#Nucleosome hashtag - Bluesky

2 months ago

A 3D print of the ALC1-nucleosome structure mentioned in the previous post, with a computer keyboard in the background for scale. The structure is printed in three pieces: the histones (blue), the DNA (grey) and ALC1 (blue). I was told it was pretty difficult to shove the histones into the DNA, since the plastic used to print isn't very flexible. It's looking great anyway. ALC1 is loosely attached, just like in the actual structure; in the 3D print, a piece of double-sided tape allows it to dissociate and bind again.

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!

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Original post on fediscience.org

2 months ago

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 […]

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3 months ago

Figure 5. Structure of an activation intermediate of ALC1 loosely bound to a PARylated nucleosome. (a) Cryo-EM map colored by chain assignment, following the color codes from Figure 1a for the nucleosome and Figure 2a for ALC1. (b) Atomic model, shown in the same orientations and with the same color code as the map shown in panel (a). (c) Structure of the auto-inhibited state. The antibody used for crystallization is shown as a translucent grey surface. From PDB 7EPU. (d) Structure of the intermediate state (dyad view). From this study. (e) Structure of the active state. From PDB 8B0A. In panels (c), (d) and (e), the ATPase residues mutated in the study by (Lehmann et al., 2017) are shown as spheres. In panels (c) and (d), the macro domain residues R857 and R860, found mutated in cancer, are shown as spheres and labeled, and the ADPr-binding pocket of the macro domain is indicated by an ADPr molecule (shown as balls-and-sticks) modeled by structural superimposition of the structure of the Af1521/ADPr complex from PDB 2BFQ (the Af1521 protein is not shown for clarity). In panels (b), (d) and (e), the nucleosome is shown as a translucent surface for clarity.

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 […]

[Original post on fediscience.org]

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@antibodies-dot-com.bsky.social

3 months ago

$Figure 1. Structure of the nucleosome. (a) Overview of the nucleosome (disc view). H3 is colored in blue, H4 in green, H2A in yellow, H2B in red, and DNA in grey. From PDB 1AOI. (b) Super-helical locations (SHL) are defined as the points where the major groove faces inward, toward the histone octamer. The base pair at the center of the histone octamer footprint on the DNA is called the dyad and numbered bp 0 / SHL 0 by convention. Each gyre has 7 SHLs, numbered positively on the front gyre and negatively on the back gyre (SHLs with same numbers but opposite signs refer to equivalent locations related by the pseudo 2-fold symmetry of the dyad axis, and a fractional SHL like 1.5 refers to the minor groove between two SHLs, in this example between SHLs 1 and 2). Only the front gyre is displayed here for clarity. From PDB 1AOI. (c) Electrostatic potential of the histone octamer. The H2A-H2B acidic patch is labeled. From PDB 1AOI. (d) The nucleosome’s major and minor super-grooves (gyres view). One of the major super-grooves is indicated by a continuous line (SHL 4/-5). One of the minor super-grooves is indicated by a dashed line (SHL 4.5/-4.5). Super-grooves can be unambiguously referred to by a pair of positive and negative SHLs. The synthetic minor super-groove binder is shown as white spheres. The nucleosome is shown as a surface with the same color code as in panel (a), with the DNA backbone in darker grey. From PDB 1S32.$

Figure 1. Structure of the nucleosome. (a) Overview of the nucleosome (disc view). H3 is colored in blue, H4 in green, H2A in yellow, H2B in red, and DNA in grey. From PDB 1AOI. (b) Super-helical locations (SHL) are defined as the points where the major groove faces inward, toward the histone octamer. The base pair at the center of the histone octamer footprint on the DNA is called the dyad and numbered bp 0 / SHL 0 by convention. Each gyre has 7 SHLs, numbered positively on the front gyre and negatively on the back gyre (SHLs with same numbers but opposite signs refer to equivalent locations related by the pseudo 2-fold symmetry of the dyad axis, and a fractional SHL like 1.5 refers to the minor groove between two SHLs, in this example between SHLs 1 and 2). Only the front gyre is displayed here for clarity. From PDB 1AOI. (c) Electrostatic potential of the histone octamer. The H2A-H2B acidic patch is labeled. From PDB 1AOI. (d) The nucleosome’s major and minor super-grooves (gyres view). One of the major super-grooves is indicated by a continuous line (SHL 4/-5). One of the minor super-grooves is indicated by a dashed line (SHL 4.5/-4.5). Super-grooves can be unambiguously referred to by a pair of positive and negative SHLs. The synthetic minor super-groove binder is shown as white spheres. The nucleosome is shown as a surface with the same color code as in panel (a), with the DNA backbone in darker grey. From PDB 1S32.

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 […]

[Original post on fediscience.org]

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Life Science Alliance

@lsajournal.org

3 months ago

New study in @LSAjournal reveals that CENP-A/H4 octasomes form flexible chromatin intermediates that may guide centromere assembly via CCAN. @uio.no @NCMMnews
#chromatin #centromere #CENP-A #cryo-EM #nucleosome #octasome
www.life-science-alliance.org/content/9/3/...

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Antibodies.com

4 months ago

Thalamocortical transcriptional gates coordinate memory stabilization - Nature The sequential recruitment of a thalamocortical transcriptional cascade enables memory maintenance over long timescales.

The authors use #MicroCaptureCUltra (#MCCu) to make multi-dimensional maps of how regulatory sequences are spatially organized. They are able to provide details on how #nucleosome are condensed, modified and organized in 3D touching points of regulatory elements like promoters and enhancers.

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Karolin Luger

@nucleosomepolice.bsky.social

5 months ago

@nucleosomepolice.bsky.social approves wholeheartedly. More #nucleosome #scienceart

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@proteinimaging.bsky.social

5 months ago

Close up of lilacs. The Canadian Science Publishing logo sits in the top left corner and the Canadian Science Publishing blaze emblem sits in the bottom right.

Genome welcomes unlimited fee-free open access submissions from @crkn-rcdr.bsky.social authors and provides unlimited Read Access to all @cdnsciencepub.com research. Publish with us 🍁▶️ buff.ly/oUyzd2x

🧬🔄 #genomics #chromatin #nucleosome #regulatorynetwork #generegulation #epigenome

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3D Protein Imaging

5 months ago

Here you can see a cryoEM structure of the human BAF-Lamin A/C IgF-H1-nucleosome complex (PDB code: 9J8O)

Rendering by Francisco J. Enguita made with #ProteinImager

3dproteinimaging.com/protein-imag...

#SciArt #chromatin #nucleosome #BAF #lamin #transcription #cryoem

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5 months ago

Confederation Bridge in PEI, Canada. The Canadian Science Publishing logo sits in the top left corner and the Canadian Science Publishing blaze emblem sits in the bottom right.

Publish your next breakthrough in Genome with no fees. Corresponding authors with @crkn-rcdr.bsky.social can submit unlimited OA manuscripts and benefit from unlimited read access. Discover how 🍁▶️ buff.ly/oUyzd2x

🧬🔄 #genomics #chromatin #nucleosome #regulatorynetwork #generegulation #epigenome

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7 months ago

Close up of beaver stepping into water. The Canadian Science Publishing logo sits in the top left corner and the Canadian Science Publishing blaze emblem sits in the bottom right.

Genome welcomes unlimited fee-free open access submissions from @crkn-rcdr.bsky.social authors and provides unlimited Read Access to all research. Publish with us 🍁▶️ buff.ly/oUyzd2x

🧬🔄 #genomics #transcriptionfactor #chromatin #nucleosome #regulatorynetwork #generegulation #epigenome

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@juliamaristany.bsky.social

8 months ago

Close up of lilacs. The Canadian Science Publishing logo sits in the top left corner and the Canadian Science Publishing blaze emblem sits in the bottom right.

Genome welcomes unlimited fee-free open access submissions from @crkn-rcdr.bsky.social authors and provides unlimited Read Access to all @cdnsciencepub.com research. Publish with us 🍁▶️ buff.ly/oUyzd2x

🧬🔄 #genomics #chromatin #nucleosome #regulatorynetwork #generegulation #epigenome

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Nikos Vakirlis

@vakirlis.bsky.social

8 months ago

PolyA/T tracts are known to function as #Nucleosome Depleted Regions, which prevent or reduce nucleosome formation to enable transcription of surrounding genes.

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Julia Maristany

8 months ago

Nucleosome spacing can fine-tune higher-order chromatin assembly - Nature Communications Internucleosomal linker length alters the stability and dynamics of chromatin condensates by shifting the balance between inter- and intramolecular interactions. Further, by changing the linker length...

🚨 New paper out in Nature Comms!

From the Rosen, Redding and Collepardo Labs, we uncover how #nucleosome spacing fine-tunes the architecture of #chromatin condensates.

👇 A short thread on how physical #genome organization emerges from molecular interactions:

www.nature.com/articles/s41...

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@nucleosomepolice.bsky.social

9 months ago

Confederation Bridge in PEI, Canada. The Canadian Science Publishing logo sits in the top left corner and the Canadian Science Publishing blaze emblem sits in the bottom right.

Publish your next breakthrough in Genome with no fees. Corresponding authors with @crkn-rcdr.bsky.social can submit unlimited OA manuscripts and benefit from unlimited read access. Discover how 🍁▶️ buff.ly/oUyzd2x

🧬🔄 #genomics #chromatin #nucleosome #regulatorynetwork #generegulation #epigenome

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Javier Santoyo

@jsantoyo.bsky.social

10 months ago

scNucMap: mapping the nucleosome landscapes at single-cell resolution. #SingleCell #Nucleosome #Bioinformatics
academic.oup.com/bioinformati...

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Karolin Luger

10 months ago

wish i was there! @nhoitsma.bsky.social will do a stellar job representing the lab . Also, is that a #nucleosome on the slide? 😘

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Nacho Molina

@molinalab.bsky.social

10 months ago

Just in case you missed this and it’s something that might interest you. #SingleMoleculeBiology, #Chromatin, #Transcription, #TF, #Nucleosome, #PolII, #Biophysics, #MachineLearning, #ComputationalBiology 👇

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