@BarkaiLab

Systems Biology Lab @ 🔬Weizmann Institute of Science. # Understanding design principles of biological circuits.

 Israel
barkailab.wixsite.com/barkai
Joined September 2017
  • Tweets402
  • Following894
  • Followers2.5K
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Barkai Lab retweeted
Barkai Lab@BarkaiLabApr 30
How do transcription factors (TFs) that recognize the same DNA motif end up binding different places in the genome? 🧬 We're excited to show you how we tackle this question in our new bioRxiv pre-print! doi.org/10.64898/2026.04.27.…
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A preprint‼️that's bound to ruffle some 🪶 "Widespread DNA off-targeting confounds studies of RNA chromatin occupancy" led by our @MicahGoldrich and Louis Delhaye from @pieter_mestdagh. TL;DR we show that many of lncRNA chromatin occupancy maps are flawed🧵biorxiv.org/content/10.1101/…

Widespread DNA off-targeting confounds studies of RNA chromatin occupancy

The importance of long noncoding RNA (lncRNA) functions is recognized across biological systems, but their modes of action remain poorly understood. One mechanism proposed to be particularly common...

biorxiv.org
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Barkai Lab retweeted
Ariel Amir@Ariel_43216 Oct 2025
Design principles of transcription factors with intrinsically disordered regions @eLife @BarkaiLab doi.org/10.7554/eLife.104956 We study how IDRs allow TFs to efficiently locate DNA targets while maintaining strong binding. 1/3

Design principles of transcription factors with intrinsically disordered regions

Intrinsically disordered regions in transcription factors enhance both target binding probability and search efficiency.

elifesciences.org
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Why are transcription factors disordered? Come join us in Oxford as a postdoc and we'll find out! Help publish 3 mature projects, AND develop cool new single molecule fluorescence binding assays! biophysics transcription protein:DNA interactions my.corehr.com/pls/uoxrecruit…
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10% of human transcription factors are oligomeric. Stoichiometry can be dialled to modulate transcription. We show CREB searches DNA mixtures as a dimer, and suggest this might be common amongst other members of the bZIP family which fold on binding DNA. biorxiv.org/content/10.1101/…

A basic leucine zipper uses a dimer pathway to locate its targets in DNA mixtures

The operation of Eukaryotic transcription factors remains enigmatic. Cyclic AMP-responsive element-binding protein (CREB) is a member of the basic zipper family, a superfamily of transcription...

biorxiv.org
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🧵 1/ New preprint! How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites? biorxiv.org/content/10.1101/… #TranscriptionFactors #IDPs #SingleMolecule #Biophysics

Intrinsically disordered regions facilitate Msn2 target search to drive promoter selectivity

Transcription factors (TFs) regulate gene expression by binding specific DNA motifs, yet only a fraction of putative sites is occupied in vivo . Intrinsically disordered regions (IDRs) have emerged...

biorxiv.org
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Another paradigm destroyed by @BarkaiLab - cell.com/cell-systems/fullte…. Previously they found DNA binding domains were not important and now #cooperativity is minimal and unidirectional. How to explain specificity? I am lost!!!! #papertunes - Iggy/the Stooges, “Search and Destroy.”

The architecture of binding cooperativity between densely bound transcription factors

Transcription factors (TFs) bind a subset of their potential sites, which is often attributed to TF cooperativity. Lupo et al. systematically examine binding dependencies by co-deleting multiple TFs...

cell.com
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Barkai Lab retweeted
Ariel Amir@Ariel_43218 Aug 2023
Motivated by experiments in the Barkai lab @BarkaiLab on the role of Intrinsically Disordered Regions in the search process in eukaryotes, we considered the search process of a *polymer* with multiple, weak bindings to a region flanking the target site on the DNA. 2/3
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Barkai Lab retweeted
Ariel Amir@Ariel_43218 Aug 2023
Two new works on how transcription factors efficiently search for their DNA targets: A pedagogical paper led by Ori Hachmo @OHachmo giving a different intuition for the beautiful mechanism of facilitated diffusion pubs.aip.org/aapt/ajp/articl… 1/3

Conditional probability as found in nature: Facilitated diffusion

Search processes are ubiquitous in physical and biological phenomena, often involving the random motion of molecules. In particular, transcription factors (TFs)

pubs.aip.org
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Barkai Lab retweeted
FJonas@FJonas1531 Jul 2023
Read the newest chapter of the histone timer⏲️arc in our @NAR_Open paper investigating 🧐 the role of different histone chaperones and remodelers using the . Special thanks to Gilad, it was again great working with you👨‍🔬 and the other members of the @BarkaiLab👩‍👧‍👦. (🧵)
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How do TFs find TFBSs? Specifically, what do the non-DBD, intrinsically disordered regions (IDR) contribute? @BarkaiLab shows that IDRs are essential, and seem to contribute an additive disordered hydrophobic milieu to enable generic recruitment to promoters. #EMBOPredictEvo
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.@Marko_Dunjic_ @FJonas15 @BarkaiLab and co at @WeizmannScience use genetically encoded sensors to define histone occupancy in mouse ES cells #synbio #BiotechNatureComms nature.com/articles/s41467-0…

Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells

Nature Communications - Eviction of histones from nucleosomes and their exchange with newly synthesized or alternative variants is a central epigenetic determinant. Here the authors implement a...

nature.com
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Happy to share our paper “Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells”. Together with @BarkaLab we adapted molecular sensor for histone exchange in mammals. Huge thanks to @FJonas15 and Gilad who were major force of this paper!
Yoav Mayshar@ymayshar26 Jun 2023
Our very own @Marko_Dunjic_ in fantastic collaboration with the @BarkaiLab, finally in print. We can now measure histone dynamics in steady state in transgenic mice! knockouts, histone variants, heterochromatin, this paper has it all! rdcu.be/dfmLg @WeizmannScience
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Barkai Lab retweeted
FJonas@FJonas1526 Jun 2023
Finally we can share the fruits of our collaboration: ⌛️+🐁=🤯. Well done and big thanks to everyone involved, especially @Marko_Dunjic_ 👩‍🔬and Gilad from the @BarkaiLab🕵️. Btw. here the OG yeast timer paper: nature.com/articles/s41587-0…
Yoav Mayshar@ymayshar26 Jun 2023
Our very own @Marko_Dunjic_ in fantastic collaboration with the @BarkaiLab, finally in print. We can now measure histone dynamics in steady state in transgenic mice! knockouts, histone variants, heterochromatin, this paper has it all! rdcu.be/dfmLg @WeizmannScience
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Excited to share our paper 'The molecular grammar of protein disorder guiding genome-binding locations' . A great team effort with @FJonas15 and Miri Carmi 👏. I'm grateful for the support of the @BarkaiLab 🙏. Check out the thread below for more details!👇🧵
FJonas@FJonas1521 Mar 2023
Proud to present our 🎉new paper🎉deciphering the IIDR grammar of transcription factor target specificity: doi.org/10.1093/nar/gkad184. Special shout out to my fellow code breakers 🕵️ @BennyKrupkin and MiriCarmi and the rest of the @BarkaiLab - follow 🧵 for highlights

The molecular grammar of protein disorder guiding genome-binding locations

Abstract. Intrinsically disordered regions (IDRs) direct transcription factors (TFs) towards selected genomic occurrences of their binding motif, as exempl

academic.oup.com
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Barkai Lab retweeted
FJonas@FJonas1521 Mar 2023
Proud to present our 🎉new paper🎉deciphering the IIDR grammar of transcription factor target specificity: doi.org/10.1093/nar/gkad184. Special shout out to my fellow code breakers 🕵️ @BennyKrupkin and MiriCarmi and the rest of the @BarkaiLab - follow 🧵 for highlights

The molecular grammar of protein disorder guiding genome-binding locations

Abstract. Intrinsically disordered regions (IDRs) direct transcription factors (TFs) towards selected genomic occurrences of their binding motif, as exempl

academic.oup.com
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Barkai Lab retweeted
Dvir Gur@DvirGur29 Jan 2023
For an exciting study aimed at deciphering the molecular mechanism that drives kidney stones' formation, we are searching for a postdoc\PhD student with either a chemistry, materials science, or biology background to join our vibrant interdisciplinary team.
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Barkai Lab retweeted
FJonas@FJonas154 Jan 2023
Thanks to @IDPseminars for giving me the opportunity to present our newest research. Come and join to learn about our newest results on the molecular grammar of IDRs guiding transcription factor specificity
IDPseminars@IDPseminars27 Dec 2022
We kick off the new year 🎉with a spectacular new program featuring: ⭐️ @IPritisanac ⭐️Felix Jonas (@jacobs_bremen) ⭐️Hyun Kate Lee (@UoftB) ⭐️@Dushek ⭐️@jerelleaj ⭐️@LindorffLarsen
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Our lab's very first paper is out! 🤩 Using language models we predict the function of uncharacterized genes. Kudos to the talented @Daniellemlrs, who single handedly made this old dream of Dudu's come true 👑
Burstein lab@BursteinLab29 Sep 2022
Can we "read" microbial genomes using language models? We explore this idea in our paper "Deciphering microbial gene function using natural language processing" nature.com/articles/s41467-0… 🧵

Deciphering microbial gene function using natural language processing

Nature Communications - The function of many microbial genes is yet unknown. Here the authors repurposed natural language processing algorithms to explore “gene semantics” and infer...

nature.com
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Barkai Lab retweeted
FJonas@FJonas1523 Jun 2022
7 years after the first publication from @voichek and @RBarZiv we got another step closer to understand the role of histone modifications during DNA replication!
Barkai Lab@BarkaiLab23 Jun 2022
Our new paper on Histone Exchange during DNA replication by @fjonas15 and Gilad Yaakov will appear in the upcoming June issue of @genomeresearch ! genome.cshlp.org/content/ear…
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