Sequence-specific DNA-binding of evolutionary divergent KRAB-zinc finger proteins

进化趋异的 KRAB-锌指蛋白的序列特异性 DNA 结合

• 批准号: 8705134
• 负责人: Adam Michael Blattler
• 金额: $ 3.59万
• 依托单位: UNIVERSITY OF CALIFORNIA AT DAVIS
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-07-21 至 2014-07-20
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8705134
• 关键词: Binding; Binding Sites; Biochemical; Biological Assay; Boxing; C2H2 Zinc Finger; Categories; ChIP-seq; Chromatin; Chromosomes; Chromosomes, Human, Pair 19; Chromosomes, Human, Pair 7; Communities; Complex; DNA Binding; DNA Binding Domain; Data; Development; Evolution; Family; Gene Cluster; Gene Expression; Gene Targeting; Genes; Genomics; Goals; Health; Human; Human Chromosomes; In Vitro; Malignant Neoplasms; Mammals; Mediating; Modeling; Mus; Oligonucleotides; Ontology; Phylogenetic Analysis; Physiological; Proteins; Recruitment Activity; Repression; Research; Role; Testing; Tissues; Transcription Repressor/Corepressor; Zinc Fingers; chromatin immunoprecipitation; design; human BRAF protein; human ZNF45 protein; in vivo; knock-down

DESCRIPTION (provided by applicant): KRAB domain-containing zinc finger proteins (KRAB-ZNFs) are a large, but poorly characterized family of transcriptional regulators in mammals. KRAB-ZNFs are thought to function as transcriptional repressors through a KRAB box-mediated interaction with the KAP1 corepressor complex. Despite much biochemical evidence, there are very few known target genes of KRAB-ZNFs and the physiological roles of these regulators remain essentially unknown. The genes encoding zinc finger proteins are typically found in clusters located on several different chromosomes. These clusters are thought to have arisen from tandem duplications and are present in much higher numbers in mammalian species. Recent phylogenetic analysis suggests that the KRAB ZNF gene clusters on human chromosome 19 and mouse chromosome 7 are highly related; it appears that a single mouse gene Zfp61 has given rise to a cluster of 10 human genes on chromosome 19. Each of these genes contains a KRAB transcriptional repressor domain and has varying numbers of C2H2 zinc finger DNA binding domains. Such lineage specific duplications of KRAB-ZNFs may have important implications for defining species-specific transcriptional networks and may have significant implications on development. I propose that the evolution of human specific KRAB-ZNF genes has a significant impact on lineage-specific transcriptional networks. Specifically, the divergence within the C2H2 regions of the cluster of KRAB-ZNF genes leads to diverse DNA binding activities of the 10 KRAB-ZNF transcriptional repressors. These separate factors are therefore capable of regulating 10 distinct subsets of genes that are otherwise only controlled by a single transcription repressor in mouse. I will express tagged versions of the 10 human genes and one mouse gene and analyze their targets using an in vivo chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq).

描述（由申请人提供）：含有KRAB结构域的锌指蛋白（KRAB-ZNF）是哺乳动物中一个大但特征不明的转录调节因子家族。 KRAB-ZNF 被认为通过 KRAB 盒介导的与 KAP1 辅阻遏物复合物的相互作用发挥转录阻遏物的作用。尽管有大量生化证据，但 KRAB-ZNF 的已知靶基因很少，并且这些调节因子的生理作用仍然基本上未知。编码锌指蛋白的基因通常存在于位于几个不同染色体上的簇中。这些簇被认为是由串联复制产生的，并且在哺乳动物物种中的数量要高得多。最近的系统发育分析表明，人类19号染色体上的KRAB ZNF基因簇与小鼠7号染色体上的KRAB ZNF基因簇高度相关；似乎单个小鼠基因 Zfp61 在 19 号染色体上产生了由 10 个人类基因组成的簇。这些基因中的每一个都包含一个 KRAB 转录抑制结构域，并具有不同数量的 C2H2 锌指 DNA 结合结构域。 KRAB-ZNF 的这种谱系特异性重复可能对定义物种特异性转录网络具有重要意义，并且可能对发育产生重大影响。我认为人类特异性 KRAB-ZNF 基因的进化对谱系特异性转录网络具有重大影响。具体而言，KRAB-ZNF 基因簇的 C2H2 区域内的分歧导致 10 个 KRAB-ZNF 转录抑制子的 DNA 结合活性不同。因此，这些独立的因子能够调节 10 个不同的基因子集，否则这些基因子集在小鼠中只能由单个转录抑制子控制。我将表达 10 个人类基因和一个小鼠基因的标记版本，并使用体内染色质免疫沉淀和高通量测序 (ChIP-seq) 分析其靶标。