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: 10242928
• 负责人: Maria D Chikina
• 金额: $ 46.93万
• 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 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10242928
• 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 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.

项目概要 眼睛发育受到复杂的基因调控元件网络的控制，但该领域尚未发现 尚未表征甚至鉴定出大部分涉及的调控序列。本项目将采用新 比较基因组学方法揭示基因组中数百个对眼睛至关重要的调控区域 发育和功能。该项目首先旨在精确识别染色体区域 在有视力的物种的基因组中保守，但在六种眼睛退化的失明物种中丢失或恶化 结构。这些盲目物种是 3 个不相关的物种，俗称“鼹鼠”，2 个不相关的“鼹鼠” 老鼠”和盲眼河豚。这一目标将通过强大的 RERconverge 软件来实现 由 Clark 和 Chikina 实验室开发，利用趋同进化现象来发现 具有共同性状的物种特有的基因组区域，在本例中是失明。得分最高的地区将 在斑马鱼胚胎发育模型中检测眼睛和其他组织中的表达 使用来自小鼠的序列。第二个目标将决定功能后果 视力退化物种的序列进化。为此，盲物种的序列将 使用实验表征与来自有视力的祖先的序列进行对比 开放染色质的胚胎表达和全基因组模式，以及最近 引入了计算模型。通过研究盲物种的序列变化，具体 对眼部表达重要的子序列将被识别。在第三个目标中，该项目将确定 这些新的眼部区域是否是导致人类患者先天性眼部疾病的原因。患者为 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 这是我们对眼睛功能的进化和功能分析得出的结论。由于因果突变是 在大多数眼病的​​大多数病例中，疾病与这些新疾病之间的关联尚未确定 发现的眼部调节区域可以解释这种缺陷并允许更全面的诊断 在诊所里。此外，该项目中确定的眼睛调节区域将提供基因领域 使用新的序列和表达模式进行治疗，以设计更安全、更精确的疗法。因此， 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使命 遗传性眼病的诊断和治疗。