Review
Biochemistry & Molecular Biology
Elisa Carotti, Federica Carducci, Marco Barucca, Adriana Canapa, Maria Assunta Biscotti
Summary: Transposable elements (TEs) are essential components of eukaryotic genomes, playing a crucial role in the evolution of vertebrates. However, their transposition ability can lead to genome instability, and thus silencing mechanisms have evolved to maintain the coexistence of TEs and host-coding genes. Recent studies have highlighted the presence of regulatory elements within TEs that can specifically regulate nearby genes, suggesting that TEs can be domesticated for gene expression regulation, enabling species adaptation and ensuring human health.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Matthew Naish, Michael Alonge, Piotr Wlodzimierz, Andrew J. Tock, Bradley W. Abramson, Anna Schmuecker, Terezie Mandakova, Bhagyshree Jamge, Christophe Lambing, Pallas Kuo, Natasha Yelina, Nolan Hartwick, Kelly Colt, Lisa M. Smith, Jurriaan Ton, Tetsuji Kakutani, Robert A. Martienssen, Korbinian Schneeberger, Martin A. Lysak, Frederic Berger, Alexandros Bousios, Todd P. Michael, Michael C. Schatz, Ian R. Henderson
Summary: The study used long-read sequencing to assemble the Arabidopsis genome and resolve all five centromeres. It found that centromeres consist of megabase-scale tandemly repeated satellite arrays and are invaded by retrotransposons. The centromeres are evolving through cycles of satellite homogenization and retrotransposon-driven diversification.
Article
Multidisciplinary Sciences
Savannah J. Hoyt, Jessica M. Storer, Gabrielle A. Hartley, Patrick G. S. Grady, Ariel Gershman, Leonardo G. de Lima, Charles Limouse, Reza Halabian, Luke Wojenski, Matias Rodriguez, Nicolas Altemose, Arang Rhie, Leighton J. Core, Jennifer L. Gerton, Wojciech Makalowski, Daniel Olson, Jeb Rosen, Arian F. A. Smit, Aaron F. Straight, Mitchell R. Vollger, Travis J. Wheeler, Michael C. Schatz, Evan E. Eichler, Adam M. Phillippy, Winston Timp, Karen H. Miga, Rachel J. O'Neill
Summary: Mobile elements and repetitive genomic regions play a crucial role in lineage-specific genomic innovation and can uniquely identify individual genomes. This study presents a novel approach to de novo repeat discovery and annotation of the T2T-CHM13 human reference genome, expanding our understanding of the diversity, distribution, and evolution of repetitive regions in the human genome.
Article
Biochemistry & Molecular Biology
Vanessa Fuentes Suguiyama, Jae Diana Paredes Rodriguez, Tatiane Cristina Nicomedio dos Santos, Bruno Silvestre Lira, Luis Alejandro de Haro, Joao Paulo Naldi Silva, Eduardo Leite Borba, Eduardo Purgatto, Emerson Alves da Silva, Nicolas Bellora, Fernando Carrari, Danilo da Cruz Centeno, Luisa Fernanda Bermudez, Magdalena Rossi, Nathalia de Setta
Summary: Drought is a major environmental stress that negatively affects plant growth and reproductive yield. The response to water deficit is determined by the duration and intensity of the stress, as well as the genetic makeup of the plant. The metabolic adjustments in response to water deficit involve complex gene expression regulation, including DNA-binding proteins and epigenetic modifications. In this study, Setaria italica plants exposed to different levels of water deficit were analyzed, and the results showed a progressive reduction in yield with increasing water deficit intensity. The signaling pathway modulation and metabolic adjustments were found to be associated with this response. Furthermore, certain loci related to drought perception, signaling, and regulation were consistently associated with drought responses. The analysis of the transcriptome and sRNAome also revealed potential gene regulation mechanisms involving transposable elements and sRNAs, as well as an intriguing correlation between transcript levels and sRNA accumulation. These findings provide insights into the processes that enable S. italica to overcome drought and survive under water restrictive conditions.
PLANT MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Thanit Saeliw, Songphon Kanlayaprasit, Surangrat Thongkorn, Kwanjira Songsritaya, Bumpenporn Sanannam, Chanachai Sae-Lee, Depicha Jindatip, Valerie W. Hu, Tewarit Sarachana
Summary: This study characterized the expression and sequence characteristics of transposable elements, specifically Alu elements, in the prefrontal cortex tissues of individuals with autism spectrum disorder (ASD). The study found that the differential expression of Alu elements was associated with ASD-related genes and cellular processes. Additionally, significant hypomethylation of Alu elements was observed in ASD subphenotypes, suggesting potential epigenetic involvement. These findings provide insights into the role of Alu elements in gene regulation and molecular neuropathology in ASD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Plant Sciences
Kajal Samantara, Aalok Shiv, Lorenna Lopes de Sousa, Karansher Singh Sandhu, Parichita Priyadarshini, Sourav Ranjan Mohapatra
Summary: Epigenetics is an important mechanism that can help plants cope with various stressors by altering gene expression without involving changes in DNA sequences. It provides diversity to aid plants in responding to the impacts of climate change.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Review
Biochemistry & Molecular Biology
Thanvi Srikant, Anjar Tri Wibowo
Summary: This article focuses on epiallelic variations in plants, particularly on methylated regions. It is still uncertain whether variations at individual methylated cytosines serve any regulatory function. Most epialleles in the form of methylated regions have not been assigned any biological function.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
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
Biochemistry & Molecular Biology
Xiufei Chen, Haiqi Xu, Xiao Shu, Chun-Xiao Song
Summary: The concept of epigenetics was first proposed in 1942. Chemical modifications on histones, DNA, and RNA have been identified as three key components of epigenetic modifications. These modifications play a crucial role in various biological processes and diseases, including cancer. With the advancement of sequencing technologies, scientists are now able to accurately map and quantify different types of epigenetic modifications in histones, DNA, and RNA, providing insights into gene regulation.
CELL DEATH AND DIFFERENTIATION
(2023)
Article
Biology
Thomas A. Carter, Manvendra Singh, Gabrijela Dumbovic, Jason D. Chobirko, John L. Rinn, Cedric Feschotte, Mia T. Levine
Summary: The study identified the HERVH family's expression in pluripotent stem cells, with the youngest subfamily LTR7up playing a key role in this transcription. It revealed the relationship between LTR7 sequence evolution, transcription factor binding sites, and promoter activity.
Article
Ecology
Yingjuan Su, Qiqi Huang, Zhen Wang, Ting Wang
Summary: The genetic paradox of invasive species, which refers to their ability to rapidly adapt to novel environments, can be explained by the activity of transposable elements (TEs). Mikania micrantha serves as a good example to test this explanation, as shown in a study of 21 invasive populations in southern China. The research found that M. micrantha populations exhibit high levels of TE-related genetic and epigenetic variation, and are differentiated into subpopulations.
ECOLOGY AND EVOLUTION
(2021)
Review
Biochemistry & Molecular Biology
So Young Park, Jungnam Cho, Dong-Hoon Jeong
Summary: This article summarizes and discusses recent literature on sRNA-mediated epigenetic regulation in rice, including the RdDM mechanisms and the role of TE-derived sRNAs in specific genomic loci in rice.
BIOCHEMICAL SOCIETY TRANSACTIONS
(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)
Article
Biochemistry & Molecular Biology
Taku Sasaki, Kyudo Ro, Erwann Caillieux, Riku Manabe, Gregoire Bohl-Viallefond, Pierre Baduel, Vincent Colot, Tetsuji Kakutani, Leandro Quadrana
Summary: Research has shown that anti-silencing systems have rapidly diversified in eudicots, determining specificity through gaining and losing specific domains and target sequence motifs. At least 10 distinct VANC-induced anti-silencing systems have been identified in Arabidopsis. Anti-silencing of non-autonomous VANDALs is crucial to prevent the demise of cognate autonomous TEs and ensure their propagation.
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)
Review
Neurosciences
James A. Briggs, Ernst J. Wolvetang, John S. Mattick, John L. Rinn, Guy Barry
Article
Clinical Neurology
Guy Barry, Boris Guennewig, Samantha Fung, Dominik Kaczorowski, Cynthia Shannon Weickert
FRONTIERS IN NEUROLOGY
(2015)
Editorial Material
Biochemistry & Molecular Biology
Guy Barry
Article
Oncology
Brett W. Stringer, Jens Bunt, Bryan W. Day, Guy Barry, Paul R. Jamieson, Kathleen S. Ensbey, Zara C. Bruce, Kate Goasdoue, Helene Vidal, Sara Charmsaz, Fiona M. Smith, Leanne T. Cooper, Michael Piper, Andrew W. Boyd, Linda J. Richards
Article
Geriatrics & Gerontology
Christin Weissleder, Samantha J. Fung, Matthew W. Wong, Guy Barry, Kay L. Double, Glenda M. Halliday, Maree J. Websters, Cynthia Shannon Weickert
FRONTIERS IN AGING NEUROSCIENCE
(2016)
Article
Psychiatry
Panos Roussos, Boris Guennewig, Dominik C. Kaczorowski, Guy Barry, Kristen J. Brennand
Article
Multidisciplinary Sciences
Guy Barry, James A. Briggs, Do Won Hwang, Sam P. Nayler, Patrick R. J. Fortuna, Nicky Jonkhout, Fabien Dachet, Jesper L. V. Maag, Pieter Mestdagh, Erin M. Singh, Lotta Avesson, Dominik C. Kaczorowski, Ezgi Ozturk, Nigel C. Jones, Irina Vetter, Luis Arriola-Martinez, Jianfei Hu, Gloria R. Franco, Victoria M. Warn, Andrew Gong, Marcel E. Dinger, Frank Rigo, Leonard Lipovich, Margaret J. Morris, Terence J. O'Brien, Dong Soo Lee, Jeffrey A. Loeb, Seth Blackshaw, John S. Mattick, Ernst J. Wolvetang
SCIENTIFIC REPORTS
(2017)
Article
Genetics & Heredity
Maina Bitar, Stefanie Kuiper, Elizabeth O'Brien, Guy Barry
Editorial Material
Biochemistry & Molecular Biology
Guy Barry
Article
Psychiatry
Boris Guennewig, Maina Bitar, Ifeanyi Obiorah, James Hanks, Elizabeth A. O'Brien, Dominik C. Kaczorowski, Yasmin L. Hurd, Panos Roussos, Kristen J. Brennand, Guy Barry
TRANSLATIONAL PSYCHIATRY
(2018)
Article
Neurosciences
Dessislava Mladenova, Guy Barry, Lyndsey M. Konen, Sandy S. Pineda, Boris Guennewig, Lotta Avesson, Raphael Zinn, Nicole Schonrock, Maina Bitar, Nicky Jonkhout, Lauren Crumlish, Dominik C. Kaczorowski, Andrew Gong, Mark Pinese, Gloria R. Franco, Carl R. Walkley, Bryce Vissel, John S. Mattick
FRONTIERS IN NEUROSCIENCE
(2018)
Article
Neurosciences
Michael Piper, Guy Barry, Tracey J. Harvey, Robert McLeay, Aaron G. Smith, Lachlan Harris, Sharon Mason, Brett W. Stringer, Bryan W. Day, Naomi R. Wray, Richard M. Gronostajski, Timothy L. Bailey, Andrew W. Boyd, Linda J. Richards
JOURNAL OF NEUROSCIENCE
(2014)
Article
Biochemistry & Molecular Biology
G. Barry, J. A. Briggs, D. P. Vanichkina, E. M. Poth, N. J. Beveridge, V. S. Ratnu, S. P. Nayler, K. Nones, J. Hu, T. W. Bredy, S. Nakagawa, F. Rigo, R. J. Taft, M. J. Cairns, S. Blackshaw, E. J. Wolvetang, J. S. Mattick
MOLECULAR PSYCHIATRY
(2014)
Article
Biochemistry & Molecular Biology
Christin Weissleder, Hayley F. North, Maina Bitar, Janice M. Fullerton, Rachel Sager, Guy Barry, Michael Piper, Glenda M. Halliday, Maree J. Webster, Cynthia Shannon Weickert
Summary: The study found that the human SEZ retains the capacity to generate neuronal progenitor cells throughout life, but this capacity is limited in schizophrenia and bipolar disorder. Increased macrophages in the SEZ of schizophrenia patients may impair neurogenesis.
MOLECULAR PSYCHIATRY
(2021)
