Genomics of cold adaptations in the Antarctic notothenioid fish radiation

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: June 9, 2023

Abstract Numerous novel adaptations characterise the radiation of notothenioids, dominant fish group in freezing seas Southern Ocean. To improve understanding evolution this iconic group, here we generate and analyse new genome assemblies for 24 species covering all major subgroups radiation, including five long-read assemblies. We present a estimate onset at 10.7 million years ago, based on time-calibrated phylogeny derived from genome-wide sequence data. identify two-fold variation size, driven by expansion multiple transposable element families, use data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, most complete reconstruction date antifreeze glycoprotein family, whose emergence enabled survival sub-zero temperatures, showing locus ancestral state. Second, trace loss haemoglobin genes icefishes, only vertebrates lacking functional haemoglobins, through clusters across notothenioid families. Both genomic loci are characterised transposon expansions that may have evolutionary history these genes.

Language: Английский

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Autonomous transposons tune their sequences to ensure somatic suppression

Nature, Journal Year: 2024, Volume and Issue: 626(8001), P. 1116 - 1124

Published: Feb. 14, 2024

Abstract Transposable elements (TEs) are a major constituent of human genes, occupying approximately half the intronic space. During pre-messenger RNA synthesis, TEs transcribed along with their host genes but rarely contribute to final mRNA product because they spliced out together intron and rapidly degraded. Paradoxically, an abundant source RNA-processing signals through which can create new introns 1 , also functional 2 or non-functional chimeric transcripts 3 . The rarity these events implies existence resilient splicing code that is able suppress TE exonization without compromising pre-mRNA processing. Here we show SAFB proteins protect genome integrity by preventing retrotransposition L1 while maintaining integrity, via prevention previously integrated TEs. This unique dual role possible L1’s conserved adenosine-rich coding sequences bound proteins. suppressive activity extends tissue-specific, giant protein-coding cassette exons, nested Tigger DNA transposons. Moreover, suppresses LTR/ERV in species still active, such as mice flies. A significant subset suppressed somatic cells activated testis, coinciding low expression postmeiotic spermatids. Reminiscent division labour between innate adaptive immune systems fight external pathogens, our results uncover RNA-based, pattern-guided, non-adaptive defence system against soma, complementing Piwi-interacting pathway germline.

Language: Английский

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An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development

Cell, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

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The sound of silence: mechanisms and implications of HUSH complex function

Trends in Genetics, Journal Year: 2023, Volume and Issue: 39(4), P. 251 - 267

Published: Feb. 6, 2023

The vertebrate genome is under constant threat of invasion by genetic parasites. Whether the host can immediately recognize and respond to invading elements has been unclear. discovery human silencing hub (HUSH) complex, finding that it provides immediate protection from products reverse transcription, have important implications for mammalian evolution. In this review, we summarize recent insights into HUSH function describe how cellular introns provide a novel means self–nonself discrimination, allowing transcriptionally repress broad range intronless elements. We discuss contributes evolution, highlight studies reporting critical role in development implicating control immune signaling cancer progression.

Language: Английский

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Repetitive elements in aging and neurodegeneration

Trends in Genetics, Journal Year: 2023, Volume and Issue: 39(5), P. 381 - 400

Published: March 17, 2023

Language: Английский

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Take a walk on the KRAB side

Trends in Genetics, Journal Year: 2023, Volume and Issue: 39(11), P. 844 - 857

Published: Sept. 14, 2023

Language: Английский

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Endogenous retroviruses in development and health

Trends in Microbiology, Journal Year: 2023, Volume and Issue: 32(4), P. 342 - 354

Published: Oct. 4, 2023

Language: Английский

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Retrotransposon-mediated evolutionary rewiring of a pathogen response orchestrates a resistance phenotype in an insect host

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(14)

Published: March 30, 2023

Ongoing host-pathogen interactions can trigger a coevolutionary arms race, while genetic diversity within the host facilitate its adaptation to pathogens. Here, we used diamondback moth (

Language: Английский

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Co-transcriptional genome surveillance by HUSH is coupled to termination machinery

Molecular Cell, Journal Year: 2023, Volume and Issue: 83(10), P. 1623 - 1639.e8

Published: May 1, 2023

The HUSH complex recognizes and silences foreign DNA such as viruses, transposons, transgenes without prior exposure to its targets. Here, we show that endogenous targets of the fall into two distinct classes based on presence or absence H3K9me3. These are further distinguished by their transposon content differential response loss HUSH. A de novo genomic rearrangement at Sox2 locus induces a switch from H3K9me3-independent H3K9me3-associated targeting, resulting in silencing. We demonstrate interacts with termination factor WDR82 and—via component MPP8—with nascent RNA. accumulates sites high RNAPII occupancy including long exons transcription manner dependent CPSF. Together, our results uncover functional diversity this vertebrate-specific exploits evolutionarily ancient machinery for co-transcriptional chromatin targeting genome surveillance.

Language: Английский

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The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes

Current Biology, Journal Year: 2023, Volume and Issue: 33(20), P. 4367 - 4380.e9

Published: Sept. 21, 2023

The mobility of transposable elements (TEs) contributes to evolution genomes. Their uncontrolled activity causes genomic instability; therefore, expression TEs is silenced by host are marked with DNA and H3K9 methylation, which associated silencing in flowering plants, animals, fungi. However, distantly related groups eukaryotes, H3K27me3 deposited the Polycomb repressive complex 2 (PRC2), an epigenetic mark gene plants animals. direct PRC2 has so far only been shown one species ciliates. To test if silences a broader range we generated mutants reduced analyzed role extant along lineage Archaeplastida diatom P. tricornutum. In this red alga C. merolae, greater proportion than genes were repressed PRC2, whereas bryophytes. contained potential cis-elements recognized transcription factors neighbor as transcriptional units PRC2. Thus, observed not but also diatoms ciliates, suggesting that silence last common ancestor eukaryotes. We hypothesize during Archaeplastida, TE fragments selected shape regulation, controlling networks regulated

Language: Английский

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