My favorite books, 2024

Nucleosome fibre topology guides transcription factor binding to enhancers - Nature Motif grammar on nucleosome fibres acts as signpost elements, directing TF combinatorial binding to enhancers.

Nucleosome fibre topology guides transcription factor binding to enhancers

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

Guide-search mechanism by signpost elements.

Three-dimensional regulatory hubs support oncogenic programs in glioblastoma www.biorxiv.org/content/10.1101/2024.12....

Spatial transcriptomic clocks reveal cell proximity effects in brain ageing Nature - A spatially resolved single-cell transcriptomics map of the mouse brain at different ages reveals signatures of ageing, rejuvenation and disease, including ageing effects associated with T...

Thrilled to see this paper out!! 🧪

Spatial transcriptomics of brain aging and 'spatial aging clocks' identify cells that have pro-aging or pro-rejuvenating effects on their neighbors!

Huge CONGRATS to Eric Sun and all authors! Fantastic collaboration with @jameszou.bsky.social!

rdcu.be/d33uQ 🧵

The physiological impact of an N-terminal Halo-tag on GIPR function in mice Aims: G protein-coupled receptors (GPCRs) modified with self-labelling enzymatic tags (e.g. Halo, SNAP, CLIP) have enabled the in vitro study of receptor expression and trafficking. We developed a Gip...

Our attempt to tag endogenous GIPR in vivo with a Halo-tag

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

Multiplexed mosaic tumor models reveal natural phenotypic variations in drug response within and between populations Many agents that show promise in preclinical cancer models lack efficacy in patients due to patient heterogeneity that is not captured in traditional assays. To address this problem, we have developed...

Our latest from the indefatigable @thejohnnyyu.bsky.social in collaboration with Weissman and Shokat labs. Meet GENEVA, which enables simultaneous phenotyping and profiling of cancer cell drug responses at scale; both in vitro and in vivo across a variety of models: www.biorxiv.org/content/10.1...

EXTRA-seq: a genome-integrated extended massively parallel reporter assay to quantify enhancer-promoter communication Precise control of gene expression is essential for cellular function, but the mechanisms by which enhancers communicate with promoters to coordinate this process are not fully understood. While seque...

Finally out! We present EXTRA-seq, a new EXTended Reporter Assay to quantify endogenous enhancer-promoter communication at kb scale!
www.biorxiv.org/content/10.1...
A 🧵about what it can do:
#SynBio #DeepLearning #GeneRegulation

Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq Abstract. In single-cell and single-nucleus RNA sequencing (RNA-seq), the coexistence of nascent (unprocessed) and mature (processed) messenger RNA (mRNA)

Reading now: Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq by @delaneyksull.bsky.social @guillaumeolesan.bsky.social @pmelsted.bsky.social @lpachter.bsky.social et al. #RNAseq #scRNAseq #snRNAseq #SingleCell #SingleNucleus

Interchromosomal contacts between regulatory regions trigger stable transgenerational epigenetic inheritance in Drosophila In some cases, non-genetic information can be inherited across generations. Fitz-James et al. investigate the mechanism by which such epigenetic information becomes heritable in fruit flies. They show that physical contact between regions of DNA within the cell is able to trigger the histone modification H3K27me3 to become heritable.

Excited to share my new paper implicating the 3D genome in epigenetic inheritance. We show that chromatin contacts are able to trigger epimutation in Drosophila. I'm very thankful for the support of Giacomo Cavalli, @psarkies.bsky.social and to all others involved!

www.cell.com/molecular-ce...

Going beyond cell clustering and feature aggregation: Is there single cell level information in single-cell ATAC-seq data? Single-cell Assay for Transposase Accessible Chromatin with sequencing (scATAC-seq) has become a widely used method for investigating chromatin accessibility at single-cell resolution. However, the re...

Have you been thinking hard about statistical modelling of scATAC-seq data? (No.)

Luckily for you, @aaronkwc.bsky.social has!

Aaron will help you grok:
What's going on?
What is TF-IDF?
Is there really single-cell level chromatin information?

Check it out 👇
www.biorxiv.org/content/10.1...

🧪🧬💻

Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues The Tabula Sapiens is a reference human cell atlas containing single cell transcriptomic data from more than two dozen organs and tissues. Here we report Tabula Sapiens 2.0 which includes data from ni...

Major milestone: Tabula Sapiens 2.0 maps tissue composition & TF expression in 175 cell types, identifying 745 ubiquitous & 890 cell type-specific TFs (many still uncharacterized -> #Codebook) w/ roles in tissue homeostasis, stress response & metabolism. #SingleCell www.biorxiv.org/content/10.1...

www.biorxiv.org/content/10.1...
Our study published today on #bioRxiv describe the identification of a deaminase that converts 5mC to T, enabling direct sequencing of the human methylome and genome. This achievement was made possible through a collaborative effort across all departments at #NEB.

Update of the FANTOM web resource: enhancement for studying noncoding genomes Abstract. The FANTOM web resource (https://fantom.gsc.riken.jp/) has been a unique resource for studying mammalian genomes, which is built on the research

Update of the FANTOM web resource: enhancement for studying noncoding genomes. #Fantom #NoncodingGenome #NAR 🧬
academic.oup.com/nar/advance-...

Synthetic GPCRs for programmable sensing and control of cell behaviour - Nature Modular synthetic G-protein-coupled receptors with nanobody-based ligand-recognition domains can be designed and used to programme transgene expression, real-time fluorescence or endogenous G-protein ...

Synthetic GPCRs for programmable sensing and control of cell behaviour. by Alice Ting Lab

"Programmable antigen-gated G-protein-coupled engineered receptors (PAGERs)"

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

Exclusive: In $1B+ bet on AI, biopharma heavyweights back new startup to upend drug R&D A star-studded mix of venture capitalists and scientists, backed by more than a billion dollars, is launching an ambitious biotech that aims to reinvent drug R&D using artificial intelligence, the gro...

endpts.com/in-biggest-e...

#Xaira #AI-Drug-Discovery

A strong case for mandating indoor air quality in public buildings science.org/doi/10.1126/...