Nucleosome papers 📚 NucPosDB database

Nucleosome aficionados! Our new review "Nucleosome spacing across cell types, diseases, and ages" is out in NAR: academic.oup.com/nar/article/54… A huge effort to pull together what we’ve learned about nucleosome spacing in many systems. Enjoy! #nucleosomics #nucleosome #chromatin #cfDNA

Great to see that this preprint used our software NucTools to calculate NRL, and reached conclusions confirming our previous paper, which reported effect of linker histones H1 on cfDNA fragmentation patterns and nucleosome spacing in cancer tissues/cfDNA link.springer.com/article/10.118…

We have a postdoctoral opening for a researcher with experience in bioinformatics of DNA sequencing and machine learning to work on the development of new methods for cancer diagnostics related to nucleosomes, chromatin and more jobs.ac.uk/job/DMK060/sen…. Apply by 21st April 2025!

Nucleosome condensate and linker DNA alter chromatin folding pathways and rates [Qiu et al, 2024] biorxiv.org/content/10.110… ▶️residue-level coarse-grained models; non-Markovian dynamics ▶️10n bp DNA linker lengths favor zigzag fibrils ▶️10n+5 bp chromatin loses unique conformations

Chromatin architecture mapping by multiplex proximity tagging [Delamarre et al. 2024] biorxiv.org/content/10.110… ▶️Nucleosome maps in 3D with Proximity Copy Paste (PCP) ▶️Connectivity of nucleosomes in S. cerevisiae ▶️Chromatin is predominantly organized in regular nucleosome arrays

Acute multi-level response to defective de novo chromatin assembly in S-phase (Dreyer et al., 2024) cell.com/molecular-cell…

1/n Looking into history of "fragile nucleosomes". The term was introduced in Xi et al, 2011 genome.cshlp.org/content/21/5/7……. But before that, MNase-sensitive nucleosomes were known as "labile nucleosomes", since 1970s academic.oup.com/nar/article/6/…. This term then continued into the NGS era

Chromatin Buffers Torsional Stress During Transcription biorxiv.org/content/10.110… [Jin Qian, Lucyna Lubkowska, Shuming Zhang, Chuang Tan, Yifeng Hong, Robert Fulbright, James Inman, Taryn Kay, Joshua Jeong, Deanna Gotte, James Berger, Mikhail Kashlev, Michelle Wang]

CTCF binding landscape is established by the epigenetic status of the nucleosome, well-positioned relative to CTCF motif orientation biorxiv.org/content/10.110…

Our new CTCF breakthrough ms has been posted today at doi.org/10.1101/2024.0… with the following Graphical Abstract:

DNA flexibility regulates transcription factor binding to nucleosomes dlvr.it/TCkpV0

Hurry up! Last day to submit abstract for "Genomics in Ageing and Disease" (Colchester, 16th September). Free Registration! Talks by @Peter_Fraser1, @_parker_aim, @GabriellaFicz, @EnrightAnton, @R_Rahbari, @ozgendeniz_, @jordanatbell, @sj_marzi & Essex PIs gate.essex.ac.uk

Single-nucleosome imaging reveals principles of transient multiscale chromatin unfolding triggered by histone ADP-ribosylation at DNA lesions dlvr.it/TCZn9R

The registration deadline for our FREE conference in Colchester is prolonged until 1st September. The conference itself is on 16th September. Short talk slots available, hurry up!

Impacts of nucleosome positioning elements and pre-assembled chromatin states on expression and retention of transgenes dlvr.it/TCCv4G

FACT-(H3-H4) complex stimulates Pol activity to coordinate DNA synthesis with nucleosome assembly dlvr.it/TBhRty

1/ 🤔 Do #chromatinlooping-mediated promoter-#enhancer interactions drive gene expression? Or is the local enrichment of transcription factors into hubs/#condensates the key factor? Our AC/DC model of gene regulation at bioRxiv doi.org/10.1101/2024.0… provides a new view on this.

We have an opening for a three-year postdoctoral position for a researcher with expertise in machine learning and genome bioinformatics, to work on cancer diagnostics (liquid biopsies). Please apply here: vacancies.essex.ac.uk/tlive_webrecru…

Determining mesoscale chromatin structure parameters from spatially correlated cleavage data using a coarse-grained oligonucleosome model dlvr.it/TBDHZZ

Registration (free!) and abstract submission now open! Please, spread the word. gate.essex.ac.uk