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Rapid evolutionary turnover underlies conserved lncRNA-genome interactions.

Jeffrey J Quinn¹, Qiangfeng C Zhang², Plamen Georgiev³

¹Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Bioengineering, Stanford University School of Medicine and School of Engineering, Stanford, California 94305, USA;

Genes & Development

|January 17, 2016

Summary

Researchers identified new long noncoding RNA (lncRNA) roles in gene regulation across species. They found that changes in repetitive RNA structures impact lncRNA function and genome interactions, linking dosage compensation to gene expression.

Keywords:

ChIRP Drosophila RNA structure dosage compensation lncRNAs roX

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Area of Science:

Evolutionary biology
Genomics
RNA biology

Background:

Long noncoding RNAs (lncRNAs) influence chromatin states, but their evolutionary origins and genome interaction dynamics remain poorly understood.
Understanding lncRNA evolution is crucial for deciphering gene regulation across species.

Purpose of the Study:

To develop a method for identifying lncRNA orthologs across species, even with low sequence similarity.
To investigate the evolutionary history and functional dynamics of roX lncRNAs in Drosophila species.

Main Methods:

An integrative strategy was employed to identify lncRNA orthologs in mammals and insects.
Genetic rescue experiments using roX orthologs and synthetic lncRNAs were performed.
Genomic occupancy mapping of roX RNAs was conducted in four Drosophila species.

Main Results:

47 new roX lncRNA orthologs were identified in Drosophilids, spanning approximately 40 million years of evolution.
The number of repetitive RNA structures within roX lncRNAs was found to determine their function.
Conserved targeting of X chromosome regions was observed, alongside rapid turnover of specific binding sites.
New binding sites frequently evolved from pre-existing RNA splicing signals, connecting dosage compensation to transcribed genes.

Conclusions:

Dynamic evolution of lncRNAs and their genomic targets is fundamental to conserved and essential lncRNA-genome interactions.
This study provides insights into the evolutionary mechanisms shaping lncRNA function and regulation.