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Leveraging comparative genomics to elucidate the genetic determinants of limb skeletal proportion

利用比较基因组学阐明肢体骨骼比例的遗传决定因素

基本信息

批准号：
10164722
负责人：
Kimberly Lynn Cooper
金额：
$ 37.86万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN DIEGO
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-04-01 至 2024-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10164722
关键词：
ATAC-seq Address Adult Animals Arm Bones Biochemical Biology Candidate Disease Gene Cartilage Chick Embryo Chiroptera Chondrocytes Chondrogenesis Cleaved cell Complex Coupled Data Data Set Development Digit structure Dipodidae Distal Dolphins Dwarfism Elements Embryo Enhancers Epiphysial cartilage Evolution Fingers Forelimb Gene Expression Gene Transfer Techniques Genes Genetic Genetic Determinism Genome Growth Hindlimb Human IGF1 gene IGFBP5 gene In Vitro Insulin-Like Growth-Factor-Binding Proteins Knowledge Laboratories Laboratory mice Leg Bones Length Limb structure Link Location Metatarsal bone structure Modeling Mus Organ Organism Orthologous Gene Pathway interactions Peptide Hydrolases Phalanx of hand Phylogenetic Analysis Positioning Attribute Public Health Radial Regulatory Element Research Resistance Role Sequence Homology Shapes Signal Pathway Signal Transduction Signaling Protein Skeletal Development Skeleton Structure Testing Tissues Toes Transgenic Mice Vertebrates Whole Organism Wing Work bone comparative comparative genomics dexterity differential expression foot gene function grasp in vivo inhibitor/antagonist long bone loss of function mutation mutant new growth organ growth overexpression predictive modeling skeletal transcriptome sequencing ulna

项目摘要

The length of each skeletal element changes independently during development and evolution to transform an embryonic skeleton with similar sized cartilages into a diverse array of adult forms and functions. Loss of function mutations of many genes produce proportionately dwarfed skeletons that suggest a common “toolkit” is required for elongation of all of the long bones. Far less well understood, however, are the mechanisms that establish the specific rate and duration of elongation at each growth plate, which together determine adult limb skeletal proportion. What are the genes that define skeletal proportion? Is differential growth controlled by modular enhancers that locally tune expression of genes common to all growth plates and/or by genes that function only in subsets of growth plates? Our laboratory is positioned to answer these profoundly important questions about how vertebrate limbs acquire form and function using two uniquely suitable species: the laboratory mouse and the lesser Egyptian jerboa. Among the nearest mouse relatives, the jerboa has the most extremely different hindlimbs with extraordinarily long feet, but its forelimbs are similar to the mouse. These similarities and differences coupled with high genome sequence homology enable the identification of genetic mechanisms that locally control skeletal growth rate. RNA-Seq analysis of mouse and jerboa forelimb and hindlimb elements revealed that 10% of orthologous genes are differentially expressed correlating with relative growth rates within and between species. These include 40 genes with strong evidence for enhancer modularity in both species. Aim 1 will implement comparative ATAC-Seq and mouse transgenesis to identify and functionally test modular enhancers in the mouse and jerboa genomes. We predict that some of these 40 genes are controlled by radius/ulna enhancers that are conserved between species and by distinct metatarsal enhancers that functionally diverged in jerboa and allowed the uncoupled evolution of jerboa hindlimb proportion. Our expression data also provides a valuable opportunity to fill critical gaps in our understanding of the genes that regulate limb skeletal growth and proportion in all vertebrates. We previously showed that IGF1 signaling is required in mice for hypertrophic chondrocyte size differences in growth plates that elongate at different rates. Although IGF1 has a well-established role in whole organism and organ growth, it is unclear how the pathway is locally regulated to modulate differential growth. In Aim 2, we will biochemically test the hypothesis that elevated protease expression in rapidly elongating skeletal elements cleaves IGF binding proteins thus freeing bioactive IGF1 protein for signaling to accelerate growth. Although six other high priority candidate genes are also expected to be critical regulators of skeletal growth, they have not yet been attributed growth plate functions. Aim 3 will implement a powerful overexpression approach in chicken embryos to test the hypothesis that each of these genes is sufficient to accelerate or inhibit limb growth rate.

每个骨骼元素的长度在发育和进化过程中独立变化