HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription [RNA-Seq]

Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during cell fate decisions, but the underlying mechanisms are not fully understood. Here we demonstrate that HRP2-DPF3a-BAF complex coordinates histone H3 lysine 36 methylation (H3K36me) and ATP-dependent chromatin remodeling to regulate chromatin dynamic and gene transcription during myogenic differentiation. To study the cellular and molecular function of HRP2-DPF3a-BAF complex during myogenic differentiation, we used RNA sequencing (RNA-seq) to generate gene expression profiling during myogenic differentiation under Hrp2/Dpf3a/Brg1 transient knockdown by siRNAs in C2C12. We identified multiple genes whose expression is significantly affected by Hrp2/Dpf3a/Brg1 levels. Overall design: For knockdown condition, C2C12 myoblasts were transfected with siRNAs against Hrp2/Dpf3a/Brg1 or control 24h before start of differentiation. Cells were harvested for gene expression profiling when differentiation was induced (0h, confluent cells) and after 48h of differentiation in differentiation medium. Two replicates were performed per siRNA.