Transcription factors operate on a limited vocabulary of binding motifs in Arabidopsis thaliana
Zenker, S.; Wulf, D.; Meierhenrich, A.; Becker, S.; Eisenhut, M.; Stracke, R.; Weisshaar, B.; Braeutigam, A.
Show abstract
Predicting gene expression from promoter sequence requires understanding of the different signal integration points within a promoter. Sequence-specific transcription factors (TFs) binding to their cognate TF binding motifs control gene expression in eukaryotes by activating and repressing transcription. Their interplay generates complex expression patterns in reaction to environmental conditions and developmental cues. We hypothesized that signals are not only integrated by different TFs binding various positions in a promoter, but also by single TF binding motifs onto which multiple TFs can bind. Analyzing 2,190 binding motifs, we identified only 76 core TF binding motifs in plants. Twenty-one TF protein families act highly specific and bind a single conserved motif. Four TF families are classified as semi-conserved as they bind up to four motifs within a family, with divisions along phylogenetic groups. Five TF families bind diverse motifs. Expression analyses revealed high competition within TF families for the same binding motif. The results show that singular binding motifs act as signal integrators in plants where a combination of binding affinity and TF abundance likely determine the output.
Matching journals
The top 8 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Polyploidization events shaped the transcription factor repertoires in legumes (Fabaceae) 97%
- MINI-AC: Inference of plant gene regulatory networks using bulk or single-cell accessible chromatin profiles 96%
- Phylogenomic analysis of the APETALA2 transcription factor subfamily across angiosperms reveals both deep conservation and lineage-specific patterns 95%
Similar papers in this journal
- Comparative Phylogenomics and Phylotranscriptomics Provide Insights into the Genetic Complexity of Nitrogen Fixing Root Nodule Symbiosis 95%
- Organ-level Gene Regulatory Network models enable the identification of central transcription factors in Solanum lycopersicum 95%
- ABI5-FLZ13 Module Transcriptionally Represses Growth-related Genes to Delay Seed Germination in Response to ABA 92%
Similar papers in this journal
- Many transcription factor families have evolutionarily conserved binding motifs in plants 100%
- ConnecTF: A platform to build gene networks by integrating transcription factor-target gene interactions 95%
- Evolutionary analysis of the LORELEI gene family in angiosperms reveals regulatory subfunctionalization 94%
Similar papers in this journal
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.