#nucleosome — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #nucleosome, aggregated by home.social.
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RE: https://fediscience.org/@Guillawme/115798148618761432
This article on an ALC1-nucleosome complex with a new conformation was accepted at @ActaCrystD in April and went online today! Check it out!
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RE: https://fediscience.org/@Guillawme/115798148618761432
This article on an ALC1-nucleosome complex with a new conformation was accepted at @ActaCrystD in April and went online today! Check it out!
-
RE: https://fediscience.org/@Guillawme/115798148618761432
This article on an ALC1-nucleosome complex with a new conformation was accepted at @ActaCrystD in April and went online today! Check it out!
-
RE: https://fediscience.org/@Guillawme/115798148618761432
This article on an ALC1-nucleosome complex with a new conformation was accepted at @ActaCrystD in April and went online today! Check it out!
-
RE: https://fediscience.org/@Guillawme/115798148618761432
This article on an ALC1-nucleosome complex with a new conformation was accepted at @ActaCrystD in April and went online today! Check it out!
-
One thing I had forgotten to post about this whole story: the fine people running our local cryoEM facility in Uppsala made a 3D print of this ALC1-#nucleosome structure and gifted it to me during the facility's end-of-year social event in December. What a sweet attention!
-
One thing I had forgotten to post about this whole story: the fine people running our local cryoEM facility in Uppsala made a 3D print of this ALC1-#nucleosome structure and gifted it to me during the facility's end-of-year social event in December. What a sweet attention!
-
One thing I had forgotten to post about this whole story: the fine people running our local cryoEM facility in Uppsala made a 3D print of this ALC1-#nucleosome structure and gifted it to me during the facility's end-of-year social event in December. What a sweet attention!
-
One thing I had forgotten to post about this whole story: the fine people running our local cryoEM facility in Uppsala made a 3D print of this ALC1-#nucleosome structure and gifted it to me during the facility's end-of-year social event in December. What a sweet attention!
-
One thing I had forgotten to post about this whole story: the fine people running our local cryoEM facility in Uppsala made a 3D print of this ALC1-#nucleosome structure and gifted it to me during the facility's end-of-year social event in December. What a sweet attention!
-
Finished reading this preprint on the ALC1-#nucleosome complex? ⬆️
The methods section details what worked, but not everything that was tried: it would be way too long for the academic article format (this methods section is already quite long).
Well, if you are curious about the thought process and decision making during data analysis, rejoice! For @HRBridges has written it all up in Part 2 of the case study in the CryoSPARC Guide!
Discuss it on the forum here: https://discuss.cryosparc.com/t/case-study-exploratory-processing-of-a-motor-bound-nucleosome-empiar-10739-part-2/24438
Or directly here on the Fediverse. -
Finished reading this preprint on the ALC1-#nucleosome complex? ⬆️
The methods section details what worked, but not everything that was tried: it would be way too long for the academic article format (this methods section is already quite long).
Well, if you are curious about the thought process and decision making during data analysis, rejoice! For @HRBridges has written it all up in Part 2 of the case study in the CryoSPARC Guide!
Discuss it on the forum here: https://discuss.cryosparc.com/t/case-study-exploratory-processing-of-a-motor-bound-nucleosome-empiar-10739-part-2/24438
Or directly here on the Fediverse. -
Finished reading this preprint on the ALC1-#nucleosome complex? ⬆️
The methods section details what worked, but not everything that was tried: it would be way too long for the academic article format (this methods section is already quite long).
Well, if you are curious about the thought process and decision making during data analysis, rejoice! For @HRBridges has written it all up in Part 2 of the case study in the CryoSPARC Guide!
Discuss it on the forum here: https://discuss.cryosparc.com/t/case-study-exploratory-processing-of-a-motor-bound-nucleosome-empiar-10739-part-2/24438
Or directly here on the Fediverse. -
Finished reading this preprint on the ALC1-#nucleosome complex? ⬆️
The methods section details what worked, but not everything that was tried: it would be way too long for the academic article format (this methods section is already quite long).
Well, if you are curious about the thought process and decision making during data analysis, rejoice! For @HRBridges has written it all up in Part 2 of the case study in the CryoSPARC Guide!
Discuss it on the forum here: https://discuss.cryosparc.com/t/case-study-exploratory-processing-of-a-motor-bound-nucleosome-empiar-10739-part-2/24438
Or directly here on the Fediverse. -
Finished reading this preprint on the ALC1-#nucleosome complex? ⬆️
The methods section details what worked, but not everything that was tried: it would be way too long for the academic article format (this methods section is already quite long).
Well, if you are curious about the thought process and decision making during data analysis, rejoice! For @HRBridges has written it all up in Part 2 of the case study in the CryoSPARC Guide!
Discuss it on the forum here: https://discuss.cryosparc.com/t/case-study-exploratory-processing-of-a-motor-bound-nucleosome-empiar-10739-part-2/24438
Or directly here on the Fediverse. -
So what does this new structure look like?
ALC1 is loosely bound to the #nucleosome, in a conformation that likely doesn't allow it to slide the nucleosome along the DNA, since the two ATPase lobes are not clamping the DNA. But we finally see the macro domain, for the first time in a nucleosome-bound structure! It interacts with the N-ATPase lobe, preventing the ATPase domain from fully clamping the DNA. So this looks a lot like an intermediate state in the transition from auto-inhibited to active ALC1.
Another striking observation from this structure is a long alpha-helix just upstream of the macro domain, that lines the nucleosome's minor super-groove.
4/5
-
So what does this new structure look like?
ALC1 is loosely bound to the #nucleosome, in a conformation that likely doesn't allow it to slide the nucleosome along the DNA, since the two ATPase lobes are not clamping the DNA. But we finally see the macro domain, for the first time in a nucleosome-bound structure! It interacts with the N-ATPase lobe, preventing the ATPase domain from fully clamping the DNA. So this looks a lot like an intermediate state in the transition from auto-inhibited to active ALC1.
Another striking observation from this structure is a long alpha-helix just upstream of the macro domain, that lines the nucleosome's minor super-groove.
4/5
-
So what does this new structure look like?
ALC1 is loosely bound to the #nucleosome, in a conformation that likely doesn't allow it to slide the nucleosome along the DNA, since the two ATPase lobes are not clamping the DNA. But we finally see the macro domain, for the first time in a nucleosome-bound structure! It interacts with the N-ATPase lobe, preventing the ATPase domain from fully clamping the DNA. So this looks a lot like an intermediate state in the transition from auto-inhibited to active ALC1.
Another striking observation from this structure is a long alpha-helix just upstream of the macro domain, that lines the nucleosome's minor super-groove.
4/5
-
So what does this new structure look like?
ALC1 is loosely bound to the #nucleosome, in a conformation that likely doesn't allow it to slide the nucleosome along the DNA, since the two ATPase lobes are not clamping the DNA. But we finally see the macro domain, for the first time in a nucleosome-bound structure! It interacts with the N-ATPase lobe, preventing the ATPase domain from fully clamping the DNA. So this looks a lot like an intermediate state in the transition from auto-inhibited to active ALC1.
Another striking observation from this structure is a long alpha-helix just upstream of the macro domain, that lines the nucleosome's minor super-groove.
4/5
-
So what does this new structure look like?
ALC1 is loosely bound to the #nucleosome, in a conformation that likely doesn't allow it to slide the nucleosome along the DNA, since the two ATPase lobes are not clamping the DNA. But we finally see the macro domain, for the first time in a nucleosome-bound structure! It interacts with the N-ATPase lobe, preventing the ATPase domain from fully clamping the DNA. So this looks a lot like an intermediate state in the transition from auto-inhibited to active ALC1.
Another striking observation from this structure is a long alpha-helix just upstream of the macro domain, that lines the nucleosome's minor super-groove.
4/5
-
As promised, here is a summary of this new preprint on the ALC1-nucleosome complex. 🧵
https://doi.org/10.1101/2025.11.10.687450
First, a reminder of some structural features of the #nucleosome.
Histones H2A and H2B form a negatively charged cleft exposed on the surface of the histone octamer, called the "acidic patch". It is recognized by many chromatin-binding factors. If you have read on these proteins, you have most likely already read about the acidic patch too.
One feature much less commonly mentioned is the "super-groove". The DNA wraps around the histone octamer in such a way that the major and minor grooves perfectly align across the two gyres. In 2004, Dervan, Luger and colleagues synthesized short polyamides able to bind to specific sequences across the super-groove (https://doi.org/10.1073/pnas.0401743101). They hypothesized that some chromatin-binding factors may recognize the super-groove, among other nucleosomal epitopes. Until 2025, there was no direct evidence for this.
1/5
-
As promised, here is a summary of this new preprint on the ALC1-nucleosome complex. 🧵
https://doi.org/10.1101/2025.11.10.687450
First, a reminder of some structural features of the #nucleosome.
Histones H2A and H2B form a negatively charged cleft exposed on the surface of the histone octamer, called the "acidic patch". It is recognized by many chromatin-binding factors. If you have read on these proteins, you have most likely already read about the acidic patch too.
One feature much less commonly mentioned is the "super-groove". The DNA wraps around the histone octamer in such a way that the major and minor grooves perfectly align across the two gyres. In 2004, Dervan, Luger and colleagues synthesized short polyamides able to bind to specific sequences across the super-groove (https://doi.org/10.1073/pnas.0401743101). They hypothesized that some chromatin-binding factors may recognize the super-groove, among other nucleosomal epitopes. Until 2025, there was no direct evidence for this.
1/5
-
As promised, here is a summary of this new preprint on the ALC1-nucleosome complex. 🧵
https://doi.org/10.1101/2025.11.10.687450
First, a reminder of some structural features of the #nucleosome.
Histones H2A and H2B form a negatively charged cleft exposed on the surface of the histone octamer, called the "acidic patch". It is recognized by many chromatin-binding factors. If you have read on these proteins, you have most likely already read about the acidic patch too.
One feature much less commonly mentioned is the "super-groove". The DNA wraps around the histone octamer in such a way that the major and minor grooves perfectly align across the two gyres. In 2004, Dervan, Luger and colleagues synthesized short polyamides able to bind to specific sequences across the super-groove (https://doi.org/10.1073/pnas.0401743101). They hypothesized that some chromatin-binding factors may recognize the super-groove, among other nucleosomal epitopes. Until 2025, there was no direct evidence for this.
1/5
-
As promised, here is a summary of this new preprint on the ALC1-nucleosome complex. 🧵
https://doi.org/10.1101/2025.11.10.687450
First, a reminder of some structural features of the #nucleosome.
Histones H2A and H2B form a negatively charged cleft exposed on the surface of the histone octamer, called the "acidic patch". It is recognized by many chromatin-binding factors. If you have read on these proteins, you have most likely already read about the acidic patch too.
One feature much less commonly mentioned is the "super-groove". The DNA wraps around the histone octamer in such a way that the major and minor grooves perfectly align across the two gyres. In 2004, Dervan, Luger and colleagues synthesized short polyamides able to bind to specific sequences across the super-groove (https://doi.org/10.1073/pnas.0401743101). They hypothesized that some chromatin-binding factors may recognize the super-groove, among other nucleosomal epitopes. Until 2025, there was no direct evidence for this.
1/5
-
As promised, here is a summary of this new preprint on the ALC1-nucleosome complex. 🧵
https://doi.org/10.1101/2025.11.10.687450
First, a reminder of some structural features of the #nucleosome.
Histones H2A and H2B form a negatively charged cleft exposed on the surface of the histone octamer, called the "acidic patch". It is recognized by many chromatin-binding factors. If you have read on these proteins, you have most likely already read about the acidic patch too.
One feature much less commonly mentioned is the "super-groove". The DNA wraps around the histone octamer in such a way that the major and minor grooves perfectly align across the two gyres. In 2004, Dervan, Luger and colleagues synthesized short polyamides able to bind to specific sequences across the super-groove (https://doi.org/10.1073/pnas.0401743101). They hypothesized that some chromatin-binding factors may recognize the super-groove, among other nucleosomal epitopes. Until 2025, there was no direct evidence for this.
1/5
-
RE: https://fediscience.org/@Guillawme/111534984107819771
Something really cool happened to me this year!
@HRBridges re-processed a #cryoEM dataset from some previous work of mine and colleagues (publicly available as EMPIAR-10739; see quoted post below for a summary of this work). She significantly improved the results we had struggled to obtain at the time of the initial analysis, and wrote it up as a case study for the CryoSPARC Guide: https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-end-to-end-and-exploratory-processing-of-a-motor-bound-nucleosome-empiar-10739
This is already super cool! Even cooler: she found a structure we had not found in this dataset. And it is a significant piece of result both to complete our understanding of ALC1 (the protein under study) and more broadly to understand one more way in which chromatin-binding factors can recognize the #nucleosome
We wrote an article about it, the preprint went online in November (now trying to get it peer-reviewed, but it might take some time; I can only work on this in my free time): https://doi.org/10.1101/2025.11.10.687450I wrote some more about the back story here: https://www.gaullier.org/en/blog/2025/12/28/new-preprint-on-alc1
Long story short: this preprint would not have materialized, had we not both attended the CCP-EM Spring Symposium this year and discussed at the poster session.I will write a summary thread about this new preprint in the near future (hopefully before the spring semester hits me; it's going to be busy...).
-
RE: https://fediscience.org/@Guillawme/111534984107819771
Something really cool happened to me this year!
@HRBridges re-processed a #cryoEM dataset from some previous work of mine and colleagues (publicly available as EMPIAR-10739; see quoted post below for a summary of this work). She significantly improved the results we had struggled to obtain at the time of the initial analysis, and wrote it up as a case study for the CryoSPARC Guide: https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-end-to-end-and-exploratory-processing-of-a-motor-bound-nucleosome-empiar-10739
This is already super cool! Even cooler: she found a structure we had not found in this dataset. And it is a significant piece of result both to complete our understanding of ALC1 (the protein under study) and more broadly to understand one more way in which chromatin-binding factors can recognize the #nucleosome
We wrote an article about it, the preprint went online in November (now trying to get it peer-reviewed, but it might take some time; I can only work on this in my free time): https://doi.org/10.1101/2025.11.10.687450I wrote some more about the back story here: https://www.gaullier.org/en/blog/2025/12/28/new-preprint-on-alc1
Long story short: this preprint would not have materialized, had we not both attended the CCP-EM Spring Symposium this year and discussed at the poster session.I will write a summary thread about this new preprint in the near future (hopefully before the spring semester hits me; it's going to be busy...).
-
RE: https://fediscience.org/@Guillawme/111534984107819771
Something really cool happened to me this year!
@HRBridges re-processed a #cryoEM dataset from some previous work of mine and colleagues (publicly available as EMPIAR-10739; see quoted post below for a summary of this work). She significantly improved the results we had struggled to obtain at the time of the initial analysis, and wrote it up as a case study for the CryoSPARC Guide: https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-end-to-end-and-exploratory-processing-of-a-motor-bound-nucleosome-empiar-10739
This is already super cool! Even cooler: she found a structure we had not found in this dataset. And it is a significant piece of result both to complete our understanding of ALC1 (the protein under study) and more broadly to understand one more way in which chromatin-binding factors can recognize the #nucleosome
We wrote an article about it, the preprint went online in November (now trying to get it peer-reviewed, but it might take some time; I can only work on this in my free time): https://doi.org/10.1101/2025.11.10.687450I wrote some more about the back story here: https://www.gaullier.org/en/blog/2025/12/28/new-preprint-on-alc1
Long story short: this preprint would not have materialized, had we not both attended the CCP-EM Spring Symposium this year and discussed at the poster session.I will write a summary thread about this new preprint in the near future (hopefully before the spring semester hits me; it's going to be busy...).
-
RE: https://fediscience.org/@Guillawme/111534984107819771
Something really cool happened to me this year!
@HRBridges re-processed a #cryoEM dataset from some previous work of mine and colleagues (publicly available as EMPIAR-10739; see quoted post below for a summary of this work). She significantly improved the results we had struggled to obtain at the time of the initial analysis, and wrote it up as a case study for the CryoSPARC Guide: https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-end-to-end-and-exploratory-processing-of-a-motor-bound-nucleosome-empiar-10739
This is already super cool! Even cooler: she found a structure we had not found in this dataset. And it is a significant piece of result both to complete our understanding of ALC1 (the protein under study) and more broadly to understand one more way in which chromatin-binding factors can recognize the #nucleosome
We wrote an article about it, the preprint went online in November (now trying to get it peer-reviewed, but it might take some time; I can only work on this in my free time): https://doi.org/10.1101/2025.11.10.687450I wrote some more about the back story here: https://www.gaullier.org/en/blog/2025/12/28/new-preprint-on-alc1
Long story short: this preprint would not have materialized, had we not both attended the CCP-EM Spring Symposium this year and discussed at the poster session.I will write a summary thread about this new preprint in the near future (hopefully before the spring semester hits me; it's going to be busy...).
-
RE: https://fediscience.org/@Guillawme/111534984107819771
Something really cool happened to me this year!
@HRBridges re-processed a #cryoEM dataset from some previous work of mine and colleagues (publicly available as EMPIAR-10739; see quoted post below for a summary of this work). She significantly improved the results we had struggled to obtain at the time of the initial analysis, and wrote it up as a case study for the CryoSPARC Guide: https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-end-to-end-and-exploratory-processing-of-a-motor-bound-nucleosome-empiar-10739
This is already super cool! Even cooler: she found a structure we had not found in this dataset. And it is a significant piece of result both to complete our understanding of ALC1 (the protein under study) and more broadly to understand one more way in which chromatin-binding factors can recognize the #nucleosome
We wrote an article about it, the preprint went online in November (now trying to get it peer-reviewed, but it might take some time; I can only work on this in my free time): https://doi.org/10.1101/2025.11.10.687450I wrote some more about the back story here: https://www.gaullier.org/en/blog/2025/12/28/new-preprint-on-alc1
Long story short: this preprint would not have materialized, had we not both attended the CCP-EM Spring Symposium this year and discussed at the poster session.I will write a summary thread about this new preprint in the near future (hopefully before the spring semester hits me; it's going to be busy...).
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#Chromatin fiber's #genomic 'memory' governs the building blocks of life, study reveals.
https://phys.org/news/2025-02-chromatin-fiber-genomic-memory-blocks.html
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#Chromatin fiber's #genomic 'memory' governs the building blocks of life, study reveals.
https://phys.org/news/2025-02-chromatin-fiber-genomic-memory-blocks.html
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#Chromatin fiber's #genomic 'memory' governs the building blocks of life, study reveals.
https://phys.org/news/2025-02-chromatin-fiber-genomic-memory-blocks.html
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#Chromatin fiber's #genomic 'memory' governs the building blocks of life, study reveals.
https://phys.org/news/2025-02-chromatin-fiber-genomic-memory-blocks.html
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#Chromatin fiber's #genomic 'memory' governs the building blocks of life, study reveals.
https://phys.org/news/2025-02-chromatin-fiber-genomic-memory-blocks.html
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#Chromatin fiber's #genomic 'memory' governs the building blocks of life, study reveals.
https://phys.org/news/2025-02-chromatin-fiber-genomic-memory-blocks.html
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#Chromatin fiber's #genomic 'memory' governs the building blocks of life, study reveals.
https://phys.org/news/2025-02-chromatin-fiber-genomic-memory-blocks.html
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#Chromatin fiber's #genomic 'memory' governs the building blocks of life, study reveals.
https://phys.org/news/2025-02-chromatin-fiber-genomic-memory-blocks.html
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#Chromatin fiber's #genomic 'memory' governs the building blocks of life, study reveals.
https://phys.org/news/2025-02-chromatin-fiber-genomic-memory-blocks.html
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Repressed but ready to go: How #bivalency holds developmental #genes in a poised state for #expression.
#histones #H3K27me3 #H3K4me3 #Nucleosome #KAT6B
https://phys.org/news/2025-02-repressed-ready-bivalency-developmental-genes.html
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Repressed but ready to go: How #bivalency holds developmental #genes in a poised state for #expression.
#histones #H3K27me3 #H3K4me3 #Nucleosome #KAT6B
https://phys.org/news/2025-02-repressed-ready-bivalency-developmental-genes.html
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Repressed but ready to go: How #bivalency holds developmental #genes in a poised state for #expression.
#histones #H3K27me3 #H3K4me3 #Nucleosome #KAT6B
https://phys.org/news/2025-02-repressed-ready-bivalency-developmental-genes.html
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Repressed but ready to go: How #bivalency holds developmental #genes in a poised state for #expression.
#histones #H3K27me3 #H3K4me3 #Nucleosome #KAT6B
https://phys.org/news/2025-02-repressed-ready-bivalency-developmental-genes.html
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Repressed but ready to go: How #bivalency holds developmental #genes in a poised state for #expression.
#histones #H3K27me3 #H3K4me3 #Nucleosome #KAT6B
https://phys.org/news/2025-02-repressed-ready-bivalency-developmental-genes.html
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6/n In addition to the above shown examples for #MolecularMachines, here a few more #molecules we presented in #AugmentedReality at #IdeenExpo: #Tubulin-stathmin complex, #antibody, #nucleosome particle, #SARSCoV2 #polymerase.
#DIYbio #MINT #STEM #chem #AR #education #TiltFive -
6/n In addition to the above shown examples for #MolecularMachines, here a few more #molecules we presented in #AugmentedReality at #IdeenExpo: #Tubulin-stathmin complex, #antibody, #nucleosome particle, #SARSCoV2 #polymerase.
#DIYbio #MINT #STEM #chem #AR #education #TiltFive -
6/n In addition to the above shown examples for #MolecularMachines, here a few more #molecules we presented in #AugmentedReality at #IdeenExpo: #Tubulin-stathmin complex, #antibody, #nucleosome particle, #SARSCoV2 #polymerase.
#DIYbio #MINT #STEM #chem #AR #education #TiltFive -
6/n In addition to the above shown examples for #MolecularMachines, here a few more #molecules we presented in #AugmentedReality at #IdeenExpo: #Tubulin-stathmin complex, #antibody, #nucleosome particle, #SARSCoV2 #polymerase.
#DIYbio #MINT #STEM #chem #AR #education #TiltFive -
6/n In addition to the above shown examples for #MolecularMachines, here a few more #molecules we presented in #AugmentedReality at #IdeenExpo: #Tubulin-stathmin complex, #antibody, #nucleosome particle, #SARSCoV2 #polymerase.
#DIYbio #MINT #STEM #chem #AR #education #TiltFive -
A #cryoem model of the RSF–NCP complex reveals distinct binding characteristics compared with the SNF2h–NCP complex and biochemical analyses indicate that RSF possesses unique chromatin-remodeling properties #ChromatinRemodeling #RSF #Nucleosome https://t.co/ZP6ZglquKq