One striking feature of the large KRAB domain-containing zinc finger protein (KZFP) family is its rapid evolution, leading to hundreds of member genes with various origination time in a certain mammalian genome. However, a comprehensive genome-wide and across-taxa analysis of the structural and expressional features of KZFPs with different origination time is lacking. This type of analysis will provide valuable clues about the functional characteristics of this special family. In this study, we found several conserved paradoxical phenomena about this issue. 1) Ordinary young domains/proteins tend to be disordered, but most of KRAB domains are completely structured in 64 representative species across the superclass of Sarcopterygii and most of KZFPs are also highly structured, indicating their rigid and unique structural and functional characteristics; as exceptions, old-zinc-finger-containing KZFPs have relatively disordered KRAB domains and linker regions, contributing to diverse interacting partners and functions. 2) In general, young or highly structured proteins tend to be spatiotemporal specific and have low abundance. However, by integrated analysis of 29 RNA-seq datasets, including 725 samples across early embryonic development, embryonic stem cell differentiation, embryonic and adult organs, tissues in 7 mammals, we found that KZFPs tend to express ubiquitously with medium abundance regardless of evolutionary age and structural disorder degree, indicating the wide functional requirements of KZFPs in various states. 3) Clustering and correlation analysis reveal that there are differential expression patterns across different spatiotemporal states, suggesting the specific-high-expression KZFPs may play important roles in the corresponding states. In particular, part of young-zinc-finger-containing KZFPs are highly expressed in early embryonic development and ESCs differentiation into endoderm or mesoderm. Co-expression analysis revealed that young-zinc-finger-containing KZFPs are significantly enriched in five co-expression modules. Among them, one module, including 13 young-zinc-finger-containing KZFPs, showed an ‘early-high and late-low’ expression pattern. Further functional analysis revealed that they may function in early embryonic development and ESC differentiation via participating in cell cycle related processes. This study shows the conserved and special structural, expressional features of KZFPs, providing new clues about their functional characteristics and potential causes of their rapid evolution.

中文翻译：

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KRAB锌指蛋白进化、结构和表达特征之间的保守矛盾关系揭示了它们的特殊功能特征

包含大 KRAB 域的锌指蛋白 (KZFP) 家族的一个显着特征是其快速进化，导致在某个哺乳动物基因组中产生数百个具有不同起源时间的成员基因。然而，缺乏对具有不同起源时间的 KZFP 的结构和表达特征的全基因组和跨分类群的全面分析。这种类型的分析将为了解这个特殊家族的功能特征提供有价值的线索。在这项研究中，我们发现了几个关于这个问题的保守的悖论现象。1) 普通的年轻结构域/蛋白质往往是无序的，但大多数 KRAB 结构域在整个 Sarcopterygii 超类的 64 个代表性物种中完全结构化，并且大多数 KZFP 也是高度结构化的，表明其刚性和独特的结构和功能特征；作为例外，含旧锌指的 KZFP 具有相对无序的 KRAB 域和链接器区域，有助于形成多种相互作用的伙伴和功能。2) 一般来说，年轻的或高度结构化的蛋白质往往具有时空特异性且丰度低。然而，通过对 29 个 RNA-seq 数据集的综合分析，包括早期胚胎发育、胚胎干细胞分化、胚胎和成体器官、7 种哺乳动物的组织的 725 个样本，我们发现 KZFP 倾向于以中等丰度无处不在地表达，而不管进化年龄如何和结构无序程度，表明 KZFPs 在各种状态下的广泛功能要求。3）聚类和相关性分析表明，不同时空状态之间存在差异表达模式，表明特定高表达的 KZFPs 可能在相应状态中发挥重要作用。特别是，部分含年轻锌指的 KZFPs 在早期胚胎发育和 ESCs 分化为内胚层或中胚层中高度表达。共表达分析显示，含有年轻锌指的 KZFP 在五个共表达模块中显着富集。其中，一个模块，包括 13 个含年轻锌指的 KZFP，显示出“早高晚低”的表达模式。进一步的功能分析表明，它们可能通过参与细胞周期相关过程在早期胚胎发育和 ESC 分化中发挥作用。