Transcription factor YY1 can control AID‐mediated mutagenesis in mice

Abstract

Activation-induced cytidine deminase (AID) is crucial for controlling the immunoglobulin (Ig) diversification processes of somatic hypermutation (SHM) and class switch recombination (CSR). AID initiates these processes by deamination of cytosine, ultimately resulting in mutations or double strand DNA breaks needed for SHM and CSR. Levels of AID control mutation rates, and off-target non-Ig gene mutations can contribute to lymphomagenesis. Therefore, factors that control AID levels in the nucleus can regulate SHM and CSR, and may contribute to disease. We previously showed that transcription factor YY1 can regulate the level of AID in the nucleus and Ig CSR. Therefore, we hypothesized that conditional knock-out of YY1 would lead to reduction in AID localization at the Ig locus, and reduced AID-mediated mutations. Using mice that overexpress AID (IgκAID yy1 ) or that express normal AID levels (yy1 ), we found that conditional knock-out of YY1 results in reduced AID nuclear levels, reduced localization of AID to the Sμ switch region, and reduced AID-mediated mutations. We find that the mechanism of YY1 control of AID nuclear accumulation is likely due to YY1-AID physical interaction which blocks AID ubiquitination.

YY1 control of mitochondrial‐related genes does not account for regulation of immunoglobulin class switch recombination in mice

“…Deletion of YY1 in splenic B cells results in a dramatic reduction in Eμ‐3’RR enhancer long‐distance DNA loops, nuclear activation‐induced cytidine deaminase (AID) levels, as well as immunoglobulin heavy chain (IgH) CSR [24, 33, 34]. To determine if YY1 might regulate CSR through regulation of mitochondrial‐related genes, we performed RNA‐seq analyses comparing naïve splenic B cells with those induced to undergo CSR by treatment with bacterial lipopolysaccharide (LPS) plus IL4 before and after conditional knockout of YY1.…”

“…To determine genes regulated by YY1, we used an ex vivo deletion system that deletes the yy1 gene through action of recombinant TAT‐CRE protein [4, 24, 33]. Using yy1 f/f mice, which contain the first yy1 exon flanked by loxP sites [33, 34, 39, 40], splenic B cells were isolated, and cells were either mock treated or treated with recombinant TAT‐CRE protein to delete the yy1 gene [33], and then cultured in LPS plus IL4 for 3 days to induce CSR. During this time, YY1 protein decays to nearly undetectable levels and CSR drops dramatically [33] (see also Supporting Information Fig.…”

“…During this time, YY1 protein decays to nearly undetectable levels and CSR drops dramatically [33] (see also Supporting Information Fig. 1 and 2B), coincident with significant drops in long‐distance DNA loops between the Eμ and 3’RR enhancers [24, 33, 34]. RNA was prepared from these samples for RNA‐seq analyses.…”

“…Instead, our data argue that the YY1 impact on CSR and long‐distance DNA loops is not due to changes in mitochondrial or glycolytic energy production, or to changes in gene expression, but is perhaps due to YY1 playing a structural role in DNA loop formation or in regulation of nuclear AID levels [33, 34]. YY1‐related long‐distance DNA looping systems involving promoter–enhancer, enhancer–enhancer, and promoter–promoter interactions have been observed in many cell types and it has been argued that YY1 plays a structural role in DNA loop formation [31, 63].…”

“…Yin Yang 1 (YY1) is a ubiquitously expressed zinc finger transcription factor that plays fundamental roles in gene expression, proliferation, differentiation, embryogenesis, replication, and apoptosis [1‐35]. YY1 was first identified as a key regulator of viral genes, ribosomal protein genes, and the immunoglobulin kappa (Igκ) 3′ enhancer [28, 35, 36], and regulates a huge variety of genes.…”