Hung Po-Cheng, Yang Tzu-Hsien, Liaw Hung-Jiun, Wu Wei-Sheng
BMC Genomics. 2014;15 Suppl 9(Suppl 9):S5. doi: 10.1186/1471-2164-15-S9-S5. Epub 2014 Dec 8.
Histone modification and remodeling play crucial roles in regulating gene transcription. These post-translational modifications of histones function in a combinatorial fashion and can be recognized by specific histone-binding proteins, thus regulating gene transcription. Therefore, understanding the combinatorial patterns of the histone code is vital to understanding the associated biological processes. However, most of the datasets regarding histone modification and chromatin regulation are scattered across various studies, and no comprehensive search and query tool has yet been made available to retrieve genes bearing specific histone modification patterns and regulatory proteins.
For this reason, we developed the Yeast Nucleosome Atlas database, or the YNA database, which integrates the available experimental data on nucleosome occupancy, histone modifications, the binding occupancy of regulatory proteins, and gene expression data, and provides the genome-wide gene miner to retrieve genes with a specific combination of these chromatin-related datasets. Moreover, the biological significance analyzer, which analyzes the enrichments of histone modifications, binding occupancy, transcription rate, and functionality of the retrieved genes, was constructed to help researchers to gain insight into the correlation among chromatin regulation and transcription.
Compared to previously established genome browsing databases, YNA provides a powerful gene mining and retrieval interface, and is an investigation tool that can assist users to generate testable hypotheses for studying chromatin regulation during transcription. YNA is available online at http://cosbi3.ee.ncku.edu.tw/yna/.
组蛋白修饰和重塑在调节基因转录中起着关键作用。这些组蛋白的翻译后修饰以组合方式发挥作用，并且可以被特定的组蛋白结合蛋白识别，从而调节基因转录。因此，了解组蛋白密码的组合模式对于理解相关的生物学过程至关重要。然而，大多数关于组蛋白修饰和染色质调控的数据集分散在各种研究中，并且尚未有一个全面的搜索和查询工具可用于检索具有特定组蛋白修饰模式的基因和调控蛋白。
出于这个原因，我们开发了酵母核小体图谱数据库，即YNA数据库，它整合了关于核小体占有率、组蛋白修饰、调控蛋白的结合占有率和基因表达数据的现有实验数据，并提供全基因组基因挖掘工具来检索具有这些染色质相关数据集特定组合的基因。此外，构建了生物学意义分析器，用于分析检索到的基因的组蛋白修饰、结合占有率、转录率和功能的富集情况，以帮助研究人员深入了解染色质调控与转录之间的相关性。
与先前建立的基因组浏览数据库相比，YNA提供了一个强大的基因挖掘和检索界面，是一种可以帮助用户生成可测试假设以研究转录过程中染色质调控的研究工具。YNA可在http://cosbi3.ee.ncku.edu.tw/yna/在线获取。
