Determining gene targets and pathways for primate-specific zinc finger proteins

Kruppel型锌指（ZNF）基因座是人类最大的基因家族之一。在哺乳动物中， 大多数ZNF基因是单一亚型，编码的蛋白质中，DMA结合锌指阵列是 连接到一个染色质相互作用域，称为KRAB，赋予一个强大的转录抑制因子 活动虽然某些KRAB-ZNF基因座是高度保守的，但正在进行的片段性重复事件使KRAB-ZNF基因座的基因组序列发生了改变。 在每个哺乳动物谱系中创造了大量独特的基因组。在404个人类KRAB- ZNF基因座是灵长类动物特有的，即使是最近的重复基因也有不同的方式，表明 选择具有不同DNA识别位点的新型蛋白质。这个单基因家族包含了五分之一的 所有预测的人类转录因子基因座，和现有的数据表明，广泛的作用，在调节 对人类健康至关重要的过程。然而，由于已知调控靶点和途径， 只有少数KRAB-ZNF蛋白，大多数家族成员的功能仍然是一个猜测的问题。 我们假设这个动态基因家族在塑造人类健康相关的基因中发挥了重要作用。 生物学，包括高度保守和灵长类特有的特征。拟议的研究计划是 旨在通过25个KRAB-ZNF基因的功能分析来解决这一假设。作为主要焦点 我们将分析由25个基因编码的蛋白质，这些基因参与了最近灵长类特异性的复制， 强调最适合实验分析的旁系同源蛋白。具体而言，我们将（1） 通过操纵基因表达来确定由每种ZNF蛋白调节的基因和途径， 人细胞;（2）使用染色质确定ZNF蛋白在人染色质中结合的基因组区域 免疫沉淀技术;和（3）鉴定和验证限定有利的DNA序列的共有DNA基序。 使用生物信息学和实验方法相结合的每种蛋白质的识别位点。本研究 将提供一个第一次深入了解这个大家庭的人类转录抑制因子的功能， 使我们能够研究它们在调节人类免疫、生殖、发育、癌症中的作用 易感性和其他过程中，KRAB-ZNF基因已经牵连。我们生成的数据 将提供新的指导方针，以预测额外的家庭成员的功能，并评估潜在的 KRAB-ZNF基因的获得、缺失、突变和失调对人类健康的影响。

Kruppel-type zinc finger (ZNF) loci comprise one of the largest of all human gene families. In mammals, the majority of ZNF genes are of a single subtype, encoding proteins in which DMA-binding zinc finger arrays are attached to a chromatin-interacting domain, called KRAB, that confers a potent transcriptional represser activity. Although certain KRAB-ZNF loci are highly conserved, ongoing segmental duplication events have created largely unique gene sets in each mammalian lineage. More than one-third of the 404 human KRAB- ZNF loci are primate-specific, and even the most recent duplicate genes have diverged in ways that indicate a selection for novel proteins with distinct DNA recognition sites. This single gene family comprises one-fifth of all predicted human transcription factor loci, and available data suggest broad roles in regulating processes that are critical to human health. However, since regulatory targets and pathways are known for only a handful of KRAB-ZNF proteins the functions of most family members remain a matter of conjecture. We hypothesize that this dynamic gene family has played a significant role in shaping human health-related biology, including both deeply conserved and primate-specific traits. The proposed research program is designed to address this hypothesis through functional analysis of 25 KRAB-ZNF genes. As a primary focus we will analyze proteins encoded by 25 genes involved in the most recent primate-specific duplications with emphasis on paralogous proteins that are most amenable to experimental analysis. Specifically, we will (1) determine genes and pathways that are regulated by each ZNF protein by manipulating gene expression in human cells; (2) define genomic regions to which the ZNF proteins bind in human chromatin using chromatin immunoprecipitation techniques; and (3) identify and validate consensus DNA motifs defining favored recognition sites for each protein using combined bioinformatics and experimental approaches. This study will provide a first in-depth look at functions for this large family of human transcriptional repressers, permitting us to examine their roles in regulating in human immunity, reproduction, development, cancer susceptibility and other processes in which KRAB-ZNF genes have been implicated. The data we generate will provide new guidelines to predict the functions of additional family members and to assess the potential impact of the gain, loss, mutation and dsyregulation of KRAB-ZNF genes on human health.