Cistromic and gene expression analyses associated with HDAC3, SCAP and SREBP1c in mouse livers. Mus musculus

HDAC3 is a repressor of lipogenic gene expression whereas nuclear SREBP1c is a potent activiator that is controlled by SCAP. Since these factors share many lipogenic gene targets, we sought to determine their molecular crosstalk by ChIP-sequencing. We also tested whether ectopic expression of nSREBP1c interferes with HDAC3 binding near lipognic genes. To faciliate these pulldowns, we ectoipcally expressed HA-tagged nSREBP1c in mouse livers in vivo using AAV8 viruses and the thyroxine-binding globulin promoter for hepatocyte-specifc expression. ChIP-sequencing identified over 7,000 HA-nSREBP1c binding sites, almost 50% of which were in the same vicinity as HDAC3 peaks. However, ectopic expression of nSREBP1c did not disrupt HDAC3 binding indicating that these factors indepedently bind near lipogenic genes and are regulated by distinct regulatory pathways. Gene expression changes in livers of HDAC3 liver specific knockout (LKO), SCAP LKO, and double LKO mice are provided. Overall design: C57Bl/6 mice were injected with adeno-associated virus serotype 8 (AAV8) viruses expressing either GFP (control), HA-nSREBP1c, or Cre. Anti-HDAC3 or anti-HA antibodies were used for ChIP. For inputs, mouse livers lacking HDAC3 were used for HDAC3 ChIPs, and mouse livers expressing GFP were used for HA ChIPs. For gene expression, mice injected with AAV8:GFP were used as controls and indicated floxed mice were injected with AAV8:Cre.