Sim Sakong
@simsakong.bsky.social
Biophysicist in🇨🇭/ bridging postDoc in LCBM, EPFL
Ph.D. in Suter’s lab and Fierz’s lab, EPFL
#targetsearch #transcription #singlemoleculeimaging
Ph.D. in Suter’s lab and Fierz’s lab, EPFL
#targetsearch #transcription #singlemoleculeimaging
Reposted by Sim Sakong
Electrostatic properties of disordered regions control transcription factor search and pioneer activity https://www.biorxiv.org/content/10.1101/2025.03.07.641980v1
March 12, 2025 at 3:51 PM
Electrostatic properties of disordered regions control transcription factor search and pioneer activity https://www.biorxiv.org/content/10.1101/2025.03.07.641980v1
Reposted by Sim Sakong
Impressions from the LCBM Xmas party.!Happy holidays!!! 🎄🎁🎅🏽
December 16, 2023 at 5:15 PM
Impressions from the LCBM Xmas party.!Happy holidays!!! 🎄🎁🎅🏽
Exciting research update 🎉
How do eukaryotic TFs find target sites on the chromatinized genome? How does DNA state—naked or nucleosomal—shape their search strategy?
We investigated how the charge of disordered regions flanking DBDs influences target search and pioneering activity. Check it out! 👇
How do eukaryotic TFs find target sites on the chromatinized genome? How does DNA state—naked or nucleosomal—shape their search strategy?
We investigated how the charge of disordered regions flanking DBDs influences target search and pioneering activity. Check it out! 👇
📣 New preprint from the lab – Massive work entirely driven by super-talented @simsakong.bsky.social , jointly betw. @beatfierz.bsky.social lab and mine – combining in vitro and in vivo TF single molecule imaging
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
March 12, 2025 at 6:46 PM
Exciting research update 🎉
How do eukaryotic TFs find target sites on the chromatinized genome? How does DNA state—naked or nucleosomal—shape their search strategy?
We investigated how the charge of disordered regions flanking DBDs influences target search and pioneering activity. Check it out! 👇
How do eukaryotic TFs find target sites on the chromatinized genome? How does DNA state—naked or nucleosomal—shape their search strategy?
We investigated how the charge of disordered regions flanking DBDs influences target search and pioneering activity. Check it out! 👇
Reposted by Sim Sakong
Check out our #openaccess article "A Site-Specific Click Chemistry Approach to Di-Ubiquitylate H1 Variants Reveals Position-Dependent Stimulation of the DNA Repair Protein RNF168"
▶️ tinyurl.com/27uxumme
@beatfierz.bsky.social
▶️ tinyurl.com/27uxumme
@beatfierz.bsky.social
A Site‐Specific Click Chemistry Approach to Di‐Ubiquitylate H1 Variants Reveals Position‐Dependent Stimulation of the DNA Repair Protein RNF168
We developed a click chemistry approach to di-ubiquitylate histone H1 at relevant DNA repair-associated positions (H1KxUb2) to probe its effect on the E3 ligase RNF168. We demonstrate that H1KxUb2 st...
onlinelibrary.wiley.com
December 19, 2024 at 12:29 PM
Check out our #openaccess article "A Site-Specific Click Chemistry Approach to Di-Ubiquitylate H1 Variants Reveals Position-Dependent Stimulation of the DNA Repair Protein RNF168"
▶️ tinyurl.com/27uxumme
@beatfierz.bsky.social
▶️ tinyurl.com/27uxumme
@beatfierz.bsky.social
Reposted by Sim Sakong
#SIRT7 is a histone deacetylase with highly specific activity on #chromatin substrates.
We just published mechanism-based #cryoEM structures of #SIRT7 on nucleosomes to understand its activity 👇
www.nature.com/articles/s41...
(1/8) #ChemBio #ChemSky
We just published mechanism-based #cryoEM structures of #SIRT7 on nucleosomes to understand its activity 👇
www.nature.com/articles/s41...
(1/8) #ChemBio #ChemSky
February 4, 2025 at 1:13 PM
#SIRT7 is a histone deacetylase with highly specific activity on #chromatin substrates.
We just published mechanism-based #cryoEM structures of #SIRT7 on nucleosomes to understand its activity 👇
www.nature.com/articles/s41...
(1/8) #ChemBio #ChemSky
We just published mechanism-based #cryoEM structures of #SIRT7 on nucleosomes to understand its activity 👇
www.nature.com/articles/s41...
(1/8) #ChemBio #ChemSky
Reposted by Sim Sakong
Want to see how PRC1 writes the Polycomb ubiquitin mark on chromatin, in real-time? Check out our latest preprint, done all by Alexandra Teslenko at ISIC EPFL, a tour-de-force of single-molecule enzymology!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Single-molecule analysis reveals the mechanism of chromatin ubiquitylation by variant PRC1 complexes
Chromatin regulation relies on "writer" enzymes that add post-translational modifications (PTMs) to histone proteins. Variant Polycomb repressive complex 1 (PRC1) exists as several subtypes, which are...
www.biorxiv.org
November 1, 2024 at 11:29 AM
Want to see how PRC1 writes the Polycomb ubiquitin mark on chromatin, in real-time? Check out our latest preprint, done all by Alexandra Teslenko at ISIC EPFL, a tour-de-force of single-molecule enzymology!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Sim Sakong
A nice collection of state-of-the art lineage tracing methods - our Gene expression memory-based lineage tracing approach is also detailed here:
link.springer.com/protocol/10....
link.springer.com/protocol/10....
GEMLI: Gene Expression Memory-Based Lineage Inference from Single-Cell RNA-Sequencing Datasets
Gene expression memory-based lineage inference (GEMLI) is a computational tool allowing to predict cell lineages solely from single-cell RNA-sequencing (scRNA-seq) datasets and is publicly available a...
link.springer.com
January 8, 2025 at 8:58 AM
A nice collection of state-of-the art lineage tracing methods - our Gene expression memory-based lineage tracing approach is also detailed here:
link.springer.com/protocol/10....
link.springer.com/protocol/10....
Reposted by Sim Sakong
1/ Preprint haiku alert 🤓✍🏻
Cells walk a tightrope—
proteins made and then destroyed,
balance must be kept.
Yet how is this done?
A mystery in the cell,
we set out to ask.
Live imaging helps,
plus models and omics, too—
data tells the tale.
Cells walk a tightrope—
proteins made and then destroyed,
balance must be kept.
Yet how is this done?
A mystery in the cell,
we set out to ask.
Live imaging helps,
plus models and omics, too—
data tells the tale.
March 7, 2025 at 11:24 AM
1/ Preprint haiku alert 🤓✍🏻
Cells walk a tightrope—
proteins made and then destroyed,
balance must be kept.
Yet how is this done?
A mystery in the cell,
we set out to ask.
Live imaging helps,
plus models and omics, too—
data tells the tale.
Cells walk a tightrope—
proteins made and then destroyed,
balance must be kept.
Yet how is this done?
A mystery in the cell,
we set out to ask.
Live imaging helps,
plus models and omics, too—
data tells the tale.
Reposted by Sim Sakong
The dance of chromatin—
Remodelers and histones,
Who leads, who follows?
🧵 (1/6)
Remodelers and histones,
Who leads, who follows?
🧵 (1/6)
February 13, 2025 at 12:35 PM
The dance of chromatin—
Remodelers and histones,
Who leads, who follows?
🧵 (1/6)
Remodelers and histones,
Who leads, who follows?
🧵 (1/6)
Always nice to share the ideas together! Many THX to who show interest and ideas in our project 🙏 If interested in TF target search, feel free to contact us 📧 @beatfierz.bsky.social @davidsuter.bsky.social
THX to the EMBL travel grant for me to attend such great conference #EMBLOmics
THX to the EMBL travel grant for me to attend such great conference #EMBLOmics
November 23, 2024 at 12:22 PM
Always nice to share the ideas together! Many THX to who show interest and ideas in our project 🙏 If interested in TF target search, feel free to contact us 📧 @beatfierz.bsky.social @davidsuter.bsky.social
THX to the EMBL travel grant for me to attend such great conference #EMBLOmics
THX to the EMBL travel grant for me to attend such great conference #EMBLOmics