Direct RNA sequencing reveals chicken post-transcriptional modifications in response to Campylobacter jejuni inoculation.

BACKGROUND

Campylobacter jejuni (C. jejuni), is a leading cause of food-borne pathogen, poses significant threats to poultry industry and public health. Post-transcriptional modifications play crucial roles in regulating the immune system and cell functions. However, the epigenetic regulation in response to C. jejuni inoculation in chicken remains elusive.

RESULTS

The RNA transcriptional profiles and base modification alterations in the chicken cecum following C. jejuni inoculation were characterized using direct RNA sequencing and analyzed by bio-informatics and expression analysis. We identified 40,755 transcripts and 23,877 genes following C. jejuni inoculation in the chicken cecum. Of which, 10,503 novel transcripts across 8,560 genes were identified. The number of significantly differential alternative splicing events and poly(A) tails was 192 and 426, respectively (P < 0.05). Particularly, 121 significantly differentially expressed transcripts which were enriched in defense response to gram-negative bacteria, positive regulation of interleukin-6 production, innate immune response, macrophage activation (P < 0.05). Among these, 29 transcripts contained mC sites, and 37 transcripts contained mA sites. The transcripts containing mA/mC modifications displayed higher expression levels and shorter poly(A) tails than those without modifications. Functional analysis of these modules including differentially expressed transcripts (DETs), transcripts with differentially significant poly(A) tail length, mC modified DETs, and mA modified DETs showed that the negative regulation of interferon-beta production was enriched (P < 0.05). Specially, ENSGALT00000020390 (novel transcript), and ENSGALT00000053962 (IFIH1-202) were significantly enriched.

CONCLUSIONS

This study provided a post-transcriptional modification profile in the chicken cecum post C. jejuni inoculation, including alternative splicing, poly(A) tail length, mA and mC modifications. ENSGALG00000012480 and IFIH1 could be potential candidate genes as epigenetic markers following C. jejuni inoculation. The findings provide new insights into the complexity of expression regulation and data resource of the epitranscriptome, enhancing our understanding on epigenetic modification regulating C. jejuni inoculation.