Generating specificity in genome regulation through transcription factor sensitivity to chromatin

L Isbel, RS Grand, D Schübeler - Nature Reviews Genetics, 2022 - nature.com
Cell type-specific gene expression relies on transcription factors (TFs) binding DNA
sequence motifs embedded in chromatin. Understanding how motifs are accessed in …

Plant transcription factors—being in the right place with the right company

L Strader, D Weijers, D Wagner - Current opinion in plant biology, 2022 - Elsevier
Transcriptional regulation underlies many of the growth and developmental processes that
shape plants as well as their adaptation to their environment. Key to transcriptional control …

[HTML][HTML] Sequence-dependent surface condensation of a pioneer transcription factor on DNA

JA Morin, S Wittmann, S Choubey, A Klosin, S Golfier… - Nature Physics, 2022 - nature.com
Biomolecular condensates are dense assemblies of proteins that form distinct biochemical
compartments without being surrounded by a membrane. Some, such as P granules and …

Short tandem repeats bind transcription factors to tune eukaryotic gene expression

CA Horton, AM Alexandari, MGB Hayes, E Marklund… - Science, 2023 - science.org
Short tandem repeats (STRs) are enriched in eukaryotic cis-regulatory elements and alter
gene expression, yet how they regulate transcription remains unknown. We found that STRs …

[HTML][HTML] “Structure”-function relationships in eukaryotic transcription factors: the role of intrinsically disordered regions in gene regulation

JJ Ferrie, JP Karr, R Tjian, X Darzacq - Molecular Cell, 2022 - cell.com
Many principles of bacterial gene regulation have been foundational to understanding
mechanisms of eukaryotic transcription. However, stark structural and functional differences …

Transcription regulation by long non-coding RNAs: mechanisms and disease relevance

J Ferrer, N Dimitrova - Nature Reviews Molecular Cell Biology, 2024 - nature.com
Long non-coding RNAs (lncRNAs) outnumber protein-coding transcripts, but their functions
remain largely unknown. In this Review, we discuss the emerging roles of lncRNAs in the …

[HTML][HTML] Transcription factor dynamics: one molecule at a time

K Wagh, DA Stavreva, A Upadhyaya… - Annual Review of Cell …, 2023 - annualreviews.org
Cells must tightly regulate their gene expression programs and yet rapidly respond to acute
biochemical and biophysical cues within their environment. This information is transmitted to …

[HTML][HTML] Identification and functional characterization of transcriptional activators in human cells

N Alerasool, H Leng, ZY Lin, AC Gingras, M Taipale - Molecular cell, 2022 - cell.com
Transcription is orchestrated by thousands of transcription factors (TFs) and chromatin-
associated proteins, but how these are causally connected to transcriptional activation is …

Decoding gene regulation in the fly brain

J Janssens, S Aibar, II Taskiran, JN Ismail, AE Gomez… - Nature, 2022 - nature.com
The Drosophila brain is a frequently used model in neuroscience. Single-cell transcriptome
analysis,,,,–, three-dimensional morphological classification and electron microscopy …

To bind or not to bind: how Auxin Response Factors select their target genes

J Rienstra, J Hernández-García… - Journal of Experimental …, 2023 - academic.oup.com
Most plant growth and development processes are regulated in one way or another by
auxin. The best-studied mechanism by which auxin exerts its regulatory effects is through …