YY1-dependent chromatin structure stabilization of B lineage commitment

B 谱系定型的 YY1 依赖性染色质结构稳定

基本信息

批准号：
10652364
负责人：
Michael Lee Atchison
金额：
$ 49.7万
依托单位：
UNIVERSITY OF PENNSYLVANIA
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-07-15 至 2026-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10652364
关键词：
3-Dimensional Ablation B-Cell Development B-Lymphocytes Biological Assay Bone Marrow Cell Line Cell Lineage Cell Maintenance Cells Chromatin Chromatin Structure Coupled DNA Binding Data Defect Development Disease Distal Embryonic Development Epigenetic Process Erythroid Cells Future Gene Expression Gene Expression Profile Gene Rearrangement Generations Genes Genetic Transcription Genomics Hematopoietic Hematopoietic stem cells IGK@ gene cluster IgK Immune In Vitro Knock-out Laboratories Lymphoid Macrophage Mediating Megakaryocytes Modeling Mus Nuclear Pathway interactions Pattern Play Polycomb Process Regulation Regulator Genes Repression Role Signal Transduction Specific qualifier value Structure System T-Lymphocyte Testing Therapeutic Tissues Transcript Transcription Initiation Transcriptional Activation YY1 Transcription Factor conditional knockout experimental study in vivo in vivo evaluation insight knock-down leukemia/lymphoma mutant neutrophil notch protein permissiveness prevent progenitor programs stem cells transcription factor

项目摘要

During B cell lineage commitment, a dynamic shift of genes between transcriptionally restricted and transcriptionally permissive compartments at the pre-pro-B to pro-B cell transition results in activation of the B lineage program and repression of alternative lineage programs. While B lineage commitment is generally believed to be driven by lineage-specific transcription factors, we have made the surprising discovery that conditional knock-out of the ubiquitous transcription factor YY1 results in loss of B lineage commitment, allowing subsequent development into the T cell lineage both in vitro and in vivo. Pioneer transcription factors such as Ebf1 promote transcription of B lineages genes and repress expression of alternative lineage genes to initiate B lineage commitment, but stable commitment requires changes in chromatin structures at the pro-B cell stage. As YY1 is a key factor controlling lineage-specific gene regulatory long-range chromatin interactions (LRCIs), we hypothesize that YY1 knock-out in pro-B cells results in loss of chromatin LRCIs that stably maintain B lineage-specific gene expression. Consistent with this, we found reduction of B lineage transcripts after YY1 knock-out. YY1 can also mediate Polycomb Group (PcG) repression, and we found that YY1 knock-out resulted in increased expression of alternative lineage genes, suggesting that YY1 loss abrogates repressive chromatin structures needed to prevent expression of these genes. Thus, we hypothesize that YY1 knock-out in pro-B cells results in lost chromatin structures that stably maintain lineage-specific gene expression, as well as loss of repressive chromatin structures needed to prevent alternative lineage gene expression, thus leading to lost B lineage commitment. To test this, we will determine chromatin folding patterns, nuclear localization of key genes, chromatin accessibility, and epigenetic structures in wild-type and YY1-null pro-B cells to define the genomic structures regulated by YY1 during B lineage commitment. To determine if analogous effects of YY1 are operative in the T lineage, we will determine if YY1 loss promotes lineage plasticity of YY1-null DN3 cells. YY1 is also necessary in pro-B cells for Igk locus contraction required for rearrangement of distal Vk genes. It has been suggested that YY1 plays a structural role in regulating chromatin structures, but it is unclear if this requires the YY1 transcriptional activation, PcG, or self-association functions. We will utilize an established panel of YY1 mutants that are compromised in these functions to assess in parallel, the mechanisms of YY1 regulation of chromatin structures needed for B lineage commitment, and those needed for Igk locus contraction and Jk-Vk rearrangement. As YY1 is involved in embryogenesis and development of multiple tissue types, determining how YY1 controls genomic structures to specify B lineage commitment will provide a new paradigm for the function of a ubiquitous factor in lineage-specific development.

在 B 细胞谱系定型期间，基因在转录限制和转录限制之间动态转变前 B 细胞向前 B 细胞转变时的转录允许区室导致激活 B 谱系计划和对替代谱系计划的镇压。虽然 B 血统承诺是通常认为是由谱系特异性转录因子驱动的，我们做出了令人惊讶的发现条件性敲除普遍存在的转录因子 YY1 会导致 B 谱系丧失承诺，允许随后在体外和体内发育成 T 细胞谱系。先锋转录因子如 Ebf1 促进 B 谱系基因的转录并抑制 B 谱系基因的表达替代谱系基因启动 B 谱系承诺，但稳定的承诺需要改变原 B 细胞阶段的染色质结构。由于YY1是控制谱系特异性基因的关键因素调节性长程染色质相互作用 (LRCI)，我们假设 pro-B 细胞中 YY1 敲除导致稳定维持 B 谱系特异性基因表达的染色质 LRCI 丢失。持续的由此，我们发现 YY1 敲除后 B 谱系转录本减少。 YY1也可以调解 Polycomb Group (PcG) 抑制，我们发现 YY1 敲除导致表达增加替代谱系基因，表明 YY1 丢失消除了抑制性染色质结构需要阻止这些基因的表达。因此，我们假设 pro-B 细胞中的 YY1 敲除导致稳定维持谱系特异性基因表达的染色质结构丢失，以及丢失阻止替代谱系基因表达所需的抑制性染色质结构，从而导致失去了B血统的承诺。为了测试这一点，我们将确定染色质折叠模式、核野生型和 YY1 缺失中关键基因的定位、染色质可及性和表观遗传结构 pro-B 细胞定义 B 谱系定型期间受 YY1 调节的基因组结构。到确定 YY1 的类似效应是否在 T 谱系中起作用，我们将确定 YY1 是否丢失促进 YY1 缺失 DN3 细胞的谱系可塑性。 YY1 对于 Igk 位点在 pro-B 细胞中也是必需的远端 Vk 基因重排所需的收缩。有人建议YY1扮演调节染色质结构中的结构作用，但尚不清楚这是否需要 YY1 转录激活、PcG 或自关联功能。我们将利用一组已建立的 YY1 突变体在这些功能中受到损害，以并行评估，YY1 调节的机制 B 谱系定型所需的染色质结构，以及 Igk 位点收缩所需的染色质结构 Jk-Vk 重排。由于YY1参与多种组织类型的胚胎发生和发育，确定 YY1 如何控制基因组结构以指定 B 谱系承诺将提供新的方法谱系特定发展中普遍存在的因素的功能范式。