Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Post-transcriptional regulation of circadian rhythm by miRNA in mouse liver

ABSTRACT: Gene regulatory circuit of circadian rhythm has been well studied at the transcriptional level. However, recent published Nascent-sequencing and proteomic data indicates that post-transcriptional mechanisms play essential roles in modulating temporal gene expression for proper circadian function. miRNAs are 19-25 nucleotides long small RNAs now well-known for their regulatory roles in the development and diseases through post-transcriptional and translational controls in a wide range of species. We systematically analyzed the miRNAs in mouse liver by Agilent microarray. Then by combining our results with the published high-through liver circadian microarray data, we identified nine mouse liver circadian miRNAs. ice were housed under a 12-h light/12-h dark regimen with food and water available ad libitum. ZT0 is defined as the time when the lights are turned on. Two mouse livers were collected every four hours in two consecutive days. Then the two samples for each time point were pooled together. The mouse liver RNAs were extracted according Agilent protocol. miRNA microarrays were manufactured by Agilent Technologies, and each contains probes for 670 mouse and miRNAs. Labeling and hybridization of total RNA were performed according to the manufacturer's protocol with no modification.

ORGANISM(S): Mus musculus

SUBMITTER: Haifang Wang

PROVIDER: E-GEOD-59423 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Recent advances in the study of human embryonic stem cells (hESCs) and induced-pluripotent stem cells (iPS) highlight their importance as both model systems for basic research and avenues for therapeutic applications. To gain better insight into these cells, a clearer understanding of their molecular properties is crucial. In this study, we analyze changes in the expression profile of microRNAs (miRNAs) and mRNAs in nine different, National Institutes of Health (NIH)-approved hESC lines. By examining both undifferentiated hESCs and cells exposed to an undirected differentiation scheme at early stages, we found those miRNAs and mRNAs enriched in the hESC lines, and those miRNAs and mRNAs initially regulated upon commitment. In comparing these profiles with those of an embryonal carcinoma (EC) cell line, NTera-2, we observed distinct patterns of miRNA expression in hESCs. Furthermore, we identify several new hESC-enriched miRNAs that respond rapidly to differentiation cues, in addition to miRNAs from a large cluster of hESC-enriched miRNAs located on chromosome 19, and miRNAs from the miR-302 cluster and the miR-17~92 family of clusters. We show that key miRNAs in the chromosome 19 cluster are highly enriched in hESCs in comparison to NTera-2, and might therefore serve as future diagnostic markers for stem cell capacity. Examination of changes in mRNA expression during early commitment further reveals that many differentiation-regulated genes are possible candidates for regulation by these hESC-enriched miRNAs. A set of 9 different NIH-approved hESC lines were treated with conditions to promote either maintenance of an undifferentiated state (mouse embryonic fibroblast- conditioned media) or undirected differentiation of the hESCs into various cell lineages (DMEM + 20% FBS). RNA was harvested from the cells and subjected to miRNA microarray analysis. An embryonal carcinma cell line, NTera-2, which shows similar growth characteristics to hESCs was used an additional comparative sample. Additionally, human placental RNA samples were used as internal controls for miRNA microarray slide (Agilent Technologies). The miRNA expression data was used to analyze differential miRNA expression in each specific cell line, as well as large-scale comparisons of the undifferentiated and differentiated hESC lines.

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Post-transcriptional regulation of circadian rhythm by miRNA in mouse liver

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