Epigenomics And Chromatin
Nowadays, the interactions between the epigenomics and transcriptomics are widely studied. The interplay between the chromatin and transcription factors is very complicated (Angelini & Costa 2014). Chromatin is composed of DNA that is wrapped around nucleosomes to form domains of accessible (open) and inaccessible (closed) chromatin. The histone proteins regulate the chromatin accessibility. Accessible chromatin can facilitate association of transcription factors to DNA (Angelini & Costa 2014). Some transcription factors are capable of modifying the chromatin around their binding site, which can then recruit new transcription factors and chromatin-modifying factors to the region. Such changes cause cell differentiation so the chromatin domains
and transcription factor binding can be used as markers for cell type-specific regulation (Angelini & Costa 2014).
Expression profiling by itself is not efficient enough to understand the mechanism of PR regulation. However, it is crucial to identify the genes targeted and induced by the PR or by secondary interactions with mediators downstream on the chromatin. But to further understand more on mechanism of PR regulation, ChIP-seq can be employed. Chromatin immune precipitation (ChIP) is capable of revealing the protein-DNA interactions i.e. transcription factor binding locations, core transcriptional machinery and histone modifications (Park 2009; Rye et al. 2011). In ChIP, antibodies are used to select specific proteins or nucleosomes, which enriches for DNA fragments that are bound to these proteins or nucleosomes (Angelini & Costa 2014; Park 2009). The DNA fragments of interest are sequenced directly instead of being hybridized on an array (Angelini & Costa 2014; Park 2009). Additionally, it has higher resolution, fewer artefacts, and greater coverage, single nucleotide resolution (Angelini & Costa 2014). By availing the recent advances in high-throughput sequencing coupled with chromatin immunoprecipitation (ChIP-Seq) genome wide mapping of such domains and further investigation of enhancer and promoter regions can be done (Angelini & Costa 2014; O’Geen, Echipare & Farnham 2011). Additionally, studying protein-DNA interactions is also necessary for proper understanding of transcriptional regulation of progesterone that can aid in deciphering the gene regulatory networks that underlie complex biological processes such as ovulation (Park 2009; Sacco, Baldassarre & Masotti 2011).
and transcription factor binding can be used as markers for cell type-specific regulation (Angelini & Costa 2014).
Expression profiling by itself is not efficient enough to understand the mechanism of PR regulation. However, it is crucial to identify the genes targeted and induced by the PR or by secondary interactions with mediators downstream on the chromatin. But to further understand more on mechanism of PR regulation, ChIP-seq can be employed. Chromatin immune precipitation (ChIP) is capable of revealing the protein-DNA interactions i.e. transcription factor binding locations, core transcriptional machinery and histone modifications (Park 2009; Rye et al. 2011). In ChIP, antibodies are used to select specific proteins or nucleosomes, which enriches for DNA fragments that are bound to these proteins or nucleosomes (Angelini & Costa 2014; Park 2009). The DNA fragments of interest are sequenced directly instead of being hybridized on an array (Angelini & Costa 2014; Park 2009). Additionally, it has higher resolution, fewer artefacts, and greater coverage, single nucleotide resolution (Angelini & Costa 2014). By availing the recent advances in high-throughput sequencing coupled with chromatin immunoprecipitation (ChIP-Seq) genome wide mapping of such domains and further investigation of enhancer and promoter regions can be done (Angelini & Costa 2014; O’Geen, Echipare & Farnham 2011). Additionally, studying protein-DNA interactions is also necessary for proper understanding of transcriptional regulation of progesterone that can aid in deciphering the gene regulatory networks that underlie complex biological processes such as ovulation (Park 2009; Sacco, Baldassarre & Masotti 2011).