Article
Cell Biology
Rene Massimiliano Marsano, Patrizio Dimitri
Summary: Transposable elements (TEs) are abundant components of constitutive heterochromatin and their accumulation in the genome may be influenced by reduced recombination and lack of functional genes. However, recent studies suggest that constitutive heterochromatin contains active genes and the accumulation of TEs may play a role in centromere and telomere structure.
Article
Biochemistry & Molecular Biology
Marzia Rossato, Luca Marcolungo, Luca De Antoni, Giulia Lopatriello, Elisa Bellucci, Gaia Cortinovis, Giulia Frascarelli, Laura Nanni, Elena Bitocchi, Valerio Di Vittori, Leonardo Vincenzi, Filippo Lucchini, Kirstin E. Bett, Larissa Ramsay, David James Konkin, Massimo Delledonne, Roberto Papa
Summary: High-throughput genotyping allows for the analysis of genetic diversity in large populations and genome-wide association studies. In this study, the researchers used CRISPR-Cas9 technology to remove repetitive elements in the lentil genome, thus focusing the sequencing data on coding and regulatory regions. This method significantly increased genotyping accuracy and the number of genotyped bases compared to non-depleted libraries.
Article
Multidisciplinary Sciences
Fernando Rodriguez, Irina A. Yushenova, Daniel DiCorpo, Irina R. Arkhipova
Summary: This study discovered a DNA methyltransferase, N4CMT, derived from bacteria in bdelloid rotifers that can deposit 4mC on active transposons and certain tandem repeats, thereby silencing these genes. This suggests that horizontal gene transfer has the potential to drive regulatory innovation in eukaryotes.
NATURE COMMUNICATIONS
(2022)
Review
Plant Sciences
Stephanie P. Klein, Sarah N. Anderson
Summary: Transposable elements (TEs) are a significant component of plant genomes, and growing evidence suggests that they play a crucial role in driving phenotypic diversity and stress responses in plants. The lack of evolutionary conservation in TE families and locus insertions necessitates collaboration among TE experts across diverse species for utilizing TE variation in crop improvement.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Review
Plant Sciences
Elizabeth A. Hemenway, Mary Gehring
Summary: The establishment, maintenance, and removal of epigenetic modifications in plants provide an additional layer of regulation beyond genetic factors, allowing for control of developmental processes and adaptation to the environment. Epigenetic inheritance, which can refer to information not encoded in the DNA sequence inherited between generations or epigenetic modifications reset between generations, is of great interest in understanding the functions and mechanisms in plants. This article discusses examples of epigenetic dynamics and maintenance during growth and development stages and their functional consequences, as well as the dynamic nature of epigenetic states in response to stress and their impact on transposable element regulation. The emerging area of research focuses on understanding how epigenetic resetting occurs during normal development and in response to stress.
ANNUAL REVIEW OF PLANT BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Irina R. Arkhipova, Irina A. Yushenova, Fernando Rodriguez
Summary: DNA methylation is a prominent feature of epigenetics, with DNA methyltransferases being transferred from prokaryotes to eukaryotes and co-opted into epigenetic regulatory systems. While the role of C5-methylcytosine in epigenetics is well-studied, the epigenetic effects of other methylated bases are less understood. The discovery of N4-methylcytosine of bacterial origin in metazoan DNA challenges the existing paradigms of eukaryotic regulatory systems' origin and evolution.
Article
Biology
Pengju Zhao, Lihong Gu, Yahui Gao, Zhangyuan Pan, Lei Liu, Xingzheng Li, Huaijun Zhou, Dongyou Yu, Xinyan Han, Lichun Qian, George E. Liu, Lingzhao Fang, Zhengguang Wang
Summary: This study found that transposable elements (TEs), particularly young short interspersed nuclear elements (SINEs), play important roles in genetic polymorphisms, chromatin architecture, gene regulatory networks, and genomic evolution in pigs. Silencing of young SINEs was observed through histone modifications, DNA methylation, and decreased accessibility, but some active young SINE transcripts showed tissue-specific expression. The presence of population-specific dimorphic SINEs suggested their involvement in local adaptation, and these SINEs were found to be associated with candidate genes related to complex traits in pigs.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Rory J. Craig
Summary: HUH endonucleases are involved in the replication of diverse plasmids and viral genomes. Replitron transposons are a group of eukaryotic transposons encoding Rep HUH endonuclease. Replitrons have a distinct structure compared to other transposons, and they are closely related to circular Rep-encoding single-stranded DNA viruses. This study reveals the evolutionary origin and diversity of Replitrons in eukaryotes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Plant Sciences
Yafang Xiao, Zengde Xi, Fei Wang, Jianbo Wang
Summary: Epigenetic modifications of transposable elements (TEs) play a crucial role in the establishment and evolution of allopolyploids, promoting adaptation to new environments. TE modification levels tend to be similar to those of the diploid parents, with the An subgenome showing higher modification rates. This imbalance may contribute to subgenome dominance.
Article
Plant Sciences
Maria Luz Annacondia, Dimitrije Markovic, Juan Luis Reig-Valiente, Vassilis Scaltsoyiannes, Corne M. J. Pieterse, Velemir Ninkovic, R. Keith Slotkin, German Martinez
Summary: Environmental stresses, such as infestation by green peach aphids, can lead to activation of transposable elements and loss of DNA methylation in plants, ultimately affecting gene expression and plant immunity. Plants deficient in DNA and H3K9 methylation show increased resistance to aphid infestation, highlighting the significant role of DNA methylation in regulating plant transcriptional response and defense mechanisms.
Article
Biochemistry & Molecular Biology
Aline Muyle, Danelle Seymour, Nikos Darzentas, Elias Primetis, Brandon S. Gaut, Alexandros Bousios
Summary: This study reveals that TE capture triggers an intragenomic conflict, potentially leading to pseudogenization of less-constrained genes, while not affecting the function of important genes.
Review
Biotechnology & Applied Microbiology
Yuxin Pan, Yuhui Zhuang, Tao Liu, Hua Chen, Lihui Wang, Rajeev K. Varshney, Weijian Zhuang, Xiyin Wang
Summary: Peanut is a globally important oil and protein crop with a large genome. The sequencing of diploid and tetraploid peanut genomes has provided insights into their genome structures, evolution, and biological characteristics. The sequencing efforts revealed a subgenome bias in gene retention and gene expression, which may be related to LTR explosions after tetraploidization. Important genes, such as those involved in fatty acid and triacylglycerol pathways, NBS-LRR, and seed size determination, were found to be enriched after polyploidization events. The genome sequencing achievement has laid a solid foundation for advancing peanut crop enhancement and systems biology research, despite peanut lagging behind other crops in terms of genomic resources.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Review
Plant Sciences
Matin Miryeganeh
Summary: Plants adapt to climate change by altering their DNA, and mangroves are promising models for studying this due to their natural exposure to environmental changes.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Cell Biology
Pierre Capy
Summary: During evolution, various types of sequences pass through genomes, serving as a useful source of genetic variability for adaptation and evolution. These sequences, acquired through horizontal transfers, can undergo processes like taming, domestication, and exaptation, impacting host genomes differently.
Article
Biochemistry & Molecular Biology
Mengyu Zhang, Weikang Sun, Xiaoxin You, Dongge Xu, Lingling Wang, Jingping Yang, Erguang Li, Susu He
Summary: This study analyzed publicly available datasets and found that EBV-associated gastric cancer (EBVaGC) has a repression of L1 transcription compared with EBV-negative gastric cancer (EBVnGC). Retrotransposition-associated young and full-length L1s (FL-L1s) were found to be the most repressed L1s in EBVaGC. Increased deposition of H3K9me3 on FL-L1s was observed, potentially attributed to increased TASOR expression and the interaction between viral DNA and the TASOR enhancer. This study uncovers a regulation mechanism of L1 expression by chromatin topology remodeling associated with viral-host genome interaction in EBVaGC.
NUCLEIC ACIDS RESEARCH
(2023)
