Gene regulatory network inference in the era of single-cell multi-omics
P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
Transcription factors: Bridge between cell signaling and gene regulation
P Weidemüller, M Kholmatov, E Petsalaki… - …, 2021 - Wiley Online Library
Transcription factors (TFs) are key regulators of intrinsic cellular processes, such as
differentiation and development, and of the cellular response to external perturbation …
differentiation and development, and of the cellular response to external perturbation …
G-quadruplexes are transcription factor binding hubs in human chromatin
Background The binding of transcription factors (TF) to genomic targets is critical in the
regulation of gene expression. Short, double-stranded DNA sequence motifs are routinely …
regulation of gene expression. Short, double-stranded DNA sequence motifs are routinely …
Molecular co-occupancy identifies transcription factor binding cooperativity in vivo
C Sönmezer, R Kleinendorst, D Imanci, G Barzaghi… - Molecular cell, 2021 - cell.com
Gene activation requires the cooperative activity of multiple transcription factors at cis-
regulatory elements (CREs). Yet, most transcription factors have short residence time …
regulatory elements (CREs). Yet, most transcription factors have short residence time …
Decoding enhancer complexity with machine learning and high-throughput discovery
GD Smith, WH Ching, P Cornejo-Páramo, ES Wong - Genome biology, 2023 - Springer
Enhancers are genomic DNA elements controlling spatiotemporal gene expression. Their
flexible organization and functional redundancies make deciphering their sequence-function …
flexible organization and functional redundancies make deciphering their sequence-function …
Dual specificity and target gene selection by the MADS-domain protein FRUITFULL
H Van Mourik, P Chen, C Smaczniak, S Boeren… - Nature Plants, 2023 - nature.com
How transcription factors attain their target gene specificity and how this specificity may be
modulated, acquiring different regulatory functions through the development of plant tissues …
modulated, acquiring different regulatory functions through the development of plant tissues …
Elucidating the biology of transcription factor–DNA interaction for accurate identification of cis-regulatory elements
M Hajheidari, SC Huang - Current opinion in plant biology, 2022 - Elsevier
Transcription factors (TFs) play a critical role in determining cell fate decisions by integrating
developmental and environmental signals through binding to specific cis-regulatory …
developmental and environmental signals through binding to specific cis-regulatory …
High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins
Cooperative DNA-binding by transcription factor (TF) proteins is critical for eukaryotic gene
regulation. In the human genome, many regulatory regions contain TF-binding sites in close …
regulation. In the human genome, many regulatory regions contain TF-binding sites in close …
Toward a mechanistic understanding of DNA binding by forkhead transcription factors and its perturbation by pathogenic mutations
S Dai, L Qu, J Li, Y Chen - Nucleic acids research, 2021 - academic.oup.com
Forkhead box (FOX) proteins are an evolutionarily conserved family of transcription factors
that play numerous regulatory roles in eukaryotes during developmental and adult life …
that play numerous regulatory roles in eukaryotes during developmental and adult life …
Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements
Neuronal stimulation induced by the brain‐derived neurotrophic factor (BDNF) triggers gene
expression, which is crucial for neuronal survival, differentiation, synaptic plasticity, memory …
expression, which is crucial for neuronal survival, differentiation, synaptic plasticity, memory …