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Generating specificity in genome regulation through transcription factor sensitivity to chromatin

Abstract

Cell type-specific gene expression relies on transcription factors (TFs) binding DNA sequence motifs embedded in chromatin. Understanding how motifs are accessed in chromatin is crucial to comprehend differential transcriptional responses and the phenotypic impact of sequence variation. Chromatin obstacles to TF binding range from DNA methylation to restriction of DNA access by nucleosomes depending on their position, composition and modification. In vivo and in vitro approaches now enable the study of TF binding in chromatin at unprecedented resolution. Emerging insights suggest that TFs vary in their ability to navigate chromatin states. However, it remains challenging to link binding and transcriptional outcomes to molecular characteristics of TFs or the local chromatin substrate. Here, we discuss our current understanding of how TFs access DNA in chromatin and novel techniques and directions towards a better understanding of this critical step in genome regulation.

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Fig. 1: Chromatin features at active regulatory elements.
Fig. 2: Nucleosome sensitivity.
Fig. 3: A scheme illustrating the use of occupancy in the genome as an indicator of chromatin sensitivity.
Fig. 4: Initiating and maintaining open chromatin.

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Acknowledgements

L.I. acknowledges the Australian National Health and Medical Research Council CJ Martin Fellowship APP1148380. R.S.G. acknowledges European Molecular Biology Organization (EMBO) Long-Term Fellowships. R.S.G. and L.I. acknowledge the European Union (EU) Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant (705354 to R.S.G. and 748760 to L.I.). D.S. acknowledges support from the Novartis Research Foundation, the Swiss National Science Foundation (310030B_176394) and the European Research Council under the EU Horizon 2020 research and innovation programme grant agreements (ReadMe-667951 and DNAaccess-884664). The authors thank N. Thomä, A. Michael, B. Cohen and members of the Schübeler laboratory for insightful discussions and critical feedback on the manuscript. They similarly thank the reviewers for their insightful comments.

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Glossary

Chromatin sensitivity

The propensity of transcription factors (TFs) to be inhibited from binding motifs due to reversible chromatin features such as modification of DNA (CpG methylation) or presence and actions of chromatin proteins (such as nucleosomes).

Methylation-sensitive

Refers to transcription factor (TF) motifs that are bound with lower affinity when CpG dinucleotides within the motif are methylated.

Methylation-preferred

Refers to transcription factor (TF) motifs that are bound with higher affinity when CpG dinucleotides within the motif are methylated.

Micrococcal nuclease

(MNase). An enzyme that generates cuts preferentially within linker DNA between nucleosomes and in nucleosome-depleted regions. Coupling MNase digestion of chromatin with next-generation sequencing generates maps of nucleosome position and density.

DNase I hypersensitive site

A chromatin region with a high rate of cleavage by DNase I due to its preference for open chromatin. DNase I hypersensitivity generally reflects transcription factor (TF) binding and a local reduction in nucleosome occupancy.

Genomic footprinting

The use of an ectopically supplied enzyme that adds chemical groups to DNA but is itself sensitive to the factors binding DNA, such as transcription factors (TFs) or nuclesomes. Its activity can subsequently be read out by sequencing.

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Isbel, L., Grand, R.S. & Schübeler, D. Generating specificity in genome regulation through transcription factor sensitivity to chromatin. Nat Rev Genet (2022). https://doi.org/10.1038/s41576-022-00512-6

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