Recurrent evolution of vertebrate transcription factors via transposase capture [ChIP-Seq]
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ABSTRACT:
PROVIDER: PRJNA625725 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11554724_1.fastq.gz | Fastqsanger.gz | |||
| SRR11554724_2.fastq.gz | Fastqsanger.gz | |||
| SRR11554725_1.fastq.gz | Fastqsanger.gz | |||
| SRR11554725_2.fastq.gz | Fastqsanger.gz | |||
| SRR11554726_1.fastq.gz | Fastqsanger.gz |
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Project description:Recurrent evolution of vertebrate transcription factors via transposase capture
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Project description:How novel genes and cellular functions evolve is a central question in biology. Exon shuffling represents a potent mechanism to assemble new protein architectures. Here we show that DNA transposons, which are mobile and pervasive in genomes, have provided a recurrent supply of both exons and splice sites to assemble novel protein-coding genes in vertebrates. We find that transposase domains have been captured, primarily via alternative splicing, to form new fusion proteins at least 99 times independently over ~350 million years of tetrapod evolution. Evolution favors fusion of transposase DNA-binding domains to host regulatory domains, especially the Krüppel-associated Box (KRAB), suggesting transposase capture frequently yields new transcriptional repressors. Consistent with this model, we show that four KRAB-transposase fusion proteins born independently in different mammalian lineages repress gene expression in a sequence-specific fashion. Genetic knockout and rescue of the bat-specific KRABINER fusion protein in cell culture demonstrates that it binds its cognate transposons genome wide and controls a network of genes and cis-regulatory elements. Transposase capture is thus a powerful mechanism whereby transcription factors and their associated cis-regulatory networks can evolve by repurposing DNA transposon families, which provide both DNA binding domains and pre-existing genomic binding sites.
2020-05-08 | GSE148788 | GEO
Project description:How novel genes and cellular functions evolve is a central question in biology. Exon shuffling represents a potent mechanism to assemble new protein architectures. Here we show that DNA transposons, which are mobile and pervasive in genomes, have provided a recurrent supply of both exons and splice sites to assemble novel protein-coding genes in vertebrates. We find that transposase domains have been captured, primarily via alternative splicing, to form new fusion proteins at least 99 times independently over ~350 million years of tetrapod evolution. Evolution favors fusion of transposase DNA-binding domains to host regulatory domains, especially the Krüppel-associated Box (KRAB), suggesting transposase capture frequently yields new transcriptional repressors. Consistent with this model, we show that four KRAB-transposase fusion proteins born independently in different mammalian lineages repress gene expression in a sequence-specific fashion. Genetic knockout and rescue of the bat-specific KRABINER fusion protein in cell culture demonstrates that it binds its cognate transposons genome wide and controls a network of genes and cis-regulatory elements. Transposase capture is thus a powerful mechanism whereby transcription factors and their associated cis-regulatory networks can evolve by repurposing DNA transposon families, which provide both DNA binding domains and pre-existing genomic binding sites.
2020-05-08 | GSE148787 | GEO
Project description:Genes with novel cellular functions may evolve through exon shuffling, which can assemble novel protein architectures. Here, we show that DNA transposons provide a recurrent supply of materials to assemble protein-coding genes through exon shuffling. We find that transposase domains have been captured-primarily via alternative splicing-to form fusion proteins at least 94 times independently over the course of ~350 million years of tetrapod evolution. We find an excess of transposase DNA binding domains fused to host regulatory domains, especially the Krüppel-associated box (KRAB) domain, and identify four independently evolved KRAB-transposase fusion proteins repressing gene expression in a sequence-specific fashion. The bat-specific KRABINER fusion protein binds its cognate transposons genome-wide and controls a network of genes and cis-regulatory elements. These results illustrate how a transcription factor and its binding sites can emerge.
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Project description:The brain requires complex mechanisms of genome regulation to encode and store behavioural information. In mammals, DNA methylation deposited at non-CG dinucleotides characterises brain epigenomes. However, it is unclear to what extent this non-canonical form of DNA methylation is evolutionarily conserved. To test this we profile brain cytosine methylation across the major vertebrate lineages, amphioxus, honeybee and octopus, finding that non-CG methylation in adult brain methylomes is restricted to vertebrates. In vertebrates, the genomic patterns of non-CG do not recapitulate those of CG methylation, yet both patterns are deeply conserved. Whereas low levels of gene body CG methylation demarcate a set of developmental transcription factors across tissues and species, a distinct set of neurodevelopmental genes accumulate non-CG methylation in neural tissues. We further show that the establishment of this methylation context coincides with the origin of the “writer” of non-CG methylation, the methyltransferase DNMT3A, and the “reader”, the methyl-CpG binding protein 2 (MeCP2), fuelled by the ancestral whole genome duplication in vertebrates. Surprisingly, MeCP2 evolved in a stepwise process, from an ancestral MBD4 protein with a dual role in transcriptional regulation and DNA repair in chordates. In sum, we show how a novel neural epigenomic layer assembled at the root of vertebrates and gained new regulatory roles partly independent from CG methylation, which could have fostered the sophisticated cognitive repertoires found in the vertebrate lineage.
2020-10-26 | GSE141609 | GEO
Project description:Vertebrates have highly methylated genomes at CpG positions while most invertebrates have sparsely methylated genomes. Therefore, hypermethylation is considered a major innovation that shaped the genome and the regulatory roles of DNA methylation in vertebrates. However, here we report that the marine sponge Amphimedon queenslandica, belonging to one of the earliest branching animal lineages, has evolved a hypermethylated genome with remarkable similarities to that of a vertebrate. Despite major differences in genome size and architecture, independent acquisition of hypermethylation reveal common distribution patterns and repercussions for genome regulation between both lineages. Genome wide depletion of CpGs is counterbalanced by CpG enrichment at unmethylated promoters, mirroring CpG islands. Furthermore, a subset of CpG-bearing transcription factor motifs are enriched at Amphimedon unmethylated promoters. We find that the animal-specific transcription factor NRF has conserved methyl-sensitivity over 700 million years, indicating an ancient cross-talk between transcription factors and DNA methylation. Finally, the sponge shows vertebrate-like levels of 5-hydroxymethylcytosine, the oxidative derivative of cytosine methylation involved in active demethylation. Hydroxymethylation is concentrated in regions that are enriched for transcription factor motifs and show developmentally dynamic demethylation. Together, these findings push back the links between DNA methylation and its regulatory roles to the early steps of animal evolution. Thus, the Amphimedon methylome challenges the prior hypotheses about the origins of vertebrate genome hypermethylation and its implications for regulatory complexity.
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Project description:Evolution of CpH methylation in vertebrate brains
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