Histone modification and remodeling play crucial roles in regulating gene transcription. These post-translational modifications of histones alter chromatin structure, thus facilitating the binding between protein domains and histones that regulate DNA accessibility during transcription. An emerging theme is that multivalent interactions between specifically modified histones and domains of protein complexes allosterically regulate the activity of a protein complex. Therefore, understanding the combinatorial pattern of the histone code is vital to understand the biological processes. However, most of these chromatin-regulating datasets are scattering in several literatures. And no comprehensive investigation tool on these data is available.

To decipher the mechanism of transcriptional regulation, we developed the Yeast Nucleosome Atlas database, or the YNA database, to integrate available experimental data of nucleosome occupancy, histone modifications, factors for chromatin regulation, and expression profiles. In addition, to acquire experimentally testable hypotheses, we implemented the genome-wide gene miner to provide the interface for researchers to fetch gene lists by custom-defined filtering criteria based on those previously published datasets. Moreover, the biological significance analyzer, which addresses the issues concerning the enrichment of histone modification and binding proteins, expression profiles, and functional categories, was constructed to help researchers propose testable hypotheses for downstream analysis.

Compared to previously established genome browsing databases, YNA provides the integrative and comprehensive information about global chromatin structure and gene regulation. Most importantly, YNA provides gene mining and analyzing functions for advanced analysis.