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Chris Clarkson

@chrsclrksn.bsky.social

Bioinformatician working on tandem repeats

9 Posts51 Follower 294 Folgt

medRxivpreprint @medrxivpreprint.bsky.social · 3mo ago

Ancestry-specific and multi-ancestry genome-wide association studies of restless legs syndrome https://www.medrxiv.org/content/10.64898/2026.04.28.26351960v1

Teif lab @teiflab.bsky.social · 5mo ago

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/)).

Nacho Molina @molinalab.bsky.social · last yr.

Time for a short thread! We developed HiddenFoot, a biophysics-inspired approach to decode single-molecule footprinting data and infer TF, nucleosome, and RNA Pol II binding profiles on individual DNA molecules. One molecule at a time! www.biorxiv.org/content/10.1... 1/6

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

Daniel S. Goldberg @profgoldberg.bsky.social · last yr.

#vanitas #memes

I'm anxious, overwhelmed and have a
bad headache
Have you tried consuming nothing but coffee and terrifying news updates?

Chris Clarkson @chrsclrksn.bsky.social · last yr.

Really interesting looking position- highly recommend! www.jobs.gla.ac.uk/job/research...

Research Assistant/Associate

Job PurposeTo contribute to/make a leading contribution to the project ‘Somatic instability in Huntington disease’ working with Prof. Darren Monckton. Prof Monckton’s team use human genetic analyse...

jobs.gla.ac.uk

Kevin Mitchell @wiringthebrain.bsky.social · 2y ago

More thoughts on these issues here: If genomics is the answer, what's the question? www.wiringthebrain.com/2018/12/if-g...

If genomics is the answer, what's the question? A commentary on PsychENCODE

There was much excitement in the press and in the psychiatric research community recently as a flurry of papers was p...

wiringthebrain.com

Teif lab @teiflab.bsky.social · 2y ago

Most previous epigenetic age predictors were focused on DNA methylation. Our own model suggested nucleosome positioning as an age predictor a year ago onlinelibrary.wiley.com/doi/full/10....

Aging clock based on nucleosome reorganisation derived from cell‐free DNA

We show that aging is associated with an increase in the distance between nucleosomes, which can be used to predict a person's age and conduct age classification. We developed the first aging clock b...

onlinelibrary.wiley.com

Nature Portfolio @natureportfolio.nature.com · 2y ago

An essay in Nature discusses how it’s an astonishing achievement that all of statistics and much of science depends on probability considering no one’s sure what it is. 🧪

Why probability probably doesn’t exist (but it is useful to act like it does)

All of statistics and much of science depends on probability — an astonishing achievement, considering no one’s really sure what it is.

go.nature.com

Chris Clarkson @chrsclrksn.bsky.social · 2y ago

The lab of (amazing!) Arianna Tucci and I are delighted to share our published work on the repeat expansion locus in THAP11:

movementdisorders.onlinelibrary.wiley.com

Jeremy Allen @jeremy-data.bsky.social · 2y ago

My fav starter packs so far, a thread: stats: go.bsky.app/Ki7PjpS stats: go.bsky.app/7TBN5rX causal inference: go.bsky.app/FdemGAZ package devs: go.bsky.app/N1569Qh data peeps: go.bsky.app/8TdEfdK medical stats: go.bsky.app/ArqEz36 bioinformatics: go.bsky.app/Ha64Gmv r-ladies: go.bsky.app/Vgxwa2F

Post nicht verfügbar.

Kurianlab @kurianlab.bsky.social · 2y ago

www.biorxiv.org/content/10.1...

RNA editing is a molecular clock in unmodified human cells

Despite major advances in spatial RNA sequencing, the ability to extract temporal information in RNA sequencing experiments is still limited. Here, we describe Transcriptome Timestamping (T2), a syste...

biorxiv.org