Invertebrate DNA Methylation and Gene Regulation

Dixon, Groves; Matz, Mikhail V.

doi:10.21203/rs.3.rs-1104133/v1

Cited by 2 publications

(2 citation statements)

References 30 publications

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“…There is evidence for epigenetic modifications via histone variants in some species (75)(76)(77) . Perhaps the simplest mechanistic explanation would be gene regulation by methylation, but studies on invertebrates suggest methylation is unlikely to be modifying expression (78)(79)(80) . It is possible that, while these genes have significantly different expression patterns, they have no functional effect on development.…”

Section: Comparison Of Reciprocal F1 Gene Expression With Ll and Ppmentioning

confidence: 99%

Maternal patterns of inheritance alter transcript expression in eggs

Zakas

Harry

2022

Preprint

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Modifications to early development can lead to evolutionary diversification. The early stages of development are under maternal control, as mothers produce eggs loaded with nutrients, proteins and mRNAs that direct early embryogenesis. Maternally provided mRNAs are the only expressed genes in initial stages of development and are known to be tightly regulated. Differences in maternal mRNA provisioning could lead to phenotypic changes in embryogenesis and ultimately evolutionary changes in development. However, the extent to which variation in maternal mRNA provisioning impacts ontogeny or life-history is unknown. Here, we use a species with dimorphic development— where females make eggs and larvae of different sizes and life-history modes—to investigate the extent of variation in maternal mRNA provisioning to the egg. We examine the effect of gene expression differences on subsequent generations of egg provisioning and determine the regulatory architecture underlying mRNA provisioning differences. We find that there is significant variation in gene expression across eggs of different development modes, and that both parent-of-origin and allele-specific effects contribute to mRNA expression differences. We also find that offspring of intraspecific crosses differentially provision their eggs based on their parents' cross direction. This effect of allelic expression based on parent-of-origin has not been previously demonstrated in reproductive traits like oogenesis.

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Section: Comparison Of Reciprocal F1 Gene Expression With Ll and Ppmentioning

confidence: 99%

Maternal patterns of inheritance alter transcript expression in eggs

Zakas

Harry

2022

Preprint

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“…Other epigenetic mechanisms can influence transcription levels, such as DNA methylation, which represses genes transcription in vertebrates via the modulation of tFs activity (Law and Jacobsen, 2010). In invertebrates, methylation patterns are also associated with the regulation of transcription (Dixon and Matz, 2021), but the correlation between transcription and methylation is less clear than in vertebrates (Dunwell and Pfeifer, 2014;Lyko et al, 2000). Transcription is a highly dynamic and plastic process with high rates of transcripts gain and loss in closely related species, as well as among populations and individuals (Zhao et al, 2014;Grandchamp et al, 2022Grandchamp et al, , 2023aNeme and Tautz, 2016;Iyengar and Bornberg-Bauer, 2023), suggesting fast transcripts turnover.…”

Section: Introductionmentioning

confidence: 99%

DNA Transposons favour denovotranscript emergence through enrichment of transcription factor binding motifs

Lebherz,

Fouks,

Schmidt

et al. 2023

Preprint

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De novogenes emerge from non-coding regions of genomes via succession of mutations. Among others, such mutations activate transcription and create a new open reading frame (ORF). Although the mechanisms underlying ORFs emergence are well documented, relatively little is known about the mechanisms enabling new transcription events. Yet, in many species a continuum between absent and very prominent transcription has been reported for essentially all regions of the genome.In this study we searched forde novotranscripts by using newly assembled genomes and transcriptomes of seven inbred lines ofDrosophila melanogaster, originating from six European and one African population. This setup allowed us to detect line specificde novotranscripts, and compare them to their homologous non-transcribed regions in other lines, as well as genic and intergenic control sequences. We studied the association with transposable elements and the enrichment of transcription factor motifs upstream ofde novoemerged transcripts and compared them with regulatory elements.We found thatde novotranscripts overlap with TEs more often than expected by chance. The emergence of new transcripts correlates with high CpG islands and regions of TEs activity. Moreover, upstream regions ofde novotranscripts are highly enriched with regulatory motifs. Such motifs abound in new transcripts overlapping with TEs, particularly DNA TEs, and are more conserved upstreamde novotranscripts than upstream their non-transcribed homologs. Overall, our study demonstrates that TEs insertion is important for transcript emergence, partly by introducing new regulatory motifs from DNA TE families.

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Invertebrate DNA Methylation and Gene Regulation

Cited by 2 publications

References 30 publications

Maternal patterns of inheritance alter transcript expression in eggs

Maternal patterns of inheritance alter transcript expression in eggs

DNA Transposons favour denovotranscript emergence through enrichment of transcription factor binding motifs

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