The Dfam Community Resource of Transposable Element Families, Sequence Models, and Genome Annotations

Storer, Jessica M.; Hubley, Robert; Rosen, Jeb; Wheeler, Travis J.; Smit, Arian F. A.

doi:10.21203/rs.3.rs-76062/v1

Cited by 74 publications

(92 citation statements)

References 43 publications

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“…The genomic landscape of zebrafish TEs Using RepeatMasker to annotate the Danio rerio reference genome (GRCv11), we mapped the location of sequences related to a total of 1931 nonredundant TE families catalogued in Dfam and Repbase (Bao et al, 2015;Storer et al, 2021). These families include representatives of all major classes and subclasses of eukaryotic TEs, including LTR, non-LTR (LINEs and SINEs) and tyrosine recombinase retroelements, as well as DDE-type DNA transposons, rolling-circle elements (RC, i.e.…”

Section: Resultsmentioning

confidence: 99%

A genomic portrait of zebrafish transposable elements and their spatiotemporal embryonic expression

Chang

Rovira

Wells

et al. 2021

Preprint

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There is considerable interest in understanding the effect of transposable elements (TEs) on embryonic development. Studies in humans and mice are limited by the difficulty of working with mammalian embryos, and by the relative scarcity of active TEs in these organisms. Zebrafish is an outstanding model for the study of vertebrate development and over half of its genome consists of diverse TEs. However, zebrafish TEs remain poorly characterized. Here we describe the demography and genomic distribution of zebrafish TEs and their expression throughout embryogenesis using bulk and single-cell RNA sequencing data. These results reveal a highly dynamic genomic ecosystem comprising nearly 2,000 distinct TE families, which vary in copy number by four orders of magnitude and span a wide range of ages. Longer retroelements tend to be retained in intergenic regions, whilst short interspersed nuclear elements (SINEs) and DNA transposons are more frequently found nearby or within genes. Locus-specific mapping of TE expression reveals extensive TE transcription during development. While two thirds of TE transcripts are likely driven by nearby gene promoters, we still observe stage and tissue-specific expression patterns in self-regulated TEs. Long terminal repeat (LTR) retroelements are most transcriptionally active immediately following zygotic genome activation, whereas DNA transposons are enriched amongst transcripts expressed in later stages of development. Single-cell analysis reveals several endogenous retroviruses expressed in specific somatic cell lineages. Overall, our study provides an important resource for using zebrafish as a model to study the impact of TEs on vertebrate development.

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Section: Resultsmentioning

confidence: 99%

A genomic portrait of zebrafish transposable elements and their spatiotemporal embryonic expression

Chang

Rovira

Wells

et al. 2021

Preprint

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“…These elements are characterized by two inverted terminal repeats, and an open reading frame (ORF) ( Wicker et al, 2007 ). The identified motifs are found on average once per element at positions 205/541 and 1005/1071 in TDR18 and TC1DR3 model sequences, respectively ( Storer et al, 2021 ). To further validate these associations, we interrogated previously published heart and forebrain WGBS DNA methylomes ( Ross et al, 2020 ; de Mendoza et al, 2021 ).…”

Section: Resultsmentioning

confidence: 99%

Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish Brain

Ross

Hesselson

Bogdanović

2021

Front. Cell Dev. Biol.

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DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes; however, non-CG methylation (mCH) is also detectable in vertebrate tissues, most notably in the nervous system. In mammals it is well established that mCH is targeted to CAC trinucleotides by DNMT3A during nervous system development where it is enriched in gene bodies and associated with transcriptional repression. Nevertheless, the conservation of developmental mCH accumulation and its deposition by DNMT3A is largely unexplored and has yet to be functionally demonstrated in other vertebrates. In this study, by analyzing DNA methylomes and transcriptomes of zebrafish brains, we identified enrichment of mCH at CAC trinucleotides (mCAC) at defined transposon motifs as well as in developmentally downregulated genes associated with developmental and neural functions. We further generated and analyzed DNA methylomes and transcriptomes of developing zebrafish larvae and demonstrated that, like in mammals, mCH accumulates during post-embryonic brain development. Finally, by employing CRISPR/Cas9 technology, we unraveled a conserved role for Dnmt3a enzymes in developmental mCAC deposition. Overall, this work demonstrates the evolutionary conservation of developmental mCH dynamics and highlights the potential of zebrafish as a model to study mCH regulation and function during normal and perturbed development.

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“…To refine and improve the quality of the TE consensus sequences, we then turned it over to DFAM (Storer et al 2021) who processed the ab initio library. First, any sequences mostly composed of tandem repeats were removed using a custom script to remove any sequences that were greater than 80% masked and/or had a sequence less than 100 bp.…”

Section: Methodsmentioning

confidence: 99%

The transposable element-rich genome of the cereal pestSitophilus oryzae

Parisot

Vargas-Chávez

Goubert

et al. 2021

Preprint

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Background Among beetles, the rice weevil Sitophilus oryzae is one of the most important pests causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. Results We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce a 770 Mbp assembly, the best for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect symbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 Kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino-acids required for insect development and cuticle biosynthesis. Conclusions In addition to being an agricultural pest and a valuable endosymbiotic system, S. oryzae can be a remarkable model for studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.

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The Dfam Community Resource of Transposable Element Families, Sequence Models, and Genome Annotations

Cited by 74 publications

References 43 publications

A genomic portrait of zebrafish transposable elements and their spatiotemporal embryonic expression

A genomic portrait of zebrafish transposable elements and their spatiotemporal embryonic expression

Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish Brain

The transposable element-rich genome of the cereal pestSitophilus oryzae

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