Chromosome-level genome assembly of Triplophysa bombifrons using PacBio HiFi sequencing and Hi-C technologies by Chengxin Wang, Site Luo, Yong Song, Liting Yang, Xinyue Wang, Shengao Chen

“…This study introduces a chromosome-level genome assembly for T. bombifrons, achieved through the integration of PacBio long-read sequencing and Hi-C chromatin interaction mapping. The assembly reveals a genome structure comprising 25 chromosomes and an overall size of 655.95 Mb. …”
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The SIX1/LDHA Axis Promotes Lactate Accumulation and Leads to NK Cell Dysfunction in Pancreatic Cancer by Wanli Ge, Lingdong Meng, Shouji Cao, Chaoqun Hou, Xiaole Zhu, Dongya Huang, Qiang Li, Yunpeng Peng, Kuirong Jiang

“…PC cells and NK cells were cocultured to study the effect of SIX1 overexpression in PC cells on NK cell function. Chromatin immunoprecipitation (ChIP) assays were used to study the relationship between SIX1 and lactate dehydrogenase A (LDHA). …”
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Transsulfuration pathway activation attenuates oxidative stress and ferroptosis in sickle primary erythroblasts and transgenic mice by Caixia Xi, Junfeng Pang, Weinan Xue, Yang Cui, Na Jiang, Wenbo Zhi, Huidong Shi, Anatolij Horuzsko, Betty S. Pace, Xingguo Zhu

“…This DMF-upregulated DNA hydroxymethylation affects CBS locus chromatin structure modifications and upregulates gene expression. …”
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Novel Pathogenic Variant in TGFBR2 Confirmed by Molecular Modeling Is a Rare Cause of Loeys-Dietz Syndrome by Michael T. Zimmermann, Raul A. Urrutia, Patrick R. Blackburn, Margot A. Cousin, Nicole J. Boczek, Eric W. Klee, Colleen Macmurdo, Paldeep S. Atwal

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Evolutionary origins and functional diversification of Auxin Response Factors by Jorge Hernández-García, Vanessa Polet Carrillo-Carrasco, Juriaan Rienstra, Keita Tanaka, Martijn de Roij, Melissa Dipp-Álvarez, Alejandra Freire-Ríos, Isidro Crespo, Roeland Boer, Willy A. M. van den Berg, Simon Lindhoud, Dolf Weijers

“…We reveal the shared origin of ARFs from preexisting domains, uncovering a protein fold homologous to the ARF DNA-binding fold in a conserved eukaryotic chromatin regulator. Building on this, we reconstruct the complete evolutionary history of ARFs, including the divergence events leading to the appearance of the ARF classes and defining the main molecular targets for their functional diversification. …”
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Significance of Apoptosis in the Process of Tumorigenesis in Colorectal Mucosa and Adenomas in FAP Patients by Hildegard Weiß, Karl‐Heinz Jacobasch, Wolfgang Haensch, Brigitte Streller, Brigitte Hieke

“…In addition, transcriptional capacity was determined by chromatin in situ testing. For both, DNA flow cytometry was used. …”
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Identification of Genes Regulating Gene Targeting by a High-Throughput Screening Approach by Fabien Delacôte, Christophe Perez, Valérie Guyot, Catherine Mikonio, Pierrick Potrel, Jean-Pierre Cabaniols, Christophe Delenda, Frédéric Pâques, Philippe Duchateau

“…We showed that siRNAs directed against the ATF7IP gene, encoding a protein involved in chromatin remodeling, stimulated HGT by a factor of three to eight, at various loci and in different cell types. …”
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Reconstruction of gene regulatory networks from single cell transcriptomic data by M. A. Rybakov, N. A. Omelyanchuk, E. V. Zemlyanskaya

“…We pay specific attention to state-of-the-art methods for GRN reconstruction from single-cell transcriptomes recruiting other omics data, primarily transcription factor binding sites and open chromatin profiles (scATAC-seq), in order to increase inference accuracy. …”
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Prolonged exposure to insulin might cause epigenetic alteration leading to insulin resistance by Shehnaz Bano, Shyam More, Dattatray S. Mongad, Abdul Khalique, Dhiraj P. Dhotre, Manoj K. Bhat, Vasudevan Seshadri

“…Transcriptomic analysis of the insulin‐sensitive and resistance cells uncover altered signalling networks involved in chromatin remodelling, Rho GTPases, and ubiquitination. …”
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Phosphorylation of histone H3Ser10 in plant cell division by D. B. Loginova, O. G. Silkova

“…Histones, the major protein components of chromatin, undergo post-translational modifications, which particularly affect the structural and functional organization of chromosomes. …”
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Transcription Factor FXR Activates DHRS9 to Inhibit the Cell Oxidative Phosphorylation and Suppress Colon Cancer Progression by Jinlai Zhao, Yigang Wang, Yang Wang, Jianchao Gao, Haichao Yang, Xiaotang Wu, Hua Li

“…The binding relationship between FXR and its downstream gene dehydrogenase/reductase member 9 (DHRS9) was verified through luciferase reporter assay and chromatin immunoprecipitation assay. The changes of oxidative phosphorylation were detected by Western blot and oxygen consumption rate determination. …”
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KLF5 loss sensitizes cells to ATR inhibition and is synthetic lethal with ARID1A deficiency by Samah W. Awwad, Colm Doyle, Josie Coulthard, Aldo S. Bader, Nadia Gueorguieva, Simon Lam, Vipul Gupta, Rimma Belotserkovskaya, Tuan-Anh Tran, Shankar Balasubramanian, Stephen P. Jackson

“…Mechanistically, we show that KLF5 protects cells from replication stress, at least in part through regulating BRD4 recruitment to chromatin. Overall, our work identifies KLF5 as a potential target for eradicating ARID1A-deficient cancers.…”
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Rad3 decorates critical chromosomal domains with gammaH2A to protect genome integrity during S-Phase in fission yeast. by Sophie Rozenzhak, Eva Mejía-Ramírez, Jessica S Williams, Lana Schaffer, Jennifer A Hammond, Steven R Head, Paul Russell

“…Here, we use ChIP-on-chip analysis to map genomic loci decorated by phosphorylated histone H2A (gammaH2A), a Rad3 substrate that establishes a chromatin-based recruitment platform for Crb2 and Brc1 DNA repair/checkpoint proteins. …”
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Replication-IDentifier links epigenetic and metabolic pathways to the replication stress response by Sophie C. van der Horst, Leonie Kollenstart, Amandine Batté, Sander Keizer, Kees Vreeken, Praveen Pandey, Andrei Chabes, Haico van Attikum

“…During Repli-ID, the replicative polymerase epsilon (Pol ε) is tracked at a barcoded origin of replication by chromatin immunoprecipitation (ChIP) coupled to next-generation sequencing of the barcode in thousands of hydroxyurea-treated yeast mutants. …”
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Multi-Omics Insights into Regulatory Mechanisms Underlying Differential Deposition of Intramuscular and Abdominal Fat in Chickens by Yuxin Xing, Chenglin Ma, Hongbo Guan, Jianing Shen, Ying Shen, Guoxi Li, Guirong Sun, Yadong Tian, Xiangtao Kang, Xiaojun Liu, Hong Li, Weihua Tian

“…This review systematically summarizes the regulatory mechanisms underlying intramuscular and abdominal fat traits at chromatin, genomic, transcriptional, post-transcriptional, translational, and epigenetic-modification scales. …”
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Genome-Wide Expression of MicroRNAs Is Regulated by DNA Methylation in Hepatocarcinogenesis by Jing Shen, Shuang Wang, Abby B. Siegel, Helen Remotti, Qiao Wang, Iryna Sirosh, Regina M. Santella

“…Six miRNAs were validated in 56 additional paired HCC tissues, and significant inverse correlations were observed for miR-125b and miR-199a, which is consistent with the inactive chromatin pattern found in HepG2 cells. Conclusion. …”
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Senescence-Associated Molecular and Epigenetic Alterations in Mesenchymal Stem Cell Cultures from Amniotic Fluid of Normal and Fetus-Affected Pregnancy by Jūratė Savickienė, Sandra Baronaitė, Aistė Zentelytė, Gražina Treigytė, Rūta Navakauskienė

“…These differences correlated with changes in the level of chromatin modifiers (DNMT1 and HDAC1) and polycomb group proteins (EZH2, SUZ12, and BMI1) paralleling with changes in the expression of repressive histone marks (H3K9me3 and H3K27me3) and stemness markers (Oct4, Nanog, Sox2, and Rex1). …”
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Characterizing the regulatory effects of H2A.Z and SWR1-C on gene expression during hydroxyurea exposure in Saccharomyces cerevisiae. by Hilary T Brewis, Peter C Stirling, Michael S Kobor

“…Chromatin structure and DNA accessibility are partly modulated by the incorporation of histone variants. …”
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Epigenetic Induction of Definitive and Pancreatic Endoderm Cell Fate in Human Fibroblasts by Rangarajan Sambathkumar, Eric Kalo, Rob Van Rossom, Marijke M. Faas, Paul de Vos, Catherine M. Verfaillie

“…We demonstrated that histone deacetylase inhibitor (HDACi) Trichostatin A (TSA) combined with a chromatin remodeling medium (CRM) induced expression of a number of definitive endoderm and early and late pancreatic marker genes. …”
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R-loops acted on by RNase H1 influence DNA replication timing and genome stability in Leishmania by Jeziel D. Damasceno, Emma M. Briggs, Marija Krasilnikova, Catarina A. Marques, Craig Lapsley, Richard McCulloch

“…Furthermore, we demonstrate that such differential organisation of R-loops, RNase H1 and DNA replication timing across the parasite’s chromosomes correlates with size-dependent differences in chromatin accessibility, G quadruplex distribution and sequence content. …”
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