Transposable elements shape the evolution of mammalian development

Senft, Anna D.; Macfarlan, Todd S.

doi:10.1038/s41576-021-00385-1

Cited by 184 publications

(168 citation statements)

References 275 publications

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“…The large number of SERV proviral integrations, with several hundreds of fixed loci having been detected in the average OWM species, profoundly alter the architecture of the OWM genomes, not only by their presence and coding capacity, but also by recombination of homologous viral sequences, and by the ability of LTRs to function as novel promoters and influence gene expression. The important role of transposable elements in reshaping mammalian development, and especially in ERV-driving lineage-specific evolution of the placenta, has been recognized [ 54 , 55 ]. ERVs that have lost env coding capacity can become “superspreaders”, multiplying disproportionately and taking over a considerable part of the host genome [ 56 , 57 ].…”

Section: Discussionmentioning

confidence: 99%

Analysis of Simian Endogenous Retrovirus (SERV) Full-Length Proviruses in Old World Monkey Genomes

Kuyl

2022

Genes

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Simian endogenous retrovirus, SERV, is a successful germ line invader restricted to Old World monkey (OWM) species. (1) Background: The availability of high-quality primate genomes warrants a study of the characteristics, evolution, and distribution of SERV proviruses. (2) Methods: Cercopithecinae OWM genomes from public databases were queried for the presence of full-length SERV proviruses. A dataset of 81 Cer-SERV genomes was generated and analyzed. (3) Results: Full-length Cer-SERV proviruses were mainly found in terrestrial OWM, and less so in arboreal, forest- dwelling monkeys. Phylogenetic analysis confirmed the existence of two genotypes, Cer-SERV-1 and Cer-SERV-2, with Cer-SERV-1 showing evidence of recent germ-line expansions. Long Terminal Repeat (LTR) variation indicated that most proviruses were of a similar age and were estimated to be between <0.3 and 10 million years old. Integrations shared between species were relatively rare. Sequence analysis further showed extensive CpG methylation-associated mutations, variable Primer Binding Site (PBS) use with Cer-SERV-1 using PBSlys3 and Cer-SERV-2 using PBSlys1,2, and the recent gain of LTR motifs for transcription factors active during embryogenesis in Cer-SERV-1. (4) Conclusions: sequence analysis of 81 SERV proviruses from Cercopithecinae OWM genomes provides evidence for the adaptation of this retrovirus to germ line reproduction.

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Section: Discussionmentioning

confidence: 99%

Analysis of Simian Endogenous Retrovirus (SERV) Full-Length Proviruses in Old World Monkey Genomes

Kuyl

2022

Genes

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“…Heterochromatin is a mosaic of simple DNA repeats and a patchwork of complete and incomplete transposable elements (TEs) that cluster in "transposon graveyards" [11][12][13][14][15]. Nearly all eukaryotic genomes carry heterochromatic regions with copious numbers of TEs [14].…”

Section: Heterochromatin: From the Dark To The Lightmentioning

confidence: 99%

“…Transposons deploy self-encoded integrases, endonucleases, and transposases to move around genomes. As they move, they carry with them promoters, transcription factor binding sites, and polyadenylation signals [12,[15][16][17][18]. Consequently, TEs have the capacity to alter transcriptional regulation, promote ectopic recombination, and generate chromosome rearrangements within host genomes.…”

Section: Heterochromatin: From the Dark To The Lightmentioning

confidence: 99%

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Shining Light on the Dark Side of the Genome

Wallrath

Rodriguez-Tirado

Geyer

2022

Cells

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Heterochromatin has historically been considered the dark side of the genome. In part, this reputation derives from its concentration near centromeres and telomeres, regions of the genome repressive to nuclear functions such as DNA replication and transcription. The repetitive nature of heterochromatic DNA has only added to its “darkness”, as sequencing of these DNA regions has been only recently achieved. Despite such obstacles, research on heterochromatin blossomed over the past decades. Success in this area benefitted from efforts of Sergio Pimpinelli and colleagues who made landmark discoveries and promoted the growth of an international community of researchers. They discovered complexities of heterochromatin, demonstrating that a key component, Heterochromatin Protein 1a (HP1a), uses multiple mechanisms to associate with chromosomes and has positive and negative effects on gene expression, depending on the chromosome context. In addition, they updated the work of Carl Waddington using molecular tools that revealed how environmental stress promotes genome change due to transposable element movement. Collectively, their research and that of many others in the field have shined a bright light on the dark side of the genome and helped reveal many mysteries of heterochromatin.

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“…Transposable elements (TEs) are a reservoir of new transcription factor binding sites for protein-coding genes [1][2][3] . Developmental programs that activate TE-derived regulatory elements could, in principle, manifest in lineage-specific TE mobility.…”

mentioning

confidence: 99%

LINE-1 retrotransposon activation intrinsic to interneuron development

Bodea

Ferreiro

Sánchez‐Luque

et al. 2022

Preprint

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Transposable elements (TEs) are a reservoir of new transcription factor binding sites for protein-coding genes. Developmental programs that activate TE-derived regulatory elements could, in principle, manifest in lineage-specific TE mobility. While somatic LINE-1 (L1) retrotransposon insertions have been detected in human neurons, the impact of L1 insertions on neurodevelopmental gene regulation, and whether L1 mobility is restricted to certain neuronal lineages, is unknown. Here, we reveal programmed L1 activation by SOX6, a transcription factor critical for parvalbumin (PV+) interneuron development. PV+ neurons harbor unmethylated and euchromatic L1 promoters, express L1 mRNA, and permit L1 transgene mobilization in vivo. Elevated L1 expression in adult dentate gyrus PV+ neurons is however attenuated by environmental enrichment. Nanopore sequencing of PV+ neurons identifies unmethylated L1 loci providing alternative promoters to core PV+ neuron genes, such as CAPS2. These data depict SOX6-mediated L1 activation as an ingrained component of the mammalian PV+ neuron developmental program.

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Transposable elements shape the evolution of mammalian development

Cited by 184 publications

References 275 publications

Analysis of Simian Endogenous Retrovirus (SERV) Full-Length Proviruses in Old World Monkey Genomes

Analysis of Simian Endogenous Retrovirus (SERV) Full-Length Proviruses in Old World Monkey Genomes

Shining Light on the Dark Side of the Genome

LINE-1 retrotransposon activation intrinsic to interneuron development

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