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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

基本信息

批准号：
10927633
负责人：
Maria D Chikina
金额：
$ 46.91万
依托单位：
UNIVERSITY OF PITTSBURGH AT PITTSBURGH
依托单位国家：
美国
项目类别：
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/10927633
关键词：
Acceleration Address Affect Automobile Driving Binding Biological Assay Blindness Catalogs Characteristics Child Chromatin Clinic Code Computer Models Computing Methodologies DNA DNA Sequence Data Deterioration 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 Ocular Onchocerciasis 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

项目摘要

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控元件的复杂网络控制，但该领域并非如此然而，表征甚至识别了所涉及的大多数调控序列。该项目将使用新的比较基因组学方法揭示基因组中对眼睛至关重要的数百个调控区域发展和功能。该项目的第一个目标是精确识别出在有视力的物种的基因组中保存，但在6个眼睛退化的盲目物种中丢失或恶化结构。这些盲种是3个不相关的物种，共同的名字是“鼹鼠”，2个不相关的“鼹鼠”- 老鼠“，还有一只盲河海豚。这一目标将使用功能强大的RERConverge软件来实现在克拉克和奇基纳实验室开发，利用收敛进化现象来发现物种特有的基因组区域共享一种特征，在这种情况下，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的表达使用来自鼠标的它们的序列。第二个目标将决定视力衰退物种的序列进化。为此，来自盲目物种的序列将与它们有视力的祖先的序列进行对比，使用实验表征开放染色质的胚胎表达和全基因组模式，以及最近通过介绍了计算模型。通过研究盲目物种的序列变化，特定的将确定对眼睛表达重要的子序列。在第三个目标中，项目将确定这些新的眼睛区域是否对人类患者的先天性眼病负有责任。患者为没有发现原因突变的人将在数千个保守的非编码区进行测序这从我们对眼睛功能的进化和功能分析中浮出水面。因为因果突变是在大多数眼科疾病的大多数病例中没有确定，疾病和这些新的已发现的眼部调节区域可以解释这种缺陷，并可以进行更全面的诊断在诊所里。此外，在这个项目中确定的眼睛调节区将提供基因领域使用新的序列和表达模式进行治疗，以设计更安全和更精确的治疗方法。因此，该项目直接满足了国家眼科研究所的使命，提供了更好的途径遗传性眼病的诊断和治疗。