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 眼睛发育受基因调节元素的复杂网络的控制，但该领域尚未 然而，涉及的大多数调节序列都被表征甚至确定。这个项目将使用新的 比较基因组学方法揭示了基因组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 在视力物种的基因组中保守，但眼睛消退的六个盲物种丢失或恶化 结构。这些盲物种是3种无关的物种，带有常用名称为“ mole”，2个无关的“摩尔 - 大鼠”和盲河海豚。将使用强大的Rerconverge软件实现此目标 在Clark和Chikina Labs中开发的，这些实验室利用了收敛进化现象的发现 在这种情况下，具有特征的物种独有的基因组区域。那么得分最高的地区将 在胚胎发育模型中分配在眼睛和其他组织中的表达 使用他们的鼠标序列。第二个目标将决定 视力消退的物种中的序列演变。为此，盲物种的序列将 使用实验表征将目光祖先的序列形成鲜明对比 开放染色质的胚胎表达和全基因组的模式，以及最近 引入的计算模型。通过研究盲物种的序列变化， 将确定对眼表达重要的子序列。在第三个目标中，该项目将确定 如果这些新的眼部区域是人类患者的先天性眼部疾病。患者 未发现因果突变的人将在数千个保守的非编码区域进行测序 这是我们眼功能的进化和功能分析浮出水面。由于因果突变是 在大多数眼科疾病的大多数情况下未发现，疾病与这些新近的关联 发现的眼部监管区域将解释这种辩护并允许更全面的诊断 在诊所。此外，该项目中确定的眼睛调节区域将提供基因领域 具有新序列和表达模式的治疗，以设计更安全，更精确的疗法。那， 该项目通过提供更好的途径来直接解决国家眼科研究所的任务 遗传眼病的诊断和治疗。