FUNCTIONAL GENOMICS AND MECHANISM OF BCL11B ACTION IN LYMPHOCYTE COMMITMENT

BCL11B 在淋巴细胞定型中的作用基因组学和机制

基本信息

批准号：
10393519
负责人：
ELLEN V. ROTHENBERG
金额：
$ 63.23万
依托单位：
CALIFORNIA INSTITUTE OF TECHNOLOGY
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-05-04 至 2024-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10393519
关键词：
3-Dimensional Acute Affect Binding Binding Sites Biological CRISPR/Cas technology Cell Lineage Cells ChIP-seq Chromatin Chromatin Loop Clustered Regularly Interspaced Short Palindromic Repeats Complex DNA DNA Binding Defect Development Developmental Gene Developmental Process Diagnosis Disease Dissection E protein Gene Expression Gene Expression Profile Gene Expression Regulation Genes Genetic Predisposition to Disease Genetic Transcription Genetic study Genome Genome Mappings Genomic Segment Genomic approach Genomics Human Genetics ID2 gene Immune Immune system Investments Knock-out Knockout Mice Light Link Location Lymphocyte Lymphoid Cell Maps Mature T-Lymphocyte Mediating Molecular Natural Killer Cells Nuclear Hormone Receptors Output Pattern Property Proteomics Radiation Regulation Regulator Genes Research Personnel Resolution Resources Role Site System T-Cell Development T-Cell Lymphoma T-Lymphocyte T-Lymphocyte Subsets Techniques Testing Time Transcriptional Regulation Work Zinc Fingers alpha-beta T-Cell Receptor cell type chicken ovalbumin upstream promoter-transcription factor cofactor functional genomics gene network genetic corepressor genome-wide leukemia loss of function preference protein complex protein function recruit retroviral transduction transcription factor

项目摘要

ABSTRACT/PROJECT SUMMARY Bcl11b is a bifunctional zinc finger transcription factor that is crucial for the lineage commitment of TCRαβ T cells. The Bcl11b gene is activated precisely at the developmental transition when the cells undergo commitment, and it sustains αβ T-cell identity and functions of multiple T-cell subsets thereafter. Genes that it keeps silent during initial T-cell commitment include key regulators of all innate lymphoid cells (ILCs) and natural killer cells (NK). Some of these genes are also continuously repressed by Bcl11b in mature T cells. However, surprisingly, Bcl11b is also expressed in one particular class of innate lymphoid cells, ILC2 cells. ILC2 cells also require Bcl11b for their identity, yet at the same time, they express Bcl11b along with Id2 and other genes that Bcl11b normally silences in T cells. A major question is how Bcl11b works so differently in ILC2 and early developing T cells (pro-T cells). We propose to determine how this works using functional genomics and gene network dissection to shed light on the mechanisms that make the difference. Our preliminary evidence from ChIP-seq and proteomic analyses shows that Bcl11b binds to distinct, only partially overlapping sets of sites in the two cellular contexts, and interacts with different transcriptional partners; and this is correlated with regulation of almost completely nonoverlapping sets of Bcl11b-sensitive genes in the two contexts. To interpret these differences, we first distinguish functional from probably-nonfunctional sites where Bcl11b binds DNA, by identifying its impact on complexes of co-regulators that assemble with it. Thus, the subset of sites is mapped where Bcl11b has a locally indispensable nucleation role for chromatin-modulating cofactors and/or other specific interaction partners. Second, we plan to map genomic regions where higher-order chromatin looping interactions and compartment boundaries can also be shown to depend on Bcl11b expression. These results will identify the Bcl11b binding sites in each cell context where that binding is molecularly functional. To determine the underlying causes of these differences, we will test how Bcl11b's own site binding preferences may be established through the presence of other transcription factors. We have identified at least two other important sequence-specific transcription factors, e.g., that (1) interact extensively with Bcl11b at many of its binding sites in the T-cell context, yet (2) are under-represented in ILC2 cells. Using retroviral transduction and CRISPR technology adapted to pro-T cells, we will introduce or delete putative interaction partners reciprocally in ILC2 and pro-T cells, to evaluate critically what roles they may have in guiding the binding and function of Bcl11b. We will apply this approach to explain how Bcl11b nucleates functionally different sites in pro-T cells and ILC2s. Finally, an interaction of particular importance is the gene network circuit through which we have shown Bcl11b to support E proteins in establishing the T-lineage commitment regulatory state. Using conditional double knockouts, we will resolve the subsets of Bcl11b gene regulation effects that are mediated through this circuit from those that are controlled directly.

摘要/项目摘要 Bcl11b 是一种双功能锌指转录因子，对于 TCRαβ T 的谱系定型至关重要当细胞经历发育转变时，Bcl11b 基因被精确激活。承诺，并在此后维持 αβ T 细胞身份和多个 T 细胞亚群的功能。在初始 T 细胞定型期间保持沉默的因素包括所有先天淋巴细胞 (ILC) 和天然淋巴细胞的关键调节因子杀伤细胞 (NK) 中的一些基因也会被成熟 T 细胞中的 Bcl11b 持续抑制。令人惊讶的是，Bcl11b 也在一类特定的先天淋巴细胞（ILC2 细胞）中表达。需要 Bcl11b 来确定其身份，但同时，它们也表达 Bcl11b 以及 Id2 和其他基因，这些基因 Bcl11b 通常在 T 细胞中沉默，一个主要问题是 Bcl11b 在 ILC2 和早期的作用有何不同。我们建议使用功能基因组学和基因来确定其如何发挥作用。网络剖析以揭示产生差异的机制。我们来自 ChIP-seq 和蛋白质组学分析的初步证据表明，Bcl11b 仅与不同的结合两个细胞环境中部分重叠的位点集，并与不同的转录伙伴相互作用；这与 Bcl11b 敏感基因组几乎完全不重叠的调节相关为了解释这些差异，我们首先区分功能性站点和可能非功能性站点。其中 Bcl11b 通过识别其对与其组装的共调节子复合物的影响来结合 DNA，因此，绘制了 Bcl11b 位点子集，其中 Bcl11b 对染色质调节具有局部不可缺少的成核作用其次，我们计划绘制高阶基因组区域。染色质环相互作用和区室边界也取决于 Bcl11b 表达。这些结果将识别每个细胞环境中的 Bcl11b 结合位点，其中该结合是分子上的为了确定这些差异的根本原因，我们将测试 Bcl11b 自身的位点结合方式。我们至少已经确定了其他转录因子的存在可以建立偏好。另外两个重要的序列特异性转录因子，例如，(1) 在许多方面主要与 Bcl11b 相互作用其在 T 细胞环境中的结合位点，但 (2) 在使用逆转录病毒转导的 ILC2 细胞中代表性不足。和适应亲T细胞的CRISPR技术，我们将引入或删除假定的相互作用伙伴在 ILC2 和 pro-T 细胞中相互相互作用，以批判性地评估它们在指导结合和 Bcl11b 的功能我们将应用这种方法来解释 Bcl11b 如何在功能上使不同位点成核。最后，一个特别重要的相互作用是基因网络回路。我们已经证明 Bcl11b 支持 E 蛋白建立 T 谱系承诺调节状态。条件双敲除，我们将解析所介导的 Bcl11b 基因调控效应的子集通过该电路直接控制。

项目成果

期刊论文数量（13）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Epigenetic Dynamics in the Function of T-Lineage Regulatory Factor Bcl11b.

T 谱系调节因子 Bcl11b 功能的表观遗传动力学。

DOI：
发表时间：
2021
期刊：
影响因子：
0
作者：
Sidwell, Tom;Rothenberg, Ellen V
通讯作者：
Rothenberg, Ellen V

Cell type-specific actions of Bcl11b in early T-lineage and group 2 innate lymphoid cells.

Bcl11b 在早期 T 谱系和第 2 组先天淋巴细胞中的细胞类型特异性作用。

DOI：
发表时间：
2020
期刊：
影响因子：
0
作者：
Hosokawa, Hiroyuki;Romero;Yang, Qi;Motomura, Yasutaka;Levanon, Ditsa;Groner, Yoram;Moro, Kazuyo;Tanaka, Tomoaki;Rothenberg, Ellen V
通讯作者：
Rothenberg, Ellen V

Dynamic control of the T-cell specification gene regulatory network.

T 细胞规范基因调控网络的动态控制。