Comment

The development of mass spectrometry-based single-cell proteomics technologies opens unique opportunities to understand the functional crosstalk between cells that drive tumor development.

Recent technological advances in mass spectrometry promise to add single-cell proteomics to the biologist’s toolbox. Here we discuss the current status and what is needed for this exciting technology to lead to biological insight — alone or as a complement to other omics technologies.

Increasing evidence suggests that the spatial distribution of biomolecules within cells is a critical component in deciphering single-cell molecular heterogeneity. State-of-the-art single-cell MS imaging is uniquely capable of localizing biomolecules within cells, providing a dimension of information beyond what is currently available through in-depth omics investigations.

We argue that the study of single-cell subcellular organelle omics is needed to understand and regulate cell function. This requires and is being enabled by new technology development.

Mammalian cells have about 30,000 times as many protein molecules as mRNA molecules, which has major implications in the development of proteomics technologies. We discuss strategies that have been helpful for counting billions of protein molecules by liquid chromatography–tandem mass spectrometry and suggest that these strategies can benefit single-molecule methods, especially in mitigating the challenges posed by the wide dynamic range of the proteome.

Human neuroscience is enjoying burgeoning population data resources: large-scale cohorts with thousands of participant profiles of gene expression, brain scanning and sociodemographic measures. The depth of phenotyping puts us in a better position than ever to fully embrace major sources of population diversity as effects of interest to illuminate mechanisms underlying brain health.

Dramatic advances in protein structure prediction have sparked debate as to whether the problem of predicting structure from sequence is solved or not. Here, I argue that AlphaFold2 and its peers are currently limited by the fact that they predict only a single structure, instead of a structural distribution, and that this realization is crucial for the next generation of structure prediction algorithms.

Long-read sequencing has made closed microbial genomes a routine task, and the dramatic increase in quality and quantity now paves the way to a complete microbial tree of life through genome-centric metagenomics.

Advances in long-read sequencing technologies have broadened our understanding of genetic variation in the human population, uncovered new complex structural variants and offered an opportunity to elucidate new variant associations with disease.

Long-read sequencing has become a widely employed technology that enables a comprehensive view of RNA transcripts. Here, we discuss the importance of long-read sequencing in interpreting the variables along RNA molecules, such as polyadenylation sites, transcription start sites, splice sites and other RNA modifications. In addition, we highlight the history of short-read and long-read technologies and their advantages and disadvantages, as well as future directions in the field.

The year 2022 will be remembered as the turning point for accurate long-read sequencing, which now establishes the gold standard for speed and accuracy at competitive costs. We discuss the key bioinformatics techniques needed to power long reads across application areas and close with our vision for long-read sequencing over the coming years.

As long-read sequencing technologies continue to advance, the possibility of obtaining maps of DNA and RNA modifications at single-molecule resolution has become a reality. Here we highlight the opportunities and challenges posed by the use of long-read sequencing technologies to study epigenetic and epitranscriptomic marks and how this will affect the way in which we approach the study of health and disease states.

High-resolution sequencing methods that capture the epigenetic landscape within the T cell receptor (TCR) gene loci are pivotal for a fundamental understanding of the epigenetic regulatory mechanisms of the TCR repertoire. In our opinion, filling the gaps in our understanding of the epigenetic mechanisms regulating the TCR repertoire will benefit the development of strategies that can modulate the TCR repertoire composition by leveraging the dynamic nature of epigenetic modifications.

Nanopore direct RNA sequencing (DRS) reads continuous native RNA strands. Early adopters have used this technology to document nucleotide modifications and 3′ polyadenosine tails on RNA strands without added chemistry steps. Individual strands ranging in length from 70 to 26,000 nucleotides have been sequenced. In our opinion, broader acceptance of nanopore DRS by molecular biologists and cell biologists will be accelerated by higher basecall accuracy and lower RNA input requirements.

Recent studies have revealed multifaceted roles of long noncoding RNAs (lncRNAs) in gene regulation, accompanying an increased understanding of lncRNA processing, localization, interacting macromolecules and structural modules. Here, progress and recently developed technological advances for understanding lncRNA biogenesis, modes of action and cellular phenotypes are highlighted, and challenges and opportunities towards higher-resolution and in vivo studies in this field are discussed.

In recent years, the number of annotated noncoding RNAs (ncRNAs) and RNA-binding proteins (RBPs) has increased dramatically. The wide range of RBPs identified highlights the enormous potential for RNA in virtually all aspects of cell biology, from transcriptional regulation to metabolic control. Yet, there is a growing gap between what is possible and what has been demonstrated to be functionally important. Here we highlight recent methodological developments in the study of RNA–protein interactions, discuss the challenges and opportunities for exploring their functional roles, and provide our perspectives on what is needed to bridge the gap in this rapidly expanding field.

The EQIPD framework for rigor in animal experiments aims to unify current recommendations based on evidence behind their rationale and was prospectively tested for feasibility in multicenter animal experiments.

Light microscopy enables researchers to observe cellular mechanisms with high spatial and temporal resolution. However, the increasing complexity of current imaging technologies, coupled with financial constraints of potential users, hampers the general accessibility and potential reach of cutting-edge microscopy. Open microscopy can address this issue by making well-designed and well-documented hardware and software solutions openly available to a broad audience. In this Comment, we provide a definition of open microscopy and present recent projects in the field. We discuss current and future challenges of open microscopy and their implications for funders, policymakers, researchers and scientists. We believe that open microscopy requires a holistic approach. Sample preparation, designing and building of hardware components, writing software, data acquisition and data interpretation must go hand in hand to enable interdisciplinary and reproducible science to the benefit of society.

The study of human–animal chimeras is fraught with technical and ethical challenges. In this Comment, we discuss the importance and future of human–monkey chimera research within the context of current scientific and regulatory obstacles.

The release of the first telomere-to-telomere (T2T) human genome sequence marks a milestone for human genomics research and holds promise of complete genomes for evolutionary genomic studies. Here we describe the advances that this new human genome assembly represents and explore the potential insights that the complete genome sequence could bring to evolutionary genomics. We also discuss the potential challenges to be faced in applying this new sequencing strategy to a broad spectrum of extant species.