Identification and Characterisation of Putative Enhancer Elements in Mouse Embryonic Stem Cells

Area of Science:

• * Genomics and epigenetics
• * Mammalian cell biology
• * Gene regulation

Background:

• * Enhancer elements are crucial for cell-type-specific transcription.
• * Identifying enhancer activity is key to understanding cell identity and function.
• * Chromatin modifications serve as markers for enhancer states.

Purpose of the Study:

• * To determine enhancer activity in mouse embryonic stem (ES) cells.
• * To characterize global properties of enhancers using chromatin modification data.
• * To classify enhancers into distinct functional groups.

Main Methods:

• * Grouping enhancers into 5 categories based on H3K4me1, H3K27ac, and H3K27me3 modifications.
• * Analyzing binding of pluripotency factors, RNA polymerase II (polII), and polycomb complex components.
• * Identifying sequence motifs enriched at different enhancer types.

Main Results:

• * Active enhancers (H3K4me1/H3K27ac) bind pluripotency factors and are near pluripotency genes.
• * Poised enhancers (H3K4me1-only) show RNA polII (8WG16) enrichment, suggesting preparation for transcription.
• * Bivalent enhancers (H3K4me1/H3K27me3) are near bivalent genes and bind polycomb components, with a specific 'CTTTCTC' motif.

Conclusions:

• * Three histone modifications (H3K4me1, H3K27ac, H3K27me3) effectively distinguish active, bivalent, and poised enhancers.
• * Each enhancer type exhibits unique sequence features and protein binding profiles.
• * This classification provides insights into enhancer function and regulation in ES cells.