Reviews & Analysis

The 3D organization of the genome is crucial for gametogenesis, embryogenesis and cell differentiation through its modulation of transcription, DNA replication and cell division. Recent studies have highlighted the roles of 3D chromatin dynamics, such as the formation of enhancer–promoter interactions in mammalian development.

The functions of many regulatory RNAs depend on how their 3D structure changes in response to cellular conditions. Recent studies have revealed that RNA exists as a dynamic ensemble of conformations, which form with different probabilities in different cellular conditions and thus modulate RNA function.

Integrin extracellular matrix receptors establish contacts between the cell interior and the cell microenvironment. Integrins are subjected to complex biochemical and mechanical regulation, which allows cells to respond to extracellular matrix with different physicochemical properties and fine-tunes cell behaviour.

CRISPR–Cas systems have revolutionized genome editing, and the CRISPR–Cas toolkit has been expanding to include single-base editing enzymes, targeting RNA and fusing inactive Cas proteins to effectors that regulate various nuclear processes. Consequently, CRISPR–Cas systems are being tested for gene and cell therapies.

Phosphoinositide 3-kinases (PI3Ks) are lipid kinases that generate 3-phosphoinositides, which govern cellular signal transduction and membrane trafficking. The PI3K family comprises three classes of enzymes, which include several isoforms and complexes; the myriad of cellular functions and means of regulation of these enzymes are now coming into focus.

Nonsense-mediated mRNA decay (NMD) is a quality and quantity control mechanism for degrading mutated mRNAs to protect the integrity of the transcriptome and proteome and unmutated mRNAs to control their quantity. NMD dysfunction in humans is associated with intellectual disability and cancer.

Cellular metabolism is rewired in proliferating cells to support their increased need for macromolecule biosynthesis. A better understanding of how cells utilize nutrients for biosynthetic pathways and how they overcome the metabolic challenges associated with high proliferation rates can lead to better control of cell proliferation and improved cancer treatments.

Cilia, and primary cilia in particular, are important signalling organelles with established roles in odorant, light and Hedgehog morphogen signal transduction. Cilia are enriched in signalling receptors and effectors and in specific lipids. Addressing how this unique composition is established and maintained is key to understanding cell signalling.

Components of the ribosome-associated protein quality control (RQC) pathway recognize truncated proteins resulting from the stalling of ribosomes on mRNAs during translation and target them for degradation. Defects in RQC can lead to disease, and recent insights have revealed RQC mechanisms in the cytosol and on mitochondria and the endoplasmic reticulum that involve the E3 ligase listerin and/or the formation of carboxy-terminal alanine and threonine tails.

Genome organization can regulate gene expression, but can gene expression regulate genome organization? Recent studies reveal that, although not required for higher-level genome organization, transcription has a role in the formation and stabilization of genomic subdomains and enhancer–promoter interactions.

Following DNA damage, the transcription factor p53 determines whether cells undergo apoptosis or cell cycle arrest and DNA repair. To enable different cellular outcomes, p53 is regulated through its temporal expression dynamics and post-translational modification, and by interactions with chromatin, chromatin regulators and transcription factors.

Metabolites can actively regulate biological processes and may directly modulate phenotype. The current challenge of metabolomics is to provide a platform for the discovery of such bioactive metabolites and — in combination with other omics technologies — to determine their biological functions.

The haematopoietic stem cell (HSC) niche in the bone marrow ensures haematopoiesis by regulating the function of HSCs and progenitor cells. An improved understanding of this regulation in homeostasis, ageing and cancer should aid the development of therapies to rejuvenate aged HSCs or niches and treat malignancies.

By opposing protein ubiquitylation, deubiquitylating enzymes (DUBs) regulate various cellular processes, including protein degradation, the DNA damage response, cell signalling and autophagy. Many DUBs show high specificity for ubiquitin chain architecture and/or the protein substrate that they recognize, and have emerged as exciting therapeutic targets within the field of proteostasis.

Misfolded proteins have a high propensity to form potentially toxic aggregates. Cells employ a complex network of processes, involving chaperones and proteolytic machineries that ensure proper protein folding and remodel or degrade misfolded species and aggregates. This proteostasis network declines with age, which can be linked to human degenerative diseases.

Spatial proteomics improves our understanding of protein function by revealing the subcellular localizations of proteins and their movement between compartments. This Review discusses spatial proteomics approaches, their successful application in cell biology and ways to improve integration of spatial proteomics data.

BCL-2 family proteins are the mediators of apoptotic cell death. The balance between pro-apoptotic and pro-survival BCL-2 family members is differently regulated in various physiological contexts to modulate cellular apoptotic susceptibility. Perturbation of this balance causes excessive or insufficient cell death, leading to diseases such as neurodegeneration and cancer.

Circadian rhythms align organismal functions with phases of rest and activity. Accordingly, circadian oscillations occur in many physiological processes, including various metabolic functions. In turn, metabolic cues are emerging as regulators of the circadian clock. This crosstalk between metabolism and circadian rhythms has important implications for human health.

Recent functional and proteomic studies have revealed the remarkable complexity of mitochondrial protein organization and interactions. This Review discusses how the mitochondrial protein import machinery functions as a key organizer of these protein networks, its involvement in the formation of membrane contact sites, and how defects in protein import can lead to disease.

An increase in white adipose tissue is associated with obesity and reduced metabolic function. Interestingly, however, adipose tissue expansion through the generation of new adipocytes (adipogenesis), rather than through increasing adipocyte size, can prevent this metabolic decline. Thus, a better understanding of adipogenesis can inform new strategies to increase metabolic health in humans.