CrosstalkDB

CrosstalkDB catalogs and statistically analyzes co-existing post-translational modifications on histone proteins using mass spectrometry data to study PTM crosstalk.

Key Features:

• Data organization: Systematically organizes observed and reported co-existing histone marks identified through mass spectrometry experiments on histone proteins and derived peptides.
• Statistical analysis: Implements statistical methods to assess sample-specific co-frequency patterns and to identify positive and negative interactions between pairs of methylation and acetylation marks.
• Conservation across species and cell types: Reveals conserved features of PTM crosstalk across different cell types and species to highlight recurrent histone mark interactions.
• Acetylation and methylation interplay: Reports positive crosstalk between proximal acetylated residues and negative crosstalk for distal acetylations, and delineates discrete methylation states at H3 Lys-9, Lys-27, and Lys-36.

Scientific Applications:

• Chromatin biology: Enables investigation of relationships among co-existing histone marks, their deposition order, hierarchy, and distinct biological functions.
• Epigenetic studies: Elucidates PTM crosstalk to inform mechanisms of epigenetic regulation, gene expression, and cellular differentiation.
• Comparative genomics: Facilitates comparative analyses of PTM conservation across species to identify evolutionarily conserved regulatory mechanisms.

Methodology:

Mass spectrometry on long peptides derived from histone proteins combined with statistical analysis of co-existing modifications and co-frequency patterns.