expression and novel miRNA candidates of putative relevance in CLL pathogenesis

“…In normal tissues, about 25 to 40% of cloned small RNAs correspond to miRNAs. 19,41 In the case of CLL, miRNAS represented about 10 % of small RNAs and included a total of 13 known miRNAs. This is in agreement with previous reports indicating a reduced accumulation of miRNAs in neoplastic tissues, 19,42 which was associated with an impaired processing of miRNA precursors.…”

MicroRNA expression profiles of human leukemias

“…We previously showed that mRAP readily allows the isolation of 41 Â 10 6 miRNA concatamers from p1 Â 10 4 cells and is thus suitable for miRNA profiling of clinical specimens. 5 Indeed, mRAP functioned well with the small number of purified specimens in the present study, with the result that sequencing capacity, rather than specimen quantity, is likely to be the limiting factor for the size of the final data set in most studies.…”

“…3 In T-cell acute lymphoblastic leukaemia, ABL1 can be fused with NUP214 (a gene located in 9q34) on episomes 4 or with EML1 by a t(9;14)(q34;q32) translocation. 5 Moreover, a recent publication described a t(1;9)(q24;q34) translocation in a B-cell acute lymphoblastic leukaemia case with a putative RCSD1-ABL1 fusion without molecular confirmation. 6 Here we report the cytogenetic and molecular analysis of a t(9;10)(q34;q23) translocation, from a case of B-lineage ALL, with recombination of ABL1 to a new partner gene, ZMIZ1 (zinc-finger MIZ-type containing 1).…”

“…We recently developed a sensitive method, mRAP (micro RNA amplification profiling) 5 that readily allows the isolation of miRNA clones from p1 Â 10 4 cells. To examine the miRNA expression profiles for leukemias with mRAP, we first purified CD34 þ cells from individuals (n ¼ 12) with de novo acute myeloid leukemia, acute myeloid leukemia secondary to myelodysplastic syndrome, acute lymphoid leukemia or biphenotypic acute leukemia (Table 1).…”

Potential role of miR-29b in modulation ofDnmt3aandDnmt3bexpression in primordial germ cells of female mouse embryos

“…Expression of miRNAs has been shown to be tightly regulated in a developmental stage-dependent, as well as in an organ-dependent, manner (Aboobaker et al 2005;Wienholds et al 2005;Ason et al 2006;Takada et al 2006a), suggesting that they may play important roles in embryonic development and tissue organization. The miRNAs miR-1 and miR-124, for example, are specifically expressed in muscle and the central nervous system, respectively, in zebrafish, medaka, mouse, and fly, suggesting that the function of these miRNAs is conserved across animal phyla .…”