iiinova — where your digital self keeps evolving

Emil Marklund

@marklundem.bsky.social

Assistant Professor at @scilifelab.se and @stockholm-uni.bsky.social. Intrigued by what makes life work at the molecular level.

Posts Replies Media

Emil Marklund @marklundem.bsky.social · 01/12/2025

Thank you Marek!

000

Emil Marklund @marklundem.bsky.social · 28/11/2025

Thank you Carolyn!

000

Emil Marklund @marklundem.bsky.social · 28/11/2025

Thank you!

010

Emil Marklund @marklundem.bsky.social · 27/11/2025

Celebrating with Julia Schaepe, William Greenleaf, and all other authors! @stockholm-uni.bsky.social, @scilifelab.se, @vetenskapsradet.bsky.social, @strategiska.bsky.social (6/6)

070

Emil Marklund @marklundem.bsky.social · 27/11/2025

🧬We do not need to invoke highly cooperative biological state changes, such as phase separation or condensation, to describe 𝘪𝘯 𝘷𝘪𝘷𝘰 transcription factor binding in our observed contexts. In sum, we can understand chromatin states 𝘪𝘯 𝘷𝘪𝘷𝘰 with “classical” and interpretable biochemistry. (5/6)

180

Emil Marklund @marklundem.bsky.social · 27/11/2025

🧬 A thermodynamic model with 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰-derived affinities predicts 𝘪𝘯 𝘷𝘪𝘷𝘰 chromatin states in human cells across KLF motif grammars. Our models predict chromatin states with few physical and interpretable free parameters, in contrast to highly parameterized “black box” deep learning models. (4/6)

140

Emil Marklund @marklundem.bsky.social · 27/11/2025

🧬 Motif flanking bases that KLF1 does not make direct contacts with in the crystal structure drive ~40-fold affinity variation. Distal flanking sequences helical turns away (≥10.5 bp) from the core motif tune affinity ~2-fold, in a manner consistent with sequence-dependent search of the motif (3/6)

120

Emil Marklund @marklundem.bsky.social · 27/11/2025

🧬 Differences in DNA binding affinity are driven by differences in motif recognition. This is the same binding mechanism that we previously found for the bacterial TF l𝘢𝘤 repressor, which is structurally dissimilar to KLF1, implying a universal mechanism across domains of life and TF types. (2/6)

130

Emil Marklund @marklundem.bsky.social · 27/11/2025

📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social www.cell.com/cell/fulltex... Key findings in a thread (1/6):

39833