Department of Statistics, University of California Riverside, Riverside, CA, 92521, USA.
Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, 98195, USA.
Biol Sex Differ. 2022 Jul 23;13(1):40. doi: 10.1186/s13293-022-00452-0.
KDM6A is a demethylase encoded by a gene with female-biased expression due to escape from X inactivation. Its main role is to facilitate gene expression through removal of the repressive H3K27me3 mark, with evidence of some additional histone demethylase-independent functions. KDM6A mutations have been implicated in congenital disorders such as Kabuki Syndrome, as well as in sex differences in cancer.
Kdm6a was knocked out using CRISPR/Cas9 gene editing in F1 male and female mouse embryonic stem cells (ES) derived from reciprocal crosses between C57BL6 x Mus castaneus. Diploid and allelic RNA-seq analyses were done to compare gene expression between wild-type and Kdm6a knockout (KO) clones. The effects of Kdm6a KO on sex-biased gene expression were investigated by comparing gene expression between male and female ES cells. Changes in H3K27me3 enrichment and chromatin accessibility at promoter regions of genes with expression changes were characterized by ChIP-seq and ATAC-seq followed by diploid and allelic analyses.
We report that Kdm6a KO in male and female embryonic stem (ES) cells derived from F1 hybrid mice cause extensive gene dysregulation, disruption of sex biases, and specific parental allele effects. Among the dysregulated genes are candidate genes that may explain abnormal developmental features of Kabuki syndrome caused by KDM6A mutations in human. Strikingly, Kdm6a knockouts result in a decrease in sex-biased expression and in preferential downregulation of the maternal alleles of a number of genes. Most promoters of dysregulated genes show concordant epigenetic changes including gain of H3K27me3 and loss of chromatin accessibility, but there was less concordance when considering allelic changes.
Our study reveals new sex-related roles of KDM6A in the regulation of developmental genes, the maintenance of sex-biased gene expression, and the differential expression of parental alleles.
KDM6A 是一种由基因编码的去甲基酶，由于逃避 X 染色体失活，其表达具有雌性偏倚。其主要作用是通过去除抑制性 H3K27me3 标记来促进基因表达，并有一些额外的组蛋白去甲基酶非依赖性功能的证据。KDM6A 突变与先天性疾病如歌舞伎综合征有关，也与癌症中的性别差异有关。
使用 CRISPR/Cas9 基因编辑在来自 C57BL6 x Mus castaneus 正反交的 F1 雄性和雌性小鼠胚胎干细胞（ES）中敲除 Kdm6a。进行二倍体和等位基因 RNA-seq 分析，以比较野生型和 Kdm6a 敲除（KO）克隆之间的基因表达。通过比较雄性和雌性 ES 细胞之间的基因表达，研究 Kdm6a KO 对性别偏倚基因表达的影响。通过 ChIP-seq 和 ATAC-seq 以及二倍体和等位基因分析，对具有表达变化的基因的启动子区域的 H3K27me3 富集和染色质可及性变化进行表征。
我们报告说，来自 F1 杂种小鼠的雄性和雌性胚胎干细胞（ES）中 Kdm6a KO 导致广泛的基因失调、性别偏见的破坏和特定的亲本等位基因效应。失调基因中有候选基因，这些基因可能解释了人类 KDM6A 突变引起的歌舞伎综合征的异常发育特征。引人注目的是，Kdm6a 敲除导致许多基因的性别偏倚表达减少，并且优先下调母本等位基因。大多数失调基因的启动子显示出一致的表观遗传变化，包括 H3K27me3 的获得和染色质可及性的丧失，但在考虑等位基因变化时一致性较小。
我们的研究揭示了 KDM6A 在调节发育基因、维持性别偏倚基因表达和差异表达亲本等位基因方面的新的性别相关作用。
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