[
Bioessays,
2017]
Chromatin composition differs across the genome, with distinct compositions characterizing regions associated with different properties and functions. Whereas many histone modifications show local enrichment over genes or regulatory elements, marking can also span large genomic intervals defining broad chromatin domains. Here we highlight structural and functional features of chromatin domains marked by histone modifications, with a particular emphasis on the potential roles of H3K27 methylation domains in the organization and regulation of genome activity in metazoans.
[
Sci Adv,
2022]
The movement of selfish DNA elements can lead to widespread genomic alterations with potential to create novel functions. We show that transposon expansions in Caenorhabditis nematodes led to extensive rewiring of germline transcriptional regulation. We find that about one-third of Caenorhabditis elegans germline-specific promoters have been co-opted from two related miniature inverted repeat transposable elements (TEs), CERP2 and CELE2. These promoters are regulated by HIM-17, a THAP domain-containing transcription factor related to a transposase. Expansion of CERP2 occurred before radiation of the Caenorhabditis genus, as did fixation of mutations in HIM-17 through positive selection, whereas CELE2 expanded only in C. elegans. Through comparative analyses in Caenorhabditis briggsae, we find not only evolutionary conservation of most CERP2 co-opted promoters but also a substantial fraction that are species-specific. Our work reveals the emergence and evolutionary conservation of a novel transcriptional network driven by TE co-option with a major impact on regulatory evolution.
Cerrato, C., Dong, Y., Dernburg, A.F., Ahringer, J., Janes, J., Carelli, F.N., Appert, A.
[
International Worm Meeting,
2019]
Transposable elements (TEs) are DNA sequences capable of inserting into new genomic locations. Although new TE integrations are usually neutral or deleterious for the host, TE amplification can disperse protein binding sites in the genome, and thus generate new regulatory elements. Distinct classes of TEs have been shown to be enriched at promoters or enhancers active in specific tissues or cell types. TE expansion has, therefore, the potential to drive the evolution of gene regulatory networks. To date, nonetheless, these observations have been mostly limited to correlation analyses or tested in cell lines. Here we provide evidence that two classes of DNA transposons have been co-opted as new regulatory elements in C. elegans. We found that a pair of DNA motifs, strongly enriched in germline-specific promoters, are part of the inverted repeat sequences of CERP2 and CELE2, two inactive DNA transposons. Through reporter assays, we validated the activity of the two motifs, confirming their role in driving germline-specific regulatory elements in vivo. Comparative analyses revealed that CERP2-associated motifs are found across the whole Caenorhabditis clade but not in other nematodes, whereas the CELE2-expanded motifs are C. elegans-specific. By annotating regulatory elements in the sister species C. briggsae, we confirmed that C. elegans-specific repeat expansions led to the emergence of a number of germline promoters which could not be identified at the orthologous locations in C. briggsae. Finally, using chromatin immunoprecipitation assays, we found that two fast evolving proteins important for germ line function have binding associated with the CERP2/CELE2 motifs. Overall, our work provides strongly suggests that distinct waves of TE expansion have shaped the germline regulatory network in the Caenorhabditis genus.