Genomic and proteomic resolution of heterochromatin and its restriction of alternate fate genes (RNA-seq)

Heterochromatic regions in mammalian cells suppress recombination, silence transcription, and are crucial for maintaining cell differentiation. Genomic and biochemical characterization of heterochromatin has relied on the associated histone modifications H3K9me3 and H3K27me3, yet these marks are also found in euchromatic regions that permit transcription. We employed a biophysical method to isolate sonication resistant heterochromatin from human somatic cells, mapped its genomic organization compared to histone modifications, and used proteomics to reveal an extensive number of heterochromatin-bound proteins. We discriminate subtypes of H3K9me3- and H3K27me3-marked domains, in sonication-resistant heterochromatin versus euchromatin, and we present a resource of hundreds of proteins that preferentially bind heterochromatin, a set enriched for RNA-binding proteins and proteins that oppose iPS reprogramming. The sonication-resistant heterochromatin landscape includes repressed genes for alternative lineages that are resistant to activation by introduced transcription factors. Depletion of identified heterochromatin-associated proteins reduces this barrier, rendering alternative-lineage genes more competent for transcriptional activation. Overall design: This study was designed to assess the role of human SUV39H1 and RBMX/RBMXL1 in impeding the activation of heterochromatic genes by transcription factors. RNA-seq was performed in human BJ foreskin fibroblasts treated with siRNAs in two main experimental protocols: cells expressing the hepatic transcription factors FOXA3/HNF1A/HNF4A ("hepatic TF" protocol) and cells expressing no ectopic transcription factors ("no TF" protocol). There are a total of 12 RNA-seq samples: two experimental protocols, three siRNAs per protocol, and two biological replicates per siRNA/protocol. The three siRNAs are: non-targeting control siRNA, siRNA against SUV39H1, and siRNA co-targeting RBMX and RBMX/L1