Methods in Brief

Here is a selection of recently published methods papers curated by Nature Methods editors.

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Every month, Nature Methods editors meet and discuss recently published method-y papers that beyond Nature titles. We then select the papers that interest a broad audience and cover these papers on the journal page as Research Highlights. Yet, we cannot highlight all the exciting method papers in the Research Highlight section. In this post, we present the highlight candidates that we have discussed in the editorial meeting.

3D Genomics

Payne et al. In situ genome sequencing resolves DNA sequence and structure in intact biological samples. Science (2021). doi: 10.1126/science.aay3446
The authors developed in situ genome sequencing (IGS) that bridges sequencing and imaging to map genome structure. They generated an in situ sequencing library by amplifying genome and introducing spatial barcodes in the amplicons in the fixed cells so that they can maintain spatial and sequence information. The researchers applied IGS to cultured human cells and intact mouse embryos to study genome structures at base resolution in single cells.

Takei et al. Integrated spatial genomics reveals global architecture of single nuclei. Nature (2021). doi: 10.1038/s41586-020-03126-2
The authors reported DNA seqFISH+ to target thousands of loci in single cells. They examined nuclei at 1-Mb resolution for the entire genome, and 25-kb resolution for different regions that are at least 1.5 Mb in size.  The combination of DNA seqFISH+ with multiplexed immunofluorescence and RNA seqFISH offers a spatial multimodal approach to map chromosome structures, chromatin states and gene expression. This multimodal approach enables further study in nuclear organization and cell states.

Biophysics

Walker et al. Predicting the stability of homotrimeric and heterotrimeric collagen helices. Nat. Chem. (2021). doi: 10.1038/s41557-020-00626-6
This is a method called SCEPTTr, for predicting melting temperatures of synthetic homotrimeric and heterotrimeric collagen helices. They synthesize triple helices using several single substituted amino acid mutants and measure their stability experimentally . Using this data they design a scoring scheme, using which they can predict the stability of any synthetic triple helix.

Cell Biology

Zhang et al. Optogenetic manipulation of cellular communication using engineered myosin motors. Nat. Cell Biol. (2021). doi: 10.1038/s41556-020-00625-2
A suite of optogenetic tools was developed to study and manipulate artificial multi-headed myosin motors. These tools allowed the selective transport of cargo with light. The researchers used these tools to control the dynamics of cytoskeletal structures and study at the molecular level what occurs during limb amputation in axolotls.

Computational biology

Avsec et al. Base-resolution models of transcription-factor binding reveal soft motif syntax. Nat. Genet. (2021). doi: 10.1038/s41588-021-00782-6
High-resolution functional genomics data uncovers the complexity of the rules governing transcription factor-DNA binding. Using a deep learning model, BPNet, the authors analyze base-resolution ChIP–nexus data to identify motifs and syntax for cooperative TF binding.

CRISPR

Park et al. Recording of elapsed time and temporal information about biological events using Cas9. Cell (2021). doi: 10.1016/j.cell.2021.01.014
This paper reports that Cas9 and gRNA can generate indels at steady rates. The researchers leveraged this property and developed a “DNA clocks” to record the duration of biological events (e.g., chemical exposure) in mammalian cells by using the accumulated indel frequency.

Hanna et al. Massively parallel assessment of human variants with base editor screens. Cell (2021). doi: 10.1016/j.cell.2021.01.012
This paper reports a cytosine base editor (CBE)-based screen system. The authors applied the base editing screen to assay loss-of-function mutations in BRCA1 and BRCA2 as well as point mutations that confer drug sensitivity or resistance. In addition, they generated a library of sgRNAs that are predicted to to generate 52,034 ClinVar variants in 3,584 genes.

Cuella-Martin et al. Functional interrogation of DNA damage response variants with base editing screens. Cell (2021). doi: 10.1016/j.cell.2021.01.041
This paper also reports a base editing screen to characterize nucleotide variants in DNA damage response genes. The researchers developed a CRISPR-based cytosine base editing screen to reveal loss- and gain-of function mutations in DNA damage response genes.

Immunology

Song et al. Development of the Nude Rabbit Model. Stem Cell Reports (2021). doi: 10.1016/j.stemcr.2021.01.010
In this paper Song et al, have developed a nude rabbit model which harbor a FOXN1 mutation. NuRabbits are immunodeficient and lack a functional thymus. Given the longer lifespan and size of rabbits compared to mice, this model may be useful for applications like longer monitoring of tumor growth in cancer studies.

Watkins et al. Persistent antigen exposure via the eryptotic pathway drives terminal T cell dysfunction. Science Immunology (2021). doi: 10.1126/sciimmunol.abe1801
In this study, Watkins et al used phage display to first identify a Fab fragment that can selectively bind erythrocytes. Then they conjugated an antigen of choice to the fragment to develop a tolerogen and injected it in mice. Exposure to the tolerogen induced anergic signatures in both antigen-specific CD4+ and CD8+ T cells and presents as an effective method to control an aberrant immune response.

Sugata et al. Affinity-matured HLA class II dimers for robust staining of antigen-specific CD4+ T cells. Nat. Biotechnol. (2021). doi: 10.1038/s41587-021-00836-4
In this paper, Sugata et al have developed efficient HLA class II dimers for the detection of antigen specific CD4+ T cells.  They do so by screening cDNA libraries of HLAs on CD4+ T cells to identify strong binders which were then dimerized. Affinity matured dimers were able to detect high-avidity T cells with greater specificity than tetramers or dextramers.

Microscopy

Sunbul et al. Super-resolution RNA imaging using a rhodamine-binding aptamer with fast exchange kinetics. Nat. Biotechnol. (2021). doi: 10.1038/s41587-020-00794-3
RhoBAST is an RNA aptamer that binds a fluorogenic rhodamine dye with fast association and dissociation kinetics for imaging tagged RNAs. The binding properties make it a suitable probe for single-molecule localization microscopy that is not limited by photobleaching. RhoBAST was used for super-resolution imaging in live and fixed cells.

Zhao et al. Ultra-bright Raman dots for multiplexed optical imaging. Nat. Commun. (2021). doi: 10.1038/s41467-021-21570-0
Raman-active nanoparticles (Rdots) are ultra-bright and compact probes for stimulated Raman scattering microscopy. Rdots incorporate Carbow dyes and other Raman active molecules into polymeric nanoparticles around 20 nm in size and can be used for even single-molecule detection. The performance of the Rdots was demonstrated in cells and tissues.

Clowsley et al. Repeat DNA-PAINT suppresses background and non-specific signals in optical nanoscopy. Nat Commun. (2021). doi: 10.1038/s41467-020-20686-z
Repeat DNA-PAINT improves DNA-PAINT by reducing background and enhancing resolution. In Repeat DNA-PAINT, multiple binding sites for labeled imager strands are present on each docker oligonucleotide. This reduces the concentration of imager strand needed for high quality imaging while reducing background. Repeat DNA-PAINT can also reduce photoinduced target-site loss and can accelerate sampling, all without affecting spatial resolution.

Neuroscience

Gala et al. Consistent cross-modal identification of cortical neurons with coupled autoencoders. Nat. Comput. Sci. (2021). doi: 10.1038/s43588-021-00030-1
Cellular identities are inferred from multimodal Patch-seq data and translated across modalities with the help of a coupled autoencoder framework. Gala et al. use this approach to describe transcriptomic and electrophysiological characteristics of 33 GABAergic cell types in the mouse visual cortex.

Guttikonda et al. Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer’s disease. Nat. Neurosci. (2021). doi: 10.1038/s41593-020-00796-z
Culturing hiPSC-derived microglia, astrocytes and neurons together allows modelling neuroinflammatory processes and provides mechanistic insight into the increased levels of C3 complement protein in Alzheimer’s disease.

Statistical Genetics

Barbeira et al. Exploiting the GTEx resources to decipher the mechanisms at GWAS loci. Genome Biol. (2021). doi: 10.1186/s13059-020-02252-4
GWAS is powerful in identifying loci that are statistically associated with complex traits and diseases. But it’s challenging to dig out the underlying biological mechanisms. The authors leverage the rich genomic and transcriptomic data in the GTEx resources to link genetically regulated gene expression to phenotypes.

Structural Biology

Matsumoto et al. Extraction of protein dynamics information from cryo-EM maps using deep learning. Nat. Mach. Intell. (2021). doi: 10.1038/s42256-020-00290-y
DEFMap, is a deep learning based method to extract protein dynamics information from CryoEM density maps. The model is trained using MD simulation data for models where CryoEM data is available, and for test cases the model is able to extract conformational changes associated with molecular recognition and allosteric effects directly from the CryoEM density maps. The dynamics data also matched well with the MD simulation data for the test cases.

Feng et al. Enhanced validation of small-molecule ligands and carbohydrates in the protein databank. Structure (2021). doi: 10.1016/j.str.2021.02.004
Enhanced validation of small-molecule ligands and carbohydrates in the protein databank
The PDB is adopting new methods to improve the validation of small molecules and carbohydrates deposited in the PDB. Augmented PDB validation report include:  
-    2D diagrams of small-molecule ligands and carbohydrates, highlighting geometric validation results; 
-    2D topological diagrams of branched oligosaccharides, and 
-    3D electron density maps for ligands and carbohydrates, illustrating the goodness-of-fit between the atomic structure and experimental data.

Lin Tang

Senior Editor, Springer Nature

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