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 …

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 …

G-quadruplexes are transcription factor binding hubs in human chromatin

J Spiegel, SM Cuesta, S Adhikari, R Hänsel-Hertsch… - Genome biology, 2021 - Springer
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 …

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 …

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 …

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 …

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 …

High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins

V Martin, F Zhuang, Y Zhang, K Pinheiro… - Nucleic Acids …, 2023 - academic.oup.com
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 …

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 …

Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements

IL Ibarra, VS Ratnu, L Gordillo, IY Hwang… - Molecular systems …, 2022 - embopress.org
Neuronal stimulation induced by the brain‐derived neurotrophic factor (BDNF) triggers gene
expression, which is crucial for neuronal survival, differentiation, synaptic plasticity, memory …