Comprehensive Identification and Characterization of HML-9 Group in Chimpanzee Genome

Area of Science:

• Genomics and Evolutionary Biology
• Molecular Biology
• Primate Genetics

Background:

• Endogenous retroviruses (ERVs), specifically Human Endogenous Retrovirus-K (HERV-K) HML-9, are remnants of ancient viral infections integrated into host genomes.
• ERVs significantly influence host genome evolution and function, but their specific roles in non-human primates, like chimpanzees, are less understood.
• Previous characterization of HERV-K HML-9 was primarily in the human genome, leaving a gap in comparative primate genomics.

Purpose of the Study:

• To characterize the distribution, genetic structure, and evolutionary history of HERV-K HML-9 in the chimpanzee genome.
• To compare HERV-K HML-9 elements in chimpanzees with those found in the human genome.
• To investigate the potential biofunctional significance of HERV-K HML-9 in chimpanzees, particularly concerning disease association.

Main Methods:

• Bioinformatic analysis of the chimpanzee genome to identify and characterize HERV-K HML-9 proviral and solo LTR elements.
• Phylogenetic analysis to determine the evolutionary relationships of identified elements.
• Estimation of integration times using the 2-LTR method and prediction of conserved motifs and cis-regulatory regions.

Main Results:

• Identified 26 proviral and 38 solo LTR elements of HML-9 in the chimpanzee genome, showing non-random integration patterns.
• HERV-K HML-9 elements integrated into the chimpanzee genome between 14-36 million years ago, and into the human genome between 18-49 million years ago.
• Bioinformatic predictions revealed enriched pathways associated with neurological and psychiatric disorders regulated by ERV LTRs in chimpanzees.

Conclusions:

• The study provides a comprehensive genomic characterization of HERV-K HML-9 in chimpanzees, highlighting its evolutionary impact.
• Comparative analysis reveals conserved features and distinct integration timelines between human and chimpanzee HML-9 elements.
• The findings suggest a significant biofunctional role for ERV LTR-regulated genes in primate evolution and disease susceptibility.