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:10.1186/s13100-020-00230-y

Cited by 356 publications

(321 citation statements)

References 52 publications

(55 reference statements)

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“…Each class of TEs comprises different clades/superfamilies and families, the diversity and complexity of which has prompted decades-long identification and classification efforts [ 29 , 30 ]. In particular, class I TEs are typically subdivided into long terminal repeat (LTR) and non-LTR retrotransposons, with the former displaying a close relationship with retroviruses and other reverse-transcribing viruses ( Figure 1 ).…”

Section: Retrotransposons and Their Impact On Mammalian Genome Evolutionmentioning

confidence: 99%

Retrotransposons as Drivers of Mammalian Brain Evolution

Ferrari

Grandi

Tramontano

et al. 2021

Life

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Retrotransposons, a large and diverse class of transposable elements that are still active in humans, represent a remarkable force of genomic innovation underlying mammalian evolution. Among the features distinguishing mammals from all other vertebrates, the presence of a neocortex with a peculiar neuronal organization, composition and connectivity is perhaps the one that, by affecting the cognitive abilities of mammals, contributed mostly to their evolutionary success. Among mammals, hominids and especially humans display an extraordinarily expanded cortical volume, an enrichment of the repertoire of neural cell types and more elaborate patterns of neuronal connectivity. Retrotransposon-derived sequences have recently been implicated in multiple layers of gene regulation in the brain, from transcriptional and post-transcriptional control to both local and large-scale three-dimensional chromatin organization. Accordingly, an increasing variety of neurodevelopmental and neurodegenerative conditions are being recognized to be associated with retrotransposon dysregulation. We review here a large body of recent studies lending support to the idea that retrotransposon-dependent evolutionary novelties were crucial for the emergence of mammalian, primate and human peculiarities of brain morphology and function.

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Section: Retrotransposons and Their Impact On Mammalian Genome Evolutionmentioning

confidence: 99%

Retrotransposons as Drivers of Mammalian Brain Evolution

Ferrari

Grandi

Tramontano

et al. 2021

Life

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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: Results and Discussion Mch Is Enriched At Defined Cac-contaimentioning

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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“…The sequences were aligned in the Clustal W program [ 29 ], using the BioEdit v7.0 editor [ 30 ]. To verify their identity, the sequences were subjected to a search against the database of Dfam ( accessed on 5 May 2021) [ 31 ] and then deposited on GenBank ( accessed on 5 May 2021) with the following accession number: MT038010.…”

Section: Methodsmentioning

confidence: 99%

Silencing of Transposable Elements Mediated by 5-mC and Compensation of the Heterochromatin Content by Presence of B Chromosomes in Astyanax scabripinnis

Barbosa

Schemczssen-Graeff

Marques

et al. 2021

Cells

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The way in which transcriptional activity overcomes the physical DNA structure and gene regulation mechanisms involves complex processes that are not yet fully understood. Modifications in the cytosine-guanine sequence of DNA by 5-mC are preferentially located in heterochromatic regions and are related to gene silencing. Herein, we investigate evidence of epigenetic regulation related to the B chromosome model and transposable elements in A. scabripinnis. Indirect immunofluorescence using anti-5-mC to mark methylated regions was employed along with quantitative ELISA to determine the total genomic DNA methylation level. 5-mC signals were dispersed in the chromosomes of both females and males, with preferential accumulation in the B chromosome. In addition to the heterochromatic methylated regions, our results suggest that methylation is associated with transposable elements (LINE and Tc1-Mariner). Heterochromatin content was measured based on the C-band length in relation to the size of chromosome 1. The B chromosome in A. scabripinnis comprises heterochromatin located in the pericentromeric region of both arms of this isochromosome. In this context, individuals with B chromosomes should have an increased heterochromatin content when compared to individuals that do not. Although, both heterochromatin content and genome methylation showed no significant differences between sexes or in relation to the occurrence of B chromosomes. Our evidence suggests that the B chromosome can have a compensation effect on the heterochromatin content and that methylation possibly operates to silence TEs in A. scabripinnis. This represents a sui generis compensation and gene activity buffering mechanism.

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The Dfam community resource of transposable element families, sequence models, and genome annotations

Cited by 356 publications

References 52 publications

Retrotransposons as Drivers of Mammalian Brain Evolution

Retrotransposons as Drivers of Mammalian Brain Evolution

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

Silencing of Transposable Elements Mediated by 5-mC and Compensation of the Heterochromatin Content by Presence of B Chromosomes in Astyanax scabripinnis

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