The contribution of transposable elements to Bos taurus gene structure

Area of Science:

• Genomics
• Evolutionary Biology
• Bioinformatics

Background:

• Transposable elements (TEs) are mobile genetic sequences that can influence genome evolution.
• Understanding TE contributions to genome evolution is crucial for deciphering genetic diversity and adaptation.
• Bovine genome evolution is shaped by various genetic factors, including TE activity.

Purpose of the Study:

• To investigate the abundance, distribution, and insertional orientation of TEs within bovine nuclear genes.
• To identify the role of TEs in shaping bovine genome evolution.
• To explore instances of TE exaptation in bovine gene sequences.

Main Methods:

• Analysis of all bovine nuclear genes using sequence build 2.1.
• Screening of exons, introns, and promoter regions using the RepeatMasker program.
• Detailed analysis of specific TE insertions, including the Charlie element in a zinc finger 452 gene homolog.

Main Results:

• Most bovine genes analyzed contained an average of 18 TE insertions.
• Retrotransposons were the predominant type of TE insertion, followed by DNA transposons.
• TEs were most frequently inserted into introns, with infrequent insertions into exons and promoters.
• Six cases of bovine genes with exon sequences entirely derived from TEs were identified.
• Detailed analysis of a Charlie DNA insertion suggests exaptation in a zinc finger 452 gene.

Conclusions:

• TEs play a substantial role in bovine genome evolution, primarily through intronic insertions.
• Exaptation of TEs into exon sequences can directly impact protein sequences and potentially alter phenotypes.
• The identified TE-derived exons, particularly in the zinc finger 452 gene, highlight novel mechanisms of gene evolution in mammals.