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Niek Wit

@niekwit.bsky.social

Bioinformatician @ University of Cambridge https://github.com/niekwit

4 Posts38 Follower 54 Folgt

Jelle van den Ameele @jellevda.bsky.social · 4mo ago

Really pleased to see this out @natsmb.nature.com: www.nature.com/articles/s41.... MitoPerturb-Seq combines #singlecell #CRISPR screening with whole-cell Multiome, to identify nuclear modifiers of mtDNA dynamics. @mitocamb.bsky.social @mrc-mbu.bsky.social @prudentlab.bsky.social and Stephen Burr

MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy - Nature Structural & Molecular Biology

Burr and Auckland et. al develop MitoPerturb-Seq, which combines single-cell screening with multiomics to link nuclear genes to mitochondrial DNA (mtDNA) dynamics. They unveil core regulators of mtDNA...

nature.com

Niek Wit @niekwit.bsky.social · 5mo ago

www.nature.com/articles/s41...

VHL synthetic lethality screens uncover CBF-β as a negative regulator of STING - Nature Communications

Biallelic inactivation of the VHL tumour suppressor gene is a hallmark of Clear cell renal cell carcinoma (ccRCC). Here the authors perform genome-wide CRISPR/Cas9 screening to identify that loss of C...

nature.com

Meng Wang @drmengwang.bsky.social · 12mo ago

New publication from our lab! It was really fun writing this review @jcb.org with my postdoc Dr. Chris Mellor and graduate student Elisabeth Larson. We explore how folate deficiency trigger DNA damage that disrupt genome stability.

Journal of Cell Biology@jcb.org · 12mo ago

New review: Mellor, Larson, and @drmengwang.bsky.social discuss the molecular mechanisms of mammalian genomic instability arising from folate deficiency and how this impacts genome biology in health and disease. rupress.org/jcb/article/... #CellMetabolism

Niek Wit @niekwit.bsky.social · 9mo ago

link.springer.com/article/10.1...

Mapping SET1B chromatin interactions with DamID using DamMapper, a comprehensive Snakemake workflow - BMC Genomics

DNA adenine methyltransferase identification followed by sequencing (DamID-seq) is a powerful method used to map genome-wide chromatin-protein interactions. However, the bioinformatic analysis of DamI...

link.springer.com

Niek Wit @niekwit.bsky.social · 9mo ago

www.cell.com/cell-stem-ce...

Hypoxia promotes airway differentiation in the human lung epithelium

Dong and colleagues uncover low oxygen-directed differentiation of human lung progenitors to airway rather than alveolar fate and show how the process is controlled by hypoxia-inducible factors. Hypox...

cell.com

Niek Wit @niekwit.bsky.social · 9mo ago

www.nature.com/articles/s41...

Hypoxia induces histone clipping and H3K4me3 loss in neutrophil progenitors resulting in long-term impairment of neutrophil immunity - Nature Immunology

Walmsley and colleagues report that systemic hypoxia induces persistent loss of histone H3K4me3 marks and epigenetic reprogramming in neutrophil progenitors, resulting in long-term impairment of subse...

nature.com

James Nathan @jamesnathanlab.bsky.social · last yr.

Delighted to share our latest work on ABHD11 as a novel deglutarylating enzyme, and its role in T cell metabolism @natchembio.nature.com rdcu.be/ewiYZ. Many congratulations to co-first authors Guine Grice, Eleanor Minogue and @hudsonwilco.bsky.social! Great team effort with Randall Johnson's lab.

Lipoyl deglutarylation by ABHD11 regulates mitochondrial and T cell metabolism

Nature Chemical Biology - Glutarate rewires cell metabolism through conjugation to proteins or fatty acids, but how glutarylation is regulated is unclear. ABHD11 was identified as a...

rdcu.be

James Nathan @jamesnathanlab.bsky.social · 11mo ago

Happy to share latest work from the lab. Led by talented first author @awmartinelli.bsky.social. Mapping the genetic landscape of iron metabolism uncovers the SETD2 methyltransferase as a modulator of iron flux | Science Advances www.science.org/doi/10.1126/... Congratulations to all the team.

Mapping the genetic landscape of iron metabolism uncovers the SETD2 methyltransferase as a modulator of iron flux

Genetic screens using endogenous reporters map key modulators of cellular iron, including the transcriptional regulator SETD2.

science.org

Emma Rawlins @labrawlins.bsky.social · 10mo ago

Delighted that Ziqi Dong's PhD paper is out for all to read! Hypoxia is fundamental to normal development, and fascinating! Thanks to all of our co-authors including @jamesnathanlab.bsky.social @jellevda.bsky.social authors.elsevier.com/sd/article/S...

James Nathan @jamesnathanlab.bsky.social · 10mo ago

Excited to share our first bioinformatics contribution! 🎉 Led by Niek Wit in collaboration with the van den Ameele lab @jellevda.bsky.social , we developed DamMapper damid-seq.readthedocs.io/en/latest/, a workflow for DamID-seq analysis, to map SET1B and HIF-1 chromatin occupancy. rdcu.be/eK2TS

Mapping SET1B chromatin interactions with DamID using DamMapper, a comprehensive Snakemake workflow

rdcu.be