# Transcriptome-Wide Analysis of N6-Methyladenosine Modification in the Liver of Geese at Different Growth Stages

## TL;DR

This study explores how RNA methylation changes in geese livers during different growth stages, revealing key genes and pathways involved in liver development and metabolism.

## Contribution

The study identifies stage-specific m6A modifications and links them to regulators like CDK1 and IGF2BP3, offering new insights into avian liver development.

## Key findings

- m6A levels in geese liver RNA decrease with age, with highest levels in newly hatched geese.
- CDK1 and IGF2BP3 are identified as key regulators of m6A-related processes in liver development.
- m6A modifications are enriched in coding sequences and 3′UTRs, affecting cell cycle and metabolism pathways.

## Abstract

This study addresses the limited understanding of dynamic RNA m6A methylation during healthy liver development in birds, using geese as a model. Our objective was to profile transcriptome-wide m6A modifications across key postnatal stages (newly hatched, fast growth, and sexual maturation) via MeRIP-seq and RNA-seq. Results revealed stage-specific m6A levels and differentially methylated peaks, predominantly in coding sequences and 3′UTRs. Integrated bioinformatic analysis identified cyclin-dependent kinase 1 (CDK1) as a potential central regulator of the cell cycle and insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) as a key m6A reader, thereby linking m6A-mediated RNA modifications to critical biological processes—including cell cycle progression, p53 signaling activation, and pyrimidine metabolism—during liver development. These findings elucidate epigenetic mechanisms governing poultry liver growth and metabolism, providing potential molecular targets for improving poultry health and productivity, thereby offering value to avian research and agricultural practices.

N6-methyladenosine (m6A) is a reversible RNA modification that dynamically regulates gene expression by modulating RNA stability, splicing, nuclear export, translation, and maturation—thereby orchestrating organismal development. In birds, including geese, the liver is a multi-functional organ central to metabolic regulation. Studies on the dynamic patterns of RNA m6A modifications during healthy liver growth and development remain limited. Here, we performed integrative methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) on liver tissues from geese at three biologically defined stages: post-hatch day 0 (0 week, P), fast growth (10 weeks, F), and sexual maturation (30 weeks, S). The level of m6A modification in total RNA extracted from liver tissues was higher in P than in F samples. Compared with other groups, the S group recorded the lowest m6A modification. In addition, 1641, 668, and 558 m6A peaks were differentially modified in the P, F, and S groups, respectively. The m6A peaks in the liver of the three groups were mainly enriched in the coding sequence and 3′ untranslated region. Moreover, integrated multi-omics analysis (MeRIP-seq and RNA-seq), combined with protein–protein interaction networks analysis, identified CDK1 as a core cell cycle regulator and IGF2BP3—a well-established m6A reader—as a consistently differentially expressed gene across all developmental stages. The m6A-regulated cell cycle, p53 signaling pathway, and pyrimidine metabolism pathway were identified in liver tissue as novel potential targets for controlling geese growth and metabolism. Together, these findings shed light on the dynamic regulation of RNA methylation during distinct growth phases in geese and advance our understanding of epigenetic mechanisms underlying poultry liver development.