Tessera

Nucleosome aficionados! Our new review "Nucleosome spacing across cell types, diseases, and ages" is out in NAR: academic.oup.com/nar/article/... A huge effort to pull together what we’ve learned about nucleosome spacing in many systems. Enjoy! @milena-bikova.bsky.social @chrsclrksn.bsky.social

Figure 1.(A) Classical gel electrophoresis experiments showing mono-, di-, tri-, tetra-, and further multinucleosome bands upon chromatin digestion. (B) The nucleosome repeat length (NRL) is defined as the genomic distance between the centres of two neighbouring nucleosomes.

Figure 2.Nucleosome mapping using MNase-seq versus ATAC-seq. (A) In MNase-seq, nucleosomes in both open and tightly packed genomic regions are accessible to digestion. MNase preferentially cleaves DNA between nucleosomes and digests DNA until it encounters a histone octamer, which provides a footprint of nucleosome-protected DNA regions. (B) Bulk MNase-seq results in averaged maps across millions of cells, effectively capturing all possible nucleosome positioning configurations. (C) Single-cell MNase-seq (scMNase-seq) results in a noisier and sparser signal. The resulting footprints still represent nucleosome-protected regions, but not all nucleosomes are represented. (D) In ATAC-seq, open regions can be accessed by the enzyme Tn5 transposase, which can insert primers in regions free from the binding of nucleosomes and transcription factors (TFs). (E) For open chromatin regions, nucleosome maps can be obtained from ATAC-seq similar to MNase-seq. (F) Closed, tightly packed chromatin regions may be less represented in ATAC-seq nucleosome maps.

Figure 5.Molecular mechanisms affecting nucleosome spacing. (A) Linker histones H1 and nonhistone chromatin proteins which compete with H1s and modulate nucleosome spacing through structural and electrostatic mechanisms. (B) Chromatin remodellers actively reposition nucleosomes following context-dependent rules. (C) Cell state-dependent chromatin boundaries formed by CTCF and other structural proteins, as well as associated recruitment of chromatin remodellers which space nucleosomes. (D) Gene activity associated with remodeller action and RNA polymerases transcribing through the nucleosomes, leading to smaller distances between nucleosomes in regulatory regions and gene bodies. (E) DNA sequence repeats of different types.

Figure 6. Examples of NRL changes in biological systems. (A) Cell differentiation leads to NRL changes between different cell types, e.g. mouse dorsal root ganglia neurons (NRL ∼165 bp) versus cortical astrocytes (NRL ∼183 bp) [175]. Schematic cell shapes are adapted from an image created in BioRender (https://BioRender.com/89trj2t). (B) Paired normal versus tumour breast tissues show NRL shortening in cancer (figure adapted from [36] under the CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/)). (C) Nucleosome positioning derived from cfDNA of human volunteers shows NRL increase with age (figure reprinted from [79] under the CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/)).

Teif lab @teiflab.bsky.social · 9mo ago

As usual this time of year, started drafting the list of gene regulation conferences for 2026, enjoy! generegulation.org/conferences-... Know of a relevant event that’s missing? Please reply below

Conferences & Schools – 2026 – Gene Regulation – Teif Lab

generegulation.org

Teif lab @teiflab.bsky.social · last yr.

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 beyond www.jobs.ac.uk/job/DMK060/s.... Application deadline: 21st April 2025

Senior Research Officer at University of Essex

Searching for an academic job? Explore this Senior Research Officer opening on jobs.ac.uk! Click to view more details and browse other academic jobs.

jobs.ac.uk

Rosana Collepardo @rcollepardo.bsky.social · 2y ago

Now is the turn of Paul Meneses from Taekjip Ha lab at Johns Hopkins and Harvard Medical School discussing single molecule measurements on native chromatin #BPS2025 @mgo-bps.bsky.social

Rosana Collepardo @rcollepardo.bsky.social · 2y ago

Rob McGinty from University of North Carolina discusses structural mechanisms of nucleosome demethylation #BPS2025 @mgo-bps.bsky.social

Rosana Collepardo @rcollepardo.bsky.social · 2y ago

Now we have Marcus Woodworth from University if Pennsylvania telling us about chromatin states in native chromatin visualised with expansion microscopy #BPS2025 @mgo-bps.bsky.social

Rosana Collepardo @rcollepardo.bsky.social · 2y ago

First is Michael Poirier from Ohio State, discussing the pathways by which H1 loads into nucleosomes #BPS2025 @mgo-bps.bsky.social

Rosana Collepardo @rcollepardo.bsky.social · 2y ago

Who's going to #BPS2025? Please join us at the MGO Symposium @mgo-bps.bsky.social on Saturday 1:30 pm Room 511ABC Featuring experiments, simulations, and all the scales by @serenasanulli.bsky.social @melikel.bsky.social @maristizabal.bsky.social @janhuemar.bsky.social and more Please repost! 🚀✨

Multiscale Genome Organisation @mgo-bps.bsky.social · 2y ago

The MGO seminar kicks off in 60 minutes. See you there! mit.zoom.us/j/91715298970

Multiscale Genome Organisation@mgo-bps.bsky.social · 2y ago

The Multiscale Genome Organisation is now on Bluesky! Our first post is to announce our next webinar. Join us next week on Tuesday, Jan. 28th at 12:00 E.T. for two exciting talks by Pablo Dans and @gfudenberg.bsky.social See you all there! Link: mit.zoom.us/j/91715298970

BPS Multiscale Genome Organization Webinar
Jan. 28th, 2025 @ 12-1 PM ET
Pablo Dans, PhD University of the Republic
Geoff Fudenberg, PhD University of Southern California

Multiscale Genome Organisation @mgo-bps.bsky.social · 2y ago

Friendly reminder of our webinar next Tuesday! See you all there!

Multiscale Genome Organisation@mgo-bps.bsky.social · 2y ago

The Multiscale Genome Organisation is now on Bluesky! Our first post is to announce our next webinar. Join us next week on Tuesday, Jan. 28th at 12:00 E.T. for two exciting talks by Pablo Dans and @gfudenberg.bsky.social See you all there! Link: mit.zoom.us/j/91715298970

Multiscale Genome Organisation @mgo-bps.bsky.social · 2y ago

The Multiscale Genome Organisation is now on Bluesky! Our first post is to announce our next webinar. Join us next week on Tuesday, Jan. 28th at 12:00 E.T. for two exciting talks by Pablo Dans and @gfudenberg.bsky.social See you all there! Link: mit.zoom.us/j/91715298970