The basic mechanisms of epigenetic regulation include DNA methylation, histone modification and mutation, chromatin remodeling, and non-coding RNA (ncRNA)-mediated regulation of gene expression. Cis-acting elements refer to specific DNA sequences in the same DNA molecule with transcriptional regulatory functions, including promoters, enhancers, etc. With the increasing availability of genomic information, it is increasingly vital to construct epigenomic maps. Lifeasible provides epigenome mapping service, which can systematically mine and identify genome-wide cis-regulatory elements and provides resources for gene regulation mechanism analysis research. This can help you characterize transcription factors during development, the interactions between transcription factors and cis-acting elements in different cell types, histone modifications, chromatin interactions, and many other epigenetic findings.

Epigenetic changes in the genome are heritable, and DNA methylation is thought to target certain genetic elements. We help you to resolve ab initio methylation associated with mutations that occur in the DNA sequence by analyzing the genome and epigenome of plants. We can perform detailed population-level analyses and whole genome DNA sequencing, whole genome methylation profiling, and gene transcription profiling on plant samples.

Epigenome mapping constructs key components

• Histone modification. In mapping the epigenome of histone modifications, we mainly use the chromatin immunoprecipitation-seq (ChIP-seq) technology related to histone modifications to identify the histone modification sites and types among different materials and then elaborate on the regulation of gene expression by histone modifications to achieve the purpose of physiological activities in combination with histone modification functions and regulatory genomes.
• DNA chemical modification. Chemical modifications of DNA mainly include 5mC, 5hmC, and 6mA modifications of DNA. For the identification of 5mC and 5hmC modifications, we used whole genome methylation sequencing (WGBS). And for 6mA detection, we accomplished it by 6mA-IP-seq. By determining DNA methylation on a genome-wide scale, you can investigate the methylation sites and the mechanisms by which they occur and explore the mechanisms by which DNA chemical modifications regulate gene expression.
• Transcription factor binding site identification. For the identification of transcription factor binding sites, we can use transcription factor ChIP-seq. The target transcription factors are captured by specific antibodies, and the DNA sequences obtained by immunoprecipitation are sequenced to obtain genome-wide binding sites. Differential analysis of binding sites allows you to explore binding differences between different materials and resolve material-specific mechanisms.
• Cis-acting element enhancer identification. For enhancer identification, we can use ChIP-seq to target histone modifications associated with active enhancers. We can identify enhancers by identifying histone H3K27ac, H3K9ac, H3K4me1, and H3K4me3 modifications and comparing the positional correlation by bio-confidence analysis. In addition, with the gradual maturation of ATAC-seq and other techniques to study chromatin openness, we can also combine chromatin open region information with histone modifications to further identify enhancers.

The construction of epigenomic maps is characterized by diversity and richness. Diversity is mainly reflected in the variability of the maps between different materials, which also reflects that epigenetic differences confer variability to the materials. The richness is mainly reflected in the richness of the content of epigenome mapping. Lifeasible can be constructed for different types of epigenetic modifications, which also reflects the richness and complexity of epigenetic regulatory mechanisms. In the post-genomic era, the construction of epigenome maps is of great significance in elaborating life regulation mechanisms for different species; please feel free to contact us for more information.

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