Nasreen Bano, PhD

Uncovering how YY1 knockout alters B-cell lineage using single-cell and 3D genomics

Nasreen Bano1, Sulagna Sanyal1, Sarah Naiyer1, Suchita Hodawadekar1, Michael L. Atchison1* 1Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA *Principal Investigator

Yin Yang 1 (YY1) is a multifunctional transcription factor that regulates gene expression by recruiting chromatin remodelers, modifying histones, and facilitating long-range chromatin interactions between enhancers and promoters. In hematopoiesis, lineage commitment is tightly controlled by transcription factors, chromatin architecture, and epigenetic regulators. During normal development, pre-pro-B cells commit exclusively to the B-cell lineage at the pro-B cell stage. In this study, we investigated the role of YY1 in B-cell lineage commitment using a conditional knockout (KO) model in pro-B cells cultured on OP9-DL4 feeder cells providing Notch signaling. Loss of YY1 disrupted B-lineage specification and promoted the emergence of alternative lineages, including T cells, macrophages, dendritic cells, and monocytes. Single-cell chromatin accessibility profiling revealed increased accessibility at alternative lineage genes and decreased accessibility at B-lineage genes in YY1 KO pro-B cells compared to wild-type. Similarly, single-cell transcriptomic analysis showed elevated expression of alternative lineage genes alongside repression of B cell-specific genes. Chromatin loops, play critical roles in gene regulation by bringing distant regulatory elements (e.g., enhancers and promoters) together. Hi-C analyses demonstrated enhanced chromatin loop interactions at alternative lineage genes whereas reduced loops were found at B lineage genes in YY1 KO pro-B cells indicating significant alterations in 3D genome organization. Together, these findings establish YY1 as a critical regulator of chromatin accessibility and 3D genome architecture required for maintaining B-cell lineage commitment and repression of alternative fates.