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Chromatin Haiku

@chromatinhaiku.bsky.social
1.3K followers 33 following 12 posts

Nuclear events Narratives in chromatin By haiku, of course

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Chromatin Haiku @chromatinhaiku.bsky.social · 27/11/2025
Transcribing Pol2 With elongation factors Kinetic control #ChromatinHaiku #SingleMolecule www.nature.com/articles/s41...
Fig. 1: Real-time observation of mammalian transcription elongation. a, Composite structural model of the human transcription EC with a set of elongation factors, as supplied in our system, decorating the Pol II surface. The model incorporates published structures for the mammalian EC (PDB 6TED), TFIIS (PDB 8A40), ELOF1 (PDB 8B3F) and a fitted AlphaFold prediction of IWS1 based on the position of Spn1 in the yeast EC (PDB 7XN7). b, Schematic of the single-molecule experimental setup. The starting location of the EC is marked by the ATTO647N-labeled RNA, while Cy3-labeled DNA probes that hybridize to the nascent RNA indicate active elongation. c, An example of transcription elongation by a single mammalian EC observed in real time. Top: kymograph showing the EC position on the DNA template, indicated by RNA (magenta) and probe (green) signals, as a function of time. Bottom: elongation trajectory extracted from the kymograph. Raw data (gray dots) were fitted to discrete linear segments (black line). Change points are marked as filled circles. The slopes for each segment are indicated, differentiating active elongation (blue) from pausing or stalling events (red). d, Eight additional examples of fitted elongation trajectories by individual mammalian ECs aligned by their starting positions. NTP, nucleoside triphosphate.Fig. 7: Summary of the distinct roles that each elongation factor serves in mammalian Pol II transcription on DNA. The relative EC activity for each factor omission condition is color coded as indicated on the right. Clockwise from the top left: ΔTFIIS increases pausing but has a minimal effect on the elongation speed; ΔP-TEFb abrogates the phosphorylation of Pol II CTD and DSIF, which in turn destabilizes the binding of PAF1C, SPT6 and RTF1, thereby severely reducing the elongation speed; ΔPAF1C exerts the most direct negative impact on EC speed and also completely abolishes RTF1 recruitment; ΔRTF1 shifts the EC from high speed to medium speed; ΔSPT6 reduces EC speed by destabilizing PAF1C binding even though SPT6 itself does not directly activate EC; ΔDSIF exerts a dual effect on EC kinetics by reducing its pausing and also lowering its speed partially via the destabilization of RTF1 binding.
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Chromatin Haiku @chromatinhaiku.bsky.social · 03/08/2025
Nascent and mature Ribosomal RNA Unbalanced in parts #ChromatinHaiku #RNAsky #28S #Chromatinsky www.biorxiv.org/content/10.1...
Figure 4E-F from the linked preprint showing the excess of 28S over 18S rRNA across cell types.
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Chromatin Haiku @chromatinhaiku.bsky.social · 03/07/2025
The Range Extender For enhancers to function At long distances #ChromatinHaiku
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Chromatin Haiku @chromatinhaiku.bsky.social · 15/06/2025
For mature oocytes H2A.Z is needed With MLL2 #ChromatinHaiku @natsmb.nature.com www.nature.com/articles/s41... www.nature.com/articles/s41...
Model figure from Mei et al., Figure legend: Small growing oocytes show canonical distributions of H3K4me3 and H2A.Z at active and bivalent gene promoters. In wild-type FGOs, H3K4me3 and H2A.Z form non-canonical broad domains across intergenic regions, whereas H2A.Z is displaced at bivalent gene promoters. In H2A.Z-DKO FGOs, non-canonical H3K4me3 at intergenic regions and H2AK119ub1 at active gene promoters are partially reduced. In Mll2-KO FGOs, ncH2A.Z is partially reduced. The distributions of H3K27me3 and H2AK119ub1 were not investigated in the Mll2-KO FGOs (marked with question marks). H2AK119ub1 at bivalent gene promoters is not shown.Model figure from Xu et al., Figure legend: Maternal depletion of H2A.Z results in aberrant meiosis resumption. Only a few FGOs survived to MII oocytes, with abnormal chromosome alignment. H2A.Z is acetylated (red) at active promoters and enhancers in mouse FGOs. Genes with low CG densities are preferentially downregulated in H2A.ZmKO FGOs. In mESCs, growing oocytes, and early embryos, in addition to active promoters and enhancers, H2A.Z and H2A.Zac are also present at inactive promoters with high CG densities, including Polycomb-target genes.
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Chromatin Haiku @chromatinhaiku.bsky.social · 13/12/2024
Pol2 stimulates SETD2 methylation Of histone H3 #ChromatinHaiku #H3K36 www.science.org/doi/10.1126/...
Fig. 1. Biochemical reconstitution of H3K36me3 deposition by SETD2 during transcription.
(A) Schematic of RNA extension-coupled histone mark deposition assay in the presence of all NTPs. (B) Denaturing gel of RNA products and Western blot analysis reveals transcription stimulates H3K36me3 deposition by SETD2. SETD2 concentration is 3.5 μM. (C) Schematic of RNA extension-coupled histone mark deposition assay with pause sites (bp −31, bp −15, and bp +27). (D) Denaturing gel of RNA products and Western blot analysis reveals transcription stimulates H3K36me3 deposition by SETD2 on partially transcribed downstream nucleosome. SETD2 concentration is 3.5 μM. (E) Denaturing gel of RNA products and Western blot analysis reveals transcription stimulates H3K36me3 deposition by SETD2 on transferred upstream nucleosome (bp +115). SETD2 concentration is 700 nM. RNA extension gel and Western blot from (E) is the same as in fig. S13F.
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Chromatin Haiku @chromatinhaiku.bsky.social · 15/11/2024
STK19 Transcription coupled repair With TFIIH #ChromatinHaiku www.cell.com/cell/fulltex... www.cell.com/cell/fulltex... www.cell.com/molecular-ce...
Graphical abstract for one of the papersGraphical abstract for one of the papersGraphical abstract for one of the papers
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Chromatin Haiku @chromatinhaiku.bsky.social · 13/11/2024
Polycomb restores H2A ubiquitin By read-write action #ChromatinHaiku #ncPRC1-RYBP www.nature.com/articles/s41...
Figure 2 from the paper: Two distinct acidic patch interactions and ubiquitin binding stabilize the ncPRC1RYBP complex on the nucleosome, suggesting an intra-nucleosome read–write mechanism.
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Reposted by Chromatin Haiku
Francesca Mattiroli @fmattiroli.bsky.social · 12/11/2024
Being haiku-ed is an honor! You were so fast, too 🤩
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Chromatin Haiku @chromatinhaiku.bsky.social · 12/11/2024
Depleting CAF-1 Slows replisome, chromatin G0 arrest #ChromatinHaiku @fmattiroli.bsky.social www.cell.com/molecular-ce...
Graphical abstract for paper. Written abstract is as follows:

Long-term perturbation of de novo chromatin assembly during DNA replication has profound effects on epigenome maintenance and cell fate. The early mechanistic origin of these defects is unknown. Here, we combine acute degradation of chromatin assembly factor 1 (CAF-1), a key player in de novo chromatin assembly, with single-cell genomics, quantitative proteomics, and live microscopy to uncover these initiating mechanisms in human cells. CAF-1 loss immediately slows down DNA replication speed and renders nascent DNA hyper-accessible. A rapid cellular response, distinct from canonical DNA damage signaling, is triggered and lowers histone mRNAs. In turn, histone variants’ usage and their modifications are altered, limiting transcriptional fidelity and delaying chromatin maturation within a single S-phase. This multi-level response induces a p53-dependent cell-cycle arrest after mitosis. Our work reveals the immediate consequences of defective de novo chromatin assembly during DNA replication, indicating how at later times the epigenome and cell fate can be altered.
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Chromatin Haiku @chromatinhaiku.bsky.social · 12/11/2024
A giant virus With its own nucleosomes And linker histone #ChromatinHaiku
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Chromatin Haiku @chromatinhaiku.bsky.social · 12/11/2024
Limiting factors For nuclear receptors Live cell imaging #ChromatinHaiku #SingleMoleculeTracking #ProximityAssistedPhotoactivation www.biorxiv.org/content/10.1...
Figure 4. A model for RARα limited chromatin binding of RARα-RXRα heterodimers.

(A) Pool of RXRα (red) and RXR partners (RARα – blue, other T2NRs-yellow) along with some number of chromatin bound RARα-RXRα heterodimers exist under normal conditions. (B) When the pool of free RXRα is increased, the number of chromatin bound RARα-RXRα heterodimers does not change. (C) When the pool of RARα is increased, chromatin binding RARα-RXRα heterodimers increases, until it reaches saturation. Note: For simplicity we have omitted to show heterodimerization of other T2NRs (yellow) with RXRα (red).
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Chromatin Haiku @chromatinhaiku.bsky.social · 12/11/2024
DNMT3 Developmental methyl A key role for B #chromatinhaiku www.youtube.com/watch?v=u2e0... www.biorxiv.org/content/10.1...
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Komal Yasmin
YouTube video by Fragile Nucleosome
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