Reviews & Analysis

Pioneer transcription factors bind closed chromatin regions, alter local accessibility and activate target genes. A study reveals that the SOX9 transcription factor drives cell fate switching by activating hair follicle cell enhancers, while simultaneously repressing epidermal enhancers via sequestration of epigenetic factors.

Molecular insight into mechanisms that mediate the selective autophagy of lipid droplets (that is, lipophagy) has been lacking. This study identifies spartin, a protein mutated in a complex hereditary spastic paraplegia called Troyer syndrome, as a receptor that targets lipid droplets to the lysosome for degradation.

The Human BioMolecular Atlas Program (HuBMAP) presents its production phase: the generation of spatial maps of functional tissue units across organs from diverse populations and the creation of tools and infrastructure to advance biomedical research.

Reprogramming of somatic cells is an inherently inefficient process. A new study has now identified histone H3K36 methylation as a crucial reprogramming barrier that operates downstream of TGFβ signalling. Global inhibition of H3K36 methylation induced PRC2-dependent silencing of mesenchymal genes and dramatically increased reprogramming efficiency.

Class 3 phosphatidylinositol-3-kinase (PI3K) has a surprising nuclear function as a coactivator of the circadian clock Bmal1–Clock transcription factor complex for rhythmic purine nucleotide metabolism. This finding opens new avenues for establishing the roles of nuclear subunits of class 3 PI3K in metabolic homeostasis.

The compact state of chromatin induced by the methylation of lysine 9 on histone H3 has long been implicated in a heritable state of transcriptional repression. A study now shows that transient deposition of H3K9me3 helps to stabilize stalled DNA replication forks, while its reversal enables accurate fork restart.

The PHD–pVHL pathway is essential for oxygen-dependent prolyl hydroxylation of HIFA. A recent study identifies RIPK1 as a hydroxylation target in this pathway during hypoxia-induced cell death and presents a 2.8 Å resolution crystal structure of the pVHL–elongin B/C complex bound to hydroxylated RIPK1.

Mitochondria are dynamic organelles, changing their morphology and functional capacity in response to physiological and metabolic cues. A study uncovers a role for the typically nutrient-responsive mTORC2 during fasting in vivo to promote mitochondrial fission via the activation of a signalling pathway that involves NDRG1 and CDC42.

The rabbit is an important model species for developmental and translational research. Here, we used histological imaging and single-cell transcriptomics to characterize gastrulation and early organogenesis in the rabbit. We identified substantial transcriptional differences between the rabbit and mouse, highlighting the power of cross-species comparative genomics to elucidate early human development.

The nuclear envelope participates in the spatial regulation of DNA repair, but the mechanisms behind this are unclear. A study now reports that a nuclear envelope-localized nuclease, NUMEN/ENDOD1, guides the choice of DNA-repair pathway by inhibiting the resection of DNA ends and aberrant recombination, ensuring genome stability.

Disruptions in the autophagy–lysosome pathway in neurons have been implicated in Alzheimer’s disease. A study now reports that autophagy is also critical for disease-associated microglia surrounding amyloid plaques and is protective against microglial senescence and neuropathology in an Alzheimer’s disease mouse model.

Desmosomes and keratin are now found to regulate the distribution and dynamics of the endoplasmic reticulum (ER). This suggests that a range of ER functions may be coordinated by this intercellular adhesive and cytoskeletal network.

A new study shows that the enzymes involved in de novo pyrimidine synthesis and ferroptosis form a complex called the pyrimidinosome, which is controlled by AMPK. Cancer cells low in AMPK expression rely on the pyrimidinosome, suggesting that co-inhibition of AMPK and the pyrimidinosome represents a potential cancer treatment strategy.

Receptor-mediated endocytosis delivers low-density lipoproteins (LDLs) to late endosomes, from where cholesterol is trafficked to mitochondria. Zhou et al. report that LDL-containing endosomes fuse with mitochondria, supplying cholesterol for steroid biosynthesis and enabling mitochondrial degradation of the LDL receptor.

How mucosal-associated invariant T (MAIT) cells acquire memory-like features after infection and the factors that control this process have been unclear. A study now defines two subsets of antigen-adapted MAIT cells emerging after immunization that differ in functions, lung localization and metabolic requirements.

Accumulation of senescent cells and compositional changes in gut microbiota have been independently reported to occur as a function of age. A study now suggests that these two seemingly disparate processes are more intimately linked than previously appreciated via a B cell–IgA–microbiota axis.

This study reveals that thermogenic stimuli activate mitochondrial proteolysis via LONP1 to sustain the succinate levels required for efficient conversion of white adipocytes to beige adipocytes. Our work highlights mitochondrial proteases (mitoproteases) as a link between environmental stimuli, metabolite levels and cell identity switching.

The loss of the polybromo-1 (PBRM1) subunit in a class of SWI/SNF chromatin remodelling complexes in clear cell renal cell carcinoma redirects the deficient complexes to aberrant enhancer regions. The catalytic subunit SMARCA4 of the PBRM1-deficient complexes recruits the nuclear factor-κB transcription factor to drive pro-tumorigenic programs.

In cancer, alternative polyadenylation has been shown to lead to altered 3′ UTRs with different regulatory potentials. A study now suggests a mechanism that leads to 3′ UTR lengthening and translational repression of a subset of metastasis-suppressing genes, revealing a new prospective therapeutic vulnerability.

The selenoprotein glutathione peroxidase 4 (GPX4) is the guardian of ferroptosis, a form of cell death earmarked by unrestrained lipid peroxidation. A new study shows that the metabolic enzyme creatinine kinase B (CKB) phosphorylates GPX4, which may influence the susceptibility of cancer cells to ferroptosis.