3D genome organization in tissue regeneration involves long-range chromatin loops

Palmira Llorens-Giralt  ¹ , Carlos Camilleri-Robles  ¹ , Leo Zuber  ^{2   3} , Jenisha Khadka  ⁴ , Maria Marti-Marimon  ^{2   3} , Andrea Crespo-Pera  ¹ , Florenci Serras  ¹ , Maria Cristina Gambetta  ⁴ , Marc A Marti-Renom  ^{2   3   5} , Montserrat Corominas  ¹

Affiliations

• PMID: 42566522
• PMCID: PMC13450218
• DOI: 10.1126/sciadv.aea8281

Abstract

The three-dimensional (3D) organization of the genome plays a fundamental role in gene expression regulation, yet how changes in genome architecture influence transcriptional responses during tissue regeneration remains poorly understood. Here, we used Hi-C to profile 3D chromatin conformation during Drosophila wing imaginal disc regeneration. We found that, although compartments and topologically associating domains (TADs) are largely maintained, regeneration is accompanied by reduced compartmentalization and decreased boundary insulation. We identified three long-range chromatin loops with increased contact frequency during regeneration. Targeted deletion of their anchors revealed that these loops are essential for proper disc regeneration but dispensable for normal wing development. Furthermore, disruption of any of these loops resulted in convergent changes in both gene expression and H3K4me1 3D environment, suggesting their coordinated activity during regeneration. These findings provide functional evidence that 3D genome architecture actively contributes to the regenerative process.

Optimization of Gastruloid Pre-culture Conditions for Reproducible Germ Layer Composition

Marloes Blotenburg  ¹ , Beril Esin  ² , Shruthi Buddharaju  ² , Peter Zeller  ³

Affiliations

• PMID: 41071232
• DOI: 10.1007/7651_2025_667

Abstract

Gastruloids are an in vitro model that mimics key aspects of gastrulation and can be used to study implantation-stage embryonic development. Even though current protocols have contributed significantly to our understanding of developmental biology, further improvements in terms of consistency and reproducibility are still required. In this chapter, we present a detailed pre-culture protocol optimized for the generation of gastruloids from 129S1/SvImJ/ C57BL/6 mouse embryonic stem cells (mESCs). Additionally, we provide information on the steps of the protocol open to optimization and present a workflow for selecting optimal conditions and evaluating the gastruloid formation outcome when using different cell lines. Overall, this workflow facilitates a step-by-step approach toward generating gastruloids from any cell line in a highly reproducible manner by optimizing the mESC pre-culture conditions.

Metabolomic Insights into HCF-1-dependent Regulation of Liver Homeostasis

Srabaita Roy  ¹ , Shruti Kaushal  ² , Ridhima Tandon  ¹ , Jaspreet K Dhanjal  ^{2   3} , Winship Herr  ⁴ , Saran Kumar  ¹ , Shilpi Minocha  ^{1   4}

Affiliations

• PMID: 42495516
• PMCID: PMC13393160 (available on 2027-09-01)
• DOI: 10.1016/j.jceh.2026.103602

Abstract

Background: Host cell factor-1 (HCF-1) is a conserved transcriptional and epigenetic coregulator known to influence hepatocyte proliferation, liver regeneration, and lipid metabolism. While its role in transcriptional control and chromatin dynamics has been explored, the metabolic consequences of HCF-1 loss remain incompletely understood.

Objective: To investigate the metabolic alterations triggered by hepatocyte-specific HCF-1 loss in murine liver and their potential relevance to metabolic-associated fatty liver disease (MAFLD).

Methods: Using Alb-Cre-ERT2 ^tg ; Hcfc1 ^hepKO/Y mice, we performed targeted metabolomic profiling of liver tissues across a seven-day time course post-knockout using the AbsoluteIDQ® p180 platform (Biocrates Life Science AG). Global changes in metabolic signatures were examined in conjunction with histological, biochemical, ultrastructural, and protein-level assessments of hepatic pathology and compared with published human metabolomic datasets.

Results: HCF-1 deficiency caused rapid and progressive metabolic rewiring, characterized by elevated bile acids, phosphatidylcholines, lysophosphatidylcholines, and acylcarnitines, with concurrent depletion of sphingolipids. Key dysregulated pathways included β-oxidation, mitochondrial energy metabolism, unsaturated fatty acid biosynthesis, and peroxisomal lipid processing. Electron microscopy revealed marked mitochondrial structural abnormalities, accompanied by impaired mitochondrial function and a significant reduction in PGC1α protein levels, a key regulator of mitochondrial biogenesis and oxidative metabolism. Temporal and integrative analysis revealed early bile acid and amino acid imbalance, advancing to severe lipid dysregulation, key effects that resemble aspects of the MAFLD-to-metabolic-associated steatohepatitis (MASH) transition. Comparative pathway mapping demonstrated substantial overlap between murine and human metabolic alterations, suggesting convergence on common metabolic pathways and supporting the translational relevance of the findings.

Conclusion: Our results uncover a crucial role for HCF-1 in maintaining hepatic metabolic homeostasis. By integrating metabolomic insights with known epigenetic and transcriptional functions, this study strengthens the view of HCF-1 as a multifaceted regulator whose loss disrupts core hepatic processes associated with MAFLD progression.

Protocol for mapping gene essentiality changes in yeast using inducible gene deletion mutants

Sabine van Schie  ¹ , Jolanda van Leeuwen  ²

Affiliations

• PMID: 42475181
• DOI: 10.1016/j.xpro.2026.104723

Free article

Abstract

Gene essentiality can differ among genetically distinct individuals. In this protocol, we describe a systematic approach for identifying genes that are essential in a laboratory strain of the budding yeast Saccharomyces cerevisiae but vary in essentiality across other yeast isolates. This approach relies on a collection of inducible essential gene deletion mutants in the laboratory background. We describe steps for crossing this collection to a yeast isolate of interest, selecting haploid segregant progeny, inducing essential gene loss, and determining viability. For complete details on the use and execution of this protocol, please refer to Batté et al.¹.