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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.
Applying SHAPE-seq to analyze cotranscriptional folding of the B. cereus crcB fluoride riboswitch at nucleotide resolution shows that the folding pathway undergoes a ligand-dependent bifurcation that influences terminator formation via coordinated structural transitions.
READ is a new crystallographic approach to visualize conformational ensembles of heterogeneous and dynamic molecules. READ is applied here to structurally characterize the various folding states of client Im7 bound to chaperone Spy.
EaSeq, a user-friendly and freely available software tool, offers fast and comprehensive ChIP-sequencing data analyses, enabling experimentalists to easily extract information and generate hypotheses from genome-wide datasets.
Using the M2 stem-loop region to tag 16S pre-rRNA allows one-step isolation of assembly intermediates of the small ribosomal subunit from wild-type Escherichia coli. Characterization of these RNPs reveals multiple independent pathways for rRNA maturation.
It has been challenging to label endogenous genomic sequences in living cells, and this has limited attempts to study the dynamics of nuclear architecture in genome function. In a newly developed methodology, transcription activator–like effectors (TALEs) were used to label endogenous repetitive genomic sequences to visualize nuclear positioning and chromatin dynamics in cultured mouse cells and embryos.
SUMOylation is a dynamic protein post-translational modification that regulates many eukaryotic proteins. Now a methodology using commercially available monoclonal antibodies coupled to MS analysis leads to the enrichment and identification of endogenous targets for SUMO1 and for SUMO2/3 in HeLa cells and mouse liver. This protocol can be adapted for other tissues and organs.
Previous studies have shown the potential for convergent transcription as a way to induce gene silencing. This Technical Report now demonstrates that introducing convergent transcription plasmids into either fission yeast or mammalian cells can be used to mediate long-term transcriptional gene silencing of endogenous genes, with major advantages over other gene silencing strategies.