bims-crepig 2025-06-29 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2025–06–29
thirty-one papers selected by
Connor Rogerson, University of Cambridge

Regulatory roles of three-dimensional structures of chromatin domains.
REM transcription factors and GDE1 shape the DNA methylation landscape through the recruitment of RNA polymerase IV transcription complexes.
Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes.
Multi-omics and biochemical reconstitution reveal CDK7-dependent mechanisms controlling RNA polymerase II function at gene 5'- and 3' ends.
NF-YCs modulate RNA polymerase II-mediated transcription to regulate FLM expression.
Starvation activates ECM-remodeling gene transcription and putative enhancers in fibroblasts despite inducing quiescence.
Super-enhancers orchestrate transcriptional dysregulation and metabolic reprogramming in uveal melanoma.
The lincRNA Pantr1 is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1.
Critical roles of IKAROS and HDAC1 in regulation of heterochromatin and tumor suppression in T-cell acute lymphoblastic leukemia.
Reverse engineering neuron-type-specific and type-orthogonal splicing-regulatory networks using diverse cellular transcriptomes.
Differential Transcriptional Activity of ΔNp63β Is Encoded by an Isoform-Specific C-Terminus.
Manipulating condensation of thermo-sensitive SUF4 protein tunes flowering time in Arabidopsis thaliana.
Coordinated chromatin modifications mediated by AREB and MYB transcription factors sustain drought tolerance in Populus.
Telomeres stall DNA loop extrusion by condensin.
Eomes directs the formation of spatially and functionally diverse extraembryonic hematovascular tissues.
Predicting gene expression using millions of yeast promoters reveals cis-regulatory logic.
BET inhibitors reduce tumor growth in preclinical models of gastrointestinal gene signature-positive castration-resistant prostate cancer.
An intrinsically disordered region of histone demethylase KDM5A activates catalysis through interactions with the nucleosomal acidic patch and DNA.
The transcription factor ZFP64 promotes activity-dependent synapse elimination during postnatal cerebellar development.
Structural basis for higher-order DNA binding by a bacterial transcriptional regulator.
Quantification of intrinsic regulatory factors refines human hematopoietic progenitor definitions and reveals early erythroid lineage priming.
Identification of a minimal Alu domain required for retrotransposition.
PADI4-mediated citrullination of histone H3 stimulates HIV-1 transcription.
mirror determines the far posterior domain in butterfly wings.
Dynamic properties of enhancer and promoter during DNA damage in hepatocellular carcinoma.
Constitutive expression of the transcriptional co-activator IκBζ promotes melanoma growth and immunotherapy resistance.
Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling.
The PURB-HOTAIR complex regulates p53-dependent promoter-specific transcriptional activation.
UniClo: scarless hierarchical DNA assembly without sequence constraint.
A Drosophila single-cell 3D spatiotemporal multi-omics atlas unveils panoramic key regulators of cell-type differentiation.
Atoh1 is required for the formation of lateral line electroreceptors and hair cells, whereas Foxg1 represses an electrosensory fate.

Genome Biol. 2025 Jun 27. 26(1): 184

Regulatory roles of three-dimensional structures of chromatin domains.

Kelly Yichen Li, Qin Cao, Savio Ho-Chit Chow, Chiara Nicoletti, Pier Lorenzo Puri, Huating Wang, Danny Leung, Kevin Y Yip.

BACKGROUND: Transcriptional enhancers usually, but not always, regulate genes within the same topologically associating domain (TAD). We hypothesize that this incomplete insulation is partially due to three-dimensional structures of corresponding chromatin domains in individual cells: whereas enhancers and genes buried inside the core of a domain interact mostly with other regions in the same domain, those on the surface can more easily interact with the outside.
RESULTS: Here we show that a simple measure, the intra-TAD ratio, can quantify the coreness of a region with respect to the single-cell domains to which it belongs. We show that domain surfaces are permissive for high gene expression. Cell type-specific active cis-regulatory elements, active histone marks, and transcription factor binding sites are enriched on domain surfaces, most strongly in chromatin subcompartments typically considered inactive.
CONCLUSIONS: These findings suggest a model of gene regulation that involves positioning active cis-regulatory elements on domain surfaces. We also find that disease-associated non-coding variants are enriched on domain surfaces.

DOI: https://doi.org/10.1186/s13059-025-03659-7
Nat Cell Biol. 2025 Jun 27.

REM transcription factors and GDE1 shape the DNA methylation landscape through the recruitment of RNA polymerase IV transcription complexes.

Zhongshou Wu, Yan Xue, Shuya Wang, Yuan-Hsin Shih, Zhenhui Zhong, Suhua Feng, Jonathan Draper, Allen Lu, Carsten A Hoeke, Jihui Sha, Lu Li, James Wohlschlegel, Keqiang Wu, Steven E Jacobsen.

In plants, the maintenance of DNA methylation is controlled by several self-reinforcing loops involving histone methylation and non-coding RNAs. However, how methylation is initially patterned at specific genomic loci is largely unknown. Here we describe four Arabidopsis REM transcription factors, VDD, VAL, REM12 and REM13, that recognize specific sequence regions and, together with the protein GENETICS DETERMINES EPIGENETICS1 (GDE1), recruit RNA polymerase IV transcription complexes. This targeted recruitment leads to the production of 24-nucleotide small interfering RNAs that guide DNA methylation to specific genomic sites in plant female reproductive tissues. In the absence of GDE1, polymerase IV transcription complexes are directed to loci bound by an alternative transcription factor, REM8, highlighting the role of REM transcription factors and GDE1 proteins as positional cues for epigenetic modulation. These findings establish a direct connection between sequence-specific transcription factors and the spatial regulation of siRNA production and DNA methylation, offering new insights into the genetic control of epigenetic patterning.

DOI: https://doi.org/10.1038/s41556-025-01691-0
Genome Res. 2025 Jun 23. pii: gr.279684.124. [Epub ahead of print]

Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes.

Anna Nordin, Chaitali Chakraborty, Mattias Jonasson, Orgena Dano, Gianluca Zambanini, Pierfrancesco Pagella, Silvia Remeseiro, Claudio Cantu.

Wnt signaling plays a pivotal role during development and homeostasis. Upon pathway activation, CTNNB1 (also known as beta-catenin) drives the expression of target genes from regulatory regions bound by TCF/LEF transcription factors. Gene regulation, however, entails the interplay between sequence information and 3D genome structure, yet the impact of Wnt signaling on genome structure has been poorly explored. Here we investigate how Wnt signaling influences CTCF and cohesin, key regulators of 3D genome organization. We identify a series of novel CTCF binding sites that emerge upon Wnt stimulation: CTCF redistributions under Wnt (RUW). RUW sites are characterized by CTCF, cohesin and TCF/LEF occupancy and are dependent on beta-catenin. Beta-catenin and CTCF colocalize upon pathway activation, and disruption of selected binding sites perturbs target gene regulation. Moreover, Wnt signaling reorganizes the 3D genome as evidenced by genome-wide alterations in CTCF-bound loops. This work reveals a previously unexplored role for CTCF in the regulation of Wnt signaling.

DOI: https://doi.org/10.1101/gr.279684.124
Cell Rep. 2025 Jun 25. pii: S2211-1247(25)00675-8. [Epub ahead of print]44(7): 115904

Multi-omics and biochemical reconstitution reveal CDK7-dependent mechanisms controlling RNA polymerase II function at gene 5'- and 3' ends.

Olivia Luyties, Lynn Sanford, Jessica Rodino, Michael Nagel, Taylor Jones, Jenna K Rimel, Christopher C Ebmeier, Megan Palacio, Grace S Shelby, Kira Cozzolino, Finn Brennan, Axel Hartzog, Mirzam B Saucedo, Lotte P Watts, Sabrina Spencer, Jennifer F Kugel, Robin D Dowell, Dylan J Taatjes.

  CDK7 regulates RNA polymerase II (RNAPII) initiation, elongation, and termination through incompletely understood mechanisms. Because contaminating kinases prevent reliable CDK7 analysis with nuclear extracts, we reconstitute RNAPII transcription with purified factors. We show that CDK7 inhibition slows and/or pauses RNAPII promoter-proximal transcription and suppresses re-initiation, and these effects are Mediator and TFIID dependent. Similarly in human cells, CDK7 inhibition reduces transcriptional output by suppressing RNAPII initiation and/or re-initiation. Moreover, widespread 3' end readthrough transcription occurs in CDK7-inhibited cells; mechanistically, this results from rapid nuclear depletion of RNAPII elongation and termination factors (e.g., DSIF, Integrator, NELF, SPT6, PPP1R10/PNUTS, and SCAF8), including high-confidence CDK7 kinase targets. Collectively, these results define how CDK7 governs RNAPII function at gene 5' ends and 3' ends and reveal that nuclear abundance of elongation and termination factors is kinase dependent. Because 3'-readthrough transcription is commonly induced during stress, our results further suggest that regulated suppression of CDK7 activity enables this transcriptional response.

Keywords:  3’-readthrough transcription; CDK7; CP: Molecular biology; Mediator; PRO-seq; RNA polymerase II; TFIID; in vitro transcription; promoter escape; promoter-proximal pausing; proteomics; re-initiation

DOI:  https://doi.org/10.1016/j.celrep.2025.115904
Plant J. 2025 Jun;122(6): e70293

NF-YCs modulate RNA polymerase II-mediated transcription to regulate FLM expression.

Xiani Yao, Ao Chen, Mingyang Jian, Xiaoming Li, Xu Liu, Xingliang Hou, Chunyu Zhang, Kangjia Li.

  The proper transition to flowering is a critical process for the success of plant reproduction and must be highly orchestrated. Nuclear Factor-Y subunit C (NF-YCs), which are closely related to histone H2A, exert diverse chromatin-mediated regulation over plant development events including flowering. However, the mechanisms by which NF-YCs regulate RNA polymerase II (Pol II) during gene transcription remain elusive. Here, we demonstrate that NF-YCs physically interact with EARLY FLOWERING 7 (ELF7), a core component of RNA Pol II-associated factor 1 complex (PAF1c), both in vitro and in vivo. We show that NF-YCs regulate flowering in an ELF7-dependent manner by repressing the expression of the floral repressor FLOWERING LOCUS M (FLM). Further analyses reveal that NF-YCs antagonize the binding of ELF7 to FLM chromatin, thereby suppressing ELF7-mediated RNA Pol II transcription at the FLM locus. Collectively, our findings uncover a novel chromatin-mediated regulatory mechanism in which NF-YCs, in association with ELF7, control the transcription of FLM to modulate flowering time.

Keywords:  Arabidopsis; ELF7; NF‐YC; RNA polymerase II; flowering time

DOI:  https://doi.org/10.1111/tpj.70293
Cell Rep. 2025 Jun 24. pii: S2211-1247(25)00667-9. [Epub ahead of print]44(7): 115896

Starvation activates ECM-remodeling gene transcription and putative enhancers in fibroblasts despite inducing quiescence.

Stefano Secchia, Vera Beilinson, Xiaoting Chen, Melanie Gucwa, Lee A Denson, Emily R Miraldi, Matthew T Weirauch, Kohta Ikegami.

  Depletion of growth factors and nutrients induces cellular quiescence, which often accompanies transcriptional silencing and chromatin compaction. Paradoxically, such depletion occurs in pathological microenvironments in which fibroblasts are activated to orchestrate tissue remodeling. The relationship between fibroblast activation and growth factor and nutrient depletion remains unclear. Here, we report that serum depletion in cell culture, a model for growth factor and nutrient depletions, extensively activates transcription in fibroblasts despite inducing quiescence. Activated genes were enriched for extracellular matrix (ECM) structural components and proteases. ECM-related transcription accompanied the activation of putative distal enhancers but not promoters. The activated putative enhancers were enriched for non-coding variants associated with inflammatory bowel disease (IBD) risk, suggesting an alteration in the ECM-remodeling gene regulatory network in IBD. This study implicates nutrient and growth factor depletion in activating the ECM-remodeling gene program in fibroblasts, challenging the prevailing view linking such depletion to transcriptional dormancy.

Keywords:  Bru-seq; CP: Genomics; CP: Molecular biology; H3K27ac; enhancer; extracellular matrix remodeling; inflammatory bowel disease; nascent transcription; nutrient; quiescence; starvation; uPA; urokinase-type plasminogen activator

DOI:  https://doi.org/10.1016/j.celrep.2025.115896
Commun Biol. 2025 Jun 23. 8(1): 951

Super-enhancers orchestrate transcriptional dysregulation and metabolic reprogramming in uveal melanoma.

Hui Pan, Weihuan Shao, Huixue Wang, Shengfang Ge, Lingyu Zhang, Xiaofang Xu, Yefei Wang, Ai Zhuang.

Uveal melanoma (UM) is the most common intraocular malignancy in adults and frequently metastasizes. Somatic mutations and chromatin aberrations have been implicated in the pathogenesis of this deadly disease. Despite rapid progress in elucidating the genetic landscape of UM, the epigenetic architecture underlying UM pathogenesis remains incompletely understood. Here, we describe a super-enhancer-mediated epigenetic pipeline through genome-scale histone acetylation and transcriptional profiling. We first characterized the active landscape of super-enhancer profiles in UM via chromatin immunoprecipitation sequencing (ChIP-seq). We identified master transcription factors specifically driven by UM-specific super-enhancers, and our pipeline identified transcription factor AP-2 alpha (TFAP2A), which is highly associated with metabolism and oncogenesis, as the top essential regulator in UM. TFAP2A occupied predicted super-enhancers associated with the oncogene Solute Carrier Family 7 member 8 (SLC7A8) in UM, thereby elucidating a mechanism for regulating oncogene expression. Collectively, our data illustrate the potential for epigenetic targeting of super-enhancer-mediated oncogene dependencies in UM, highlighting an epigenetic vulnerability that can be exploited for precision therapy.

DOI: https://doi.org/10.1038/s42003-025-08338-8
Nucleic Acids Res. 2025 Jun 20. pii: gkaf539. [Epub ahead of print]53(12):

The lincRNA Pantr1 is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1.

Fabian Gather, Tudor Rauleac, Ipek Akol, Ganeshkumar Arumugam, Camila L Fullio, Teresa Müller, Dimitrios Kleidonas, Ruth Geiss-Friedlander, Andre Fischer, Andreas Vlachos, Rolf Backofen, Tanja Vogel.

Derailed gene expression programs within the developing nervous system, encompassing both transcriptional and post-transcriptional processes, can cause diverse neurodevelopmental diseases (NDD). The NDD FOXG1-syndrome lacks full understanding of the mechanistic role of its eponymous gene product. While it is known that FOXG1 acts in part at the chromatin by binding to regulative regions, it is unclear what factors control its presence at specific sites. Long non-coding RNAs (lncRNAs) can mediate site-directed transcription factor binding, but their potential role in FOXG1-syndrome has not been described. Here, we show that FOXG1 localisation is regulated at selected loci through the lncRNA Pantr1. We identified FOXG1 as an upstream transcriptional activator of Pantr1 in human and mice. Further, we discovered that FOXG1 has the ability to associate with RNAs. Both transcriptional regulation of Pantr1 by FOXG1 and binding of both partners build up a regulative network that impacts the localisation of FOXG1 at selected genomic loci. Specifically, Pantr1 facilitates cooperative presence of FOXG1/NEUROD1 at specific sites, and Pantr1 reduction leads to redistribution of FOXG1 to comparably more generic binding sites. The rescue of impaired dendritic outgrowth upon FOXG1 reduction by simultaneous overexpression of Pantr1 underlines the importance of the FOXG1/Pantr1 regulative network.

DOI: https://doi.org/10.1093/nar/gkaf539
Leukemia. 2025 Jun 24.

Critical roles of IKAROS and HDAC1 in regulation of heterochromatin and tumor suppression in T-cell acute lymphoblastic leukemia.

Yali Ding, Bing He, Daniel Bogush, Joseph Schramm, Chingakham Singh, Katarina Dovat, Julia Randazzo, Diwakar Tukaramrao, Jeremy Hengst, Charyguly Annageldiyev, Avinash Kudva, Dhimant Desai, Arati Sharma, Vladimir S Spiegelman, Suming Huang, Chi T Viet, Glenn Dorsam, Giselle Saulnier Scholler, James Broach, Feng Yue, Sinisa Dovat.

The IKZF1 gene encodes IKAROS - a DNA binding protein that acts as a tumor suppressor in T-cell acute lymphoblastic leukemia (T-ALL). IKAROS can act as a transcriptional repressor via recruitment of histone deacetylase 1 (HDAC1) and chromatin remodeling, however the mechanisms through which IKAROS exerts its tumor suppressor function via heterochromatin in T-ALL are largely unknown. We studied human and mouse T-ALL using a loss-of-function and IKZF1 re-expression approach, along with primary human T-ALL, and normal human and mouse thymocytes to establish the role of IKAROS and HDAC1 in global regulation of facultative heterochromatin and transcriptional repression in T-ALL. Results identified novel IKAROS and HDAC1 functions in T-ALL: Both IKAROS and HDAC1 are essential for EZH2 histone methyltransferase activity and formation of facultative heterochromatin; recruitment of HDAC1 by IKAROS is critical for establishment of H3K27me3 histone modification and repression of active enhancers; and IKAROS-HDAC1 complexes promote formation and expansion of H3K27me3 Large Organized Chromatin lysine (K) domains (LOCKs) and Broad Genic Repression Domains (BGRDs) in T-ALL. Our results establish the central role of IKAROS and HDAC1 in activation of EZH2, global regulation of the facultative heterochromatin landscape, and silencing of active enhancers that regulate oncogene expression.

DOI: https://doi.org/10.1038/s41375-025-02651-1
Cell Rep. 2025 Jun 24. pii: S2211-1247(25)00669-2. [Epub ahead of print]44(7): 115898

Reverse engineering neuron-type-specific and type-orthogonal splicing-regulatory networks using diverse cellular transcriptomes.

Daniel F Moakley, Melissa Campbell, Miquel Anglada-Girotto, Huijuan Feng, Andrea Califano, Edmund Au, Chaolin Zhang.

  Cell-type-specific alternative splicing (AS) enables differential gene isoform expression between diverse neuron types with distinct identities and functions. Current studies linking individual RNA-binding proteins (RBPs) to AS in a limited number of neuron types underscore the need for holistic modeling. Here, we use network reverse engineering to derive a map of the neuron-type-specific AS-regulatory landscape of 133 mouse neocortical cell types using pseudobulk transcriptomes derived from single-cell data. We infer the regulons of 350 RBPs and their cell-type-specific activities, among which we validate Elavl2 as a key RBP for medial ganglionic eminence (MGE)-specific splicing in GABAergic interneurons using an in vitro embryonic stem cell (ESC) differentiation system. We also identify a module of exons and candidate regulators specific to long- and short-projection neurons across multiple neuronal classes. This study provides a resource for elucidating splicing-regulatory programs that drive neuronal molecular diversity, including those that do not align with gene-expression-based classifications.

Keywords:  CP: Molecular biology; CP: Neuroscience; Elavl2; RNA splicing regulation; RNA-binding proteins; network inference; neuronal subtypes

DOI:  https://doi.org/10.1016/j.celrep.2025.115898
Mol Cell Biol. 2025 Jun 23. 1-17

Differential Transcriptional Activity of ΔNp63β Is Encoded by an Isoform-Specific C-Terminus.

Abby A McCann, Morgan A Sammons.

  p63 is a clinically relevant transcription factor heavily involved in development and disease. Mutations in the p63 DNA-binding domain cause severe developmental defects and overexpression of p63 plays a role in the progression of epithelial-associated cancers. Unraveling the specific biochemical mechanisms underlying these phenotypes is made challenging by the presence of multiple p63 isoforms and their shared and unique contributions to development and disease. Here, we explore the function of the p63 isoforms ΔNp63ɑ and ΔNp63β to determine the contribution of C-terminal splice variants on known and unique molecular and biochemical activities. Using RNA-seq and ChIP-seq on isoform-specific cell lines, we show that ΔNp63β regulates both canonical ΔNp63ɑ targets and a unique set of genes with varying biological functions. We demonstrate that most genomic binding sites are shared, however the enhancer-associated histone modification H3K27ac is highly enriched at ΔNp63β binding sites relative to ΔNp63ɑ. An array of ΔNp63β C-terminal mutants demonstrates the importance of isoform-specific C-terminal domains in regulating these unique activities. Our results provide novel insight into differential activities of p63 C-terminal isoforms and suggest future directions for dissecting the functional relevance of these and other transcription factor isoforms in development and disease.

Keywords:  Transcription factor; gene regulation; transcription

DOI:  https://doi.org/10.1080/10985549.2025.2514529
Cell Rep. 2025 Jun 25. pii: S2211-1247(25)00683-7. [Epub ahead of print]44(7): 115912

Manipulating condensation of thermo-sensitive SUF4 protein tunes flowering time in Arabidopsis thaliana.

Heather M Meyer, Takashi Hotta, Andrey V Malkovskiy, Yixian Zheng, David W Ehrhardt.

  Intrinsically disordered proteins (IDPs) can undergo environmentally responsive phase separation, raising the question of whether organisms use phase behavior to regulate development. Many plants rely on seasonal temperatures to control flowering time. Yet, how plants coordinate their developmental states with temperature is poorly understood. Here, we investigate the role of temperature-sensitive phase separation using the IDP and flowering-time regulator SUPPRESSOR OF FRIGIDA 4 (SUF4). SUF4 plays a well-defined role in seasonal flowering by activating the floral repressor FLOWERING LOCUS C (FLC). We show that at warm temperatures (20°C), SUF4 forms nuclear condensates that co-localize with key flowering regulators (FRIGIDA and EARLY FLOWERING 7 [ELF7]), whereas at 4°C, these condensates disperse into the nucleoplasm. Moreover, progressive alterations to the amino acid composition of SUF4's disordered region lead to corresponding changes in temperature-dependent condensation, SUF4's ability to bind and transcribe FLC, and flowering time. These findings reveal how temperature-sensitive condensation can drive seasonal development in plants.

Keywords:  CP: Plants; ELF7; FLC; FRI; SUF4; flowering time; intrinsically disordered proteins; nuclear condensates; phase separation; temperature-dependent transcription

DOI:  https://doi.org/10.1016/j.celrep.2025.115912
Plant Physiol. 2025 Jun 25. pii: kiaf271. [Epub ahead of print]

Coordinated chromatin modifications mediated by AREB and MYB transcription factors sustain drought tolerance in Populus.

Jinghui Gao, Xiaoqian Wu, Rui Zhai, Huizi Liu, Jinfeng Zhao, Chenguang Zhou, Shuang Li, Wei Li.

Sustained drought tolerance in plants relies on transcriptional memory through successive stress cycles, yet the chromatin-based mechanisms underlying this memory remain unclear. Previously, we revealed that PtrMYB161 overexpression in Populus trichocarpa results in phenotypes characteristic of drought tolerance. Here, we confirm that such transgenesis instills an epigenetic path to gene transregulation for drought tolerance. PtrMYB161 binds directly to the MYB-core motif in the promoter of PtrNAC120, a drought response/tolerance gene, to recruit the histone acetyltransferase (HAT) dimer GENERAL CONTROL NON-DEREPRESSIBLE5-1-ALTERATION/DEFICIENCY IN ACTIVATION2b-3 (PtrGCN5-1-PtrADA2b-3), forming the ternary protein complex (PtrMYB161-PtrGCN5-1-PtrADA2b-3). This ternary system enables enhanced acetylation of nucleosome histone 3 lysine-9, -14, and -27 (H3K9, H3K14, and H3K27) for enriched RNA Pol II occupancy in the PtrNAC120 promoter to elevate its expression for drought tolerance. Unlike PtrAREB1-2, an important drought-inducible transcription factor that can also mediate PtrNAC120 transactivation for tolerance, PtrMYB161 expression remains unaffected by drought. However, under drought conditions, induced PtrAREB1-2 could form HAT ternary complexes, PtrAREB1-2-PtrGCN5-1-PtrADA2b-3, and bind to PtrAREB1-binding sites (ABREs) in the PtrNAC120 promoter for PtrNAC120's enhanced H3K acetylation, RNA Pol II occupancy, and transactivation for drought tolerance. PtrMYB161-PtrGCN5-1-PtrADA2b-3-mediated PtrNAC120 transactivation was induced following severe, prolonged drought stress (below 40% Relative Soil Water Content) and PtrAREB1-2-induced PtrNAC120 transactivation. Further loss- and gain-of-function transgenesis experiments in whole plants and stem differentiating xylem protoplasts suggest that, under stress, the PtrAREB1-2 regulatory system activates an ancillary regulation mediated by PtrMYB161. Our findings propose coordinated epigenetic regulations mediated by HAT complexes to jointly sustain drought tolerance in Populus.

DOI: https://doi.org/10.1093/plphys/kiaf271
Cell Rep. 2025 Jun 24. pii: S2211-1247(25)00671-0. [Epub ahead of print]44(7): 115900

Telomeres stall DNA loop extrusion by condensin.

Brian T Analikwu, Alice Deshayes, Jaco van der Torre, Thomas M Guérin, Allard J Katan, Claire Béneut, Roman Barth, Jamie Phipps, Vittore Scolari, Xavier Veaute, Didier Busso, Karine Dubrana, Stefano Mattarocci, Cees Dekker, Stéphane Marcand.

  DNA loop extrusion by SMC proteins is a key process underlying chromosomal organization. It is unknown how loop extruders interact with telomeres where DNA is densely covered with proteins. Using complementary in vivo and in vitro single-molecule approaches, we study how loop-extruding condensin interacts with Rap1, the telomeric DNA-binding protein of Saccharomyces cerevisiae. We show that dense linear Rap1 arrays can completely halt DNA loop extrusion, with a blocking efficiency depending on the array length and the DNA gap size between proteins. In anaphase cells, dense Rap1 arrays are found to accumulate condensin and to cause a local chromatin decompaction, as monitored with a microscopy-based approach, with direct implications for the resolution of dicentric chromosomes produced by telomere fusions. Our findings show that linear arrays of DNA-bound proteins can efficiently halt DNA loop extrusion by SMC proteins, which may impact cellular processes from telomere functions to transcription and DNA repair.

Keywords:  CP: Molecular biology; SMC complexes; Saccharomyces cerevisiae; chromatin; condensin; dicentric chromosome; loop extrusion; single-molecule assay; telomere

DOI:  https://doi.org/10.1016/j.celrep.2025.115900
Dev Cell. 2025 Jun 20. pii: S1534-5807(25)00333-8. [Epub ahead of print]

Eomes directs the formation of spatially and functionally diverse extraembryonic hematovascular tissues.

Bart Theeuwes, Luke T G Harland, Alexandra M Bisia, Ita Costello, Mai-Linh N Ton, Tim Lohoff, Stephen J Clark, Ricard Argelaguet, Nicola K Wilson, Wolf Reik, Elizabeth K Bikoff, Elizabeth J Robertson, Berthold Göttgens.

  During mouse gastrulation, extraembryonic mesoderm (ExEM) contributes to the extraembryonic yolk sac (YS) and allantois, both of which are essential for successful gestation. Although the genetic networks coordinating intra-embryonic mesodermal subtype specification are well studied, ExEM diversification remains poorly understood. Here, we identify that embryoid body (EB) in vitro differentiation generates distinct lineages of mesodermal cells, matching YS and allantois development. Combining in vitro and in vivo mouse models, we discover that Eomesodermin (Eomes) controls the formation of YS-fated ExEM but is dispensable for allantois formation. Furthermore, simultaneous disruption of Eomes and T impedes the specification of any YS or allantois mesoderm, indicating compensatory roles for T during allantois formation upon Eomes depletion. Our study highlights previously unrecognized functional and mechanistic diversity in ExEM diversification and endothelial development and introduces a tractable EB model to dissect the signaling pathways and transcriptional networks driving the formation of key extraembryonic tissues.

Keywords:  Eomes; allantois; embryogenesis; embryonic stem cell models; endothelial development; extraembryonic mesoderm; scRNA + ATAC-seq; scRNA-seq; single-cell analysis; yolk sac

DOI:  https://doi.org/10.1016/j.devcel.2025.06.001
Bioinform Adv. 2025 ;5(1): vbaf130

Predicting gene expression using millions of yeast promoters reveals cis-regulatory logic.

Tirtharaj Dash, Susanne Bornelöv.

Motivation: Gene regulation involves complex interactions between transcription factors. While early attempts to predict gene expression were trained using naturally occurring promoters, gigantic parallel reporter assays have vastly expanded potential training data. Despite this, it is still unclear how to best use deep learning to study gene regulation. Here, we investigate the association between promoters and expression using Camformer, a residual convolutional neural network that ranked fourth in the Random Promoter DREAM Challenge 2022. We present the original model trained on 6.7 million sequences and investigate 270 alternative models to find determinants of model performance. Finally, we use explainable AI to uncover regulatory signals.
Results: Camformer accurately decodes the association between promoters and gene expression ( r2=0.914 ± 0.003 , ρ=0.962 ± 0.002 ) and provides a substantial improvement over previous state of the art. Using Grad-CAM and in silico mutagenesis, we demonstrate that our model learns both individual motifs and their hierarchy. For example, while an IME1 motif on its own increases gene expression, a co-occurring UME6 motif instead strongly reduces gene expression. Thus, deep learning models such as Camformer can provide detailed insights into cis-regulatory logic.
Availability and implementation: Data and code are available at: https://github.com/Bornelov-lab/Camformer.

DOI: https://doi.org/10.1093/bioadv/vbaf130
J Clin Invest. 2025 Jun 24. pii: e180378. [Epub ahead of print]

BET inhibitors reduce tumor growth in preclinical models of gastrointestinal gene signature-positive castration-resistant prostate cancer.

Shipra Shukla, Dan Li, Woo Hyun Cho, Dana M Schoeps, Holly M Nguyen, Jennifer L Conner, Marjorie L Roskes, Anisha Tehim, Gabriella Bayshtok, Mohini R Pachai, Juan Yan, Nicholas A Teri, Eric Campeau, Sarah Attwell, Patrick Trojer, Irina Ostrovnaya, Anuradha Gopalan, Ekta Khurana, Eva Corey, Ping Chi, Yu Chen.

  A subgroup (~20-30%) of castration-resistant prostate cancer (CRPC) aberrantly expresses a gastrointestinal (GI) transcriptome governed by two GI-lineage-restricted transcription factors, HNF1A and HNF4G. In this study, we found that expression of GI transcriptome in CRPC correlates with adverse clinical outcomes to androgen receptor signaling inhibitor treatment and shorter overall survival. Bromo- and extra-terminal domain inhibitors (BETi) downregulated HNF1A, HNF4G, and the GI transcriptome in multiple CRPC models, including cell lines, patient-derived organoids, and patient-derived xenografts, while AR and the androgen-dependent transcriptome were largely spared. Accordingly, BETi selectively inhibited growth of GI transcriptome-positive preclinical models of prostate cancer. Mechanistically, BETi inhibited BRD4 binding at enhancers globally, including both AR and HNF4G bound enhancers while gene expression was selectively perturbed. Restoration of HNF4G expression in the presence of BETi rescued target gene expression without rescuing BRD4 binding. This suggests that inhibition of master transcription factors expression underlies the selective transcriptional effects of BETi.

Keywords:  Cell biology; Drug therapy; Epigenetics; Genetics; Oncology

DOI:  https://doi.org/10.1172/JCI180378
J Mol Biol. 2025 Jun 20. pii: S0022-2836(25)00367-5. [Epub ahead of print] 169301

An intrinsically disordered region of histone demethylase KDM5A activates catalysis through interactions with the nucleosomal acidic patch and DNA.

Ali M Palla, Chien-Chu Lin, Michael J Trnka, Emme M Leao, Nektaria Petronikolou, Alma L Burlingame, Robert K McGinty, Danica Galonić Fujimori.

  Lysine demethylase 5A (KDM5A) plays a key role in the regulation of chromatin accessibility by catalyzing the removal of trimethyl marks on histone H3K4 (H3K4me3). KDM5A is also an oncogenic driver, with overexpression of KDM5A observed in various cancers, including breast, lung, and ovarian cancer. Past studies have characterized the functions of KDM5A domains, including KDM5A interactions with the histone H3 tail, but have yet to identify the broader mechanisms that drive KDM5A binding to the nucleosome. Through investigation of binding and catalysis on nucleosome substrates, we uncovered multivalent interactions of KDM5A with the H2A/H2B acidic patch and DNA that play crucial roles in the regulation of catalytic activity. We also identified an intrinsically disordered region (IDR) containing bifunctional arginine-rich motifs capable of binding to both the histone H2A/H2B acidic patch and nucleosomal DNA that is necessary for catalysis on nucleosome substrates. Our findings both elucidate previously unknown mechanisms that regulate KDM5A catalytic activity and reveal the ability of an IDR to engage in multiple interactions with chromatin.

Keywords:  Jumonji-domain-containing histone demethylases; chromatin modifiers; epigenetics; intrinsically disordered proteins; lysine methylation

DOI:  https://doi.org/10.1016/j.jmb.2025.169301
iScience. 2025 Jun 20. 28(6): 112746

The transcription factor ZFP64 promotes activity-dependent synapse elimination during postnatal cerebellar development.

Jianling Zhang, Takaki Watanabe, Taisuke Miyazaki, Miwako Yamasaki, Kohtarou Konno, Yuto Okuno, Kyoko Matsuyama, Takayuki Noro, Masahiko Watanabe, Naofumi Uesaka, Masanobu Kano.

  Eliminating redundant synapses formed around birth is essential for shaping functionally mature neural circuits during postnatal development. Each Purkinje cell (PC) in the neonatal mouse cerebellum receives synaptic inputs from multiple climbing fibers (CFs). Only one CF is strengthened and extends its innervation over PC dendrites, whereas the other CFs are eventually pruned during postnatal development. These events are believed to require proper gene expression, but the underlying mechanisms are not yet understood. Here, we report that the transcription factor ZFP64 in PCs mediates part of CF synapse elimination events presumably downstream of P/Q-type voltage-dependent Ca2+ channels (P/Q-VDCCs). PC-specific knockdown (KD) of ZFP64 during postnatal development delayed the elimination of redundant CF synapses and the dendritic extension of CF innervation. The KD of semaphorin 3A (Sema3A) in PCs partially restored the effects of ZFP64 or P/Q-VDCC KD. We propose that ZFP64 promotes developmental CF synapse elimination by regulating Sema3A expression.

Keywords:  Developmental biology; Molecular physiology; Neuroscience

DOI:  https://doi.org/10.1016/j.isci.2025.112746
PLoS Genet. 2025 Jun;21(6): e1011749

Structural basis for higher-order DNA binding by a bacterial transcriptional regulator.

Frederik Oskar Graversgaard Henriksen, Lan Bich Van, Ditlev Egeskov Brodersen, RagnhildBager Skjerning.

Transcriptional regulation by binding of transcription factors to palindromic sequences in promoter regions is a fundamental process in bacteria. Some transcription factors have multiple dimeric DNA-binding domains, in principle enabling interaction with higher-order DNA structures; however, mechanistic and structural insights into this phenomenon remain limited. The Pseudomonas putida toxin-antitoxin (TA) system Xre-RES has an unusual 4:2 stoichiometry including two potential DNA-binding sites, compatible with a complex mechanism of transcriptional autoregulation. Here, we show that the Xre-RES complex interacts specifically with a palindromic DNA repeat in the promoter in a 1:1 molar ratio, leading to transcriptional repression. We determine the 2.7 Å crystal structure of the protein-DNA complex, revealing an unexpected asymmetry in the interaction and suggesting the presence of a secondary binding site, which is supported by structural prediction of the binding to the intact promoter region. Additionally, we show that the antitoxin can be partially dislodged from the Xre-RES complex, resulting in Xre monomers and a 2:2 Xre-RES complex, neither of which repress transcription. These findings highlight a dynamic, concentration-dependent model of transcriptional autoregulation, in which the Xre-RES complex transitions between a non-binding (2:2) and a DNA-binding (4:2) form.

DOI: https://doi.org/10.1371/journal.pgen.1011749
Cell Rep. 2025 Jun 25. pii: S2211-1247(25)00684-9. [Epub ahead of print]44(7): 115913

Quantification of intrinsic regulatory factors refines human hematopoietic progenitor definitions and reveals early erythroid lineage priming.

Patricia Favaro, David R Glass, Luciene Borges, Reema Baskar, Avery Lam, Warren Reynolds, Daniel Ho, Trevor Bruce, Dmitry Tebaykin, Thomas Koehnke, Vanessa M Scanlon, Ilya Shestopalov, Sean C Bendall.

  Hematopoietic stem and progenitor cell (HSPC) transplantation is an essential therapy for hematological conditions, but finer definitions of human HSPC subsets with associated function could enable better tuning of grafts and more routine, lower-risk application. To deeply phenotype HSPCs, following a screen of 328 antigens, we quantified 41 surface proteins and functional regulators on millions of CD34+ and CD34- cells, spanning four primary hematopoietic tissues: bone marrow, mobilized peripheral blood, cord blood, and fetal liver. We propose more granular definitions of HSPC subsets and present detailed differentiation trajectories of erythroid and myeloid lineages. These aspects of our revised human hematopoietic model are validated with corresponding epigenetic analysis, in vitro clonal differentiation assays, and an in vivo cell tracing model. Overall, we demonstrate the utility of using molecular regulators as surrogates for cellular identity and functional potential, providing a framework for description, prospective isolation, and cross-tissue comparison of HSPCs in humans.

Keywords:  ATAC-sequencing; CP: Developmental biology; erythrocyte/megakaryocyte lineage; hematopoietic stem and progenitor cell; human hematopoiesis; in vivo lineage tracing; mass cytometry; molecular regulator; single cell; trajectory analysis; transcription factor

DOI:  https://doi.org/10.1016/j.celrep.2025.115913
Nucleic Acids Res. 2025 Jun 20. pii: gkaf526. [Epub ahead of print]53(12):

Identification of a minimal Alu domain required for retrotransposition.

John B Moldovan, John Yin, John V Moran.

Alu elements are primate-specific retrotransposons that comprise ∼11% of human DNA. Alu sequences contain an internal RNA polymerase III promoter, and the resultant Alu RNA transcripts mobilize by a replicative process termed retrotransposition, which requires the long interspersed element-1 open reading frame 2-encoded protein (ORF2p). Here, we used HeLa cell-based retrotransposition assays to define a minimal Alu domain necessary for retrotransposition. We demonstrate that Alu transcripts expressed from a cytomegalovirus (CMV) RNA polymerase II promoter can efficiently undergo retrotransposition. The use of an external CMV promoter to express Alu RNA allowed us to construct separation-of-function mutations to examine the effects of large deletions within the Alu sequence on retrotransposition. Deletion mutagenesis demonstrated that a 46-nucleotide (nt) domain located at the 5' end of the Alu RNA transcript is necessary for retrotransposition. Consistent with current models, the 46-nt 5' Alu domain associates with SRP9/14 in HeLa-HA cell extracts and can promote retrotransposition in HeLa-HA cells. We propose that the 46-nt 5' Alu domain forms a discrete structure that allows for SRP9/14 binding and ribosomal association, thereby allowing the Alu poly(A) tract to compete with the L1 poly(A) tail for ORF2p RNA binding to mediate its retrotransposition.

DOI: https://doi.org/10.1093/nar/gkaf526
Nat Commun. 2025 Jun 25. 16(1): 5393

PADI4-mediated citrullination of histone H3 stimulates HIV-1 transcription.

Luca Love, Bianca B Jütte, Birgitta Lindqvist, Hannah Rohdjess, Oscar Kieri, Piotr Nowak, J Peter Svensson.

HIV-1 infection establishes a reservoir of long-lived cells with integrated proviral DNA that can persist despite antiretroviral therapy (ART). Certain reservoir cells can be reactivated to reinitiate infection. The mechanisms governing proviral latency and transcriptional regulation of the provirus are complex. Here, we identify a role for histone H3 citrullination, a post-translational modification catalyzed by protein-arginine deiminase type-4 (PADI4), in HIV-1 transcription and latency. PADI4 inhibition by the small molecule inhibitor GSK484 reduces HIV-1 transcription after T cell activation in ex vivo cultures of CD4+ T cells from people living with HIV-1 in a cross-sectional study. The effect is more pronounced in individuals with active viremia compared to individuals under effective ART. Cell models of HIV-1 latency show that citrullination of histone H3 occurs at the HIV-1 promoter upon T cell stimulation, which facilitates proviral transcription. HIV-1 integrates into genomic regions marked by H3 citrullination and these proviruses are less prone to latency compared to those in non-citrullinated chromatin. Inhibiting PADI4 leads to compaction of the HIV-1 promoter chromatin and an increase of heterochromatin protein 1α (HP1α)-covered heterochromatin, in a mechanism partly dependent on the HUSH complex. Our data reveal a novel mechanism to explain HIV-1 latency and transcriptional regulation.

DOI: https://doi.org/10.1038/s41467-025-61029-0
Elife. 2025 Jun 25. pii: RP96904. [Epub ahead of print]13

mirror determines the far posterior domain in butterfly wings.

Martik Chatterjee, Xin Yi Yu, Noah K Brady, Connor Amendola, Gabriel C Hatto, Robert D Reed.

  Insect wings, a key innovation that contributed to the explosive diversification of insects, are recognized for their remarkable variation and many splendid adaptations. Classical morphological work subdivides insect wings into several distinct domains along the anteroposterior (AP) axis, each of which can evolve relatively independently to produce the myriad forms we see in nature. Important insights into AP subdivision of insect wings come from work in Drosophila melanogaster; however, they do not fully explain the diversity of AP domains observed across broad-winged insects. Here, we show that the transcription factor mirror acts as a selector gene to differentiate a far posterior domain in the butterfly wing, classically defined as the vannus, and has effects on wing shape, scale morphology, and color pattern. Our results support models of how selector genes may facilitate evolutionarily individuation of distinct AP domains in insect wings outside of Drosophila and suggest that the D. melanogaster wing blade has been reduced to represent only a portion of the archetypal insect wing.

Keywords:  Iroquois genes; broad-winged insect; butterfly; evolutionary biology; wing domain

DOI:  https://doi.org/10.7554/eLife.96904
iScience. 2025 Jun 20. 28(6): 112565

Dynamic properties of enhancer and promoter during DNA damage in hepatocellular carcinoma.

Jinyuan Zhang, Tianyu Ma, Longjun Xian, Zhiyun Guo.

  DNA damage is a critical factor contributing to tumorigenesis, however, the dynamic changes in multi-omics signatures of enhancers and promoters during the DNA damage response (DDR) remain poorly understood. In this study, we discovered that the expression levels, chromatin accessibility, and element activity of distal/proximal enhancers and promoters exhibited obvious dynamic similarity and duality of characteristics at different stages of DNA damage in hepatocellular carcinoma (HCC). Furthermore, we found that the pre-damage accessibility and activity status of enhancers and promoters played an important role in determining their regulatory features following DNA damage in HCC. Finally, we identified transcription factors (TFs) with significantly altered activity in response to DNA damage, with notable differences between p53 binding activity in enhancers and promoters during the DDR. Overall, these findings reveal the complex dynamic changes within cis-regulatory elements in response to DNA damage.

Keywords:  Cancer; Genomics; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2025.112565
Nat Commun. 2025 Jun 25. 16(1): 5387

Constitutive expression of the transcriptional co-activator IκBζ promotes melanoma growth and immunotherapy resistance.

Antonia Kolb, Ana-Marija Kulis-Mandic, Matthias Klein, Anna Stastny, Maximilian Haist, Vanessa Votteler, Beate Weidenthaler-Barth, Tobias Sinnberg, Antje Sucker, Gabriele Allies, Lea Jessica Albrecht, Alpaslan Tasdogan, Andrea Tuettenberg, Matthias M Gaida, Carsten Deppermann, Henner Stege, Dirk Schadendorf, Stephan Grabbe, Klaus Schulze-Osthoff, Daniela Kramer.

IκBζ, a rather unknown co-regulator of NF-κB, can either activate or repress a subset of NF-κB target genes. While its role as an inducibly expressed, transcriptional regulator of cytokines and chemokines in immune cells is established, IκBζ's function in solid cancer remains unclear. Here we show that IκBζ protein is constitutively expressed in a subfraction of melanoma cell lines, and around 30% of all melanoma cases, independently of its mRNA levels or known mutations. Deleting IκBζ in melanoma abrogates the activity and chromatin association of STAT3 and NF-κB, thereby reducing the expression of the pro-proliferative cytokines IL-1β and IL-6, thus impairing melanoma cell growth. Additionally, IκBζ suppresses Cxcl9, Cxcl10, and Ccl5 expression via HDAC3 and EZH2, which impairs the recruitment of NK and CD8+ T cells into the tumor, causing resistance to α-PD-1 immunotherapy in mice. Thus, tumor-derived IκBζ may serve as a therapeutic target and prognostic marker for melanoma with high tumor cell proliferation, cytotoxic T- and NK-cell exclusion, and unfavorable immunotherapy responses.

DOI: https://doi.org/10.1038/s41467-025-60929-5
Proc Mach Learn Res. 2024 Jul;235 43632-43648

Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling.

Yair Schiff, Chia-Hsiang Kao, Aaron Gokaslan, Tri Dao, Albert Gu, Volodymyr Kuleshov.

Large-scale sequence modeling has sparked rapid advances that now extend into biology and genomics. However, modeling genomic sequences introduces challenges such as the need to model long-range token interactions, the effects of upstream and downstream regions of the genome, and the reverse complementarity (RC) of DNA Here, we propose an architecture motivated by these challenges that builds off the long-range Mamba block, and extends it to a BiMamba component that supports bi-directionality, and to a MambaDNA block that additionally supports RC equivariance. We use MambaDNA as the basis of Caduceus, the first family of RC equivariant bi-directional long-range DNA language models, and we introduce pre-training and fine-tuning strategies that yield Caduceus DNA foundation models. Caduceus outperforms previous long-range models on downstream benchmarks; on a challenging long-range variant effect prediction task, Caduceus exceeds the performance of 10x larger models that do not leverage bi-directionality or equivariance. Code to reproduce our experiments is available here.
Nat Struct Mol Biol. 2025 Jun 25.

The PURB-HOTAIR complex regulates p53-dependent promoter-specific transcriptional activation.

Zhangchuan Xia, Ning Kon, Zhenyi Su, Jingjie Yi, Xu Hua, Hui Zhou, Zhiguo Zhang, Wei Gu.

p53 executes its diverse functions through different transcriptional targets but the precise mechanism of promoter-specific regulation by p53 remains largely unknown. Through biochemical purification, we identify purine-rich element binding protein B (PURB), a dual DNA/RNA-binding protein, which acts as a transcriptional corepressor for p53 in a manner dependent on p53 acetylation status. PURB is overexpressed in human cancers, and its knockdown induces p53-dependent activation of p21 but has no effect on other major promoters such as PUMA and MDM2. In contrast to other p53 corepressors, PURB can recognize a unique DNA element at the p21 promoter, with the loss of this element not affecting p53-mediated transactivation but abrogating the ability of p53 to recruit PURB to the p21 promoter for repression. Mechanistically, PURB requires its sequence-specific binding with long noncoding RNA (lncRNA) HOX transcript antisense RNA (HOTAIR) to exert its repressive role. In turn, HOTAIR interacts directly with EZH2 and, bridged by the PURB-HOTAIR complex, p53 can recruit the EZH2 histone methyltransferase to target promoters for transcriptional repression. Further analysis of p53 targets reveals several promoters that may serve as targets for PURB binding, suggesting that this mechanism of PURB-dependent promoter-specific regulation may not be limited to p21. These data establish a mode of lncRNA-mediated regulation of p53 transcription in a sequence-specific manner and reveal a previously unanticipated mechanism for acetylation-mediated promoter-specific regulation through a cis-regulatory element recognized by the PURB-HOTAIR complex.

DOI: https://doi.org/10.1038/s41594-025-01597-3
Nucleic Acids Res. 2025 Jun 20. pii: gkaf548. [Epub ahead of print]53(12):

UniClo: scarless hierarchical DNA assembly without sequence constraint.

Carol N Flores-Fernández, Da Lin, Katherine Robins, Chris A O'Callaghan.

Type IIS restriction enzyme-mediated DNA assembly is efficient but has sequence constraints and can result in unwanted sequence scars. To overcome these drawbacks, we developed UniClo, a type IIS restriction enzyme-mediated method for universal and flexible DNA assembly. This is achieved through a combination of vector engineering, DNA methylation using recombinant methylases, and steric blockade using CRISPR-dCas9 technology to regulate this methylation. Type IIS restriction enzyme sites within fragments to be assembled are methylated using recombinant methylases, while the fragment-flanking outer sites are protected from methylation by a recombinant dCas9-sgRNA complex. During the subsequent assembly reaction, only the protected flanking sites are cut as only they are unmethylated. Fragments are correctly assembled, despite containing internal sites for the single type IIS restriction enzyme used for the one-pot assembly. The assembled plasmid can be used as a donor plasmid in a subsequent assembly round with the same type IIS restriction enzyme and the assembly vector engineering ensures removal of potential scars by a trimming process. This simplifies assembly design and only three vectors are required for any multi-round assembly. These vectors all use the same pair of overhangs. UniClo provides a simple scarless approach for hierarchical assembly of any sequence and has wide potential application.

DOI: https://doi.org/10.1093/nar/gkaf548
Cell. 2025 Jun 24. pii: S0092-8674(25)00629-4. [Epub ahead of print]

A Drosophila single-cell 3D spatiotemporal multi-omics atlas unveils panoramic key regulators of cell-type differentiation.

Mingyue Wang, Qinan Hu, Zhencheng Tu, Lingshi Kong, Tengxiang Yu, Zihan Jia, Yuetian Wang, Jiajun Yao, Rong Xiang, Zhan Chen, Yan Zhao, Yanfei Zhou, Qing Ye, Kang Ouyang, Xianzhe Wang, Yinqi Bai, Zhenyu Yang, Hanxiang Wang, Yanru Wang, Hanxiang Jiang, Tao Yang, Jing Chen, Yunting Huang, Ni Yin, Wenyuan Mo, Wenfu Liang, Chang Liu, Xiumei Lin, Chuanyu Liu, Ying Gu, Wei Chen, Longqi Liu, Xun Xu, Yuhui Hu.

  The development of a multicellular organism is a highly intricate process tightly regulated by numerous genes and pathways in both spatial and temporal manners. Here, we present Flysta3D-v2, a comprehensive multi-omics atlas of the model organism Drosophila spanning its developmental lifespan from embryo to pupa. Our datasets encompass 3D single-cell spatial transcriptomic, single-cell transcriptomic, and single-cell chromatin accessibility information. Through the integration of multimodal data, we generated developmentally continuous in silico 3D models of the entire organism. We further constructed tissue development trajectories that uncover the detailed profiles of cell-type differentiation. With a focus on the midgut, we identified transcription factors involved in midgut cell-type regulation and validated exex as a key regulator of copper cell development. This extensive atlas provides a rich resource and serves as a systematic platform for studying Drosophila development with integrated single-cell data at ultra-high spatiotemporal resolution.

Keywords:  3D developmental model; Drosophila development; Drosophila exex; Flysta3D; single-cell multi-omics; spatial transcriptomics

DOI:  https://doi.org/10.1016/j.cell.2025.05.047
Elife. 2025 Jun 25. pii: e96285. [Epub ahead of print]14

Atoh1 is required for the formation of lateral line electroreceptors and hair cells, whereas Foxg1 represses an electrosensory fate.

Martin Minařík, Alexander S Campbell, Roman Franěk, Michaela Vazačová, Miloš Havelka, David Gela, Martin Pšenička, Clare V H Baker.

  In electroreceptive jawed fishes and amphibians, individual lateral line placodes form lines of neuromasts on the head containing mechanosensory hair cells, flanked by fields of ampullary organs containing electroreceptors - modified hair cells that respond to weak electric fields. Extensively shared gene expression between neuromasts and ampullary organs suggests that conserved molecular mechanisms are involved in their development, but a few transcription factor genes are restricted either to the developing electrosensory or mechanosensory lateral line. Here, we used CRISPR/Cas9-mediated mutagenesis in G0-injected sterlet embryos (Acipenser ruthenus, a sturgeon) to test the function of three such genes. We found that the 'hair cell' transcription factor gene Atoh1 is required for both hair cell and electroreceptor differentiation in sterlet, and for Pou4f3 and Gfi1 expression in both neuromasts and ampullary organs. These data support the conservation of developmental mechanisms between hair cells and electroreceptors. Targeting ampullary organ-restricted Neurod4 did not yield any phenotype, potentially owing to redundancy with other Neurod genes that we found to be expressed in sterlet ampullary organs. After targeting mechanosensory-restricted Foxg1, ampullary organs formed within neuromast lines, suggesting that Foxg1 normally represses their development, whether directly or indirectly. We speculate that electrosensory organs may be the 'default' developmental fate of lateral line primordia in electroreceptive vertebrates.

Keywords:  developmental biology

DOI:  https://doi.org/10.7554/eLife.96285