Recent advances in understanding the 3D structure of chromosomes has led to increased focus on the role of genome architecture in regulating gene transcription. Above the nucleosomal level, DNA elements like a gene promoter can form loop with distal enhancer element to drive gene transcription. Such loop can be lineage specific and is thus believed to play a crucial role during immune cell development and differentiation. However, how such loop is established and maintained is poorly understood.
Bcl11b is a critical transcription factor during T cell development, it is needed for the proper development of T lymphocytes and the deletion of it can skew the developing thymocytes towards natural killer or myeloid lineages. Here the genomic architecture of Bcl11b in T and B lymphocytes was investigated using chromosome conformation capture coupled with high-throughput sequencing (Hi-C) and CRISPR/Cas9 genome editing technologies.
Hi-C data of T and B lymphocytes on the Bcl11b regions revealed a T cell specific interaction between the Bcl11b promoter and a distal (~850 kb) cis-element 3’ downstream, the location of which is consistent with the previously characterised enhancer element of Bcl11b. By exploiting the CRISPR/Cas9 gene editing technology, the enhancer was bi-allelically deleted in the T cell lymphoma cell line EL4 and the expression of Bcl11b was found to be down-regulated but not abolished.
This preliminary work provides a framework of how a cis-regulatory region of the genome can be manipulated and this approach would further allow us to understand the role of the cistrome during immune development and differentiation.