Genome-Wide Analysis Identifies Rag1 and Rag2 as Novel Notch1 Transcriptional Targets in Thymocytes

Abstract

Recombination activating genes 1 (Rag1) and Rag2 are expressed in immature lymphocytes and essential for generating the vast repertoire of antigen receptors. Yet, the mechanisms governing the transcription of Rag1 and Rag2 remain to be fully determined, particularly in thymocytes. Combining cDNA microarray and ChIP-seq analysis, we identify Rag1 and Rag2 as novel Notch1 transcriptional targets in acute T-cell lymphoblastic leukemia (T-ALL) cells. We further demonstrate that Notch1 transcriptional complexes directly bind the Rag1 and Rag2 locus in not only T-ALL but also primary double negative (DN) T-cell progenitors. Specifically, dimeric Notch1 transcriptional complexes activate Rag1 and Rag2 through a novel cis-element bearing a sequence-paired site (SPS). In T-ALL and DN cells, dimerization-defective Notch1 causes compromised Rag1 and Rag2 expression; conversely, dimerization-competent Notch1 achieves optimal upregulation of both. Collectively, these results reveal Notch1 dimerization-mediated transcription as one of the mechanisms for activating Rag1 and Rag2 expression in both primary and transformed thymocytes. Our data suggest a new role of Notch1 dimerization in compelling efficient TCRβ rearrangements in DN progenitors during T-cell development.

An opinion on the debatable function of brain resident immune protein, T-cell receptor beta subunit in the central nervous system

“…The principal function of T-cells is to provide a highly specific line of immunological defense against foreign pathogen invasion and distinguish between self- and non-self-antigens ( Gascoigne, 2008 , Marshall et al, 2018 ). This role of T-cells heavily relies on recombination-acting genes ( Rag 1 and Rag 2 ) which produce a vast diversity of antigen receptors on T-cells and immunoglobulin receptors on B-cells, to defend against foreign pathogenic insult ( Dong et al, 2021 , Kumari et al, 2021 , Miyazaki et al, 2020 ). There are four well-defined antigen receptor polypeptides (α, β, γ, δ) on T-cells which occur either in α/β or in γ/δ heterodimeric combinations ( Davis and Bjorkman, 1988 ).…”

Lymphoid cell development from fetal hematopoietic progenitors and human pluripotent stem cells

“…Nevertheless, the generation of CD3 + cells in this system was limited and could only be achieved by transferring cells onto OP9‐DLL4 stroma. As such, the limitations of this specific organoid system to support T cell differentiation possibly reflected suboptimal access of developing cells to Notch ligands that are required for both expression of RAG genes and T cell development 110 …”

Established and Emerging Methods for Protecting Linear DNA in Cell-Free Expression Systems

“…While being crucial to linear DNA end protection, Ku proteins are also involved in VDJ recombination to create antigen receptor gene rearrangements [24]. For the rearrangements to occur, the Rag 1 and 2 proteins are needed to induce a site-specific double-strand break [25]. The double-strand breaks leave the ends of each strand exposed, allowing for Ku proteins to bind.…”