Transcriptional regulatory networks underlying gene expression changes in Huntington's disease. Mus musculus

Transcriptional changes occur presymptomatically and throughout Huntington’s disease (HD), motivating the study of transcriptional regulatory networks (TRNs) in HD. We reconstructed a genome-scale model for the target genes of 718 transcription factors (TFs) in the mouse striatum by integrating a model of genomic binding sites with transcriptome profiling of striatal tissue from HD mouse models. We identified 48 differentially expressed TF-target gene modules associated with age- and CAG repeat length-dependent gene expression changes in Htt CAG knock-in mouse striatum, and replicated many of these associations in independent transcriptomic and proteomic datasets. 13 of 48 of these predicted TF-target gene modules were also differentially expressed in striatal tissue from human disease. We experimentally validated a specific model prediction that SMAD3 regulates HD-related gene expression changes using chromatin immunoprecipitation and deep sequencing (ChIP-seq) of mouse striatum. We found CAG repeat length-dependent changes in the genomic occupancy of SMAD3 and confirmed our model’s prediction that many SMAD3 target genes are down-regulated early in HD. Overall design: Duplicate ChIP samples for each antibody from four-month-old HttQ111/+ and from age-matched wildtype mice. For each ChIP preparation, chromatin DNA was prepared using the combined striatal tissue from both hemispheres of three mice. IPs were performed using Abcam Anti-SMAD3 antibody ab28379 [ChIP grade] or Anti-RNA polymerase II CTD repeat YSPTSPS antibody [8WG16] [ChIP Grade] ab817. Sequencing libraries were prepared from the isolated ChIP DNA and from input DNA controls. Libraries were sequenced on an Illumina HiSeq 2500 sequencer to a depth of ~17-25 million paired-end 25 bp reads per sample