Ariel Kaplan
@arielkaplan.bsky.social
Single molecule biophysics, Optical Tweezers, Chromatin, Transcription, Polymerases, Helicases
Associate Professor, Technion-Israel Institute of Technology
https://kaplan.net.technion.ac.il/
Associate Professor, Technion-Israel Institute of Technology
https://kaplan.net.technion.ac.il/
Pinned
Ariel Kaplan
@arielkaplan.bsky.social
· May 27
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 as ...
www.biorxiv.org
1/
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?
www.biorxiv.org/content/10.1...
#TranscriptionFactors #IDPs #SingleMolecule #Biophysics
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?
www.biorxiv.org/content/10.1...
#TranscriptionFactors #IDPs #SingleMolecule #Biophysics
Reposted by Ariel Kaplan
Oldies but Goldies. from 2007. Light-powering Escherichia coli with proteorhodopsin www.pnas.org/doi/10.1073/...
June 10, 2025 at 12:56 PM
Oldies but Goldies. from 2007. Light-powering Escherichia coli with proteorhodopsin www.pnas.org/doi/10.1073/...
Reposted by Ariel Kaplan
Marine Asgard Archaea’s Light-Harvesting Rhodopsin Revealed scienmag.com/marine-asgar...
Marine Asgard Archaea's Light-Harvesting Rhodopsin Revealed
In a groundbreaking advancement that challenges existing paradigms of microbial photobiology, researchers have unveiled novel structural insights into how marine Asgard archaea harness light energy.
scienmag.com
May 31, 2025 at 12:57 PM
Reposted by Ariel Kaplan
There are 2 previous historical cases of countries destroying their science and universities, crippling them for decades: Lysenkoism in the USSR and Nazi Germany. The Trump administration will be the 3rd.
It's not just budgets but research, institutions, expertise, and training the next generation.
It's not just budgets but research, institutions, expertise, and training the next generation.
May 31, 2025 at 4:43 AM
There are 2 previous historical cases of countries destroying their science and universities, crippling them for decades: Lysenkoism in the USSR and Nazi Germany. The Trump administration will be the 3rd.
It's not just budgets but research, institutions, expertise, and training the next generation.
It's not just budgets but research, institutions, expertise, and training the next generation.
Reposted by Ariel Kaplan
Reposted by Ariel Kaplan
Nice work by the Kurumizaka Lab in @natcomms.nature.com
Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis
www.nature.com/articles/s41...
Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis
www.nature.com/articles/s41...
Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis - Nature Communications
The authors establish the ChIP-CryoEM method, which combines chromatin immunopurification coupled with cryo-electron microscopy, to visualize native human RNAPII elongation complexes in action, with a...
www.nature.com
May 29, 2025 at 7:09 AM
Nice work by the Kurumizaka Lab in @natcomms.nature.com
Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis
www.nature.com/articles/s41...
Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis
www.nature.com/articles/s41...
Reposted by Ariel Kaplan
1/
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?
www.biorxiv.org/content/10.1...
#TranscriptionFactors #IDPs #SingleMolecule #Biophysics
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?
www.biorxiv.org/content/10.1...
#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 as ...
www.biorxiv.org
May 27, 2025 at 10:11 PM
1/
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?
www.biorxiv.org/content/10.1...
#TranscriptionFactors #IDPs #SingleMolecule #Biophysics
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?
www.biorxiv.org/content/10.1...
#TranscriptionFactors #IDPs #SingleMolecule #Biophysics
Reposted by Ariel Kaplan
Super cool work on the function of intrinsically disordered regions in regulating transcription factor DNA binding.
1/
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?
www.biorxiv.org/content/10.1...
#TranscriptionFactors #IDPs #SingleMolecule #Biophysics
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?
www.biorxiv.org/content/10.1...
#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 as ...
www.biorxiv.org
May 28, 2025 at 10:53 AM
Super cool work on the function of intrinsically disordered regions in regulating transcription factor DNA binding.
Reposted by Ariel Kaplan
The energy landscape of a single disordered protein (tau) and the impact of PTMs is resolved. An important step to understanding the function and dysfunction of disordered proteins from their conformational ensemble. Not yet peer reviewed. www.biorxiv.org/content/10.1...
Direct observation of conformational dynamics of intrinsically disordered proteins at the single-molecule level
Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) are integral to many biological processes, including neurotransmitter regulation, microtubule regulat...
www.biorxiv.org
May 28, 2025 at 6:56 PM
The energy landscape of a single disordered protein (tau) and the impact of PTMs is resolved. An important step to understanding the function and dysfunction of disordered proteins from their conformational ensemble. Not yet peer reviewed. www.biorxiv.org/content/10.1...
Reposted by Ariel Kaplan
How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Conservation of regulatory elements with highly diverged sequences across large evolutionary distances
Nature Genetics - Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence...
rdcu.be
May 27, 2025 at 12:19 PM
How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
1/
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?
www.biorxiv.org/content/10.1...
#TranscriptionFactors #IDPs #SingleMolecule #Biophysics
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?
www.biorxiv.org/content/10.1...
#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 as ...
www.biorxiv.org
May 27, 2025 at 10:11 PM
1/
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?
www.biorxiv.org/content/10.1...
#TranscriptionFactors #IDPs #SingleMolecule #Biophysics
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?
www.biorxiv.org/content/10.1...
#TranscriptionFactors #IDPs #SingleMolecule #Biophysics
Reposted by Ariel Kaplan
And, again, WHERE IS #BIGPHARMA in defending #basicscience? laying low? playing dead? Waiting it out? Do SOMETHING! SPEAK UP! Use your gigantic lobbying machine to defend us instead of peddling your wares and increasing your profits. Or do you think highly trained workforce grows on trees?
May 2, 2025 at 11:55 AM
And, again, WHERE IS #BIGPHARMA in defending #basicscience? laying low? playing dead? Waiting it out? Do SOMETHING! SPEAK UP! Use your gigantic lobbying machine to defend us instead of peddling your wares and increasing your profits. Or do you think highly trained workforce grows on trees?
Reposted by Ariel Kaplan
Wow - this is also the cofactor for the lyase activity of Cyp17A1 - required for production of androgens from pregnenolone/progesterone.
Cytochrome b5 occurrence in giant and other viruses belonging to the phylum Nucleocytoviricota www.nature.com/articles/s44...
Cytochrome b5 occurrence in giant and other viruses belonging to the phylum Nucleocytoviricota - npj Viruses
npj Viruses - Cytochrome b5 occurrence in giant and other viruses belonging to the phylum Nucleocytoviricota
www.nature.com
February 18, 2025 at 7:47 AM
Wow - this is also the cofactor for the lyase activity of Cyp17A1 - required for production of androgens from pregnenolone/progesterone.
Reposted by Ariel Kaplan
Congratulations to Prof. Nabieh Ayoub on receiving the Award for Outstanding Excellence in Teaching for the Spring Semester of 2024 biology.technion.ac.il/en/congratul...
Congratulations to Prof. Nabieh Ayoub on receiving the Award for Outstanding Excellence in Teaching for the Spring Semester of 2024 - פקולטה לביולוגיה Biology Faculty
The Faculty of Biology commends Prof. Ayoub for his significant contributions to teaching, his dedication to students, and his academic excellence. This recognition reflects his deep commitment to adv...
biology.technion.ac.il
January 2, 2025 at 11:18 AM
Congratulations to Prof. Nabieh Ayoub on receiving the Award for Outstanding Excellence in Teaching for the Spring Semester of 2024 biology.technion.ac.il/en/congratul...
Reposted by Ariel Kaplan
Did you know that there is an enzyme called ATAC, which is not related to ATAC-seq? :) academic.oup.com/nar/advance-...
This paper reports a very interesting finding that ATAC and SAGA increase TF binding to DNA target sites on nucleosome by an order of magnitude independent of histone acetylation
This paper reports a very interesting finding that ATAC and SAGA increase TF binding to DNA target sites on nucleosome by an order of magnitude independent of histone acetylation
ATAC and SAGA histone acetyltransferase modules facilitate transcription factor binding to nucleosomes independent of their acetylation activity
Abstract. Transcription initiation involves the coordination of multiple events, starting with activators binding specific DNA target sequences, which recr
academic.oup.com
December 8, 2024 at 11:00 AM
Did you know that there is an enzyme called ATAC, which is not related to ATAC-seq? :) academic.oup.com/nar/advance-...
This paper reports a very interesting finding that ATAC and SAGA increase TF binding to DNA target sites on nucleosome by an order of magnitude independent of histone acetylation
This paper reports a very interesting finding that ATAC and SAGA increase TF binding to DNA target sites on nucleosome by an order of magnitude independent of histone acetylation
Reposted by Ariel Kaplan
Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪
There are already many articles for which there is more attention on Bluesky than on other comparable micro-blogging sites, meaning the academic community and the general public have clearly adopted Bluesky as one of its core places to disseminate and discuss new research.
A Place of Joy.
A Place of Joy.
December 3, 2024 at 2:10 PM
Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪
Reposted by Ariel Kaplan
Best practice mass photometry: A guide to optimal single molecule mass measurement https://www.biorxiv.org/content/10.1101/2024.12.03.624087v1
Best practice mass photometry: A guide to optimal single molecule mass measurement https://www.biorxiv.org/content/10.1101/2024.12.03.624087v1
Mass photometry (MP) has emerged as a powerful approach to study biomolecular structure, dynamics an
www.biorxiv.org
December 4, 2024 at 1:49 PM
Best practice mass photometry: A guide to optimal single molecule mass measurement https://www.biorxiv.org/content/10.1101/2024.12.03.624087v1
Reposted by Ariel Kaplan
As you make have seen, there is a special issue of JMB on "Controlling Transcription Elongation and Termination: More Than a Means to An End" curated by my colleague here at Pitt Karen Arndt and by Steve Buratowski from Harvard Medical School 🧪🧵 1/ www.sciencedirect.com/science/arti...
Controlling Transcription Elongation and Termination: More Than a Means to An End
www.sciencedirect.com
November 27, 2024 at 3:00 PM
As you make have seen, there is a special issue of JMB on "Controlling Transcription Elongation and Termination: More Than a Means to An End" curated by my colleague here at Pitt Karen Arndt and by Steve Buratowski from Harvard Medical School 🧪🧵 1/ www.sciencedirect.com/science/arti...
Reposted by Ariel Kaplan
Single-molecule states link transcription factor binding to gene expression www.nature.com/articles/s41...
Single-molecule states link transcription factor binding to gene expression - Nature
A study uses single-molecule footprinting to measure protein occupancy at regulatory elements on individual molecules in human cells and describes how different properties of transcription factor bind...
www.nature.com
November 20, 2024 at 8:34 PM
Single-molecule states link transcription factor binding to gene expression www.nature.com/articles/s41...
Reposted by Ariel Kaplan
"Dark TFs": new manuscript mapped 166 uncharacterized human transcription factors, finding half bind genomic "dark matter," often closed chromatin rich in transposable elements.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 19, 2024 at 11:41 PM
"Dark TFs": new manuscript mapped 166 uncharacterized human transcription factors, finding half bind genomic "dark matter," often closed chromatin rich in transposable elements.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Ariel Kaplan
Genome access is transcription factor-specific and defined by nucleosome position https://www.sciencedirect.com/science/article/pii/S1097276524006634
September 16, 2024 at 3:30 PM
Genome access is transcription factor-specific and defined by nucleosome position https://www.sciencedirect.com/science/article/pii/S1097276524006634
Reposted by Ariel Kaplan
Regulation of transcription by condensates, great review by @bsabari.bsky.social and coll.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Transcription regulation by biomolecular condensates - Nature Reviews Molecular Cell Biology
Transcriptional condensates, which are formed through dynamic multivalent interactions between proteins, RNA and chromatin, regulate transcription by compartmentalizing its machinery in the crowded nu...
www.nature.com
November 13, 2024 at 6:56 PM
Regulation of transcription by condensates, great review by @bsabari.bsky.social and coll.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ariel Kaplan
So, here I am. The nucleosome police now flies under their official tag. Please follow me if you are interested in #chromatin, #nucleosome, #cryoEM, #scienceeducation, #hiking, #quilting, and #nature. Help me figure out this platform!
September 23, 2023 at 3:55 PM
So, here I am. The nucleosome police now flies under their official tag. Please follow me if you are interested in #chromatin, #nucleosome, #cryoEM, #scienceeducation, #hiking, #quilting, and #nature. Help me figure out this platform!