Clusters of lineage-specific genes are anchored by ZNF274 in repressive perinucleolar compartments [RNA-seq]

Epigenetic mechanisms influencing chromatin architecture are key to the spatio-temporal control of transcription. Here we identify ZNF274 as a new regulator of chromosome compartmentalization that silences lineage-specific gene clusters. ZNF274 is a SCAN-bearing member of the Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs). Ablation of ZNF274 results in the transcriptional activation of genomic neighbourhoods encompassing, among others, zinc finger and protocadherin-encoding genes, with loss of H3K9me3 repressive mark, altered 3D genome conformation and de novo CTCF binding. In contrast to other factors that have been implicated in chromatin anchoring, ZNF274 is necessary both for transcriptional silencing and nucleolar tethering. While the establishment of silencing depends on the KRAB domain, we demonstrate that the SCAN domain is required to gather ZNF274 complexes at the nucleolus and efficiently spread heterochromatin. Thus, ZNF274 orchestrates the segregation of developmentally regulated gene clusters at nucleoli to allow timely and selective activation of cell-restricted alleles. RNAseq was performed in biological replicates on independent wild-type (wt) and ZNF274 knock-out (ZNF274KO) clones in hEK293T cell line and H1 hES cell line differentiated into NPC.

影响染色质构象的表观遗传调控机制，是转录过程时空精准调控的核心环节。本研究鉴定出ZNF274为染色体区室化的新型调控因子，可沉默谱系特异性基因簇。ZNF274属于携带SCAN结构域的含KRAB（Krüppel-associated box）结构域锌指蛋白（KZFPs）家族成员。敲除ZNF274会导致包含锌指基因、原钙粘蛋白编码基因在内的多个基因组邻域发生转录激活，同时伴随H3K9me3抑制性修饰丢失、三维基因组构象改变以及全新CTCF结合位点的形成。与其他已被证实参与染色质锚定的调控因子不同，ZNF274同时具备转录沉默与核仁锚定的功能。尽管转录沉默的建立依赖于KRAB结构域，本研究证实SCAN结构域是将ZNF274复合物募集至核仁并高效扩散异染色质的必需结构。综上，ZNF274可统筹调控核仁处发育调控基因簇的分离，以实现细胞限制性等位基因的适时选择性激活。本研究对hEK293T细胞系，以及分化为神经前体细胞（neural progenitor cells, NPC）的H1人类胚胎干细胞（human embryonic stem cell, hES）系中的独立野生型（wild-type, wt）与ZNF274敲除（ZNF274 knock-out, ZNF274KO）克隆，开展了生物学重复的RNA测序（RNA-seq）实验。