Technical Reports

Here the authors present an artificial-intelligence-based automated method for improved protein structure determination from cryo-EM density maps by efficiently integrating map information and structure prediction.

Inspired by the advance in protein structure prediction, CryoAtom builds protein models directly from cryogenic electron microscopy maps, producing more complete models, reducing the resolution requirement and accelerating modeling.

AlphaSync synchronizes AlphaFold Protein Structure Database predictions with UniProt sequences, providing up-to-date protein structures with residue-level annotations for humans, model organisms and pathogens through an accessible web interface and application programming interface.

Li et al. further develop a high-throughput peptide-centric local stability assay that speeds up sample preparation 100-fold and extends protein–ligand identification to membrane proteins, tissues and bacteria.

Here, the authors develop a systematic approach (Dip3D) for unraveling diploid high-order genome interactions for low-heterozygosity genomes using Pore-C. Using Dip3D they obtain an almost complete diploid three-dimensional genome interaction map for a human genome.

Here the authors present deep quantitative glycoprofiling (DQGlyco), a method that enables high-throughput analysis of protein glycosylation dynamics. Using DQGlyco, they link gut microbiome composition to brain glycoproteins and provide insights into glycoform functionality and tissue specificity.

Here the authors develop a method to quantify all combinations of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine at individual CpG dyads, including in single cells, to identify the relationship between the local 5mC density, histone marks and maintenance methylation fidelity.

Here the authors develop a single-cell multiomics sequencing method (scCARE-seq), which allows the simultaneous probing of 3D chromatin architecture and transcription for single cells. Using scCARE-seq they explore the relationship between the 3D genome and transcriptome in cell fate transitions and the cell cycle.

Here the authors present the INSERT-seq methodology to investigate the effect of transcribed sequence on processive transcription. The authors find that GC content and splice site sequences are important determinants of elongation potential.

The authors describe the development of ASPIR-1, a small molecule that specifically inhibits AAA proteins by covalently modifying a cysteine residue introduced by mutagenesis at the AAA ATPase site.

RBS-ID, a method to identify RNA–protein interactions by crosslinking, uses hydrofluoride to cleave RNA to simple mono-nucleoside adducts, which improves coverage and resolution of RNA binding site identification.

thCHART, a hybridization capture approach using biotinylated LNA-oligonucleotides with toehold architecture, improves the specificity of RNA enrichment and enables detection of the chromosomal spreading pattern of Drosophila roX2 lncRNA under different cellular conditions.

CRISPR–Cas9-based method to introduce site-specific S-GlcNAcylation enables dissection of the roles of protein O-GlcNAcylation. S-GlcNAc, a hydrolytically stable structural mimic of O-GlcNAc, is recognized by a range of O-GlcNAc-binding proteins.

Paired-seq allows parallel analysis of transcriptome and accessible chromatin in millions of single cells and can be used to study dynamic and cell-type-specific gene regulatory programs in complex tissues, as demonstrated here for mouse adult cerebral cortex and fetal forebrain.

A new approach to map nucleosome array regularity and spacing reveals modulation of array regularity and nucleosome repeat length depending on functional chromatin states.

A new way to virtually screen HIV-1 TAR RNA using dynamic ensembles better identifies small molecules targeting RNA secondary structures for development.

Yeast surface display platform allows nanobody discovery within two to three weeks. Examples include nanobodies for crystallographic applications, targeting nonpurified antigen or conformationally selective nanobodies to two distinct human GPCRs.

The Protein Contacts Atlas is an interactive resource of non-covalent contacts that can generate multiple representations of non-covalent contacts from PDB structures at different scales, from atoms to subunits and entire complexes.

An allele-specific CRISPR-based DNA imaging technique provides insights into allelic positioning in live mouse cells. Spatiotemporal monitoring reveals that allele positions may fluctuate during cell state transitions.

RNA-DamID, a novel approach to detect lncRNA–genome interactions in vivo with high sensitivity and accuracy, demonstrates that the initial targeting of lncRNAs in the Drosophila dosage-compensation complex is cell-type specific.