Epigenetics & Chromatin最新文献

{"title":"Detecting Protein-DNA binding in single molecules using antibody guided methylation.","authors":"Apoorva Thatavarty, Naor Sagy, Michael R Erdos, Isac Lee, Jared T Simpson, Winston Timp, Francis S Collins, Daniel Z Bar","doi":"10.1186/s13072-025-00602-9","DOIUrl":"10.1186/s13072-025-00602-9","url":null,"abstract":"<p><p>Characterization of DNA binding sites for specific proteins is of fundamental importance in molecular biology. It is commonly addressed experimentally by chromatin immunoprecipitation and sequencing (ChIP-seq) of bulk samples (10³-10⁷ cells). We have developed an alternative method that uses a Chromatin Antibody-mediated Methylating Protein (ChAMP) composed of a GpC methyltransferase fused to protein G. By tethering ChAMP to a primary antibody directed against the DNA-binding protein of interest, and selectively switching on its enzymatic activity in situ, we generated distinct and identifiable methylation patterns adjacent to the protein binding sites. This method is compatible with methods of single-cell methylation-detection and single molecule methylation identification. Indeed, as every binding event generates multiple nearby methylations, we were able to confidently detect protein binding in long single molecules.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"18 1","pages":"39"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210839/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bath: a Bayesian approach to analyze epigenetic transitions reveals a dual role of H3K27me3 in chondrogenesis.","authors":"Christoph Neu, Manuela Wuelling, Christoph Waterkamp, Daniel Hoffmann, Andrea Vortkamp","doi":"10.1186/s13072-025-00594-6","DOIUrl":"10.1186/s13072-025-00594-6","url":null,"abstract":"<p><strong>Background: </strong>Histone modifications are key epigenetic regulators of cell differentiation and have been intensively studied in many cell types and tissues. Nevertheless, we still lack a thorough understanding of how combinations of histone marks at the same genomic location, so-called chromatin states, are linked to gene expression, and how these states change in the process of differentiation. To receive insight into the epigenetic changes accompanying the differentiation along the chondrogenic lineage we analyzed two publicly available datasets representing (1) the early differentiation stages from embryonic stem cells into chondrogenic cells and (2) the direct differentiation of mature chondrocyte subtypes.</p><p><strong>Results: </strong>We used ChromHMM to define chromatin states of 6 activating and repressive histone marks for each dataset and tracked the transitions between states that are associated with the progression of differentiation. As differentiation-associated state transitions are likely limited to a reduced set of genes, one challenge of such global analyses is the identification of these rare transitions within the large-scale data. To overcome this problem, we have developed a relativistic approach that quantitatively relates transitions of chromatin states on defined groups of tissue-specific genes to the background. In the early lineage, we found an increased transition rate into activating chromatin states on mesenchymal and chondrogenic genes while mature chondrocytes are mainly enriched in transition between activating states. Interestingly, we also detected a complex extension of the classical bivalent state (H3K4me3/H3K27me3) consisting of several activating promoter marks besides the repressive mark H3K27me3. Within the early lineage, mesenchymal and chondrogenic genes undergo transitions from this state into active promoter states, indicating that the initiation of gene expression utilizes this complex combination of activating and repressive marks. In contrast, at mature differentiation stages the inverse transition, the gain of H3K27me3 on active promoters, seems to be a critical parameter linked to the initiation of gene repression in the course of differentiation.</p><p><strong>Conclusions: </strong>Our results emphasize the importance of a relative analysis of complex epigenetic data to identify chromatin state transitions associated with cell lineage progression. They further underline the importance of serial analysis of such transitions to uncover the diverse regulatory potential of distinct histone modifications like H3K27me3.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"18 1","pages":"38"},"PeriodicalIF":4.2,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12203727/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144508999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional characterization of transcriptional enhancers in an Anopheles genetic locus controlling natural resistance to the malaria parasite, Plasmodium falciparum.","authors":"Natalia Marta Zmarlak-Feher, Kathryn S Taquet, Renée Zakhia, Adrien Pain, Emma Brito-Fravallo, Cameron E Anderson, Kenneth D Vernick, Christian Mitri, Michelle M Riehle","doi":"10.1186/s13072-025-00597-3","DOIUrl":"10.1186/s13072-025-00597-3","url":null,"abstract":"<p><strong>Background: </strong>Anopheles mosquitoes and the malaria parasites they transmit remain a significant global health problem. Most genomic and functional genomic studies of mosquitoes have focused on the protein-coding genome, and comparatively little is known about the importance of noncoding transcriptional enhancers in controlling their gene expression and phenotypic variation. Here we evaluate nine enhancers previously identified in a STARR-seq screen and present in a genetic locus that was identified as a major influence on susceptibility to malaria infection in wild Anopheles coluzzii mosquitoes.</p><p><strong>Result: </strong>We developed an analytical pipeline to filter nine enhancers in the malaria susceptibility locus on chromosome 2L. First, ATAC-seq revealed that only three of the nine enhancers were located in open chromatin and thus likely to be active in somatic cells. Next, we cloned these three enhancers from malaria-susceptible and resistant mosquitoes and measured their enhancer activity by luciferase reporter assays. Only two of the three open-chromatin enhancers displayed significantly different enhancer activity between resistant and susceptible alleles. Finally, alleles of just one of these enhancers, ENH_2L-03, contained nucleotide variants which also segregated in wild mosquitoes, and ENH_2L-03 was prioritized for further study. A noncoding RNA was detected within ENH_2L-03, consistent with an enhancer RNA (eRNA), which we depleted in mosquitoes using RNAi in order to silence the enhancer activity. Transcriptional profiling of ENH_2L-03-silenced mosquitoes revealed 15 differentially expressed genes, which share a transcription factor binding motif suggestive of coordinate regulation. However, silencing ENH_2L-03 did not influence infection levels of either human or rodent malaria parasites.</p><p><strong>Conclusion: </strong>Despite the absence of an ENH_2L-03 effect on infection outcome, multiple enhancers can cooperate to influence a phenotype, and further examination of this enhancer is warranted. Overall, we provide a pipeline for the in vivo functional study of transcriptional enhancers in Anopheles, towards understanding how enhancer function may control important vector phenotypes.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"18 1","pages":"37"},"PeriodicalIF":3.5,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12186386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144477585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cell identity and 5-hydroxymethylcytosine.","authors":"Floris Honig, Adele Murrell","doi":"10.1186/s13072-025-00601-w","DOIUrl":"10.1186/s13072-025-00601-w","url":null,"abstract":"<p><p>Epigenetic factors underlie cellular identity through the regulation of transcriptional networks that establish a cell's phenotype and function. Cell conversions are directed by transcription factor binding at target DNA which induce changes to identity-specific gene regulatory programs. The degree of cell plasticity is determined by the interplay of epigenetic mechanisms to create a landscape susceptible to such binding events. 5-hydroxymethylcytosine, a key intermediate during the process of DNA demethylation, is an epigenetic modification involved in controlling these epigenetic dynamics related to cell identity. Here, the role of 5-hydroxcymethylcytosine during cell identity conversions, including its relationship with other main epigenetic mechanisms, is reviewed.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"18 1","pages":"36"},"PeriodicalIF":4.2,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12178066/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144334257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Artificial Intelligence in cancer epigenomics: a review on advances in pan-cancer detection and precision medicine.","authors":"Karishma Sahoo, Prakash Lingasamy, Masuma Khatun, Sajitha Lulu Sudhakaran, Andres Salumets, Vino Sundararajan, Vijayachitra Modhukur","doi":"10.1186/s13072-025-00595-5","DOIUrl":"10.1186/s13072-025-00595-5","url":null,"abstract":"<p><p>DNA methylation is a fundamental epigenetic modification that regulates gene expression and maintains genomic stability. Consequently, DNA methylation remains a key biomarker in cancer research, playing a vital role in diagnosis, prognosis, and tailored treatment strategies. Aberrant methylation patterns enable early cancer detection and therapeutic stratification; however, their complex patterns necessitates advanced analytical tools. Recent advances in artificial intelligence (AI) and machine learning (ML), including deep learning networks and graph-based models, have revolutionized cancer epigenomics by enabling rapid, high-resolution analysis of DNA methylation profiles. Moreover, these technologies are accelerating the development of Multi-Cancer Early Detection (MCED) tests, such as GRAIL's Galleri and CancerSEEK, which improve diagnostic accuracy across diverse cancer types. In this review, we explore the synergy between AI and DNA methylation profiling to advance precision oncology. We first examine the role of DNA methylation as a biomarker in cancer, followed by an overview of DNA profiling technologies. We then assess how AI-driven approaches transform clinical practice by enabling early detection and accurate classification. Despite their promise, challenges remain, including limited sensitivity for early-stage cancers, the black-box nature of many AI algorithms, and the need for validation across diverse populations to ensure equitable implementation. Future directions include integrating multi-omics data, developing explainable AI frameworks, and addressing ethical concerns, such as data privacy and algorithmic bias. By overcoming these gaps, AI-powered epigenetic diagnostics can enable earlier detection, more effective treatments, and improved patient outcomes, globally. In summary, this review synthesizes current advancements in the field and envisions a future where AI and epigenomics converge to redefine cancer diagnostics and therapy.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"18 1","pages":"35"},"PeriodicalIF":4.2,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12166640/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA methylation mechanisms in the maturing and ageing oocyte.","authors":"Carla Caniçais, Sara Vasconcelos, Fátima Santos, Sofia Dória, C Joana Marques","doi":"10.1186/s13072-025-00600-x","DOIUrl":"10.1186/s13072-025-00600-x","url":null,"abstract":"<p><p>Oocyte maturation involves both nuclear and cytoplasmic processes that are critical for the acquisition of oocyte competence. Granulosa cells, surrounding the oocyte, play a pivotal role in the maturation process, with mechanisms such as cAMP signaling significantly influencing oocyte development. Epigenetic mechanisms - including DNA methylation and its oxidative derivatives, histone post-translational modifications and chromatin remodeling - interfere with the accessibility of transcription factors to regulatory regions of the genome, such as promoter regions of genes, hence generally regulating gene expression profiles; however, in oocytes, transcription is largely independent of DNA methylation patterns. Here we highlight epigenetic reprogramming events occurring during oocyte development and ageing, focusing on the establishment of gamete-specific epigenetic marks, including DNA modifications at imprinted regions, and age-related epigenetic changes. We focus on the mechanisms of DNA methylation and demethylation during mouse and human oocyte maturation, alongside an exploration of how ageing impacts the oocyte epigenome and its implications for reproductive success. By providing a comprehensive analysis of the role of epigenetics in oocyte development and maturation, this review addresses the importance of comprehending these processes to enhance in vitro fertilization treatments and improve reproductive outcomes.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"18 1","pages":"34"},"PeriodicalIF":4.2,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153205/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cohesin stabilization at promoters and enhancers by common transcription factors and chromatin regulators.","authors":"Audra F Bryan, Megan Justice, Alexis V Stutzman, Daniel J McKay, Jill M Dowen","doi":"10.1186/s13072-025-00598-2","DOIUrl":"10.1186/s13072-025-00598-2","url":null,"abstract":"<p><strong>Background: </strong>Cohesin is a major regulator of three-dimensional genome organization and gene expression. Cohesin associates with DNA and dynamically extrudes a DNA loop, often bringing two cis-regulatory elements physically close together. Extruding cohesin molecules can be stalled or stabilized when they encounter a CTCF insulator protein on DNA, thereby anchoring a DNA loop. However, many enhancer-promoter loops that are bound by cohesin lack CTCF and it is not clear how cohesin is stabilized at or recruited to these sites in the genome.</p><p><strong>Results: </strong>Here, we investigated the localization of cohesin with common chromatin regulators and transcription factors on the mouse embryonic stem cell genome. The SP1 and NFYA transcription factors are ubiquitously expressed proteins known to regulate expression of genes associated with a variety of cellular processes, while WDR5 is a ubiquitous core component of multiple chromatin regulatory complexes. We found that cohesin co-bound promoters and enhancers with WDR5, with SP1, or with NFYA in mESCs. Cohesin physically interacted with and colocalized with WDR5, with SP1, or with NFYA on the same molecule of chromatin. Strikingly, depletion of WDR5, SP1, or NFYA caused a decrease in cohesin binding at shared binding sites, while depletion of cohesin did not alter binding of WDR5, SP1, or NFYA on the genome.</p><p><strong>Conclusions: </strong>These results indicate that common transcription factors and chromatin regulators stabilize cohesin at specific sites in chromatin and may thereby serve as structural regulators of enhancer-promoter loops via the stabilization of cohesin.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"18 1","pages":"33"},"PeriodicalIF":3.5,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12147376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144259250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The linker histone chaperone Prothymosin α (PTMA) is essential for efficient DNA damage repair and the recruitment of PARP1.","authors":"Ciara A McKnight, Mary E Graichen, Eric M George, David T Brown","doi":"10.1186/s13072-025-00599-1","DOIUrl":"10.1186/s13072-025-00599-1","url":null,"abstract":"<p><strong>Background: </strong>Mammalian cells have numerous DNA repair pathways to repair lesions generated by replication errors, metabolism, and exogenous agents. Cells can sense and respond to DNA damage within seconds, suggesting that there is a highly effective sensor of lesions although the mechanistic details are unclear. The DNA damage response in mammalian cells results in a localized transient de-condensation of chromatin, loss of linker histones and the recruitment of DNA repair proteins such as PARP1 and chromatin remodelers.</p><p><strong>Results: </strong>Here we investigated the interactions between poly(ADP-ribose) polymerase-1 (PARP1), the linker histone H1.0 and linker histone chaperone Prothymosin α (PTMA). Using H1.0 tagged with a photoconvertible fluorescent protein, we observed a significant increase in the initial rate of exit of H1.0 from regions of chromatin containing microirradiation-induced DNA lesions. Surprisingly, this was also seen in Parp1^-/- cells but not in stable cell lines with homozygous null mutations in the PTMA gene (Ptma^-/-). The recruitment of PARP1 to damaged DNA was inhibited by overexpression of a mutant of H1.0 with a tighter chromatin-binding affinity or by reduced expression of PTMA. Relative to the wild type, Ptma^-/- cell lines displayed increased sensitivity to DNA-damaging agents.</p><p><strong>Conclusion: </strong>We suggest that DNA damage alters the interaction of H1.0 with the nucleosome to allow the chaperone PTMA to bind and promote release of linker histones thereby initiating the local chromatin de-condensation necessary for the efficient recruitment of repair proteins such as PARP1. In this context linker histones may serve as in situ \"sensors\" of DNA damage.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"18 1","pages":"32"},"PeriodicalIF":4.2,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139302/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144235715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling the cohesin-chromatin interface: identifying protein interactions that modulate chromosome structure and function.","authors":"Natalie L Rittenhouse, Riya Gohil, June E Arricastres, Jill M Dowen","doi":"10.1186/s13072-025-00596-4","DOIUrl":"10.1186/s13072-025-00596-4","url":null,"abstract":"<p><strong>Background: </strong>The evolutionarily conserved cohesin complex is a pleiotropic regulator of chromosome structure and function, participating in sister chromatid cohesion, transcriptional regulation of genes, DNA replication, and DNA repair. Cohesin uses ATP hydrolysis to dynamically extrude DNA loops that bring together cis-regulatory elements and thus regulate gene expression. Some DNA loops are anchored by the binding of CTCF insulator proteins which can stall extruding cohesin complexes, however many DNA loops that connect enhancers and promoters lack CTCF and it is unclear how cohesin is stabilized at these cis-regulatory sites. While cohesin has been found to co-purify with a number of proteins, some of which regulate cohesin function, our current knowledge of cohesin activity is incomplete. Identification of transient or less stable interactions between cohesin and chromatin-associated proteins is crucial for understanding regulation of gene expression and chromosome structure.</p><p><strong>Results: </strong>Here we utilize a TurboID proximity labeling and mass spectrometry approach for identifying cohesin-interacting proteins. We identify > 400 cohesin-interacting proteins in NIH-3T3 cells, including previously known and potentially novel cohesin interactors. Among the cohesin interactors were chromatin remodeling complexes and histone-modifying complexes. Interactions between seven of these chromatin regulating complexes and cohesin were confirmed with co-immunoprecipitations performed in multiple cell lines. The SWI/SNF complex was found to co-purify with cohesin and SWI/SNF co-occupied enhancers and promoters with cohesin. To investigate the functional relevance of the cohesin-SWI/SNF interaction, we assessed whether the binding of cohesin to the genome is regulated by SWI/SNF or vice versa. Acute small molecule perturbations of SWI/SNF altered the amount of both SWI/SNF and cohesin on chromatin, particularly affecting cohesin binding to CTCF sites.</p><p><strong>Conclusions: </strong>This work represents the most comprehensive investigation of cohesin-interacting proteins to date. These results identify a physical link between cohesin and a vast number of chromatin-associated proteins inside of cells, including chromatin remodeling complexes and histone-modifying complexes. Furthermore, these results indicate SWI/SNF activity stabilizes cohesin on chromatin particularly at insulator sites. These cohesin interactome data are a resource for future studies aimed at characterizing the functional interactions between cohesin and numerous chromatin-associated proteins in regulating chromosome structure and gene control.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"18 1","pages":"31"},"PeriodicalIF":3.5,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12128382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144200607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The WAC-downWAC domain in the yeast ISW2 nucleosome remodeling complex forms a structural module essential for ISW2 function but not cell viability.","authors":"Ashish Kumar Singh, Sabine Ines Grünert, Lena Pfaller, Felix Mueller-Planitz","doi":"10.1186/s13072-025-00593-7","DOIUrl":"10.1186/s13072-025-00593-7","url":null,"abstract":"<p><strong>Background: </strong>ATP-dependent nucleosome remodeling complexes of the imitation switch (ISWI) family slide and space nucleosomes. The ISWI ATPase subunit forms obligate complexes with accessory subunits whose mechanistic roles remain poorly understood. In baker's yeast, the Isw2 ATPase subunit associates with Itc1, the orthologue of human ACF1/BAZ1A. Prior data suggested that the genomic deletion of the 374 N-terminal amino acids from Itc1 (hereafter called itc1^ΔN) leads to a gain-of-toxic-function phenotype with severe growth defects in the BY4741 genetic background, possibly due to defective nucleosome spacing activity of the mutant complex.</p><p><strong>Results: </strong>Here we show that the deletion encompasses a novel motif termed downWAC that forms a conserved structural module with the N-terminal WAC domain. The module is predicted to interact with DNA. However, it does not form a stable interaction interface with the remainder of the complex. Instead, it is connected through a long disordered polypeptide linker to the remainder of the complex. Curiously, the itc1^ΔN allele does not lead to measurable growth defects in haploid BY4741 and diploid BY4743 strains. It also does not alter genome-wide nucleosome organization in wild-type cells. To rule out that potentially redundant remodeling factors obscure itc1^ΔN-associated phenotypes, we repeated experiments in cells devoid of ISW1 and CHD1 remodelers with the same results. Only at known target genes of the ISW2 complex was the nucleosome organization perturbed in itc1^ΔN cells.</p><p><strong>Conclusions: </strong>We conclude that the deletion of Itc1 N-terminus is indistinguishable from the full deletion of either ITC1 or ISW2. As such, itc1^ΔN should be considered a null allele of ISW2. We propose a model, in which the WAC-downWAC module, along with a flexible protein linker, helps ISW2 in searching for its target genes and positioning + 1-nucleosomes.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"18 1","pages":"30"},"PeriodicalIF":4.2,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12093815/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144121440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}