The technological landscape and applications of single-cell multi-omics

A Baysoy, Z Bai, R Satija, R Fan - Nature Reviews Molecular Cell …, 2023 - nature.com
Single-cell multi-omics technologies and methods characterize cell states and activities by
simultaneously integrating various single-modality omics methods that profile the …

Methods and applications for single-cell and spatial multi-omics

K Vandereyken, A Sifrim, B Thienpont… - Nature Reviews Genetics, 2023 - nature.com
The joint analysis of the genome, epigenome, transcriptome, proteome and/or metabolome
from single cells is transforming our understanding of cell biology in health and disease. In …

The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes

S Brahma, S Henikoff - Nature Genetics, 2024 - nature.com
Chromatin accessibility is a hallmark of active transcription and entails ATP-dependent
nucleosome remodeling, which is carried out by complexes such as Brahma-associated …

scChIX-seq infers dynamic relationships between histone modifications in single cells

J Yeung, M Florescu, P Zeller, BA De Barbanson… - Nature …, 2023 - nature.com
Regulation of chromatin states involves the dynamic interplay between different histone
modifications to control gene expression. Recent advances have enabled mapping of …

A dynamical perspective: moving towards mechanism in single-cell transcriptomics

RJ Maizels - … Transactions of the Royal Society B, 2024 - royalsocietypublishing.org
As the field of single-cell transcriptomics matures, research is shifting focus from
phenomenological descriptions of cellular phenotypes to a mechanistic understanding of the …

Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag

S Henikoff, JG Henikoff, K Ahmad, RM Paranal… - Nature …, 2023 - nature.com
For more than a century, formalin-fixed paraffin-embedded (FFPE) sample preparation has
been the preferred method for long-term preservation of biological material. However, the …

High-throughput methods for the analysis of transcription factors and chromatin modifications: Low input, single cell and spatial genomic technologies

M Salma, C Andrieu-Soler, V Deleuze… - Blood Cells, Molecules …, 2023 - Elsevier
Genome-wide analysis of transcription factors and epigenomic features is instrumental to
shed light on DNA-templated regulatory processes such as transcription, cellular …

Epigenetic control of microglial immune responses

R Scholz, D Brösamle, X Yuan, M Beyer… - Immunological …, 2024 - Wiley Online Library
Microglia, the major population of brain‐resident macrophages, are now recognized as a
heterogeneous population comprising several cell subtypes with different (so far mostly …

Combinatorial single-cell profiling of major chromatin types with MAbID

SJA Lochs, RH van der Weide, KL de Luca… - Nature …, 2024 - nature.com
Gene expression programs result from the collective activity of numerous regulatory factors.
Studying their cooperative mode of action is imperative to understand gene regulation, but …

Nano-CUT&Tag for multimodal chromatin profiling at single-cell resolution

JR Bárcenas-Walls, F Ansaloni, B Herve… - Nature …, 2024 - nature.com
The ability to comprehensively analyze the chromatin state with single-cell resolution is
crucial for understanding gene regulatory principles in heterogenous tissues or during …