Transcription factor modularity in a gene-centered C. elegans core neuronal protein–DNA interaction network
Abstract
Transcription regulatory networks play a pivotal role in the development, function, and pathology of metazoan organisms. Such networks are comprised of protein–DNA interactions between transcription factors (TFs) and their target genes. An important question pertains to how the architecture of such networks relates to network functionality. Here, we show that a Caenorhabditis elegans core neuronal protein–DNA interaction network is organized into two TF modules. These modules contain TFs that bind to a relatively small number of target genes and are more systems specific than the TF hubs that connect the modules. Each module relates to different functional aspects of the network. One module contains TFs involved in reproduction and target genes that are expressed in neurons as well as in other tissues. The second module is enriched for paired homeodomain TFs and connects to target genes that are often exclusively neuronal. We find that paired homeodomain TFs are specifically expressed in C. elegans and mouse neurons, indicating that the neuronal function of paired homeodomains is evolutionarily conserved. Taken together, we show that a core neuronal C. elegans protein–DNA interaction network possesses TF modules that relate to different functional aspects of the complete network.
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BibTeX
@misc{vermeirssen2026transcription,
title = {{Transcription factor modularity in a gene-centered C. elegans core neuronal protein–DNA interaction network}},
author = {Vanessa Vermeirssen and M. Inmaculada Barrasa and César A Hidalgo and Jenny Aurielle B. Babon and Reynaldo Sequerra and Lynn Doucette-Stamm and Albert-László Barabási and Albertha J.M. Walhout},
howpublished = {Genome Research},
year = {2026},
month = nov,
doi = {10.1101/gr.6148107},
url = {https://hal.science/hal-05852158v1},
note = {CC BY-NC 4.0},
}
RIS
TY - UNPB
TI - Transcription factor modularity in a gene-centered C. elegans core neuronal protein–DNA interaction network
AU - Vanessa Vermeirssen
AU - M. Inmaculada Barrasa
AU - César A Hidalgo
AU - Jenny Aurielle B. Babon
AU - Reynaldo Sequerra
AU - Lynn Doucette-Stamm
AU - Albert-László Barabási
AU - Albertha J.M. Walhout
PY - 2026
DA - 2026/11/04
PB - Genome Research
DO - 10.1101/gr.6148107
UR - https://hal.science/hal-05852158v1
AB - Transcription regulatory networks play a pivotal role in the development, function, and pathology of metazoan organisms. Such networks are comprised of protein–DNA interactions between transcription factors (TFs) and their target genes. An important question pertains to how the architecture of such networks relates to network functionality. Here, we show that a Caenorhabditis elegans core neuronal protein–DNA interaction network is organized into two TF modules. These modules contain TFs that bind to a relatively small number of target genes and are more systems specific than the TF hubs that connect the modules. Each module relates to different functional aspects of the network. One module contains TFs involved in reproduction and target genes that are expressed in neurons as well as in other tissues. The second module is enriched for paired homeodomain TFs and connects to target genes that are often exclusively neuronal. We find that paired homeodomain TFs are specifically expressed in C. elegans and mouse neurons, indicating that the neuronal function of paired homeodomains is evolutionarily conserved. Taken together, we show that a core neuronal C. elegans protein–DNA interaction network possesses TF modules that relate to different functional aspects of the complete network.
SN - 1088-9051
SN - 1549-5469
ER -