Regulation of gene expression by RelA in activated B lymphocytes

B cells undergo dramatic alterations in response to antigen recognition through cell surface receptors, which requires active transcription and translation. The temporal expression of transcripts is germane and integral in determining underlying complex biological phenomena. The transcription factor RelA is rapidly expressed in the nucleus in response to BCR crosslinking, and downregulated within hours. However, many putative NF-B target genes expressed by stimulated B cells do not follow the same kinetic pattern as the transcription factor, suggesting complex transcriptional and post-transcriptional regulation. The current work seeks to explore the mechanisms by which genes are regulated by NF-B in primary murine splenic B cells in response to BCR crosslinking. To do this, we examined the kinetics of genome-wide RelA binding, the inducible transcriptome, and RNA stability of induced genes. NF-B target genes, as inferred from RelA ChIP-seq analyses and pharmacological inhibition of IKK-2 inhibitors, were amongst the most highly induced genes in response to BCR crosslinking. Highly induced transcripts had shorter half-lives (t1/2s) than those with less robust induction one hour after stimulation. The majority of inducible genes with fast t1/2s displayed exponential decay, while the majority of inducible genes with slow t1/2s displayed non-exponential decay. As exponential decay is likely to mean a single-step decay mechanism and the 3’ UTRs are known to play a critical role in RNA stability, we looked to the presence of RNABP consensus motifs in genes of various decay patterns. Our analyses revealed that hnRNPA1 binding sites were highly enriched in the 3’ UTRs of genes with fast, exponential decay. siRNA mediated knockdown of hnRNPA1 in two mature B cell lines, Bal17 and M12, revealed greater RNA stability of many genes that have fast, exponential decay and are RelA target genes based on inducible RelA binding and IKK-2 inhibition. These findings suggest a tantalizing model in which mRNA decay is dependent on transcription factors, such as RelA, that inducibly bind to its target genes and induce RNA