Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023 - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

Energy-driven genome regulation by ATP-dependent chromatin remodellers

S Eustermann, AB Patel, KP Hopfner, Y He… - … Reviews Molecular Cell …, 2024 - nature.com
The packaging of DNA into chromatin in eukaryotes regulates gene transcription, DNA
replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re) arrange …

Chromatin accessibility: methods, mechanisms, and biological insights

AR Mansisidor, VI Risca - Nucleus, 2022 - Taylor & Francis
Access to DNA is a prerequisite to the execution of essential cellular processes that include
transcription, replication, chromosomal segregation, and DNA repair. How the proteins that …

Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex

S Dong, H Li, M Wang, N Rasheed, B Zou, X Gao… - Cell Research, 2023 - nature.com
In Saccharomyces cerevisiae, cryptic transcription at the coding region is prevented by the
activity of Sin3 histone deacetylase (HDAC) complex Rpd3S, which is carried by the …

[HTML][HTML] Systematic epigenome editing captures the context-dependent instructive function of chromatin modifications

C Policarpi, M Munafò, S Tsagkris, V Carlini… - Nature Genetics, 2024 - nature.com
Chromatin modifications are linked with regulating patterns of gene expression, but their
causal role and context-dependent impact on transcription remains unresolved. Here we …

Pioneer activity distinguishes activating from non‐activating SOX2 binding sites

M Maresca, T van den Brand, H Li, H Teunissen… - The EMBO …, 2023 - embopress.org
Genome‐wide transcriptional activity involves the binding of many transcription factors (TFs)
to thousands of sites in the genome. Pioneer TFs are a class of TFs that maintain open …

Cotranscriptional RNA processing and modification in plants

S Marquardt, E Petrillo, PA Manavella - The Plant Cell, 2023 - academic.oup.com
The activities of RNA polymerases shape the epigenetic landscape of genomes with
profound consequences for genome integrity and gene expression. A fundamental event …

New genetic and epigenetic insights into the chemokine system: the latest discoveries aiding progression toward precision medicine

H Xu, S Lin, Z Zhou, D Li, X Zhang, M Yu… - Cellular & Molecular …, 2023 - nature.com
Over the past thirty years, the importance of chemokines and their seven-transmembrane G
protein-coupled receptors (GPCRs) has been increasingly recognized. Chemokine …

Dynamic nucleosome remodeling mediated by YY1 underlies early mouse development

M Sakamoto, S Abe, Y Miki, Y Miyanari… - Genes & …, 2023 - genesdev.cshlp.org
Nucleosome positioning can alter the accessibility of DNA-binding proteins to their cognate
DNA elements, and thus its precise control is essential for cell identity and function …

ZFP462 safeguards neural lineage specification by targeting G9A/GLP-mediated heterochromatin to silence enhancers

R Yelagandula, K Stecher, M Novatchkova… - Nature cell …, 2023 - nature.com
ZNF462 haploinsufficiency is linked to Weiss–Kruszka syndrome, a genetic disorder
characterized by neurodevelopmental defects, including autism. Though conserved in …