Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss

Wang, Mengchi; Wang, David; Zhang, Kai; Ngo, Vu; Fan, Shicai; Wang, Wei

doi:10.1534/genetics.120.303597

Cited by 2 publications

(2 citation statements)

References 30 publications

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“…Core promoters contain specific transcription factor binding-sites (TFBs), such as the TATA box or the Initiator sequence , that are recognized by transcription factors (TFs) ( Boeva 2016 ). Binding motifs with low identity to the consensus sequence are referred to as “minimal motif” ( Wang et al 2020a ). Transcription factors recruit the protein complexes required for transcription ( Butler and Kadonaga 2002 ).…”

Section: Introductionmentioning

confidence: 99%

DNA Transposons Favor De Novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs

Lebherz,

Fouks,

Schmidt

et al. 2024

Genome Biology and Evolution

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De novo genes 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 ORF 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 for de novo transcripts by using newly assembled genomes and transcriptomes of seven inbred lines of Drosophila melanogaster, originating from six European and one African population. This setup allowed us to detect sample specific de novo transcripts, and compare them to their homologous non-transcribed regions in other samples, as well as genic and intergenic control sequences. We studied the association with transposable elements and the enrichment of transcription factor motifs upstream of de novo emerged transcripts and compared them with regulatory elements. We found that de novo transcripts overlap with TEs more often than expected by chance. The emergence of new transcripts correlates with regions of high GC content and TE expression. Moreover, upstream regions of de novo transcripts are highly enriched with regulatory motifs. Such motifs are more enriched in new transcripts overlapping with TEs, particularly DNA TEs, and are more conserved upstream de novo transcripts than upstream their 'non-transcribed homologs'. Overall, our study demonstrates that TE insertion is important for transcript emergence, partly by introducing new regulatory motifs from DNA TE families.

show abstract

Section: Introductionmentioning

confidence: 99%

DNA Transposons Favor De Novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs

Lebherz,

Fouks,

Schmidt

et al. 2024

Genome Biology and Evolution

View full text Add to dashboard Cite

show abstract

“…Core promoters contain specific binding motifs, such as the TATA box or the Initiator sequence , that are recognized by transcription factors (tFs) (Boeva, 2016). Binding motifs with low identity to the consensus sequence are referred as minimal motif (Wang et al, 2020a). Transcription factors then recruit the protein complexes required for transcription (Butler and Kadonaga, 2002).…”

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.

show abstract

Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss

Cited by 2 publications

References 30 publications

DNA Transposons Favor De Novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs

DNA Transposons Favor De Novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs

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

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