Genomic studies of gonad development in health and disea

脑性腺发育和性二型性的功能基因组研究 尽管已鉴定出在胚胎性腺发育过程中不可或缺的关键基因，如Sry，但调节关键生物学过程的机制仍远未被了解，如原始生殖细胞向性腺细胞的转变和性二型性的启动。我们试图通过使用基因表达序列分析(SAGE)来描绘不同发育阶段男性胚胎性腺的转录组来解决这个问题。我们分析了在胚胎第10.5天(胚胎第10.5天)、E11.5、E12.5、E13.5、E15.5和E17.5的雄性胚胎性腺中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45,000个已知转录本，21,000个未鉴定的cDNA和大约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，其中有哪些染色体热点？基于基因表达的共定位，强调了在任何发展时间点的显着变化。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。

Functional Genomic Studies of Gonad Development and Sexual Dimorphism of the Brain Despite the identification of key genes, such as Sry, which are integral during embryonic gonad development, the mechanisms that regulate the critical biological processes, such as transition of the primordial germ cells to gonocytes and the initiation of sexual dimorphism, are still far from being understood. We attempt to resolve this problem by first delineating the transcriptome of male embryonic gonads at different stage of development using Serial Analysis of Gene Expression (SAGE). We profiled the genes and novel transcripts expressed in male 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.