「ゲノム・タイムマシン」がDNAの秘密を解明(”Genomic time machine” reveals secrets of our DNA)

2024-02-02

2024-02-01 スイス連邦工科大学ローザンヌ校(EPFL)

◆研究者らは、再構築された祖先のゲノムデータベースを用い、退化した可動性要素(TE)をより効果的に検出する方法を見つけました。
◆TEはゲノム内で位置を変え、遺伝的プロファイルを変異させる一方で、ゲノムの組織化と発現にも関与します。通常は識別が難しいTEの変異を祖先のゲノムと比較することで、新たに発見されたTEの数が増加し、これらが既知のものと同様に調整的な役割を果たすことが示されました。
◆TEの理解は、がんや免疫障害、エネルギー効率の高い電力グリッドなど、人間の健康や技術革新への洞察につながる可能性があります。

<関連情報>

ゲノム再構築がトランスポーザブル・エレメントのアノテーションを強化、退化したインテグラントを同定 Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Wayo Matsushima, Evarist Planet, Didier Trono
Cell Genomics Published: January 30, 2024
DOI:https://doi.org/10.1016/j.xgen.2024.100497

Highlights

•A transposon annotation pipeline through probing reconstructed ancestral genomes
•Identification of previously unannotated degenerate transposable elements (degTEs)
•DegTEs contribute various regulatory elements and transcription factor binding sites
•DegTEs form non-canonical chimeric transcripts with the host genes

Summary

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual species, which limits its scope to relatively intact TE sequences. Here, we report a novel approach to uncover previously unannotated degenerate TEs (degTEs) by probing multiple ancestral genomes reconstructed from hundreds of species. We applied this method to the human genome and achieved a 10.8% increase in coverage over the most recent annotation. Further, we discovered that degTEs contribute to various cis-regulatory elements and transcription factor binding sites, including those of a known TE-controlling family, the KRAB zinc-finger proteins. We also report unannotated chimeric transcripts between degTEs and human genes expressed in embryos. This study provides a novel methodology and a freely available resource that will facilitate the investigation of TE co-option events on a full scale.