High Throughput Next Generation Sequencing: supports genomics and epigenomics research in muscle, skin, bone and autoimmune diseases

基因组技术科积极参与了NIAMS的大量研究项目，包括： -分析T淋巴细胞的基因组组织，以了解T辅助细胞命运规范和功能的基因调控机制。ATAC-SEQ、RNA-SEQ和CHIP-SEQ已被用于绘制染色质状态图、染色质可及性图和转录组图，揭示细胞命运指定和功能的分子机制。 -用scRNAseq研究循环中的人中性粒细胞的转录亚群。中性粒细胞可以被分类为转录簇，在健康的人类受试者中可以复制。外周血中性粒细胞从相对不成熟的(NH0)细胞，通过过渡表型(NH1)，进入由相对转录不活跃(NH2)或I型干扰素诱导基因的高表达(NH3)所定义的两个终点之一。 -染色质景观和调控小鼠表皮分化的网络的研究 -抑制脾酪氨酸激酶在恢复新冠肺炎髓系稳态中作用的研究 -研究UBA1和严重成人起病自身炎症性疾病的体细胞突变。 -通过比较组蛋白标记、核小体结合、转录因子结合、DNA(去)甲基化和使用不同测序技术(CHIP-SEQ、mRNA-SEQ、全基因组甲基-SEQ、4C、Hi-C)的三维核结构，观察到B细胞细胞激活过程中表观遗传特征的变化及其对细胞激活的影响。 -RNA结合蛋白(RBPs)对转录后基因调控的影响。 -选择限制性商业惯例对翻译起始和延伸的影响。 -单细胞分辨率下中胚层诱导的ESCs的转录组学、调控句法和增强子鉴定 -体外和体内产生和分离小鼠肌源性祖细胞的方案 -指定和维持皮肤细胞谱系，并研究皮肤干细胞的调节。 -了解染色质调节因子，如Polycomb蛋白、转录因子Pst1和eRNAs在肌肉分化过程中调节基因表达的活性。 -Ezh1通过非典范调控Notch信号维持小鼠肌肉干细胞静止 -发现骨骼肌细胞特化、分化和再生过程中调节新陈代谢和表观遗传学的分子机制。 -转录学、表观遗传学和功能分析表明，中性粒细胞多样性与系统性红斑狼疮的发病机制有关。 干扰素-γ诱导肌炎局部补体的协同局部RNA过度表达 -免疫检查点抑制剂引起的肌炎的不同亚群 -通过ATAC-seq分析静止和分化的肌肉干细胞(卫星细胞)的染色质可及性和基因组组织。 -分析几种人类和小鼠疾病和分化/细胞命运模型中的单细胞转录组。 -皮肌炎和抗Mi2自身抗体患者肌肉中CHD4/NuRD调节基因的转录抑制 -FoxO保持真正的肌肉干细胞静止状态，直到老年。

The Genome Technology Section has been actively involved in a large number of NIAMS research projects, including the following: -Analysis of the genomic organization of T lymphocytes to understand gene regulatory mechanisms for T helper cell fate specification and function. ATAC-seq, RNA-Seq, and ChIP-Seq have been used to draw maps of chromatin states, chromatin accessibility, and transcriptome revealing molecular mechanisms for cell fate specification and function. - Study of transcriptional subsets of circulating human neutrophils by scRNAseq. Neutrophils can be classified into transcriptional clusters that are reproducible among healthy human subjects. Peripheral blood neutrophils shift from relatively immature (Nh0) cells, through a transitional phenotype (Nh1), into one of two endpoints defined by either relative transcriptional inactivity (Nh2) or high expression of type I IFN-inducible genes (Nh3). - Study of chromatin landscape and regulatory networks governing murine epidermal differentiation -Study on the role of Spleen tyrosine kinase inhibition to restore myeloid homeostasis in COVID-19 - Study of somatic mutations in UBA1 and severe adult-onset Autoinflammatory Disease. - Dynamics of change in the epigenetic features observed during cellular activation of B-cells and its impacts on cellular activation by comparison of histone marks, nucleosome binding, transcription factor binding, DNA (de)methylation, and 3-D nuclear structure using different sequencing technologies (ChIP-Seq, mRNA-seq, whole genome methyl-seq, 4C, Hi-C). - Impact of RNA binding proteins (RBPs) on posttranscriptional gene regulation. - Impact of select RBPs on translation initiation and elongation. - Transcriptomics, regulatory syntax, and enhancer identification in mesoderm-induced ESCs at single-cell resolution - Protocols to generate and isolate mouse myogenic progenitors both in vitro and in vivo - Specification and maintenance of cell lineages in the skin, and study of the regulation of stem cells in the skin. - Understanding the activity of chromatin regulators such as Polycomb proteins, the transcription factor Pst1, and eRNAs in regulating gene expression during muscle differentiation. - Role of Ezh1 in maintaining murine muscle stem cell quiescence through non-canonical regulation of Notch signaling - Discovering the molecular mechanisms regulating metabolism and epigenetics during specification, differentiation, and regeneration of skeletal muscle cells. - Transcriptomic, epigenetic, and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus. - Coordinated local RNA overexpression of complement induced by interferon-gamma in myositis - Distinct subsets of immune checkpoint inhibitor-induced myositis - Analysis of chromatin accessibility and genomic organization of quiescent and differentiating muscle stem cells (satellite cells) by ATAC-seq. - Analysis of single-cell transcriptome in several human and mouse models of disease and differentiation/cell fate specification. - Transcriptional derepression of CHD4/NuRD-regulated genes in the muscle of patients with dermatomyositis and anti-Mi2 autoantibodies -FoxO maintains a genuine muscle stem-cell quiescent state until geriatric age.