Specificity in clustering of gene-specific transcription factors is encoded in the genome

Shivali Dongre ¹, Nadine L Vastenhouw ¹

. 2025 Jul 8;53(13):gkaf625.

 doi: 10.1093/nar/gkaf625.

• PMID: 40650976
• PMCID: PMC12255298
• DOI: 10.1093/nar/gkaf625

Abstract

Gene-specific transcription factors (TFs) often form clusters in the nucleus. Such clusters can facilitate transcription, but it remains unclear how they form. It has been suggested that clusters are seeded by the sequence-specific binding of TFs to DNA and grow by interactions between intrinsically disordered regions (IDRs) that bring in more TFs. In this model, specificity in TF clustering must be provided by the IDRs. To investigate this model, we studied TF clustering by quantitative imaging of Nanog, Pou5f3, and Sox19b in zebrafish embryos. Using mutant TFs, we show that the formation of a TF cluster requires the DNA-binding domain (DBD) as well as at least one of its IDRs. Importantly, IDRs are not sufficient to join a pre-existing cluster. Rather, both IDR and DBD are needed. Finally, using chimeric TFs, we show that while IDRs are required to join a cluster, they are quite promiscuous, and it is the DBD that provides specificity to the clustering of a TF. Thus, for any TF to join a cluster, motif recognition is required, which explains the specificity in TF cluster formation. Taken together, our work provides an alternative model for how specificity is achieved in the organization of transcriptional machinery in the nucleus.

© The Author(s) 2025. Published by Oxford University Press on behalf of Nucleic Acids Research.

Probing condensate microenvironments with a micropeptide killswitch

Yaotian Zhang ^1 2, Ida Stöppelkamp ^# 1 2, Pablo Fernandez-Pernas ^# 3, Melanie Allram ^# 3, Matthew Charman ^# 4 5 6, Alexandre P Magalhaes ¹, Melanie Piedavent-Salomon ¹, Gregor Sommer ¹, Yu-Chieh Sung ¹, Katrina Meyer ¹, Nicholas Grams ⁵, Edwin Halko ^4 6, Shivali Dongre ⁷, David Meierhofer ¹, Michal Malszycki ¹, Ibrahim A Ilik ¹, Tugce Aktas ¹, Matthew L Kraushar ¹, Nadine Vastenhouw ⁷, Matthew D Weitzman ^4 5 6 8, Florian Grebien ^3 9 10, Henri Niskanen ¹¹, Denes Hnisz ¹²

. 2025 Jul;643(8073):1107-1116.

 doi: 10.1038/s41586-025-09141-5. Epub 2025 Jun 4.

• PMID: 40468084
• PMCID: PMC12286862
• DOI: 10.1038/s41586-025-09141-5

Abstract

Biomolecular condensates are thought to create subcellular microenvironments that have different physicochemical properties compared with their surrounding nucleoplasm or cytoplasm^1-5. However, probing the microenvironments of condensates and their relationship to biological function is a major challenge because tools to selectively manipulate specific condensates in living cells are limited^6-9. Here, we develop a non-natural micropeptide (that is, the killswitch) and a nanobody-based recruitment system as a universal approach to probe endogenous condensates, and demonstrate direct links between condensate microenvironments and function in cells. The killswitch is a hydrophobic, aromatic-rich sequence with the ability to self-associate, and has no homology to human proteins. When recruited to endogenous and disease-specific condensates in human cells, the killswitch immobilized condensate-forming proteins, leading to both predicted and unexpected effects. Targeting the killswitch to the nucleolar protein NPM1 altered nucleolar composition and reduced the mobility of a ribosomal protein in nucleoli. Targeting the killswitch to fusion oncoprotein condensates altered condensate compositions and inhibited the proliferation of condensate-driven leukaemia cells. In adenoviral nuclear condensates, the killswitch inhibited partitioning of capsid proteins into condensates and suppressed viral particle assembly. The results suggest that the microenvironment within cellular condensates has an essential contribution to non-stoichiometric enrichment and mobility of effector proteins. The killswitch is a widely applicable tool to alter the material properties of endogenous condensates and, as a consequence, to probe functions of condensates linked to diverse physiological and pathological processes.

Epigenetic modifications in the murine liver upon depletion of transcriptional coregulator host cell factor 1

Shruti Kaushal ^# 1, Debashruti Bhattacharya ^# 2, Saran Kumar ², Winship Herr ³, Jaspreet Kaur Dhanjal ^4 5, Shilpi Minocha ^6 7

. 2025 Jul 11;26(1):654.

 doi: 10.1186/s12864-025-11786-5.

• PMID: 40646491
• PMCID: PMC12247444
• DOI: 10.1186/s12864-025-11786-5

Abstract

Background: Transcriptional co-regulators fine-tune gene expression by modulating transcription factor activity and chromatin dynamics. HCF-1 (Host Cell Factor 1), a conserved transcriptional co-regulator, has been implicated in cell cycle progression, liver metabolism, and regeneration. Loss of hepatocyte-specific HCF-1 in mice leads to spontaneous NAFLD, which rapidly exacerbates to NASH and compromises liver regeneration. While its role in transcriptional regulation is well-established, the impact of HCF-1 on epigenetic modifications remains relatively unexplored.

Methods: To investigate the consequences of HCF-1 depletion, we performed histological and biochemical analyses of murine livers, assessing liver injury, lipid accumulation, and hepatocyte proliferation upon 2/3 partial hepatectomy (PH). Additionally, we conducted RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) for H3K4me3 and RNA polymerase II (POL2) to examine the epigenetic and transcriptional alterations associated with HCF-1 loss.

Results: Loss of HCF-1 results in severe liver injury, causing hallmark features of NAFLD, including steatosis, inflammation, fibrosis, and mitochondrial dysfunction. Following injury, hepatocytes typically re-enter the cell cycle to replenish lost cells. However, in the absence of HCF-1, hepatocytes fail to proliferate leading to a progressive decline in liver function. Even upon 2/3 PH, HCF-1-deficient hepatocytes remain arrested in the cell cycle, further exacerbating disease severity and preventing tissue regeneration. RNA-seq analyses revealed significant downregulation of genes involved in cell cycle progression, metabolism, and mitochondrial structure and function including those regulating oxidative phosphorylation. ChIP-seq data showed altered H3K4me3 patterns at promoter and enhancer regions of key hepatic genes. These findings indicate that HCF-1 is essential for maintaining transcriptional and epigenetic landscapes necessary for hepatocyte proliferation and regeneration.

Conclusions: Our study establishes HCF-1 as a critical regulator of hepatic homeostasis, with roles extending beyond transcriptional control to epigenetic regulation of liver function and repair. Loss of HCF-1 not only induces liver injury and NAFLD but also prevents hepatocyte proliferation, impairing regeneration and accelerating disease progression.

Tumor-instructed glutamine synthesis in cancer-associated fibroblasts promotes pro-tumor macrophages

Xiaoyun Li ^# 1 2, Sofie Hedlund Møller ^# 1 2, Jaeoh Park ^1 2, Yu-Ming Chuang ^1 2, Pei-Chun Hsueh ^1 2, Tzu-Hsuan Chang ^1 2, Kung-Chi Kao ^1 2, Hector Gallart-Ayala ³, Yi-Hao Wang ^1 2, Jhan-Jie Peng ^1 2 4 5, Alessio Bevilacqua ^1 2, Yi-Ru Yu ^1 2, Zhiyu Li ^1 2 6, Yann Kieffer ⁷, Domitille Peigney ⁷, Hugo Croizer ⁷, Yingxi Xu ^1 2, Alfred Zippelius ^8 9, Isabel C Lopez-Mejia ¹⁰, Lluis Fajas ¹⁰, Fatima Mechta-Grigoriou ⁷, Julijana Ivanisevic ³, Zhengtao Xiao ¹¹, Ming-Chih Ho ¹², Ying-Chun Shen ^13 14, Ping-Chih Ho ^1 2 15

. 2025 Sep 1;222(9):e20241426.

 doi: 10.1084/jem.20241426. Epub 2025 Jul 16.

• PMID: 40668214
• DOI: 10.1084/jem.20241426

Abstract

In the tumor microenvironment (TME), cancer-associated fibroblasts (CAFs) play a crucial role in promoting tumor progression by creating an immunosuppressive environment through cytokine secretion and antigen presentation. While previous studies have demonstrated that CAFs exhibit distinct metabolic profiles compared with normal fibroblasts, it remains unclear how these metabolic programs influence the immune landscape within tumors and which factors drive metabolic reprogramming in CAFs. Here, we found that glutamine synthesis by CAFs promotes the polarization of pro-tumorigenic tumor-associated macrophages (TAMs) and supports tumor growth by altering TAM composition, highlighting the pivotal role of CAFs in shaping the immunosuppressive TME. Mechanistically, we found that tumor-derived palmitic acid activates a signaling cascade involving TLR4, Syk, and NF-κB in fibroblasts, leading to inflammatory CAF polarization and IL-6-induced glutamine synthesis. These findings uncover a novel metabolic symbiosis whereby tumor cells manipulate TAM polarization through CAF-mediated glutamine metabolism, presenting potential therapeutic targets for cancer immunotherapy.

Canalization of flower production across thermal environments requires Florigen and CLAVATA signaling

Elizabeth S Smith ¹, Amala John ¹, Andrew C Willoughby ¹, Daniel S Jones ¹, Vinicius C Galvão ², Christian Fankhauser ², Zachary L Nimchuk ³

. 2025 Jun 25:S0960-9822(25)00688-8.

 doi: 10.1016/j.cub.2025.06.001. Online ahead of print.

• PMID: 40592331
• PMCID: PMC12225604 (available on 2026-06-25)
• DOI: 10.1016/j.cub.2025.06.001

Abstract

The maintenance of invariant developmental phenotypes across disparate environments is termed canalization, but few examples of canalization mechanisms are described. In plants, robust flower production across environmental gradients contributes to reproductive success and agricultural yields. Flowers are produced by the shoot apical meristem (SAM) in an auxin-dependent manner following the switch from vegetative growth to the reproductive phase. Although the timing of this phase change, called the floral transition, is sensitized to numerous environmental and endogenous signals, flower formation itself is invariant across environmental conditions. Previously, we found that CLAVATA peptide signaling promotes auxin-dependent flower primordia formation in cool environments but that an unknown mechanism promotes continuous flower formation at high temperatures. Here, we show that heat promotes floral primordia patterning and formation in SAMs, not by increased auxin production but through the production of the mobile flowering signal, florigen, in leaves. Florigen, which includes FLOWERING LOCUS T (FT) and its paralog TWIN SISTER OF FT (TSF) in Arabidopsis thaliana, is necessary and sufficient to buffer flower production against the loss of CLAVATA signaling and promotes heat-mediated primordia formation through specific SAM-expressed transcriptional regulators. We find that sustained florigen production is necessary for continuous flower primordia formation at warmer temperatures, contrasting florigen’s switch-like control of floral transition. Lastly, we show that CLAVATA signaling and florigen synergize to canalize flower production across broad temperature ranges. This work sheds light on the mechanisms governing the canalization of plant development and provides potential targets for engineering crop plants with improved thermal tolerance.

Targeting AMPK as a potential treatment for hepatic fibrosis in MASLD

Xavier Palomer ¹, Jue-Rui Wang ¹, Claudia Escalona ¹, Siyuan Wu ¹, Walter Wahli ², Manuel Vázquez-Carrera ³

Affiliations Expand

• PMID: 40300935
• DOI: 10.1016/j.tips.2025.03.008
• . 2025 Jun;46(6):551-566.

Abstract

Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most common chronic liver disease, and often progresses to hepatic fibrosis, cirrhosis, and liver failure. Despite its increasing prevalence, effective pharmacological treatments for MASLD-related fibrosis remain limited. Recent research has highlighted AMP-activated protein kinase (AMPK) as a key regulator of the processes that promote fibrogenesis, and AMPK activation shows potential in mitigating fibrosis. Advances in AMPK activators and deeper insights into their role in fibrotic pathways have recently revitalized interest in targeting AMPK for fibrosis treatment. This review discusses the molecular mechanisms linking AMPK to hepatic fibrosis and evaluates emerging AMPK-directed therapies. Furthermore, it addresses challenges in clinical translation. Importantly, we combine the latest mechanistic discoveries with recent therapeutic developments to provide a comprehensive perspective on AMPK as a target for hepatic fibrosis treatment.