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：
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
项目类别：
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

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确定了该项目将使用新的大部分调控序列。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盲人物种中丢失或恶化这些盲目物种是 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相同性状的物种独有的基因组区域，在这种情况下，得分最高的区域将是失明的。在胚胎发育的斑马鱼模型中分析眼睛和其他组织中的表达使用来自小鼠的序列来确定其功能后果。视力退化物种的序列进化为此，来自盲人物种的序列将被研究。使用实验表征与来自其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，以及最近通过研究盲物种的序列变化，引入了计算模型。在第三个目标中，该项目将确定对眼部表达重要的子序列。如果这些新的眼部区域是导致人类患者先天性眼部疾病的原因。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从我们对眼睛功能的进化和功能分析中得出的，因为因果突变是存在的。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此外，该项目中确定的眼部调节将提供基因领域。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。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。