Dataset Information

Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila.

ABSTRACT: High quality reference genomes are crucial to understanding genome function, structure and evolution. The availability of reference genomes has allowed us to start inferring the role of genetic variation in biology, disease, and biodiversity conservation. However, analyses across organisms demonstrate that a single reference genome is not enough to capture the global genetic diversity present in populations. In this work, we generate 32 high-quality reference genomes for the well-known model species D. melanogaster and focus on the identification and analysis of transposable element variation as they are the most common type of structural variant. We show that integrating the genetic variation across natural populations from five climatic regions increases the number of detected insertions by 58%. Moreover, 26% to 57% of the insertions identified using long-reads were missed by short-reads methods. We also identify hundreds of transposable elements associated with gene expression variation and new TE variants likely to contribute to adaptive evolution in this species. Our results highlight the importance of incorporating the genetic variation present in natural populations to genomic studies, which is essential if we are to understand how genomes function and evolve.

SUBMITTER: Rech GE

PROVIDER: S-EPMC9005704 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

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Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila.

Rech Gabriel E GE Radío Santiago S Guirao-Rico Sara S Aguilera Laura L Horvath Vivien V Green Llewellyn L Lindstadt Hannah H Jamilloux Véronique V Quesneville Hadi H González Josefa J

Nature communications 20220412 1

High quality reference genomes are crucial to understanding genome function, structure and evolution. The availability of reference genomes has allowed us to start inferring the role of genetic variation in biology, disease, and biodiversity conservation. However, analyses across organisms demonstrate that a single reference genome is not enough to capture the global genetic diversity present in populations. In this work, we generate 32 high-quality reference genomes for the well-known model spe ...[more]

PMID: 35413957

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Project description:BackgroundTransposable elements (TEs), which constitute nearly half of the human genome, have long been regarded as genomic "dark matter". However, their reactivation in tumor cells, resulting in the production of TE-chimeric transcripts (TCTs), has emerged as a potential driver of cancer progression. The complexity and full extent of these transcripts remain elusive, largely due to the limitations of short-read next-generation sequencing technologies. These methods have struggled to comprehensively capture the diversity and structure of TCTs, particularly those involving short interspersed nuclear elements (SINEs) or closely co-transcribed TEs.MethodsLeveraging full-length cDNA sequencing technology based on nanopore sequencing platform, we developed a customized pipeline for identifying and quantifying TCTs in 19 lung adenocarcinoma (LUAD) cell lines. The short-read RNA-seq dataset from a LUAD corhort (~ 200 tumor samples) was employed to validate the identified TCTs and explore their association with tumor progression. To assess the functional roles of a specific TCTs, cell migration and cell proliferation assays were performed.ResultsWe uncovered 208 unique TCT candidates in the LUAD cell lines. Our approach allowed for the identification of cryptic promoters and terminators within non-transposing TEs. Notably, we identified a chimeric transcript involving MIR_HKDC1, which appears to play a significant role in the progression of LUAD. Furthermore, the expression of these TCTs were associated with poor clinical outcomes in a cohort of LUAD patients, suggesting their potential as novel biomarkers for both LUAD progression and prognosis.ConclusionsOur study underscores the application of long-read sequencing to unravel the complex landscape of TCTs in LUAD. We provide a comprehensive characterization of TCTs in LUAD, exploring their potential regulatory roles in cancer progression. These findings contribute to a deeper understanding of the genomic intricacies underlying cancer, and offer new directions for the development of targeted therapies and personalized treatment strategies for LUAD. This research highlights the potential of TCTs as both biomarkers and therapeutic targets in the oncogenesis, offering new insights into the interplay between transposable elements and gene regulation in cancer.

Dataset Information

Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila.

Publications

Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila.

Similar Datasets

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