Article
Chemistry, Multidisciplinary
Yan Gao, Xinlei Sheng, Doudou Tan, SunJoo Kim, Soyoung Choi, Sanjita Paudel, Taeho Lee, Cong Yan, Minjia Tan, Kyu Min Kim, Sam Seok Cho, Sung Hwan Ki, He Huang, Yingming Zhao, Sangkyu Lee
Summary: This study identifies acetoacetate as the precursor for lysine acetoacetylation (Kacac), a previously uncharacterized histone post-translational modification. It also finds that HBO1 can function as both an acetyltransferase and an acetoacetyltransferase. Additionally, 33 Kacac sites are identified on mammalian histones, providing insight into the distribution of this modification across species and organs.
Article
Biochemical Research Methods
Sony Shrestha, Amuza Byaruhanga Lucky, Awtum Marie Brashear, Xiaolian Li, Liwang Cui, Jun Miao
Summary: This study profiled the histone post-translational modifications (PTMs) in the development of Plasmodium falciparum gametocytes, revealing novel PTM sites and distinct patterns from asexual stages. The results suggest that these PTMs play critical roles in gametocyte development and provide insights into the epigenetic regulation in the life cycle of the malaria parasite.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Daniel S. Saxton, Jasper Rine
Summary: Genetically identical cells can have different transcriptional states. Inheritance of silenced states relies not only on the inheritance of modified histones, but also on the presence of silencers. Strong silencers recruit Sir proteins and silence the locus in all cells, while weakening silencers can result in stable silencing in some cells but with a probability of conversion to an expressed state lacking Sir protein recruitment. The presence of different silencer states and variations in silencer-bound proteins or the concentration of a structural Sir protein can modulate the probability of a locus exhibiting the silenced or expressed state.
Article
Multidisciplinary Sciences
Shihao Zhang, Xilan Yu, Yuan Zhang, Xiangyan Xue, Qi Yu, Zitong Zha, Madelaine Gogol, Jerry L. Workman, Shanshan Li
Summary: Telomeres, organized into heterochromatin, require maintenance of silent heterochromatin for chromosome stability. The study shows that Pyruvate kinase Pyk1 phosphorylates histone H3T11 and regulates gene expression through the SESAME complex. SESAME phosphorylates H3T11 at telomeres to maintain SIR complex occupancy and prevent autophagy-mediated Sir2 degradation, ultimately enhancing telomere silencing and protecting against compromised telomere silencing during aging.
NATURE COMMUNICATIONS
(2021)
Review
Medicine, Research & Experimental
Dongze Li, Li Zhang, Yanqiu He, Tingting Zhou, Xi Cheng, Wei Huang, Yong Xu
Summary: Diabetes is a prevalent global epidemic disease that is influenced by genetic, environmental, and socioeconomic factors. Histone post-translational modifications, specifically methylation and acetylation, play significant roles in the pathophysiological changes associated with diabetes. Recent advancements in mass spectrometry have identified novel histone acylation modifications, which are yet to be thoroughly investigated for their connection to diabetes.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Multidisciplinary Sciences
Fei He, Qi Yu, Min Wang, Rongsha Wang, Xuanyunjing Gong, Feng Ge, Xilan Yu, Shanshan Li
Summary: This study reveals the inhibitory effect of H3pT11 on H3K79me3 and uncovers the histone crosstalk regulating autophagy and telomere silencing. It is also discovered that Reb1 recruits the SESAME complex to telomere regions to prevent the invasion of H3K79me3 into heterochromatin, maintaining telomere silencing.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Qianyun Mei, Qi Yu, Xin Li, Jianguo Chen, Xilan Yu
Summary: Histone loss during yeast aging compromises telomere silencing by promoting Sir2 degradation through autophagy. Reduction of core histones enhances autophagy pathway, further accelerating autophagy-mediated Sir2 degradation. Screening of histone mutants and one histone modification identifies regulators of telomere silencing via modulation of core histones-autophagy-Sir2 axis.
LIFE SCIENCE ALLIANCE
(2023)
Article
Chemistry, Analytical
Ning Xia, Ting Sun, Lin Liu, Linxu Tian, Zhifang Sun
Summary: The study introduces a novel sensing platform utilizing avidin-modified interface and biotin-labeled substrates as probes for heterogeneous analysis, combining the advantages of homogeneous and heterogeneous assays while overcoming their limitations.
Review
Pharmacology & Pharmacy
Elena Kunadis, Eleftheria Lakiotaki, Penelope Korkolopoulou, Christina Piperi
Summary: Glioblastoma is the most common primary brain tumor in adults, characterized by variable histopathology, aggressiveness, and poor clinical outcomes. Epigenetic modifications play a crucial role in GBM research, providing a potential for tumor classification and prognosis, as well as for drug targeting. Recent advances in glioma epigenetic research focus on histone modifications and the use of epigenetic therapy as a valid treatment option for glioblastoma.
PHARMACOLOGY & THERAPEUTICS
(2021)
Article
Microbiology
Samantha N. Cobos, Chaim Janani, Gabriel Cruz, Navin Rana, Elizaveta Son, Rania Frederic, Jailene Paredes Casado, Maliha Khan, Seth A. Bennett, Mariana P. Torrente
Summary: In this study, the researchers explore the link between prion states and histone modifications in yeast. They find that different prion states are associated with specific changes in histone post-translational modifications. These findings provide novel insights into the function of prions in yeast.
Review
Plant Sciences
William Agbemafle, Min May Wong, Diane C. Bassham
Summary: This review summarizes key regulatory mechanisms for modulating autophagy through post-translational modification or transcriptional regulation. Plants activate cellular responses to adapt to changing environmental conditions, one of which is autophagy, where cellular components are delivered to the vacuole for degradation. Autophagy is activated by various conditions, and the pathways controlling its activation are being elucidated. However, there is still much to discover regarding how these factors work together to properly modulate autophagy in response to specific signals.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Biochemistry & Molecular Biology
Naoya Kitamura, James J. Galligan
Summary: Post-translational modifications (PTMs) rapidly respond to stimuli, finely tuning metabolism and gene expression to maintain homeostasis. Advances in mass spectrometry have expanded the list of known PTMs, but many lack defined mechanisms for their regulation. This review discusses the current state of PTM research, including site specificity, analytical methods, chemical tools, and approaches for discovering and validating novel PTMs, providing a comprehensive list and knowledge of their regulation and metabolic origins.
BIOCHEMICAL JOURNAL
(2023)
Review
Virology
Stephen P. Goff
Summary: This review provides an overview of the silencing mechanisms of retroviral DNA, discussing its impact on virus replication, the sensing of the virus by the innate immune system, and the formation of latent proviruses. Additionally, it speculates on the potential transition to high expression from integrated proviruses in permissive cell types, as well as the silencing of proviruses even after integration in embryonic stem cells and other developmentally primitive cell types.
Article
Oncology
Roberta Noberini, Evelyn Oliva Savoia, Stefania Brandini, Francesco Greco, Francesca Marra, Giovanni Bertalot, Giancarlo Pruneri, Liam A. McDonnell, Tiziana Bonaldi
Summary: This study simplified the protein extraction process from low-amount clinical samples and developed a protocol that allows MS-based analysis of histone PTMs from laser microdissected tissue areas with as low as 1000 cells, which is approximately 500 times lower than what is required by available methods. This method opens the possibility for spatial epi-proteomics, facilitating the investigation of epigenetic features in tissue and tumor heterogeneity and aiding in the discovery of novel epigenetic biomarkers and mechanisms.
CLINICAL EPIGENETICS
(2021)
Review
Microbiology
Yiman Li, Zhihui Song, Ente Wang, Liming Dong, Jie Bai, Dong Wang, Jinyan Zhu, Chao Zhang
Summary: Invasive aspergillosis is a significant cause of death in patients with hematological malignancies and transplant recipients. Antifungal drug resistance has become a concern in managing infections, and understanding histone posttranslational modifications may provide insights for developing new antifungal drugs.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Cell Biology
Jan Padeken, Stephen Methot, Peter Zeller, Colin E. Delaney, Veronique Kalck, Susan M. Gasser
Summary: The study shows that the histone methyltransferase SET-25 in C. elegans can establish repressed chromatin domains, silencing novel insertions of transposons and tissue-specific genes during development. Two redundant pathways recruit SET-25 to its targets, with one pathway involving LIN-61 and MET-2, and the other pathway involving NRDE-3 and small RNAs, primarily targeting conserved transposons. The loss of these pathways results in the derepression of transposons in embryos, leading to increased embryonic lethality.
GENES & DEVELOPMENT
(2021)
Article
Biochemistry & Molecular Biology
Romain Forey, Antoine Barthe, Mireille Tittel-Elmer, Maxime Wery, Marie-Benedicte Barrault, Cecile Ducrot, Andrew Seeber, Nils Krietenstein, Ugo Szachnowski, Magdalena Skrzypczak, Krzysztof Ginalski, Maga Rowicka, Jennifer A. Cobb, Oliver J. Rando, Julie Soutourina, Michel Werner, Karine Dubrana, Susan M. Gasser, Antonin Morillon, Philippe Pasero, Armelle Lengronne, Jerome Poli
Summary: Mre11-Rad50-Xrs2 (MRX) plays a new role in limiting transcription in budding yeast by physically interacting and colocalizing with the transcriptional co-regulator Mediator on chromatin. MRX restricts transcription of coding and noncoding DNA by tethering transcriptionally active loci to the nuclear pore complex (NPC), promoting gene-NPC interactions, contributing to chromosome folding, and controlling gene expression. These findings suggest a distinct role for MRX in transcription and chromosome organization apart from its known function in DNA repair.
Editorial Material
Biochemistry & Molecular Biology
Noriko Saitoh, Susan M. Gasser
Article
Biochemistry & Molecular Biology
Kiran Challa, Christoph D. Schmid, Saho Kitagawa, Anais Cheblal, Vytautas Iesmantavicius, Andrew Seeber, Assaf Amitai, Jan Seebacher, Michael H. Hauer, Kenji Shimada, Susan M. Gasser
Summary: In eukaryotic cells, checkpoint activation leads to degradation of core histones, resulting in reduced nucleosome occupancy. Extensive changes in chromatin-associated protein composition were observed after DNA damage, including loss of core histones, recruitment of ubiquitin ligases, and compromised DNA strand invasion kinetics during repair. This study provides a comprehensive overview of the genome-wide chromatin response to DNA damage.
Review
Genetics & Heredity
Jeannette Fuchs, Anais Cheblal, Susan M. Gasser
Summary: Recent studies have highlighted the crucial role of DNA Polymerase 5 (DNA Pol 5) in replication forks, especially under stress conditions. Mutations affecting POLD1, amplifications of POLD2 and POLD3, and compromising the noncatalytic subunits of DNA Pol 5 are all closely related to cancer development and may open up avenues for novel therapies addressing replication stress.
TRENDS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Raphael J. Guebeli, Davide Bertoldo, Kenji Shimada, Christian B. Gerhold, Verena Hurst, Yuichiro Takahashi, Kai Harada, Ganesh K. Mothukuri, Jonas Wilbs, Masahiko Harata, Susan M. Gasser, Christian Heinis
Summary: Actin, the most abundant protein in eukaryotic cells, plays a crucial role in many cellular functions. In this study, through phage display screening, bicyclic peptides with low nanomolar affinity for G-actin were isolated, showing a strong similarity to thymosin-beta 4. These peptides were found to bind to a common region on actin and were evaluated for use as probes in various experiments, with the results indicating that G-actin peptides did not bind in cellular context likely due to competition with thymosin-beta 4.
ACS CHEMICAL BIOLOGY
(2021)
Editorial Material
Cell Biology
Susan M. Gasser, Gerd A. Blobel
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2021)
Article
Cell Biology
Stephen P. Methot, Jan Padeken, Giovanna Brancati, Peter Zeller, Colin E. Delaney, Dimos Gaidatzis, Hubertus Kohler, Alexander van Oudenaarden, Helge Grosshans, Susan M. Gasser
Summary: The deposition of H3K9me2 and H3K9me3 can repress lineage-specific and germline genes in terminally differentiated Caenorhabditis elegans tissues by restricting the activity of specific transcription factors. Changes in H3K9me during development affect gene regulation and the maintenance of cellular functions.
NATURE CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Colin E. Delaney, Stephen P. Methot, Veronique Kala, Jan Seebacher, Daniel Hess, Susan M. Gasser, Jan Padeken
Summary: Genetic and genome-wide analysis of the SETDB1-like enzyme MET-2 in Caenorhabditis elegans reveals its role in promoting transcriptional silencing and fertility through both H3K9 methylation and focus formation. MET-2 has a noncatalytic function that contributes to gene repression. In normal development, MET-2 activity helps maintain fertility, while under heat stress, MET-2 foci disperse, resulting in increased acetylation and transcriptional derepression.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Review
Cell Biology
Jan Padeken, Stephen P. Methot, Susan M. Gasser
Summary: Heterochromatin is characterized by histone H3 Lys9 methylation, which ensures transcriptional silencing of repetitive elements and genes. The methyltransferases and "readers" of H3K9me2 or H3K9me3 are highly conserved and show redundancy. Loss or mistargeting of individual H3K9 methyltransferases can lead to impaired cell differentiation, loss of tissue identity, premature aging, and/or cancer. Recent studies in mammals have shed light on the roles of H3K9-specific histone methyltransferases in transcriptional homeostasis during tissue differentiation.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2022)
Correction
Biochemistry & Molecular Biology
Colin E. Delaney, Stephen P. Methot, Veronique Kalck, Jan Seebacher, Daniel Hess, Susan M. Gasser, Jan Padeken
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Editorial Material
Genetics & Heredity
Susan M. Gasser
Summary: In this interview, Professor Susan Gasser discusses her research on genome stability, epigenetic regulation, and chromatin organization, as well as her efforts in supporting women in research. She has made significant contributions to the field of chromatin structure and has been recognized with numerous awards and honors. She continues to actively promote the careers of women scientists in Europe and Japan.
Editorial Material
Biochemistry & Molecular Biology
Marta Rodriguez-Martinez, Jens Nielsen, Sam Dupont, Jessica Vamathevan, Beverley J. Glover, Lindsey C. Crosswell, Brendan Rouse, Ben F. Luisi, Chris Bowler, Susan M. Gasser, Detlev Arendt, Tobias J. Erb, Victor de Lorenzo, Edith Heard, Kiran Raosaheb Patil
Summary: Molecular biology has great potential in addressing climate change and biodiversity loss, but it is currently not well incorporated into strategies. We call for a community-wide action to bring molecular biology to the forefront of climate change solutions.
Review
Biochemistry & Molecular Biology
Susan M. Gasser, Francoise Stutz
Summary: The covalent linkage of Ubiquitin and SUMO to lysine residues plays important roles in DNA repair pathway choice and transcription regulation. SUMOylation mainly affects cellular processes by relocalizing modified proteins, particularly in response to DNA damage.
Editorial Material
Cell Biology
Susan M. M. Gasser
Summary: The compact state of chromatin induced by methylation of H3K9 on histone H3 is believed to be involved in heritable transcriptional repression. A recent study reveals that transient deposition of H3K9me3 helps stabilize stalled DNA replication forks, while its reversal allows for accurate fork restart.
NATURE CELL BIOLOGY
(2023)
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.
