Discovery and characterization of ocular regulatory elements through evolutionary analysis

通过进化分析发现和表征眼部调节元件

• 批准号: 10445290
• 负责人: Maria D Chikina
• 金额: $ 51.6万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-07-01 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10445290
• 关键词: ATAC-seq; Address; Affect; Automobile Driving; Binding; Biological Assay; Blindness; Catalogs; Characteristics; Child; Chromatin; Clinic; Code; Computer Models; Computing Methodologies; DNA; DNA Sequence; Data; Development; Developmental Gene; Diagnosis; Disease; Embryo; Embryonic Development; Enhancers; Evolution; Exclusion; Eye; Eye Abnormalities; Eye Development; Eye diseases; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Genes; Genetic; Genome; Genomic Segment; Genomic approach; Goals; High-Throughput Nucleotide Sequencing; Human; Mammals; Marsupialia; Mission; Modeling; Mole Rats; Mole the mammal; Mus; Mutation; Names; National Eye Institute; Nucleic Acid Regulatory Sequences; Parents; Patients; Pattern; Phenotype; Process; Proteins; Regulator Genes; Regulatory Element; Research Project Grants; Retina; Safety; Sotalia; Structure; Surface; Testing; Tissues; Transgenic Organisms; Untranslated RNA; Vision; Zebrafish; blind; causal variant; comparative genomics; de novo mutation; design; diagnostic panel; gene regulatory network; gene therapy; genetic regulatory protein; genome-wide; improved; in vivo; insight; loss of function; molecular phenotype; novel; novel diagnostics; novel therapeutics; software development; spatiotemporal; tool; trait; transcription factor

Project Summary Eye development is governed by complicated networks of gene regulatory elements, but the field has not yet characterized or even identified most of the regulatory sequences involved. This project will use new comparative genomics approaches to reveal hundreds of regulatory regions in the genome crucial to eye development and function. The project first aims to precisely identify chromosomal regions that are conserved in sighted species’ genomes but lost or deteriorating in six blind species with regressed eye structures. Those blind species are 3 unrelated species with the common name “mole”, 2 unrelated “mole- rats”, and a blind river dolphin. This aim will be achieved using powerful RERconverge software developed in the Clark and Chikina labs that exploits the phenomenon of convergent evolution to discover genomic regions unique to species sharing a trait, in this case, blindness. Top-scoring regions will then be assayed for expression in the eye and other tissues in a zebrafish model of embryonic development using their sequences from mouse. The second aim will determine the functional consequences of sequence evolution in species with regressed eyesight. To this end, sequences from blind species will be contrasted with sequences from their sighted ancestor using experimental characterization of embryonic expression and genome-wide patterns of open chromatin, as well as through recently introduced computational models. By studying the sequence changes in blind species, specific subsequences important for ocular expression will be identified. In the third aim, the project will determine if these new ocular regions are responsible for congenital eye diseases in human patients. Patients for whom no causal mutation was found will be sequenced at thousands of conserved, non-coding regions that surfaced from our evolutionary and functional analyses for eye function. Since causal mutations are not identified in a majority of cases for most eye diseases, associations between disease and these newly discovered ocular regulatory regions would explain this deficit and allow more comprehensive diagnosis in the clinic. Furthermore, eye regulatory regions identified in this project will provide the field of gene therapy with new sequences and expression patterns to design safer and more precise therapies. Thus, this project directly addresses the mission of the National Eye Institute by providing avenues to better diagnosis and treatment of genetic eye diseases.

项目摘要 眼睛的发育是由复杂的基因调控元件网络控制的，但该领域并没有 但仍表征或甚至鉴定了所涉及的大多数调节序列。该项目将使用新的 比较基因组学方法揭示了基因组中对眼睛至关重要的数百个调节区域 发展和功能。该项目首先旨在精确识别染色体区域， 有视力物种的基因组保守，但在六个失明物种中失去或恶化 结构.这些盲物种是3个不相关的物种，共同名称为“鼹鼠”，2个不相关的“鼹鼠- 老鼠和一只盲眼海豚这一目标将通过功能强大的RERconverge软件实现 在克拉克和奇基纳实验室开发的，利用趋同进化的现象， 基因组区域是物种间共有的特征，在这个例子中，是失明。得分最高的地区将 在胚胎发育的斑马鱼模型中测定其在眼和其它组织中的表达 用的是老鼠的基因序列第二个目标将决定 用退化的视力进行物种的序列进化。为此，来自盲物种的序列将 与来自其有视力的祖先的序列进行对比，使用实验表征， 胚胎表达和开放染色质的全基因组模式，以及最近通过 引入了计算模型。通过研究盲物种的序列变化， 将鉴定对眼部表达重要的免疫原性。在第三个目标中，该项目将确定 这些新的眼部区域是否是人类患者先天性眼病的原因。患者 没有发现致病突变的人将在数千个保守的非编码区进行测序 从我们对眼睛功能的进化和功能分析中浮现出来。由于因果突变是 在大多数情况下，大多数眼部疾病都没有发现，疾病与这些新发现的疾病之间的联系， 发现的眼调节区可以解释这种缺陷，并允许更全面的诊断 在诊所里。此外，在本项目中鉴定的眼调节区域将为基因调控领域提供新的研究方向。 新的序列和表达模式，以设计更安全和更精确的治疗方法。因此，在本发明中， 该项目通过提供更好的途径，直接解决国家眼科研究所的使命， 遗传性眼病的诊断和治疗。