The swimming pool chromatin analogy
The adventure of our lab’s cartoon personages started in 2019 on the cover of Genome Research, associated with our article which showed that CTCF can set boundaries for one-dimensional DNA methylation spreading in chromatin (Wiehle et al, 2019). (Image credit: Yana Savinich & Teif Lab)
Wiehle L., Thorn G.J., Raddatz G., Clarkson C.T., Rippe K., Lyko F., Breiling A., Teif V.B. (2019) DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Research 29, 750-761 | Open access article
The ice and penguins chromatin analogy
In our recent Nature Communications article (Thorn et al., 2022) we developed a framework ChromHL allowing to predict from DNA sequence and protein concentrations the locations of such chromatin nanodomains (e.g. H3K9me2/3 associated heterochromatin). The DNA sequence sets the map of potential locations of nanodomains through motifs of transcription factors that can initiate and stop nanodomain spreading. The abundance of chromatin proteins such as HP1, which changes during cell differentiation refines the sequence-determined thermodynamic landscape of chromatin domains. (Image credit: Yana Savinich & Teif Lab)
Thorn G.J., Clarkson C.T., Rademacher A., Mamayusupova H., Schotta G., Rippe K. and Teif V.B. (2022) DNA sequence-dependent formation of heterochromatin nanodomains. Nature Communications 13, 1861 | Open access article
The garden chromatin analogy
Another concept of chromatin organisation was introduced in our Nucleic Acids Research article (Clarkson et al., 2019). Distances between nucleosomes decrease near chromatin boundaries and this is affected by cell differentiation. Chromatin remodellers (mice on the cartoon) are “measuring” distances between nucleosomes (bushes on the cartoon), while the anchors for such measurements are provided by CTCF proteins. (Image credit: Yana Savinich & Teif Lab)
Clarkson C.T., Deeks E.A., Samarista R., Mamayusupova H., Zhurkin V.B., Teif V.B. (2019) CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length. Nucleic Acids Res 47, 11181-11196. | Open access article
The nucleosome arrays puzzle
The latest cartoon in this series is associated with our theoretical biophysical paper (Hedley et al., 2021), which showed that nucleosome arrays with different distances between nucleosomes can recognise each other. The interaction forces between such differently arranged nucleosome arrays are very weak, but because they accumulate over large distances this effect may become significant, especially in areas of ordered chromatin sections such as DNA sequence repeats, near CTCF sites, etc. We liked this last cartoon so much that it currently serves as our “official” lab photo 🙂 (Image credit: Yana Savinich & Teif Lab)
Hedley J.G., Teif V.B. and Kornyshev A.A. (2021) Nucleosome induced homology recognition in chromatin. J. Royal Soc. Interface 18, 20210147. | Journal web site
Sisyphus, CTCF and nucleosomes
Fancy a mythological twist? This one is from the recent cover in Nucleic Acids Research, associated with this paper led by our NIH collaborators Elena Pugacheva & Co (their drawing): https://academic.oup.com/nar/article/53/12/gkaf587/8185977 Like Sisyphus eternally pushing his boulder uphill, CTCF is depicted pushing a nucleosome, the fundamental unit of chromatin, up a hill. CTCF’s constant effort causes the nucleosome to “slide” along the DNA, unwrapping at one end while wrapping at the other. But when CTCF is released from chromatin, a nucleosome takes its place. To bind again, CTCF must start the struggle anew, pushing the nucleosome aside once more.
