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
Plant Sciences
Kosuke Nozawa, Seiji Masuda, Hidetoshi Saze, Yoko Ikeda, Takamasa Suzuki, Hiroki Takagi, Keisuke Tanaka, Naohiko Ohama, Xiaoying Niu, Atsushi Kato, Hidetaka Ito
Summary: This study analyzed the transcriptional activation of the ONSEN retrotransposon in response to high-temperature stress in Arabidopsis thaliana, finding that Kyoto ecotypes showed significantly higher transcription levels due to reduced CHH methylation and a mutation in the CMT2 gene. Additionally, lower levels of repressive histone markers H3K9me2 and H3K27me1 were observed in Kyoto compared to Col-0.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Oncology
Guanzheng Liu, Chaojie Bu, Guangzhong Guo, Zhiyue Zhang, Zhiyuan Sheng, Kaiyuan Deng, Shuang Wu, Sensen Xu, Yage Bu, Yushuai Gao, Meiyun Wang, Gang Liu, Lingfei Kong, Tianxiao Li, Ming Li, Xingyao Bu
Summary: This study evaluated the genetic changes in oligodendroglioma during tumor progression using deep whole-genome sequencing. The study found that there was low rate of shared mutations between the primary and recurrent samples. Two patients showed a conversion in the IDH mutation during gene evolution under chemotherapy treatment. The PI3K/AKT and SHh signaling pathways may play a role in treatment resistance and distant relapse during oligodendroglioma evolution.
Article
Multidisciplinary Sciences
Jie Yang, Qianghu Wang, Ze-Yan Zhang, Lihong Long, Ravesanker Ezhilarasan, Jerome M. Karp, Aristotelis Tsirigos, Matija Snuderl, Benedikt Wiestler, Wolfgang Wick, Yinsen Miao, Jason T. Huse, Erik P. Sulman
Summary: Molecular classification has improved diagnosis and treatment for patients with malignant gliomas. This study proposes using DNA methylation as a clinical diagnostic platform to classify gliomas and provide subtype characteristics, showing accurate prediction and improvement over existing classifiers. The developed Unified Diagnostic Pipeline (UniD) is rapid and cost-effective, and can be applied to other malignancies.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Piotr Gawronski, Christel Enroth, Peter Kindgren, Sebastian Marquardt, Stanislaw Karpinski, Dario Leister, Poul Erik Jensen, Jeppe Vinther, Lars B. Scharff
Summary: The study revealed that mRNA secondary structure influences translation in plastids, with increased accessibility of the translation initiation region of psbA mRNA after exposure to high light. The presence of a putative regulatory protein in the 5 ' UTR of psbA was identified, which may cause structural opening of the translation initiation region, facilitating ribosome access. This suggests that changes in mRNA secondary structure could represent a general mechanism for translational regulation of psbA and other plastid genes.
Article
Plant Sciences
Niels Tol, Robin Schendel, Alex Bos, Maartje Kregten, Sylvia Pater, Paul J. J. Hooykaas, Marcel Tijsterman
Summary: Agrobacterium tumefaciens-mediated transformation is the preferred tool for generating transgenic plants, but gene targeting (GT) events occur at low frequency and are often accompanied by random integration events. The functionality of polymerase theta (Pol theta) affects the biology of GT in plants, with its deficiency preventing T-DNA integration and ectopic GT events. Insights obtained from this study can be used for developing strategies to achieve high-quality GT events in crop plants.
Article
Biochemistry & Molecular Biology
Wei Fu, Yaoguang Yu, Jie Shu, Zewang Yu, Yixiong Zhong, Tao Zhu, Zhihao Zhang, Zhenwei Liang, Yuhai Cui, Chen Chen, Chenlong Li
Summary: Three Arabidopsis SWI/SNF chromatin remodeling complexes, BAS, SAS, and MAS, have unique and shared roles, distinct organization, genomic targeting, and assembly.
Article
Agronomy
Santosh Nayak, Hem Bhandari, Vince Pantalone, Malay C. Saha, Shahjahan Ali, Carl Sams
Summary: Switchgrass is a promising species for biofuel production on marginal land, but soil salinity can limit its biomass yield. This study identified genetic variation in switchgrass and found five quantitative trait loci (QTL) associated with salinity tolerance, as well as candidate genes related to salinity tolerance.
Correction
Plant Sciences
O. Batistic, R. Waadt, L. Steinhorst, K. Held, J. Kudla
Summary: The ribosome stalling at AUG-stop sequences plays a critical role in regulating the expression of NIP5;1 in Arabidopsis thaliana in response to boron conditions, with boric acid triggering this process. Through ribosome profiling analysis, hundreds of translationally regulated genes functioning in various biological processes were identified, with a particular emphasis on the role of uORFs. The presence of minimum uORFs (AUG-stops) suggests these elements play a global role in responding to boron, as evidenced by the increased ribosome occupancy of stop codons under high-boron conditions.
Article
Plant Sciences
Cyprian A. Rajabu, Mary M. Dallas, Evangelista Chiunga, Leandro De Leon, Elijah M. Ateka, Fred Tairo, Joseph Ndunguru, Jose T. Ascencio-Ibanez, Linda Hanley-Bowdoin
Summary: SEGS-1 enhances disease symptoms in both cassava and Arabidopsis plants infected with cassava mosaic begomoviruses. It can increase viral disease severity in a heterologous host and does not require episomal DNA for disease enhancement.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Jose Cerca, Bent Petersen, Jose Miguel Lazaro-Guevara, Angel Rivera-Colon, Siri Birkeland, Joel Vizueta, Siyu Li, Qionghou Li, Joao Loureiro, Chatchai Kosawang, Patricia Jaramillo Diaz, Gonzalo Rivas-Torres, Mario Fernandez-Mazuecos, Pablo Vargas, Ross A. McCauley, Gitte Petersen, Luisa Santos-Bay, Nathan Wales, Julian M. Catchen, Daniel Machado, Michael D. Nowak, Alexander Suh, Neelima R. Sinha, Lene R. Nielsen, Ole Seberg, M. Thomas P. Gilbert, James H. Leebens-Mack, Loren H. Rieseberg, Michael D. Martin
Summary: Many island plant species exhibit a syndrome known as the 'plant island syndrome', which involves distinct phenotypic and life history traits. In this study, the researchers sequenced and analyzed the genome of the critically endangered Galapagos-endemic species Scalesia atractyloides Arnot. They identified the genomic basis of the island syndrome and determined the ancestral genomes and their divergence in this species.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Muhammad Farooq, Aalt D. J. van Dijk, Harm Nijveen, Mark G. M. Aarts, Willem Kruijer, Nguyen Thu-Phuong, Shahid Mansoor, Dick de Ridder
Summary: Prediction of growth-related complex traits in crop breeding has been revolutionized by technological advancements in genomics and phenomics. Incorporating prior biological knowledge can improve genomic prediction accuracy, with the effectiveness depending on the trait, type of knowledge, and trait heritability. Transcriptomics provides additional evidence for improvement when defining functional gene groups.
FRONTIERS IN GENETICS
(2021)
Article
Engineering, Environmental
Diwu Fan, Yong Sun, Moxian Chen, Yongli Zhu, Evgenios Agathokleous, Fuyuan Zhu, Jiangang Han
Summary: This study aimed to identify and verify key genes in regulating Cd-induced hormesis in Arabidopsis thaliana. The results showed that hormesis occurred at certain concentrations of Cd, and the antioxidant defense system and photosynthesis system played roles in hormesis. The key gene ABF1 in the metabolic pathway of abscisic acid was identified and found to be essential for Cd-induced hormesis.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Ivano Forgione, Antonella Muto, Magdalena Woloszynska, Adriana Ada Chiappetta, Michele Ferrari, Mieke Van Lijsebettens, Maria Beatrice Bitonti, Leonardo Bruno
Summary: This study explores the molecular basis of the abnormal leaf phenotype in the ddc mutant of Arabidopsis thaliana. It demonstrates that misexpression of genes related to leaf fate commitment and morphogenesis, such as CLF and KNAT6, is responsible for the abnormal phenotype. Epigenetic mechanisms, including DNA methylation and histone modifications, are proposed to regulate the expression of these genes during leaf morphogenesis in the ddc mutant.