Probing the epigenetic status at Notch target genes

Area of Science:

• Developmental Biology
• Molecular Biology
• Epigenetics

Background:

• Chromatin modifications are crucial for regulating developmentally important genes, particularly Notch target genes.
• The Notch signaling pathway involves the intracellular Notch domain (NICD) translocating to the nucleus to activate transcription via CSL (RBPJ).
• In the absence of Notch signaling, CSL recruits co-repressors to silence target genes, involving chromatin modifiers like histone acetyltransferases and methyltransferases.

Purpose of the Study:

• To provide detailed protocols for chromatin immunoprecipitation (ChIP) to investigate the chromatin status of dynamically regulated Notch target genes.
• To illustrate a method for primary analysis of ChIP-Seq data at Notch target genes using the Cistrome platform.

Main Methods:

• Chromatin immunoprecipitation (ChIP) protocols.
• ChIP-sequencing (ChIP-Seq) data analysis using the Cistrome platform.

Main Results:

• Protocols for analyzing chromatin status at Notch target genes are presented.
• An example workflow for primary ChIP-Seq data analysis at Notch target genes is demonstrated.

Conclusions:

• Chromatin-based mechanisms, involving CSL and recruited modifiers, are key to dynamic Notch target gene regulation.
• The provided ChIP protocols and analysis methods facilitate the study of epigenetic regulation in developmental gene expression.