BIOINFORMATICS OF 3 PRIME-UTR-BASED POST-TRANSCRIPTIONAL REGULATORY ELEMENTS

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 我们的工作集中在开发和使用计算工具来加深我们对基因调控的理解，重点是识别和表征控制转录后基因调控的调控序列。转录后调控序列通常嵌入前体mRNA的序列中，因此我们的分析主要基于对表达序列的研究，包括但不限于表达序列标签(EST)和索引方案，如SAGE或MPSS。我们对描述进化上保守的序列特别感兴趣，这些序列可以在我们的实验合作者使用的模型系统中进行功能测试。我所在小组的主要工作是继续改进和收集我们的一套综合序列分析数据库：pacdb、seqgen和estdb的数据。这些数据库结合在一起，代表并使我们的基于基因组的表达序列分析可用于识别功能特征，特别是侧重于识别信使核糖核酸3-加工位点(Brockman等人，2005年)。我们随后将我们的数据库用于进一步的研究，包括对后生动物mRNA 3-加工信号的广泛比较研究(Salisbury等人，2006年)，对cDNA/EST文库创建过程中转录样本的系统效应的调查(Liu和Graber，2006年)，对哺乳动物精子发生过程中3-加工信号的系统变化的调查，以及几项合作研究(Peaston等人，2004，Petkov等人，2005，Graber等人，2006和Evsikov等人2006)。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Our work is focused on the development and use of computational tools to further our understanding of gene regulation, with an emphasis on the identification and characterization of the regulatory sequences that control post-transcriptional gene regulation. Post-transcriptional regulatory sequences are typically embedded within the sequence of the precursor mRNA, therefore our analysis is largely based on studies of expressed sequences, including, but not limited to, expressed sequence tags (ESTs) and indexing schemes, such as SAGE or MPSS. We are particularly interested in the delineation of evolutionarily conserved sequences that can be tested for functionality in the model systems utilized by our experimental collaborators. The principal efforts in my group are going into the continued improvement and collection of data for our integrated set of sequence analysis databases: pacdb, seqgen, and estdb. These databases combine to represent and make useable our genome-based analysis of expressed sequences, for the identification of functional features, specifically focusing on identification of mRNA 3-processing sites (Brockman et al, 2005). We have subsequently used our databases in further studies, including a broad comparative study of metazoan mRNA 3-processing signals (Salisbury et al, 2006), an investigation of systematic effects in the sampling of transcripts during cDNA/EST library creation (Liu and Graber, 2006), an investigation of systematic changes in 3-processing during mammalian spermatogenesis, and several collaborative studies (Peaston et al, 2004, Petkov et al, 2005, Graber et al, 2006, and Evsikov et al 2006).