Identification of a chromatin-bound ERRa interactome network in mouse liver [ChIP-Seq]

Objective Estrogen-related-receptor a (ERRa) plays a critical role in the transcriptional regulation of cellular bioenergetics and metabolism, and perturbations in its activity have been associated with metabolic diseases. While several coactivators and corepressors of ERRa have been identified to date, a knowledge gap remains in understanding the extent to which ERRa cooperates with coregulators in the control of gene expression. Herein, we mapped the primary chromatin-bound ERRa interactome in mouse liver. Methods RIME (Rapid Immuno-precipitation Mass spectrometry of Endogenous proteins) analysis using mouse liver samples from two circadian time points was used to catalog ERRa-interacting proteins on chromatin. The genomic crosstalk between ERRa and its identified cofactors in the transcriptional control of precise gene programs was explored through cross-examination of genome-wide binding profiles from chromatin immunoprecipitation-sequencing (ChIP-seq) studies. The dynamic interplay between ERRa and its newly uncovered cofactor Host cell factor C1 (HCFC1) was further investigated by loss-of-function studies in hepatocytes Results Characterization of the hepatic ERRa chromatin interactome led to the identification of 48 transcriptional interactors of which 42 were previously unknown including HCFC1. Interrogation of available ChIP-seq binding profiles highlighted oxidative phosphorylation (OXPHOS) under the control of a complex regulatory network between ERRa and multiple cofactors. While ERRa and HCFC1 were found to bind to a large set of common genes, only a small fraction showed their co-localization, found predominately near the transcriptional start sites of genes particularly enriched for components of the mitochondrial respiratory chain. Knockdown studies demonstrated inverse regulatory actions of ERRa and HCFC1 on OXPHOS gene expression ultimately dictating the impact of their loss-of-function on mitochondrial respiration. Conclusions Our work unveils a repertoire of previously unknown transcriptional partners of ERRa comprised of chromatin modifiers and transcription factors thus advancing our knowledge of how ERRa regulates metabolic transcriptional programs. Overall design: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) for HCFC1 or IgG control was conducted in Hepa-6 cells treated with 200nM of siRNAs targeting ERRa (siERRa, siE), HCFC1 (siHCFC1, siH) or control siRNAs (siC) for 96h.