Integrative analysis of Poly(A)-seq and RNA-seq reveals transcriptional regulation of poly(A) tail length in tuberculosis.

UNLABELLED: Tuberculosis (TB) is a serious global health problem, and the molecular mechanisms underlying TB pathogenesis remain poorly understood to date. Differential expression of many genes is an important contributor to TB, and poly(A) tails have previously unrecognized regulatory roles in this process that may impact gene expression. In this study, we combined Poly(A)-seq and RNA-seq to preliminarily investigate the link between poly(A) tail length and gene expression regulation in TB. The results indicated that the majority of genes harbor a longer poly(A) tail in TB, and the transcript levels of these genes were likely to be precisely regulated by poly(A) tail length. Notably, we identified 22 immune/inflammation-related genes that exhibited significant variations in both poly(A) tail length and expression levels. Furthermore, we focused on CHI3L1, associated with a robust antibacterial response, and experimentally validated its poly(A) tail length and expression level, showing that alterations in CHI3L1 poly(A) tail length affect gene expression, which may be important for Mycobacterium tuberculosis infection. In conclusion, this study generates hypotheses about post-transcriptional regulation in TB granulomas and may contribute potential strategies and ideas for future TB control.

IMPORTANCE: Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a global health challenge, with granulomas-its defining histopathological feature-playing a crucial role in the host's defense and patient outcomes. While poly(A) tail processing, a critical post-transcriptional regulator of RNA lifecycle events, has been studied in diseases like repeat expansion disorders, its role in TB pathogenesis remains unexplored. This study is the first to integrate Poly(A)-seq and RNA-seq to investigate the significance of poly(A) tail length regulation in tuberculosis granulomas. Our findings provide new insights into Mtb pathogenesis and the human immune response, and offer promising avenues for developing targeted host-directed therapeutic strategies.