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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.

抽象/项目总结