Article
Plant Sciences
Zhichao Zhang, Shuai Yu, Jing Li, Yanbin Zhu, Siqi Jiang, Haoran Xia, Yue Zhou, Daqiu Sun, Meiling Liu, Cong Li, Yanshu Zhu, Yanye Ruan, Xiaomei Dong
Summary: A total of 691 possible imprinted genes were identified in the sunflower endosperm, showing conservation and intraspecific variation, with limited imprinted loci found in other species. The study suggests that demethylation in the maternal CG context may induce genomic imprinting in the endosperm.
Article
Plant Sciences
Daniel Matsusaka, Javier F. Botto, Diego H. Sanchez
Summary: This study reveals the central regulatory role of specific noncoding tandem repeats in the intersection between epigenetic silencing and gene expression, and their importance in plant stress responses.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Multidisciplinary Sciences
Xiaochao Chen, Dana R. R. MacGregor, Francesca L. L. Stefanato, Naichao Zhang, Thiago Barros-Galvao, Steven Penfield
Summary: Mother plants play a crucial role in determining the dispersal characteristics of their progeny by controlling seed dormancy. The study shows that the VEL3 histone deacetylase complex establishes an epigenetic state in the maternal plant, which regulates progeny seed dormancy. This mechanism involves the association of VEL3 with a histone deacetylase complex, preferential attachment to pericentromeric chromatin, and repression of specific genes to control seed behavior.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Hikaru Sato, Juan Santos-Gonzalez, Claudia Koehler
Summary: The study reveals that maternal alleles marked by H3K27me3 in Arabidopsis endosperm are targeted by the H3K27me3 demethylase REF6 and become activated during germination, while other maternal alleles marked by H3K27me3, H3K9me2, and CHG methylation are protected from REF6 targeting and remain silenced. This suggests that combinations of different repressive epigenetic modifications play a role in modulating access of REF6 and timing key adaptive traits.
Review
Andrology
Blake A. Caldwell, Marisa S. Bartolomei
Summary: The mammalian genome undergoes two extensive epigenetic reprogramming events during development, with DNA demethylation playing a critical role in germline cells and TET1 being crucial for imprinted gene reprogramming.
Review
Cell & Tissue Engineering
Xinhui Liu, Aamir Khan, Huan Li, Shensen Wang, Xuechai Chen, Hua Huang
Summary: Emerging evidence suggests that vitamin C enhances the reprogramming process by acting as a cofactor in DNA and histone demethylation. It also potentially plays a role in regulating RNA methylation and cellular reprogramming. This review highlights the significance of vitamin C in epigenetic regulation and its affiliation with demethylases in facilitating epigenetic reprogramming.
CURRENT STEM CELL RESEARCH & THERAPY
(2022)
Article
Plant Sciences
Qiang Han, Yu-Hung Hung, Changqing Zhang, Arthur Bartels, Matthew Rea, Hanwen Yang, Christine Park, Xiang-Qian Zhang, Robert L. L. Fischer, Wenyan Xiao, Tzung-Fu Hsieh
Summary: In Arabidopsis, the maternal linker histone H1 influences DME-mediated demethylation, but has limited effects on gene transcription and overall imprinting regulation in the endosperm.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
James P. B. Lloyd, Florence Ly, Patrick Gong, Jahnvi Pfluger, Tessa Swain, Christian Pfluger, Elliott Fourie, Muhammad Adil Khan, Brendan N. Kidd, Ryan Lister
Summary: Transcriptional activity in plants is controlled by programmable gene circuits. Synthetic gene circuits have the potential to integrate and customize signals. This study presents a suite of recombinase-based gene circuits for use in plants, which can be used to programmably manipulate transcriptional activity and have stable long-term effects.
NATURE BIOTECHNOLOGY
(2022)
Article
Plant Sciences
Hironori Takasaki, Miho Ikeda, Reika Hasegawa, Yilin Zhang, Shingo Sakamoto, Daisuke Maruyama, Nobutaka Mitsuda, Tetsu Kinoshita, Masaru Ohme-Takagi
Summary: Apomixis, the transfer of maternal germplasm to offspring without fertilization, is a useful process in crop breeding. However, most apomictic plants still require pollination for endosperm development. This study shows that the expression of the ESP3-SRDX gene in Arabidopsis allows for ovule enlargement without fertilization. The unfertilized ESP3-SRDX ovules can partially nourish embryos and exhibit gene expression similar to fertilized seeds.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Cell & Tissue Engineering
Yoichi Sekita, Yuki Sugiura, Akari Matsumoto, Yuki Kawasaki, Kazuya Akasaka, Ryo Konno, Momoka Shimizu, Toshiaki Ito, Eiji Sugiyama, Terushi Yamazaki, Eriko Kanai, Toshinobu Nakamura, Makoto Suematsu, Fumitoshi Ishino, Yoshio Kodera, Takashi Kohda, Tohru Kimura
Summary: The study reveals that AKT signaling is involved in TET-mediated DNA demethylation during cellular reprogramming, enhancing glucose metabolism and increasing levels of alpha-ketoglutarate. This leads to genome-wide changes in DNA methylation and upregulation of pluripotency genes. AKT activation promotes epigenetic reprogramming by hyperactivating TET at transcriptional and catalytic levels.
STEM CELL RESEARCH & THERAPY
(2021)
Article
Agronomy
Zhanyu Chen, Yingying Zhang, Jiating Zhang, Bei Fan, Ying Zhou, Xiyan Cui
Summary: The study on the amino acid permease (AAP) in Arabidopsis thaliana revealed differential expression patterns of AtAAP genes in different tissues. Overexpression of specific genes led to increased amino acid contents in reproductive organs, indicating the potential for improved utilization of organic nitrogen.
Article
Plant Sciences
Bing Han, Yelan Li, Di Wu, De-Zhu Li, Aizhong Liu, Wei Xu
Summary: Genomic imprinting plays a significant role in the endosperm development, storage compound accumulation, and seed germination in castor bean. The study reveals that DNA methylation has a limited role in controlling genomic imprinting, while histone modifications play a more significant role in regulating the expression of most imprinted genes.
Article
Multidisciplinary Sciences
Run Jin, Samantha Klasfeld, Yang Zhu, Meilin Fernandez Garcia, Jun Xiao, Soon-Ki Han, Adam Konkol, Doris Wagner
Summary: This study reveals that the plant pioneer transcription factor LFY promotes floral cell fate by locally unlocking chromatin through displacing histone H1 and recruiting SWI/SNF chromatin remodelers, providing biochemical evidence for a pioneer factor in plants and showing similarities with animal pioneer transcription factors.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Joao C. Sabino, Madalena R. de Almeida, Patricia L. Abreu, Ana M. Ferreira, Paulo Caldas, Marco M. Domingues, Nuno C. Santos, Claus M. Azzalin, Ana Rita Grosso, Sergio Fernandes de Almeida
Summary: The activity of TET enzymes promotes the formation of R-loops, revealing new mechanisms of gene expression regulation.
Article
Chemistry, Physical
Yang Song, Jennifer Soto, Binru Chen, Tyler Hoffman, Weikang Zhao, Ninghao Zhu, Qin Peng, Longwei Liu, Chau Ly, Pak Kin Wong, Yingxiao Wang, Amy C. Rowat, Siavash K. Kurdistani, Song Li
Summary: Deformation of the cell nucleus boosts cell reprogramming and offers potential applications in cell engineering.
Article
Biochemistry & Molecular Biology
Sangrea Shim, Hong Gil Lee, Ok-Sun Park, Hosub Shin, Kyounghee Lee, Hongwoo Lee, Jin Hoe Huh, Pil Joon Seo
Summary: During the formation of callus in plant somatic cells, DNA methylation plays a key role in coordinating cell cycle regulation. Researchers found that genes involved in cell cycle regulation were enriched during the transition from leaves to callus, forming a coexpression gene network with pluripotency regulators. Additionally, CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) was newly identified as a regulator of plant regeneration.
Article
Biochemistry & Molecular Biology
Hosub Shin, Hye Rang Park, Jeong Eun Park, Seung Hwa Yu, Gibum Yi, Jung Hyo Kim, Wonjun Koh, Hyun Hee Kim, Soo-Seong Lee, Jin Hoe Huh
Summary: The study revealed that non-homologous interactions causing unequal segregation of meiotic chromosomes are the main reason behind pollen sterility and seed abortion in xBrassicoraphanus. This abnormality leads to micronuclei formation and unbalanced gamete production, resulting in decreased fertility in hybrid lines.
Article
Biochemistry & Molecular Biology
Yong Juan Zhao, Wei Ming He, Zhi Ying Zhao, Wan Hua Li, Qian Wen Wang, Yun Nan Hou, Yongjun Tan, Dapeng Zhang
Summary: SARM1 can be activated by NMN, CZ-48, VMN and acid, with acid being even more effective through protonation of negative residues. Mutations can lead to constitutive activation of SARM1, with the E689Q mutation forming a salt bridge with R216 to maintain the autoinhibitory structure. Two inhibitory mechanisms of SARM1, through K597E mutation to inhibit activation and H685A mutation to eliminate catalytic activity, were revealed using an 'acid activation' protocol.
Article
Multidisciplinary Sciences
Gibum Yi, Hosub Shin, Kyeonglim Min, Eun Jin Lee
Summary: In this study, a meta-analysis of existing transcriptome data from six cultivars of strawberry was conducted, revealing cultivar-specific transcriptome changes and common gene expression patterns during ripening. The study identified previously undisclosed genes related to photosynthesis and amino acid and fatty acid biosynthesis, enriching the understanding of strawberry ripening at the transcriptomic level.
Article
Microbiology
Yongjun Tan, Cindy Wang, Theresa Schneider, Huan Li, Robson Francisco de Souza, Xueming Tang, Kylie D. Swisher Grimm, Tzung-Fu Hsieh, Xu Wang, Xu Li, Dapeng Zhang
Summary: This study conducted an in-depth comparative genomic analysis of Liberibacter pathogens and their nonpathogenic ancestral species, identifying various types of prophage loci and novel toxins that are evolutionarily linked to the emergence of the pathogens. Genomic genes that were lost or gained in the ancestor of the pathogens were identified, with the lost genes related to the biosynthesis of cellular building blocks and the gained genes including previously unrecognized toxins.
MICROBIOLOGY SPECTRUM
(2021)
Article
Biochemistry & Molecular Biology
Theresa Schneider, Yongjun Tan, Huan Li, Jonathan S. Fisher, Dapeng Zhang
Summary: By conducting computational analyses, the authors identified a new type of non-heme binding globin called photoglobin, which may act as a light sensor in complex prokaryotic signal transduction systems.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Plant Sciences
Hosub Shin, Jeong Eun Park, Hye Rang Park, Woo Lee Choi, Seung Hwa Yu, Wonjun Koh, Seungill Kim, Hye Yeon Soh, Nomar Espinosa Waminal, Hadassah Roa Belandres, Joo Young Lim, Gibum Yi, Jong Hwa Ahn, June-Sik Kim, Yong-Min Kim, Namjin Koo, Kyunghee Kim, Sampath Perumal, Taegu Kang, Junghyo Kim, Hosung Jang, Dong Hyun Kang, Ye Seul Kim, Hyeon-Min Jeong, Junwoo Yang, Somin Song, Suhyoung Park, Jin A. Kim, Yong Pyo Lim, Beom-Seok Park, Tzung-Fu Hsieh, Tae-Jin Yang, Doil Choi, Hyun Hee Kim, Soo-Seong Lee, Jin Hoe Huh
Summary: This study reports the hybrid genome structure of a synthetic allotetraploid, xBrassicoraphanus, and investigates chromosome behaviors, transcription network reconstruction, and genome methylation in the hybrid. The results demonstrate that hybrid genome stabilization and transcription compatibility necessitate epigenome landscape adjustment and rewiring of cis-trans interactions.
Article
Biochemistry & Molecular Biology
Huan Li, Theresa Schneider, Yongjun Tan, Dapeng Zhang
Summary: This study revealed that many proteins remain unclassified in current protein databases. By reconstructing the structure of RNase T2 and comparing it with other BECR RNases, a hidden relationship was discovered. This suggests that reconstruction and modeling of ancestral topology can be an effective strategy to identify remote relationships between proteins.
Article
Plant Sciences
Qiang Han, Yu-Hung Hung, Changqing Zhang, Arthur Bartels, Matthew Rea, Hanwen Yang, Christine Park, Xiang-Qian Zhang, Robert L. L. Fischer, Wenyan Xiao, Tzung-Fu Hsieh
Summary: In Arabidopsis, the maternal linker histone H1 influences DME-mediated demethylation, but has limited effects on gene transcription and overall imprinting regulation in the endosperm.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Jaehoon Lee, Seunga Lee, Kyunghyuk Park, Sang-Yoon Shin, Jennifer M. Frost, Ping-Hung Hsieh, Chanseok Shin, Robert L. Fischer, Tzung-Fu Hsieh, Yeonhee Choi
Summary: Through profiling DNA methylation at five stages of Arabidopsis embryogenesis, we found that the gradual increase in mCHH coincides with the expansion of small RNA expression and the spreading of mCHH to nearby sites. We also identified distinct methylation dynamics in different groups of mCHH targets, which are associated with the length, location, and cytosine frequency of transposons.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Ya-Chen Huang, Yu-tang Wang, Yee-ching Choong, Hsin-ya Huang, Yu-ru Chen, Tzung-Fu Hsieh, Yann-rong Lin
Summary: This study investigates the relationship between gene expression and temperature in foxtail millet, revealing how temperature and gene interactions affect the growth and flowering time, providing a foundation for breeding foxtail millet cultivars that can adapt to global warming.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Huan Li, Yongjun Tan, Dapeng Zhang
Summary: Bacteria have developed various molecular conflict systems, including polymorphic toxin systems (PTSs), to facilitate kin recognition and non-kin competition for growth niches and limited resources. However, the highly divergent nature of these systems makes it challenging to identify and characterize them using traditional experimental and bioinformatic approaches. In this study, the researchers used unique genome-mining strategies and pipelines based on the organizational principles of domain architectures and genomic loci to systematically discover a new type of PTS (S8-PTS) in gram-positive bacteria. They revealed the components and organization of the S8-PTS, classified the toxin domains into different superfamily groups, and identified the associated immunity proteins. Furthermore, they found that the peptidases associated with S8-PTS are similar to processing peptidases found in other secretion systems and proprotein-processing peptidases. The S8-PTSs are mostly found in animal and plant-associated bacteria, including many pathogens, suggesting their role in microbial competition and pathogen-host interactions.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Agronomy
Xin Luan, Shanwen Ke, Shuchun Liu, Guojian Tang, Dahui Huang, Minyi Wei, Yuexiong Zhang, Gang Qin, Xiang-Qian Zhang
Summary: The study found that rice caryopsis development can be genetically uncoupled from the size control of the outer glume, and OsPEX1 gene may be a new resource for improving the nutritional quality of rice.
Article
Virology
Yongjun Tan, Theresa Schneider, Prakash K. Shukla, Mahesh B. Chandrasekharan, L. Aravind, Dapeng Zhang
Summary: This study reveals the evolutionary history of ion channel proteins in the coronavirus family, unifying various protein families in different viral strains and suggesting the importance of conserved polar residues in forming water pores for virion assembly. The research demonstrates the significant role of ion channels in virion assembly and membrane budding, with different evolutionary pressures observed for structural components like M protein and ORF3, indicating potential interaction with host molecules and immune responses.