The nucleus is a busy place. Cellular proteins twist and pull DNA, folding the genome into complex three-dimensional structures that support the function of its coding regions. This arrangement is crucial for cell development, but the specific steps for different types of cells vary greatly. Establishing correct communication between genes and distant control switches in the right cells at the right time is not an easy task. In fact, few proteins have the correct functional combination to organize the genome into the correct structure.
In a new study, researchers from the La Jolla Institute of Immunology (LJI), Massachusetts General Hospital, and Harvard Medical School demonstrated how a protein called IKAROS helps the genome “weave” into the correct structure needed for B cell differentiation and the production of life-saving antibodies. The relevant research results have recently been published in the Cell journal, with the title “Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS”.
Dr. Ferhat Ay, Associate Professor of LJI who co-led this new study, said, “Without IKAROS, it is impossible to produce B cells with normal functions.”
Ay is an expert in genome structure. He studies the location of genes and how certain parts of the genome interact with each other. His laboratory developed bioinformatics tools to draw a three-dimensional genome map, which is a crucial step in understanding the genetic basis of immune cell development. In this new study, Ay Laboratory collaborated with Dr. Katia Georgopoulos from Harvard Medical School Massachusetts General Hospital. Dr. Georgopoulos has previously found that IKAROS is crucial for the development of immune cells.
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Georgopoulos said, “IKAROS plays a fundamental role in this developmental process by differentiating hematopoietic stem cells into various immune cells, including B cells.” These early studies have shown that functional loss mutations in IKAROS can lead to lymphoid malignancies in animal models and are associated with poor prognosis in children and young adult B cell precursor leukemia patients. Can IKAROS serve as an early key organizer for the three-dimensional genomic structure required for normal development of B cells?
Ay Laboratory and Georgopoulos Laboratory teamed up to use the IKAROS mouse genetic model, B cell differentiation method, bioinformatics tools, and 3D genome map to validate this hypothesis and answer major questions about immune cell development.
Dr. Yeguang Hu, a lecturer at Georgopoulos Laboratory, conducted a highly technical experiment to determine which parts of the genome come into contact with each other in the presence and absence of IKAROS. Daniela Salgado Figueroa, a doctoral student in bioinformatics at the University of California, San Diego at Ay Laboratory, led the analysis of the complex dataset generated, spanning hundreds of trillions of bytes.
These authors found that IKAROS addresses a major issue in B cell development. B cells use receptors with two arms to detect pathogens. These arms have a “light chain” area and a “heavy chain” area. When B cells recognize pathogens, they produce antibodies with matching arms.
B cells assemble heavy chain regions in the early stages of development. Ay and Georgopoulos laboratories have found that assembling light chain regions is very challenging because the genes encoding light chain regions are far apart on DNA. Ay said, “The entire region needs to be rearranged in an appropriate three-dimensional conformation. Something needs to connect them together.”
Fortunately, IKAROS appeared on site and helped complete some genome sequencing. These two laboratories have found that IKAROS binds to specific loci in the genome and uses these loci as anchors to control the formation of highly useful DNA loops. The formed DNA loop connects distant genes with their control elements, thereby activating and expressing the genes required for normal B cell development and light chain rearrangement. Equally important, this folding of the genome keeps other control elements away from genes that should not be expressed in B cells.
In subsequent experiments, these authors introduced IKAROS into human skin cells. They tested whether IKAROS can induce genome assembly in a cell type that does not produce any IKAROS on its own. IKAROS has indeed achieved it. IKAROS altered most of the three-dimensional structure of the skin cell genome and formed new DNA loops, some of which were similar to the DNA loops in the B cells they analyzed.
These authors emphasize that studying the assembly of chromatin in three-dimensional space helps people understand how healthy cells develop and how poorly folded genomes can lead to diseases such as immunodeficiency and cancer. Looking ahead, they are interested in learning more about IKAROS disruption and disease development.
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Reference
Yeguang Hu et al. Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS. Cell, 2024, doi:10.1016/j.cell.2023.10.023.