Alternative splicing variants and DNA methylation status of BDNF in inbred chicken lines

Abstract Brain-derived neurotrophic factor ( BDNF ) has multiple alternative splicing variants and plays diverse biological functions in mammals, including neuronal survival, cholesterol metabolism, cell differentiation and tumor development. However, genomic structures of chicken BDNF (c BDNF ) variants and its potential functions are still undefined. Here, we characterized two novel alternative splicing variants of c BDNF , c BDNF 1 and c BDNF 2, via combining comparative genomics methods and molecular techniques in inbred chicken line 63 and line 72 , which have been developed to be resistant and susceptible, respectively, to Marek's disease tumor since 1939. Both c BDNF s consist of a bipartite transcript, with different 5′ exons, exon I (298 bp) in c BDNF 1 and exon II (286 bp) in c BDNF 2, each of which is spliced to the common 3′ exon IV. Exon I and IV are highly conserved between chicken and mammals, whereas exon II is unique for chicken. The amino acid sequence of cBDNF1 contains 8 additional amino acids in the N terminal compared to cBDNF2. c BDNF 1 and c BDNF 2 were only expressed in the hypothalamus among eight tissues, and c BDNF 2 showed lower expression than that of c BDNF 1 in both lines. The expression level of c BDNF 1 was significantly higher in line 72 than in line 63 ( P < 0.01). Notably, the DNA methylation levels on the cis -regulatory region of c BDNF 1 was negatively correlated with its expression level, which suggests that the mRNA expression level of c BDNF 1 may be related to the DNA methylation status in the chickens. We also discussed a potential role of variant c BDNF 1 in MD tumor resistance and susceptibility.