Germany is one of the most popular destinations for students and scholars worldwide, but those pursuing academic careers face significant hurdles to success.

High-throughput chromosome conformation capture (Hi-C) is a powerful tool to investigate 3D genome architecture. Here, we present a protocol for preparing low-input Hi-C libraries from mitotic cells isolated by fluorescence-activated cell sorting (FACS) to study chromatin conformation in mitotic cells. We describe steps for mitotic arrest, harvest and fixation of cultured cells, staining with an anti-Mitotic Protein Marker (MPM2), and isolation of mitotic cells. We then detail procedures for qua...

There is great interest in modeling human HFpEF in animals to identify underlying mechanisms and ultimately improve sorely needed therapies. Our current models are a step forward but still fall short ...

A gene-editing approach enables modification of bacteria within the mouse gut

Wang et al. establish an in vivo proteomic labeling (IVPL) system combining the Btn-Ph-3F substrate with APEX2-EGFPf/f Cre crosses to map cell-type-specific proteomes in intact organs and trace patient-derived exosomal proteins. IVPL identifies LDHAL6A as a pro-metastatic driver and highlights its potential as a therapeutic target in TNBC.

Nature Reviews Genetics, Published online: 10 November 2025; doi:10.1038/s41576-025-00913-3In this Tools of the Trade article, Shaoqian Ma discusses scFLUENT-seq, a method that enables quantitative, genome-wide analysis of nascent transcription in single cells.

Li et al. show that the chromatin-associated long noncoding RNA Pvt1 is a negative regulator of Myc transcription by increasing local RNA concentration and limiting bursting from the Myc promoter. This mechanism serves to restrain Myc levels and restrict its proliferative and oncogenic activities.

Adenosine triphosphate (ATP)–dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. We investigate effects of two major remod...

Nature Protocols, Published online: 30 September 2025; doi:10.1038/s41596-025-01248-3This protocol for imaging-based highly multiplexed in situ profiling of the spatial transcriptome uses three methods: antibody-based protein comapping with STARmap PLUS, ribosome-bound mRNA mapping with RIBOmap and spatiotemporal transcriptome mapping with TEMPOmap.

Bridge recombinases are naturally occurring RNA-guided DNA recombinases that we previously demonstrated can programmably insert, excise, and invert DNA in vitro and in Escherichia coli. In this study,...

Nature Methods - Targeted deaminase-accessible chromatin sequencing (TDAC-seq) measures chromatin accessibility across long chromatin fibers at targeted loci using double-stranded DNA cytidine...

Here, the authors present a method to rapidly isolate actively translating ribosomes in a time- and cost-effective manner using poly-lysine. The method is compatible with a wide variety of cell and ti...

The human genome contains over 3 million small open reading frames (smORFs, ≤ 150 codons). Ribosome profiling and proteogenomics transformed our understanding of these sequences by showing that t...

Qin et al. show that Lig3 PARylation promotes ecDNA formation, requiring YY1-mediated DNA looping. The Lig3-YY1 complex establishes a PARylation-dependent acidic microenvironment, inducing unstable Z-DNA transition states, which are religated by Lig3, ultimately mediating the biogenesis of ecDNA.

Nature Methods - This Perspective explores advances and future directions in spatiotemporal omics methods for four-dimensional profiling.

Health and societal ramifications of extreme hunger will reverberate long after the war is over

Prime editing and base editing in mouse models and human cells effectively correct mutations in a gene that causes a childhood neurodevelopmental disorder called alternating hemiplegia of childhood. In vivo prime editing in the brain results in significant improvements in neurological symptoms and lifespan, highlighting a potential one-time gene therapy approach for the disorder.

Prime editing and base editing in mouse models and human cells effectively correct mutations in a gene that causes a childhood neurodevelopmental disorder called alternating hemiplegia of childhood. I...

A chromatin accessibility peak caller with an adaptive background model - vierstralab/hotspot3