The mouse brain transcriptome by SAGE: differences in gene expression between P30 brains of the partial trisomy 16 mouse model of Down syndrome (Ts65Dn) and normals

Abstract

Trisomy 21, or Down syndrome (DS), is the most common genetic cause of mental retardation. Changes in the neuropathology, neurochemistry, neurophysiology, and neuropharmacology of DS patients' brains indicate that there is probably abnormal development and maintenance of central nervous system structure and function. The segmental trisomy mouse (Ts65Dn) is a model of DS that shows analogous neurobehavioral defects. We have studied the global gene expression profiles of normal and Ts65Dn male and normal female mice brains (P30) using the serial analysis of gene expression (SAGE) technique. From the combined sample we collected a total of 152,791 RNA tags and observed 45,856 unique tags in the mouse brain transcriptome. There are 14 ribosomal protein genes (nine under expressed) among the 330 statistically significant differences between normal male and Ts65Dn male brains, which possibly implies abnormal ribosomal biogenesis in the development and maintenance of DS phenotypes. This study contributes to the establishment of a mouse brain transcriptome and provides the first overall analysis of the differences in gene expression in aneuploid versus normal mammalian brain cells.

Figure 1

Cumulative curve of unique tag detection through sequencing of 152,791 tags from normal male and Ts65Dn male and normal female mice brain serial analysis of gene expression (SAGE) libraries. A total of 22,115, 21,357, and 19,103 unique tags were detected after sequencing 51,561, 50,504, and 50,726 tags from normal male, Ts65Dn male, and normal female mice brain SAGE libraries, respectively.

Figure 2

Comparison of ∼50,000 tags isolated from serial analysis of gene expression (SAGE) libraries prepared from four normal male, three Ts65Dn male, and three normal female P30 mice brains. We have detected 330 tags with statistically significant differences (P ≤ 0.05) between normal and Ts65Dn male SAGE libraries, 406 differences between normal male and female SAGE libraries, and 451 differences between Ts65Dn male and normal female SAGE libraries. The complete list of tags that are overrepresented in each sample can be found in the web address http://medgen.unige.ch/research/projects/SAGE/.

Figure 3

Comparison of the observed frequencies of 36,012 unique tags detected after sequencing of ∼51,000 tags from each normal and Ts56Dn mouse serial analysis of gene expression (SAGE) libraries. The vast majority of the tags were expressed at the same or similar level in the two samples (gray circles); however, there were 330 tags with statistically significant differences (P < 0.05) between normal and Ts56Dn mouse SAGE libraries (black circles).

Figure 4

Northern blot analysis of some examples of differentially expressed genes between normal and Ts56Dn mouse serial analysis of gene expression (SAGE) libraries. Total RNA isolated from brain of four control males and four Ts65Dn male mice was blotted and hybridized with probes detecting Rbm3, p19, L30, and L5 ribosomal protein genes, clusterin, and actin transcripts. The top panel shows the results of autoradiography, the bottom panel shows the corresponding agarose gels prior to blotting (the two bands represent the 28S and 18S rRNAs). The number of tags detected in normal (N) and Ts65Dn (T) male SAGE libraries are also shown.