Article
Multidisciplinary Sciences
Dian Spakman, Tinka V. M. Clement, Andreas S. Biebricher, Graeme A. King, Manika I. Singh, Ian D. Hickson, Erwin J. G. Peterman, Gijs J. L. Wuite
Summary: In this study, an in vitro single-molecule assay was used to mimic chromatin under tension and it was demonstrated that PICH is a tension- and ATP-dependent nucleosome remodeler.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Estanislao Peixoto, Asad Khan, Zachary A. Lewis, Rafael Contreras-Galindo, Wioletta Czaja
Summary: Robust and tightly regulated DNA repair is crucial for maintaining genome stability and preventing cancer. HELLS, a chromatin remodeler, plays important roles in DNA repair, genome stability, and cancer-associated pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Corinna Lieleg, Ana Novacic, Sanja Musladin, Andrea Schmid, Goezde Gueclueler Akpinar, Slobodan Barbaric, Philipp Korber
Summary: Chromatin remodeling by ATP-dependent enzymes is crucial for genomic processes. The recruitment of remodelers, such as the SWI/SNF complex, in the removal of nucleosomes in yeast PHO gene induction is specific and may affect the outcome of remodeling.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Ieva Vaicekauskaite, Rasa Sabaliauskaite, Juozas Rimantas Lazutka, Sonata Jarmalaite
Summary: Ovarian cancer is the fifth leading cause of women's death from cancers, with high mortality rate due to late presence and lack of modern diagnostic tools. It is a highly heterogeneous disease, leading to early treatment failure. Exploring molecular mechanisms of ovarian cancer can enhance our understanding and provide new treatment options.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Neurosciences
Chen Dong, Chuntao Zhao, Xiang Chen, Kalen Berry, Jiajia Wang, Feng Zhang, Yunfei Liao, Rong Han, Sean Ogurek, Lingli Xu, Li Zhang, Yifeng Lin, Wenhao Zhou, Mei Xin, Daniel A. Lim, Kenneth Campbell, Masato Nakafuku, Ronald R. Waclaw, Q. Richard Lu
Summary: This study identifies the stage-dependent functions of CHD8 in neurogenesis, including the regulation of neural stem/progenitor cell proliferation and survival, the production of transit-amplifying intermediate progenitors (IPCs), and the activation of neurogenesis-promoting factors. It also reveals that CHD8 controls chromatin accessibility to activate neurogenesis-promoting factors and repress apoptotic programs. In the adult brain, CHD8 depletion impairs neurogenesis but does not affect NSC proliferation and survival, and this impairment can be partially restored with fluoxetine treatment.
JOURNAL OF NEUROSCIENCE
(2022)
Article
Immunology
Naomi Goldman, Aditi Chandra, Isabelle Johnson, Matthew A. Sullivan, Abhijeet R. Patil, Ashley Vanderbeck, Atishay Jay, Yeqiao Zhou, Emily K. Ferrari, Leland Mayne, Jennifer Aguilan, Hai-Hui Xue, Robert B. Faryabi, E. John Wherry, Simone Sidoli, Ivan Maillard, Golnaz Vahedi
Summary: The functional and mechanistic importance of an intrinsically disordered region of TCF-1 in T cell development is shown in this study. Deletion of this region leads to an early developmental block in T cells and causes lineage infidelity. The intrinsically disordered N terminus of TCF-1 is critical for T cell lineage fidelity.
Article
Immunology
Ana C. F. Ferreira, Aydan C. H. Szeto, Paula A. Clark, Alastair Crisp, Patrycja Kozik, Helen E. Jolin, Andrew N. J. McKenzie
Summary: The study found that ADNP plays an indispensable role in immune reactions to allergens by recruiting proteins such as CHD4 and BRG1, serving as a critical bridge in gene activation and promoting T cell differentiation. The absence of ADNP impairs the ability of GATA3 and AP-1 to initiate histone acetylation and DNA accessibility, resulting in impaired expression of type 2 cytokines. These results demonstrate the importance of ADNP in promoting immune cell specialization.
Article
Cell Biology
Nadine Hosny El Said, Francesco Della Valle, Peng Liu, Andreu Paytuvi-Gallart, Sabir Adroub, Juliette Gimenez, Valerio Orlando
Summary: This study reveals the significant role of PRC2 and long non-coding RNAs in oxidative stress response, and identifies Malat-1 as the first lncRNA involved in PRC2-Ezh1 function.
CELL DEATH & DISEASE
(2021)
Article
Biochemistry & Molecular Biology
Roberto Amigo, Carlos Farkas, Cristian Gidi, Matias Hepp, Natalia Cartes, Estefania Tarifeno, Jerry L. Workman, Jose L. Gutierrez
Summary: This study compares the properties and interactions of Hmo1 and Hho1 proteins, and finds that Hmo1 belongs to the HMGB family while Hho1 belongs to the linker histones family. In addition, Hmo1 and Hho1 display differential effects on chromatin remodeling complexes.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2022)
Article
Multidisciplinary Sciences
Nicolas Page, Sylvain Lemeille, Ilena Vincenti, Bogna Klimek, Alexandre Mariotte, Ingrid Wagner, Giovanni Di Liberto, Jonathan Kaye, Doron Merkler
Summary: The study characterizes the transcriptional and epigenetic landscape of self-reactive CD8+ T cells in central nervous system autoimmunity, showing that the TOX gene is crucial for the maintenance of self-reactive CD8+ T cells. Continuous exposure to CNS self-antigen sustains TOX levels in self-reactive CD8+ T cells.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Roberto Amigo, Fernanda Raiqueo, Estefania Tarifeno, Carlos Farkas, Jose L. Gutierrez
Summary: The establishment and maintenance of nucleosome-free regions (NFRs) are essential processes in chromatin dynamics. This study investigates the role of transcription factors, chromatin remodeling complexes, and DNA sequences, particularly poly(dA:dT) tracts, in nucleosome remodeling. The results show that poly(dA:dT) tracts have differential effects on the activity of chromatin remodeling complexes and affect the directionality of nucleosome sliding. These findings shed light on the mechanisms underlying asymmetrical chromatin opening around poly(dA:dT) tracts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Hyeryung Yoon, Yejin Shim, Soo-Cheul Yoo, Kiyoon Kang, Nam-Chon Paek
Summary: Genetic studies show that the chromatin remodeling factor RFS promotes flowering in rice by affecting the expression of flowering time-related genes. RFS displays diurnal expression patterns under different day lengths, and mutations in RFS lead to delays in flowering and negative effects on rice yield and yield components.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Damir Baranasic, Matthias Hortenhuber, Piotr J. Balwierz, Tobias Zehnder, Abdul Kadir Mukarram, Chirag Nepal, Csilla Varnai, Yavor Hadzhiev, Ada Jimenez-Gonzalez, Nan Li, Joseph Wragg, Fabio M. D'Orazio, Dorde Relic, Mikhail Pachkov, Noelia Diaz, Benjamin Hernandez-Rodriguez, Zelin Chen, Marcus Stoiber, Michael Dong, Irene Stevens, Samuel E. Ross, Anne Eagle, Ryan Martin, Oluwapelumi Obasaju, Sepand Rastegar, Alison C. McGarvey, Wolfgang Kopp, Emily Chambers, Dennis Wang, Hyejeong R. Kim, Rafael D. Acemel, Silvia Naranjo, Maciej Lapinski, Vanessa Chong, Sinnakaruppan Mathavan, Bernard Peers, Tatjana Sauka-Spengler, Martin Vingron, Piero Carninci, Uwe Ohler, Scott Allen Lacadie, Shawn M. Burgess, Cecilia Winata, Freek van Eeden, Juan M. Vaquerizas, Jose Luis Gomez-Skarmeta, Daria Onichtchouk, Ben James Brown, Ozren Bogdanovic, Erik van Nimwegen, Monte Westerfield, Fiona C. Wardle, Carsten O. Daub, Boris Lenhard, Ferenc Muller
Summary: Zebrafish, an important model organism for studying embryonic development and human diseases, lacks a systematic functional annotation program. The international DANIO-CODE consortium addressed this issue by creating a central repository to store and process zebrafish developmental functional genomic data. They improved existing annotations and identified over 140,000 cis-regulatory elements throughout development. They also compared regulatory elements and epigenomic landscapes between zebrafish and mouse, predicting functional relationships between them. This study extends the utility of zebrafish developmental genomics to mammals.
Article
Medicine, Research & Experimental
Fabienne Gally, Sarah K. Sasse, Jonathan S. Kurche, Margaret A. Gruca, Jonathan H. Cardwell, Tsukasa Okamoto, Hong W. Chu, Xiaomeng Hou, Olivier B. Poirion, Justin Buchanan, Sebastian Preissl, Bing Ren, Sean P. Colgan, Robin D. Dowell, Ivana Yang, David A. Schwartz, Anthony N. Gerber
Summary: The G/T transversion rs35705950, located 3 kb upstream of the MUC5B start site, is identified as a key risk factor for idiopathic pulmonary fibrosis. Through analysis of accessible chromatin and nuclease sensitivity data, it is shown that this region affects the expression of MUC5B and is subject to epigenetic remodeling in IPF patients' lung tissue.
Review
Cardiac & Cardiovascular Systems
Kun Zhao, Yukang Mao, Yansong Li, Chuanxi Yang, Kai Wang, Jing Zhang
Summary: This review summarizes the emerging advances in epigenetic regulation in pathological myocardial remodeling and provides an overview of the potential mechanisms involved in this regulation.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Fatemeh Rasouli, Ali Kiani-Pouya, Lana Shabala, Leiting Li, Ayesha Tahir, Min Yu, Rainer Hedrich, Zhonghua Chen, Richard Wilson, Heng Zhang, Sergey Shabala
Summary: The halophyte quinoa responds to salinity stress by altering the protein composition of guard cells, with differential expression of proteins involved in signaling pathways and stress responses. Upregulated proteins in response to salt treatment include those related to ABA signaling and sucrose-starch metabolism, while high levels of aspartic proteinase are associated with mitigating oxidative stress induced by saline conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Pengfei Fan, Emmanuel Aguilar, Mariem Bradai, Hao Xue, Hua Wang, Tabata Rosas-Diaz, Weihua Tang, Sebastian Wolf, Heng Zhang, Lin Xu, Rosa Lozano-Duran
Summary: This study demonstrates that the establishment of xylem patterning in Arabidopsis roots is dependent on the opposing gradients of miRNAs and their targets, with BAM1 and BAM2 playing redundant roles in ensuring proper distribution and accumulation of miR165/6-targeted transcripts, ultimately affecting xylem morphology.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Plant Sciences
Heejin Yoo, Stuti Shrivastava, Joseph H. Lynch, Xing-Qi Huang, Joshua R. Widhalm, Longyun Guo, Benjamin C. Carter, Yichun Qian, Hiroshi A. Maeda, Joseph P. Ogas, John A. Morgan, Amy Marshall-Colon, Natalia Dudareva
Summary: The flux towards phenylalanine in plants is highly regulated, with ADT playing a key role; in petunia flowers with high phenylalanine levels, ADT regulation is relaxed; regulation of the d-ribulose-5-phosphate 3-epi merase gene in the pentose phosphate pathway controls flux into the shikimate pathway.
Article
Nutrition & Dietetics
Chenwei Song, Wei Lv, Yahui Li, Pan Nie, Jun Lu, Yanlou Geng, Zhang Heng, Lihua Song
Summary: The study found that low amounts of quinoa intake effectively prevented weight gain in rats fed a high-fat diet, reduced hepatic lipid and cholesterol levels, alleviated pathological injury, promoted antioxidant activity, and regulated lipid metabolism. Meanwhile, high amounts of quinoa more effectively influenced genes related to lipid metabolism and immune response.
NUTRITION & METABOLISM
(2021)
Article
Cell Biology
Shaobo Zhu, Jinge Gu, Juanjuan Yao, Yichen Li, Zheting Zhang, Wencheng Xia, Zhen Wang, Xinrui Gui, Leiting Li, Dan Li, Heng Zhang, Cong Liu
Summary: This study demonstrates the role of protein liquid-liquid phase separation (LLPS) in the heat stress response in plants by discovering the LLPS of two RNA-binding proteins, RBGD2 and RBGD4. The findings suggest that manipulation of protein LLPS could be a strategy to improve plant stress resistance.
DEVELOPMENTAL CELL
(2022)
Article
Evolutionary Biology
Joshua T. Trujillo, Jiaxin Long, Erin Aboelnour, Joseph Ogas, Jennifer H. Wisecaver
Summary: Chromatin remodelers play a vital role in chromatin assembly, transcription regulation, and DNA repair. Through a comprehensive phylogenetic analysis, this study provides insights into the evolutionary history and function of the CHD family of chromatin remodelers. The analysis reveals that the subfamilies originated from the last common ancestor of eukaryotes and have been lost independently in different lineages. In addition, distinct subfamilies were identified in plants that were absent or highly divergent in Arabidopsis thaliana, and the expansion of CHD subfamilies in vertebrates corresponds to whole genome duplication events. Analysis of protein domains also indicates transitions in domain architecture associated with CHD remodeler diversification.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Nadia Bazihizina, Jennifer Boehm, Maxim Messerer, Christian Stigloher, Heike M. Mueller, Tracey Ann Cuin, Tobias Maierhofer, Joan Cabot, Klaus F. X. Mayer, Christian Fella, Shouguang Huang, Khaled A. S. Al-Rasheid, Saleh Alquraishi, Michael Breadmore, Stefano Mancuso, Sergey Shabala, Peter Ache, Heng Zhang, Jian-Kang Zhu, Rainer Hedrich, Soenke Scherzer
Summary: Chenopodium quinoa uses epidermal bladder cells to sequester excess salt, with stalk cells acting as filters and controllers for transcellular transport.
Article
Plant Sciences
Wei Jiang, Chao Li, Leiting Li, Yali Li, Zhihao Wang, Feiyu Yu, Feng Yi, Jianhan Zhang, Jian-Kang Zhu, Heng Zhang, Yan Li, Chunzhao Zhao
Summary: This study characterizes CqCrRLK1L and CqRALF family genes in quinoa and provides evidence to support their roles in salt stress response.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Stephen M. Richards, Leiting Li, James Breen, Nelli Hovhannisyan, Oscar Estrada, Boris Gasparyan, Matthew Gilliham, Alexia Smith, Alan Cooper, Heng Zhang
Summary: The study of well-preserved millet grains from the archaeological cave site Areni-1 in Southern Armenia reveals that DNA from these grains can be preserved for at least 1000 years, serving as a genetic resource for studying the domestication history of this cereal crop.
SCIENTIFIC REPORTS
(2022)
Review
Biochemistry & Molecular Biology
Heng Zhang, Zhizhong Gong, Jian-Kang Zhu
Summary: Maintaining proper DNA methylation levels in the genome requires active demethylation of DNA. The discovery of the first eukaryotic DNA demethylase ROS1 in Arabidopsis thaliana has greatly expanded our understanding of the active DNA demethylation pathway and its regulation and biological functions in plants.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Article
Plant Sciences
Fatemeh Rasouli, Ali Kiani-Pouya, Ali Movahedi, Yuan Wang, Leiting Li, Min Yu, Mohammad Pourkheirandish, Meixue Zhou, Zhonghua Chen, Heng Zhang, Sergey Shabala
Summary: A comparative investigation was conducted to evaluate transcriptional changes in guard cells (GCs) of halophytic (Chenopodium quinoa) and glycophytic (Spinacia oleracea) species under salt stress. Salt-responsive genes in both species were mainly related to protein metabolism, secondary metabolites, signal transduction, and transport systems. Quinoa exhibited strong induction of genes related to abscisic acid signaling and biosynthesis, as well as transporters for amino acids, proline, sugars, sucrose, and potassium. Additionally, changes in cell wall-related genes and stomatal development were observed, suggesting that these variations may contribute to the higher salt tolerance and water use efficiency in quinoa.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Food Science & Technology
Lingyue Zhong, Wei Lyu, Zihan Lin, Jun Lu, Yanlou Geng, Lihua Song, Heng Zhang
Summary: A long-term high-fat diet leads to hepatic steatosis, oxidative stress, and inflammation. This study investigated the effects of different amounts of quinoa on hepatic steatosis, oxidative stress, inflammation, and gut microbiota of rats fed a high-fat diet. The results showed that quinoa intake inhibited hepatomegaly and splenomegaly, improved hepatic steatosis, restored antioxidant enzyme activity, and decreased inflammatory markers. Furthermore, quinoa intake altered the composition of gut microbiota. In conclusion, quinoa has beneficial effects in preventing nonalcoholic fatty liver disease and should be included in daily diets for prevention.
Article
Education & Educational Research
Eric D. Deemer, Amy C. Barr, Amy Belote, Mark C. Hall, Chunyu Xu, Joseph P. Ogas
Summary: This study examined the effects of an online and in-person pre-college science enrichment program on students' motivation. The results showed that students' satisfaction of needs for autonomy, competence, and relatedness grew throughout the program, regardless of the learning format. However, the type of science project undertaken by students influenced the growth in autonomy differently for online and in-person learning.
RESEARCH IN SCIENCE EDUCATION
(2023)
Article
Plant Sciences
Ali Kiani-Pouya, Leiting Li, Fatemeh Rasouli, Zheting Zhang, Jiahong Chen, Min Yu, Ayesha Tahir, Rainer Hedrich, Sergey Shabala, Heng Zhang
Summary: This study characterized the transcriptome differences between intact and EBC-free quinoa leaves in response to salt stress. EBC-free leaves retained most of the transcriptome responses to salt stress, but failed to induce certain specific processes such as increased DNA replication activity. These results reveal the critical role of EBCs in salt stress acclimation of quinoa leaves.
Article
Education & Educational Research
Eric D. Deemer, Joseph P. Ogas, Amy C. Barr, Richard D. Bowdon, Mark C. Hall, Stefan Paula, Brenda M. Capobianco, Seoyoung Lim
Summary: Engaging in authentic research as a high school student can promote motivation and retention in STEM, as well as play an important role in facilitating the socialization and assimilation of students into the broader scientific community.
RESEARCH IN SCIENCE EDUCATION
(2022)
Article
Biochemistry & Molecular Biology
Damien Marchese, Florent Guislain, Tamara Pringels, Laure Bridoux
Summary: Homopolymeric amino acid repeats are common in human proteins, particularly in transcription factors and kinases. This study focuses on homopolymeric histidine repeats (polyH) and their role in regulating embryonic development. Through bioinformatic analysis, the study identifies that polyH-containing proteins interact with cysteine-rich proteins and proteins containing cysteine repeats. The study further investigates the HOXA1 protein, a transcription factor with a long polyH motif, and finds that the polyH motif is necessary for its interaction with cysteine-rich proteins. Additionally, the study discovers that metal ions are required for the HOXA1-MDFI interaction and identifies three polyH interactors that down-regulate the transcriptional activity of HOXA1.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2024)
