Molecular processes during fat cell development revealed by gene expression profiling and functional annotation - PubMed (original) (raw)

Molecular processes during fat cell development revealed by gene expression profiling and functional annotation

Hubert Hackl et al. Genome Biol. 2005.

Abstract

Background: Large-scale transcription profiling of cell models and model organisms can identify novel molecular components involved in fat cell development. Detailed characterization of the sequences of identified gene products has not been done and global mechanisms have not been investigated. We evaluated the extent to which molecular processes can be revealed by expression profiling and functional annotation of genes that are differentially expressed during fat cell development.

Results: Mouse microarrays with more than 27,000 elements were developed, and transcriptional profiles of 3T3-L1 cells (pre-adipocyte cells) were monitored during differentiation. In total, 780 differentially expressed expressed sequence tags (ESTs) were subjected to in-depth bioinformatics analyses. The analysis of 3'-untranslated region sequences from 395 ESTs showed that 71% of the differentially expressed genes could be regulated by microRNAs. A molecular atlas of fat cell development was then constructed by de novo functional annotation on a sequence segment/domain-wise basis of 659 protein sequences, and subsequent mapping onto known pathways, possible cellular roles, and subcellular localizations. Key enzymes in 27 out of 36 investigated metabolic pathways were regulated at the transcriptional level, typically at the rate-limiting steps in these pathways. Also, coexpressed genes rarely shared consensus transcription-factor binding sites, and were typically not clustered in adjacent chromosomal regions, but were instead widely dispersed throughout the genome.

Conclusions: Large-scale transcription profiling in conjunction with sophisticated bioinformatics analyses can provide not only a list of novel players in a particular setting but also a global view on biological processes and molecular networks.

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Figures

Figure 1

Figure 1

Clustering of ESTs found to be differentially expressed during fat cell differentiation. Shown is k-means clustering of 780 ESTs found to be more than twofold upregulated or downregulated at a minimum of four time points during fat cell differentiation. ESTs were grouped into 12 clusters with distinct expression profiles. Relative expression levels (log2 ratios) for EST gene at different time points are shown and color coded according to the legend at the top (left) and expression profile (mean ± standard deviation) for each cluster (right). EST, expressed sequence tag.

Figure 2

Figure 2

Distribution of GO terms for genes/ESTs in each cluster. The GO terms listed here are those present in at least 15% of the genes within the cluster. In brackets are the number of genes/ESTs with associated GO terms and the number of genes/ESTs within the cluster. EST, expressed sequence tag; GO, Gene Ontology.

Figure 3

Figure 3

Genes in cluster 9 and significantly over-represented miRNA motifs (blue squares). miRNA, microRNA.

Figure 4

Figure 4

Cellular localization of gene products. Shown are the cellular localizations of gene products involved in (a) metabolism and (b) other biological processes during fat cell differentiation. Gene products are color coded for each of the 12 clusters (key given to the left of the figure). The numbering is given according to the de novo functional annotation (Additional data files 6, 7, 8).

Figure 5

Figure 5

Temporal activation of metabolic pathways. Summarized is the activation of metabolic pathways at different time points (0 hours, 24 hours, 3 days, and 14 days) during fat cell differentiation. Color codes are selected according to expression levels of key enzymes in these pathways at distinct time points (red = upregulated; green = downregulated).

Figure 6

Figure 6

Chromosomal localization analysis for ESTs found to be differentially expressed during fat cell differentiation. Chromosomal localization analysis for chromosome 10 from 780 ESTs shown to be more than two times upregulated or downregulated in a minimum of four time points during adipocyte differentiation. (a) Mapped ESTs to chromosome 10. (b) ESTs from cluster 10 mapped to chromosome 10. (c) Relative gene expression levels (log2 ratios) at different time points for seven ESTs mapped within a genomic interval of 5 Mb from chromosome 10. EST, expressed sequence tag.

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