Chromatin remodeling and gene expression during preimplantation development

着床前发育过程中的染色质重塑和基因表达

• 批准号: 10402284
• 负责人: Pablo Juan Ross
• 金额: $ 31.93万
• 依托单位: UNIVERSITY OF CALIFORNIA AT DAVIS
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-01 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10402284
• 关键词: ATAC-seq; Address; Affect; Bioinformatics; Biological; Biological Assay; Biology; Blushing; Cancer Biology; Cattle; Cell Cycle; Cell Differentiation process; Cells; ChIP-seq; Characteristics; Chromatin; Cloning; Communities; Data Set; Deposition; Development; Diagnosis; Disease; Embryo; Embryonic Development; Epigenetic Process; Excision; Experimental Designs; Fertility Disorders; Fertilization; Foundations; Gene Expression; Gene Expression Regulation; Genes; Genetic Transcription; Genome; Genomics; Germ Cells; Health; Histones; Human; Human Development; Incidence; Infertility; Inherited; Intervention; Knowledge; Length; Light; Link; Location; Maps; Methodology; Minor; Modeling; Molecular; Mus; Nature; Oocytes; Pluripotent Stem Cells; Pre-implantation Embryo Development; Process; Production; RNA Splicing; Research; Resolution; Resources; Role; Series; Time; Totipotent; Transcript; Transcriptional Activation; animal cloning; base; blastocyst; chromatin remodeling; demethylation; diagnostic tool; egg; embryo stage 2; experimental study; genome-wide; histone methylation; histone modification; improved; inhibitor; mortality; nuclear reprogramming; pluripotency; preimplantation; prevent; single molecule; sperm cell; stem cell biology; transcriptome sequencing; zygote

Dynamic changes in epigenetic information underlie the transition of gametic chromatin to embryonic chromatin. These changes are thought to be required to initiate embryonic gene transcription and acquisition of pluripotency. Abnormalities in these transitions likely result in embryonic arrest at early preimplantation stages. Early embryonic mortality is a major cause of infertility in dairy cattle and humans. We and others established that histone methylation changes during preimplantation development is an active and enzymatically based process. Specific Aim 1 will determine the locus-specific dynamics of histone methylation marks during preimplantation bovine development and their association with changes in gene expression. Using a rigorous experimental design, ChIP-seq and RNA-seq datasets across preimplantation bovine development will be generated to answer the following questions: 1) what is the role of repressive histone mark removal on EGA, 2) is deposition of activating histone marks related to EGA, 3) which genomic features escape histone modification remodeling, 4) what is the role of modified sperm histones for embryonic gene regulation, 5) how long does the asymmetric chromatin state persist and how does it affect embryonic gene expression, and 6) what is the epigenetic landscape of the totipotent state and how does it change with early lineage differentiation. Although it is generally accepted that the dramatic remodeling of gametic chromatin, driven by maternal factors, is required to initiate embryonic gene expression, the relationship between transcription and chromatin remodeling is poorly understood. Specific Aim 2 will determine the relationship between embryonic gene expression and chromatin remodeling during bovine preimplantation development. The nature of transcripts produced by early embryos will be determined using full-length single-molecule RNA-sequencing and global chromatin accessibility landscapes interrogated using ATAC-seq. A rigorous experimental design using transcriptional inhibition and bioinformatics analysis will determine the characteristics of transcripts produced during embryo development and the relationship between transcription and chromatin remodeling. Together, these experiments will expand our understanding of basic mechanisms underlying embryonic development. This information will aid in developing diagnostic tools and interventions to treat infertility disorders. Moreover, understanding the transition from differentiated gametes to pluripotent blastomeres will shed light on mechanisms of chromatin remodeling of differentiated cells to pluripotency, which is relevant to cloning, stem cells, and cancer biology. Therefore, the aims of this project will contribute to improve our understanding of human development and health.

表观遗传信息的动态变化是配子染色质向胚胎染色质转变的基础。这些变化被认为是启动胚胎基因转录和获得多能性所必需的。这些转变的异常可能导致胚胎着床前早期阶段的胚胎骤停。胚胎早期死亡是奶牛和人类不育的主要原因。我们和其他人建立了组蛋白甲基化变化在植入前发育是一个活跃的和酶为基础的过程。特异性目的1将确定着床前牛发育过程中组蛋白甲基化标记的位点特异性动态及其与基因表达变化的关联。通过严格的实验设计，ChIP-seq和RNA-seq数据集将生成贯穿着床前牛发育的数据集，以回答以下问题：1)的角色是什么压制在EGA删除组蛋白标记,2)是激活相关的组蛋白标记EGA沉积,3)组蛋白的化学修饰基因组功能逃避装修,4)的角色是什么修改为胚胎基因调控精子组蛋白,5)不对称的染色质状态持续多久和它如何影响胚胎基因表达,和6)的表观遗传景观全能国家和它如何改变早期谱系分化。虽然人们普遍认为，由母体因素驱动的配子染色质的戏剧性重塑是启动胚胎基因表达所必需的，但转录与染色质重塑之间的关系尚不清楚。特异性Aim 2将确定胚胎基因表达和牛着床前发育期间染色质重塑之间的关系。早期胚胎产生的转录本的性质将使用全长单分子rna测序和使用ATAC-seq查询的全球染色质可及性景观来确定。利用转录抑制和生物信息学分析的严格实验设计将确定胚胎发育过程中产生的转录本的特征以及转录和染色质重塑之间的关系。总之，这些实验将扩大我们对胚胎发育基本机制的理解。这些信息将有助于开发诊断工具和干预措施来治疗不孕症。此外，了解从分化配子到多能卵裂球的转变将揭示分化细胞染色质重塑到多能性的机制，这与克隆、干细胞和癌症生物学有关。因此，该项目的目标将有助于增进我们对人类发展和健康的理解。

项目成果

A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues.

• DOI: 10.1186/s12864-020-07078-9
• 发表时间: 2020-10-07
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Halstead MM;Kern C;Saelao P;Wang Y;Chanthavixay G;Medrano JF;Van Eenennaam AL;Korf I;Tuggle CK;Ernst CW;Zhou H;Ross PJ
• 通讯作者: Ross PJ