Dynamic and widespread control of poly(A) tail length during macrophage activation

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 m5C sites, and 37 transcripts contained m6A sites. The transcripts containing m6A/m5C 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, m5C modified DETs, and m6A 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, m6A and m5C 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.

Unveiling Tissue-Specific RNA Landscapes in Mouse Organs During Fasting and Feeding Using Nanopore Direct RNA Sequencing

Understanding tissue-specific RNA landscapes is essential for uncovering the functional mechanisms of key organs in mammals. However, current knowledge remains limited, as short-read RNA sequencing-the predominant method for assessing gene expression-depends on incomplete gene annotations and struggles to resolve the diverse transcripts produced by genes. To address these limitations, an integrative approach combining nanopore direct RNA sequencing (DRS), ATAC-Seq, and short-read RNA-seq is used. This method enabled the analysis of RNA landscapes across major mouse organs under fasting and fed conditions, representing two extremes of the caloric cycle. This study uncovered tens of thousands of novel transcripts and identified hundreds of genes with tissue-specific expression, revealing additional layers of regulated pathways within each organ that conventional short-read RNA-seq cannot resolve. By profiling transcript expression across multiple organs under identical conditions, it is conducted comparative analyses exposing significant differences in transcript isoforms and regulations. Moreover, nanopore DRS revealed dynamic changes in poly(A) tail length and m6A modifications of transcripts, many regulated in a tissue-specific manner. These changes likely contribute to functional differentiation and metabolic specialization of various organs. Collectively, this findings reveal previously unrecognized layers of gene regulation, offering new insights into the metabolic basis of organ function.

Progress in modifying and delivering mRNA therapies for cancer immunotherapy

Advancements in mRNA-based therapeutics have greatly enhanced cancer immunotherapy by using the immune system to specifically target and eradicate cancer cells. There has been notable advancement in tailoring and administering mRNA to treat cancer. Codon optimization, chemical alterations, and sequence manipulation are complex design methodologies employed in the production of mRNA vaccines and treatments. The goal is to improve the ability of the chemicals to stimulate an immune response, increase their ability to be translated into practical applications, and boost their stability. Lipid nanoparticles (LNPs) are currently the most efficient means of delivering mRNA because they can withstand degradation, enhance cellular uptake, and facilitate endosomal escape. Scientists are currently investigating the possibility of using alternate methods of delivering substances, including as exosomes, lipoplexes, and polymeric nanoparticles, to enhance the ability to target specific tissues and minimize unwanted negative consequences. In addition, recent clinical trials and preclinical investigations have demonstrated encouraging findings in terms of the advancement of strong anti-tumor immune responses, long-lasting tumor shrinkage, and enhanced patient outcomes. The remaining challenges involve optimizing the equilibrium between tolerance and immunological activation, addressing systemic toxicity, and expanding manufacturing techniques. The upcoming study seeks to improve the design and dissemination of mRNA, include it in combination drugs, and investigate its therapeutic uses outside cancer. The advancement in cancer treatment represents a change in the current approach, highlighting the significant impact of mRNA technology in revolutionizing immunotherapy and enabling tailored cancer treatments.