Figure 5 - Gene regulatory elements classification and mechanistic discussion

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Mechanistic discussion of gene regulation using cell-type and multi-omic info

Think about modality relationships, segregation using cell-type as features

DNA methylation

• Classification of DMR
• Single-base resolution analysis on specific methylation sites, both CpG and CpH (CA, CAC, CTC, etc.)
• Relationship between global mC level and fine-scale mC features

Chromatin conformation

• Relationship between methylation and chromatin conformation
• Classification of Domain, Loop, Strips
• E-E, E-P feature vs. Insulation feature
• Cell-type-specific vs. constitutive

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How to cluster loops?

• Use the compartment strength across the cell type itself
• Use other modalities across the cell types and discuss how compartment features segregated after clustering How to align left and right anchor signal (min max align?)

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Genomic imprinted genes Their cell type specificity in brain, their DMRs, their regulatory modules, their genome structures Base level mC corr structure

Tucci, Valter, Anthony R. Isles, Gavin Kelsey, Anne C. Ferguson-Smith, and Erice Imprinting Group. 2019. “Genomic Imprinting and Physiological Processes in Mammals.” Cell 176 (5): 952–65. See Table S1 260 Genes