Maik Engeholm
LightNews LightNews
mengeho.bsky.social
Maik Engeholm
@mengeho.bsky.social
16 followers 42 following 0 posts
Posts Replies Media Videos
Reposted by Maik Engeholm
xuhuihuangchem.bsky.social
Our new preprint, led by @yunruiqiu.bsky.social and
Shuming Liu (MIT), explores the use of IGME non-Markovian model to study chromatin folding in collaboration with Bin Zhang’s group at MIT. One interesting finding: memory kernels decay more slowly in nucleosome
condensates than in free solution.
yunruiqiu.bsky.social yunruiqiu.bsky.social @yunruiqiu.bsky.social · Nov 19
New preprint: The non-Markovian model and residue-level CG simulations reveal how nucleosome condensates and 10n+5 bp linker DNA shape chromatin folding pathways and folding rates. www.biorxiv.org/content/10.1...
November 19, 2024 at 11:18 PM
Reposted by Maik Engeholm
teiflab.bsky.social
Interesting new method to map nucleosomes in 3D, "Proximity Copy Paste (PCP)". www.biorxiv.org/content/10.1...
▶️ mapped connectivity of nucleosomes in S. cerevisiae
▶️ chromatin is predominantly organized into regularly spaced nucleosome arrays
▶️ metaphase chromosomes packed by arrayed cohesin hubs
PCP maps 3D genome organization at the nucleosome level. (a) Schematic of the PCP reaction on chromatin. Crosslinked chromatin is digested into nucleosomes by Caspase Activated DNAse (CAD) and then immobilized onto magnetic beads. Digested chromatin is ligated by seed and receptor molecules to the ratio of 1/10. The PCP reaction takes place on the beads where RNA tags will diffuse from the seeds and tag nearby receptors. The chromatin is then decrosslinked, the proteins and RNA removed, and a sequencing library generated by PCR. Molecules sharing the same UMI are grouped. Tag groups can be analyzed in several ways, including individual multiway tag groups or pairwise interaction matrices. (b) Plot showing the relative frequency of receptor tagging as a function of distance from the seed, the midpoints of the tagged molecules is shown. Seeds that self-tag are excluded from this analysis. (c) Plot showing the number of reads per seed tag groups for G1 data. (d) Distance decay interaction plots of PCP (orange) and Micro-C (Costantinto et al. 2020, 15 min 23°C sample) (res = 50bp). Regularly spaced nucleosome arrays are prevalent over the genome. (a) Meta analysis of PCP matrices relative to the dyad of the +1 nucleosome of genes longer than 2Kb, 50 least expressed genes (res = 10bp). (b) As a, but for the 50 most expressed genes (res = 10bp). (c) PCP map of low expressed gene RNR3 (middle, res = 25bp), Nucleosome profile (grey). Note the grid-like pattern across the entire gene body. (d) PCP map of the expressed gene FMP27 (res = 25bp), Nucleosome profile (grey). Note the grid-like pattern at the 5’ end of the gene and parallel stripes at towards the middle and 3’ end of gene. (e) Schematic of the results observed. No pattern is obtained with poorly spaced, poorly positioned nucleosomes. Dotted pattern is obtained with regularly spaced, well positioned nucleosome arrays. Striped pattern is obtained with regularly spaced delocalized arrays. The number of parallel stripes indicates the number of nucleosomes in the array. (f) Meta plot of highly transcribed, ribosomal protein genes. The genes are organized with respect to the Rap1 protein at position 0. Top panel, Rap1 ChIP-MNase in blue (Gutin et al. 2018), All reads size, Mono-nucleosomal (Nuc.) reads only and Sub-nucleosomal reads only (Sub. 20 bp < insert size < 90 bp) are represented. Medium panel represent the density of read by position relative to insert size from mapped PCP data. The bottom panel is a pile-up analysis of PCP matrix oriented relative to the RP genes (res = 10bp). Note that the gene body contains short, delocalized nucleosome arrays. (g) Frequency of tagging relative to the seed position for the subset of genes used in a and b. The most expressed genes are in red and least expressed genes in blue. (h) Frequency of tagging relative to the seed position for gene of at least 600bp. The most expressed are in orange and the least expressed is in blue.
November 16, 2024 at 4:37 PM
Reposted by Maik Engeholm
peterlewislab.bsky.social
A novel method, Proximity Copy Paste (PCP), maps nucleosome connectivity in yeast, revealing transcription-linked array differences and cohesin hubs in metaphase. Plus, stable non-canonical nucleosomes take center stage.
www.biorxiv.org/content/10.1...
November 20, 2024 at 12:47 AM