Project description:In any cell type, repetitive elements and alternative lineage genes can be silenced by heterochromatin marked by H3K9me3 and/or H3K27me3. During cellular reprogramming to pluripotency and to liver, genes marked by H3K9me3 are the most difficult to activate. Given that KRAB domain-containing, zinc finger proteins (KRAB-ZFPs) can direct repressive H3K9me3 at genes and transposable elements, we sought to identify KRAB-ZFPs that silence liver genes in non-liver lineages and could be useful for down-regulating during human fibroblast to hepatocyte (hiHep) reprogramming. We identified six KRAB-ZFPs that are essentially not expressed in liver or BJ fibroblasts, but are expressed in many other tissues. We knocked down each KRAB-ZFP during hepatic reprogramming of human fibroblasts and found that only knockdown of primate-specific ZNF695 allowed hundreds of hepatic genes in H3K9me3-heterochromatin to be derepressed. ZNF695 localizes primarily at LINE repeat elements and at gene introns that were linked to gene expression changes. ZNF695 exhibits nuclear mobility characteristics similar to well-characterized heterochromatin proteins. While most KRAB-ZFPs tested that exhibit diminution in one tissue (liver) did not functionally repress that tissue’s genes in another cell type, our strategy revealed a KRAB-ZFP that can be targeted to allow H3K9me3-heterochromatic genes to be derepressed during cellular reprogramming.
Project description:In any cell type, repetitive elements and alternative lineage genes can be silenced by heterochromatin marked by H3K9me3 and/or H3K27me3. During cellular reprogramming to pluripotency and to liver, genes marked by H3K9me3 are the most difficult to activate. Given that KRAB domain-containing, zinc finger proteins (KRAB-ZFPs) can direct repressive H3K9me3 at genes and transposable elements, we sought to identify KRAB-ZFPs that silence liver genes in non-liver lineages and could be useful for down-regulating during human fibroblast to hepatocyte (hiHep) reprogramming. We identified six KRAB-ZFPs that are essentially not expressed in liver or BJ fibroblasts, but are expressed in many other tissues. We knocked down each KRAB-ZFP during hepatic reprogramming of human fibroblasts and found that only knockdown of primate-specific ZNF695 allowed hundreds of hepatic genes in H3K9me3-heterochromatin to be derepressed. ZNF695 localizes primarily at LINE repeat elements and at gene introns that were linked to gene expression changes. ZNF695 exhibits nuclear mobility characteristics similar to well-characterized heterochromatin proteins. While most KRAB-ZFPs tested that exhibit diminution in one tissue (liver) did not functionally repress that tissue’s genes in another cell type, our strategy revealed a KRAB-ZFP that can be targeted to allow H3K9me3-heterochromatic genes to be derepressed during cellular reprogramming.
