The past few years have revealed that the genome of all studied organisms is almost entirely transcribed, generating an enormous number of non-protein-coding RNAs (ncRNAs) that are often organised in interlacing patterns with protein-coding genes. However, the functions of these RNAs remain largely untested. To identify target ncRNAs for characterisation, we analysed the expression of ncRNAs associated with key regulatory genes using mouse embryonic stem (ES) cells as a model of early development. Using a custom-designed microarray, we detected hundreds of ncRNAs whose expression is dynamically regulated during ES cell differentiation over a 16-day time course. The expression profile of many ncRNAs was either positively or negatively correlated with the expression of associated protein-coding genes with important roles in ES cell pluripotency and differentiation, such as Sox2, GATA6 and several homeobox-containing genes. We found that different isoforms of noncoding Sox2 Overlapping Transcripts (Sox2OT) transcribed from highly conserved elements have complex spatio-temporal relationships with Sox2 expression. By RT-PCR, whole-mount and brain section in situ hybridisations, we observed specific, and developmentally regulated, expression of Sox2OT transcripts in zebrafish, chicken and mouse embryos. We also identified novel spliced antisense (AS) ncRNAs that share similar expression patterns with associated homeotic genes, including Evx1,HoxB5/6 and all three Dlx clusters. We show that some of these ncRNA-mRNA pairs are spatially co-expressed in the mouse embryo and this co-regulation is maintained in adult tissues. In addition, we show that Evx1AS and HoxB5/6AS ncRNAs co-immunoprecipitate with trimethylated H3K4 histones and trithorax Mll1 chromatin fractions, involved in homeotic gene activation. These results suggest a positive role for ncRNAs in epigenetic regulation and homeotic programming. Taken together the data indicates that long ncRNAs participate in processes directing vertebrate developmental programs.
Characterization of long noncoding RNAs associated with developmental genes in vertebrates / P.P. Amaral, M.E. Dinger, T.R. Mercer, S.J. Bruce, M. Askarian Amiri, S.J. Wilkins, C. Neyt, G.M. Soldà, S.M. Sunkin, A.C. Perkins, J.S. Mattick. ((Intervento presentato al 29. convegno Lorne genome conference on the organization and expression of the genome tenutosi a Lorne, Australia nel 2008.
Characterization of long noncoding RNAs associated with developmental genes in vertebrates
G.M. Soldà;
2008
Abstract
The past few years have revealed that the genome of all studied organisms is almost entirely transcribed, generating an enormous number of non-protein-coding RNAs (ncRNAs) that are often organised in interlacing patterns with protein-coding genes. However, the functions of these RNAs remain largely untested. To identify target ncRNAs for characterisation, we analysed the expression of ncRNAs associated with key regulatory genes using mouse embryonic stem (ES) cells as a model of early development. Using a custom-designed microarray, we detected hundreds of ncRNAs whose expression is dynamically regulated during ES cell differentiation over a 16-day time course. The expression profile of many ncRNAs was either positively or negatively correlated with the expression of associated protein-coding genes with important roles in ES cell pluripotency and differentiation, such as Sox2, GATA6 and several homeobox-containing genes. We found that different isoforms of noncoding Sox2 Overlapping Transcripts (Sox2OT) transcribed from highly conserved elements have complex spatio-temporal relationships with Sox2 expression. By RT-PCR, whole-mount and brain section in situ hybridisations, we observed specific, and developmentally regulated, expression of Sox2OT transcripts in zebrafish, chicken and mouse embryos. We also identified novel spliced antisense (AS) ncRNAs that share similar expression patterns with associated homeotic genes, including Evx1,HoxB5/6 and all three Dlx clusters. We show that some of these ncRNA-mRNA pairs are spatially co-expressed in the mouse embryo and this co-regulation is maintained in adult tissues. In addition, we show that Evx1AS and HoxB5/6AS ncRNAs co-immunoprecipitate with trimethylated H3K4 histones and trithorax Mll1 chromatin fractions, involved in homeotic gene activation. These results suggest a positive role for ncRNAs in epigenetic regulation and homeotic programming. Taken together the data indicates that long ncRNAs participate in processes directing vertebrate developmental programs.
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