Review
Cell Biology
Luisa Di Stefano
Summary: This review discusses the role of chromatin marks in the regulation of transposable elements (TEs) and summarizes the research evidence in Drosophila and mammalian systems.
Article
Evolutionary Biology
Yan-Nan Liu, Rong-Mei Chen, Qi-Ting Pu, Lotanna M. Nneji, Yan-Bo Sun
Summary: This study re-analyzed transcriptomic data of chickens and found that transposable elements (TEs) play an important role in adaptive evolution, with their expression changes exceeding genetic changes. These TEs were co-expressed with diverse genes and involved in regulatory activities.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Tomoko Ichiyanagi, Hirokazu Katoh, Yoshinobu Mori, Keigo Hirafuku, Beverly Ann Boyboy, Masaki Kawase, Kenji Ichiyanagi
Summary: The currently active SINE B2 copies in mice act as mobile boundary elements that modulate chromatin modifications and gene expression, likely playing a role in the epigenomic and phenotypic diversification of the species.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Sophia Groh, Anna Viktoria Milton, Lisa Marinelli, Cara Sickinger, Angela Russo, Heike Bollig, Gustavo Pereira de Almeida, Andreas Schmidt, Ignasi Forne, Axel Imhof, Gunnar Schotta
Summary: Endogenous retroviruses (ERVs) make up a significant portion of mammalian genomes, and Morc3 has been identified as a key regulator of ERV silencing. Through interactions with the H3.3 chaperone Daxx, Morc3 plays a critical role in incorporating histone H3.3 into ERV regions.
NATURE COMMUNICATIONS
(2021)
Article
Agriculture, Dairy & Animal Science
Tao Jiang, Ziqi Ling, Zhimin Zhou, Xiaoyun Chen, Liqing Chen, Sha Liu, Yingchun Sun, Jiawen Yang, Bin Yang, Jianzhen Huang, Lusheng Huang
Summary: This study presents a genome-wide landscape of chromatin accessibility in 20 tissues of pigs using ATAC-seq. It identifies tissue-specific regulatory elements and reveals their associations with tissue-relevant biological functions. The study also investigates the presence of transposable elements in open chromatin regions and prioritizes a potential causal variant for polyunsaturated fatty acid in muscle tissue.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Aditi Singh, Xyrus X. Maurer-Alcala, Therese Solberg, Lilia Haeussermann, Silvan Gisler, Michael Ignarski, Estienne C. Swart, Mariusz Nowacki
Summary: Recruiting the chromatin remodeler ISWI1 facilitates IES recognition and precise excision in Paramecium, ensuring efficient DNA elimination.
Review
Geriatrics & Gerontology
Pouria Mosaddeghi, Mitra Farahmandnejad, Mohammad M. M. Zarshenas
Summary: Transposable elements (TEs) make up a significant portion of the human genome and their dysregulation has been linked to various human diseases. This review explores the role of TEs in age-related diseases and cancer, highlighting their impact on immune responses, chronic inflammation, and genome instability. The upregulation of TEs in precancerous cells through inflammageing and exposure to carcinogens can lead to cancer initiation and progression. Therefore, TEs may serve as therapeutic targets in aging and cancer.
Editorial Material
Plant Sciences
Scott William Roy
Summary: In modern biology, research on proximal mechanistic and ultimate evolutionary causes are usually conducted separately by different specialist communities, but they are often interrelated and mutually informative.
TRENDS IN PLANT SCIENCE
(2022)
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
Cell Biology
Rola S. Zeidan, Sung Min Han, Christiaan Leeuwenburgh, Rui Xiao
Summary: Iron plays crucial roles in physiological processes and its homeostasis involves a complex network of regulators at systemic, cellular, and molecular levels. Dysregulation of iron homeostasis is often linked to age-related pathologies, highlighting the importance of understanding the interplay between iron balance and aging in order to develop therapeutic strategies for age-related diseases.
AGEING RESEARCH REVIEWS
(2021)
Article
Biochemical Research Methods
Matej Lexa, Monika Cechova, Son Hoang Nguyen, Pavel Jedlicka, Viktor Tokan, Zdenek Kubat, Roman Hobza, Eduard Kejnovsky
Summary: This article introduces a novel approach to analyze the role of repetitive elements in the 3D organization of genomes. By combining Hi-C data, reference genome data, and tools for repeat analysis, a pipeline was constructed to identify and quantify the contacts between specific repeat families, generating heatmaps and circular diagrams for visualization. Using this pipeline with tomato data, preferential homotypic interactions of ribosomal DNA, centromeric satellites, and some LTR retrotransposon families were revealed.
Article
Biochemistry & Molecular Biology
Aicen Zhang, Wenli Zhang
Summary: Growing evidence suggests that transposons or transposable elements (TEs)-derived accessible chromatin regions (ACRs) play important roles in various biological processes. However, the function of TE-derived ACRs in regulating gene expression in the rice genome is not well understood. This study examined chromatin dynamics in different rice tissues and found that a significant portion of ACRs were derived from TEs. These TE-derived ACRs exhibited distinct levels of accessibility and conservation compared to those without TEs. Additionally, tissue-specific TE-derived ACRs were found to be involved in tissue development through the regulation of nearby gene expression. Furthermore, TE-derived ACRs were also associated with the domestication of rice and the functional divergence of duplicated genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Martin Rougee, Leandro Quadrana, Jerome Zervudacki, Valentin Hure, Vincent Colot, Lionel Navarro, Angelique Deleris
Summary: DNA methylation and H3K27me3 are two specialized systems for epigenetic silencing in plants and mammals, but the acquisition of H3K27me3 at TE sequences can depend on CURLY LEAF and does not necessarily lead to TE reactivation or increased transposition.
LIFE SCIENCE ALLIANCE
(2021)
Review
Entomology
Clement Gilbert, Jean Peccoud, Richard Cordaux
Summary: Insects play a significant role in understanding the interaction between TEs and hosts, with variable TE landscapes across insect orders possibly correlating with phylogenetic relatedness. Recent findings suggest that TEs are essential symbionts in insects, being involved in antiviral immunity and potentially having both deleterious and beneficial consequences for hosts.
ANNUAL REVIEW OF ENTOMOLOGY, VOL 66, 2021
(2021)
Article
Evolutionary Biology
Daniel K. Fabian, Handan Melike Donerta, Matias Fuentealba, Linda Partridge, Janet M. Thornton
Summary: The study found that transposable elements are generally more abundant in long-lived individuals, but there is a trend of reduced TE expression in selected populations compared to nonselected controls. Telomeric TEs are more abundant in long-lived flies, suggesting improved telomere maintenance as a promising mechanism for prolonging lifespan.
GENOME BIOLOGY AND EVOLUTION
(2021)