Genomic studies of gonad development in health and diseases.

我们分析了雄性小鼠胚胎性腺在E10.5(胚胎第10.5天)、E11.5、E12.5、E13.5、E15.5和E17.5时表达的基因和新的转录本，每个SAGE文库的平均覆盖率为152K。这6个转录本总共提供了4.5万个已知转录本，2.1万个未鉴定的cDNA和4000个新的转录本。在10个表达最丰富的转录本中，有5个编码核糖体蛋白，与在人类胚胎干细胞中观察到的类似。在A型精原细胞中表达最丰富的转录本有6个，包括细胞色素b氧化酶5b亚基(Cox5)、细胞色素b-245、β多肽(Cybb)、肿瘤蛋白、翻译控制蛋白1(Tpt1)、核糖体蛋白L19(Rpl19)、泛素A-52残基核糖体蛋白融合产物1(Uba52)和一个未鉴定的基因。将非监督聚类分析应用于胚胎性腺转录本，得到了性腺发育早期(E10.5-E12.5)和晚期(E13.5-E17.5)两个主要阶段的基因组指纹图谱。 为了确定性腺发育过程中最活跃的染色体区域，我们创建了算法，根据Unigene分配将SAGE标签分配到相应的染色体位置，并使用完整的小鼠基因组信息以染色体图形格式显示。因此，创建了胚胎性腺发育的染色体热图，其中基于基因表达的共定位，突出了在任何发育时间点具有显著变化的染色体热点。这一染色体热图将有助于确定发育过程中特定时间点不同区域的重要性，以及染色体复制或缺失造成的潜在后果。此外，通过链接到不同的突变和功能注释数据库，包括在线孟德尔人类遗传(OMIM)和EASE，可以提取和进一步分析重要染色体簇的生物学意义。

We profiled the genes and novel transcripts expressed in male mouse embryonic gonads at E10.5 (embryonic day 10.5), E11.5, E12.5, E13.5, E15.5 and E17.5 with an average of 152K coverage for each of the SAGE libraries. The 6 transcriptomes gave a total of 45,000 known transcripts, 21,000 uncharacterized cDNAs, and 4000 novel transcripts. Among the 10 most abundantly expressed transcripts, 5 encoded ribosomal proteins, similar to that observed in human embryonic stem cells. Six of the most abundantly expressed transcripts including cytochrome b oxidase, subunit 5b (Cox5), cytochrome b-245, beta polypeptide (Cybb), tumor protein, translationally-controlled 1 (Tpt1), ribosomal protein L19 (Rpl19), ubiquitin A-52 residue ribosomal protein fusion product 1 (Uba52), and an uncharacterized cDNA, were also among the 10 most abundant transcripts in type A spermatogonia. Application of unsupervised clustering analysis to the embryonic gonad transcriptomes yielded distinct genomic fingerprints of two major stages in gonad development, namely early (E10.5-E12.5) and late (E13.5-E17.5) stages. To identify the chromosomal regions most active during gonad development, we created algorithms to assign the SAGE tags to the corresponding chromosomal position based on the Unigene assignments and displayed in chromosome graphic format using the completed mouse genome information. Consequently, a chromosome heatmap of embryonic gonad development was created in which chromosomal hotspots with significant changes at any time point of development were highlighted based on co-localization of gene expression. This chromosome heatmap will be useful for determining the importance of different regions at specific time point during the developmental process and the potential consequences due to chromosome duplication or deletion. Furthermore, the biological implication of significant chromosomal clusters can be extracted and further analyzed by linking to different mutation and functional annotation databases including Online Mendelian Inheritance in Man (OMIM) and EASE.