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
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
Kosuke Hashimoto, Eeva-Mari Jouhilahti, Virpi Tohonen, Piero Carninci, Juha Kere, Shintaro Katayama
Summary: This study reveals that the LTR families MLT2A1 and MLT2A2 are primarily expressed in human four-cell and eight-cell embryos, as well as in some adult somatic tissues, particularly the pineal gland. Certain MLT2A elements function as promoters and first exons of protein-coding genes specifically in the human pineal gland but not in macaques, suggesting recent exaptation of these LTRs during primate evolution. This analysis provides insights into the transition from germline insertion to somatic expression of LTR retrotransposons.
Article
Agronomy
Yangyang Sun, Haiming Han, Xiao Wang, Bohui Han, Shenghui Zhou, Meng Zhang, Weihui Liu, Xiuquan Li, Xiaomin Guo, Yuqing Lu, Xinming Yang, Jinpeng Zhang, Xu Liu, Lihui Li
Summary: This study developed a set of oligo probes based on ND-FISH assays to identify P-genome chromosomes in wheat. These probes simplify the experimental process, save costs and time, and improve detection efficiency.
MOLECULAR BREEDING
(2022)
Article
Biochemistry & Molecular Biology
Saisai Wang, Mohamed Diaby, Mikhail Puzakov, Numan Ullah, Yali Wang, Patrick Danley, Cai Chen, Xiaoyan Wang, Bo Gao, Chengyi Song
Summary: This study focused on the structure and diversity of the DD37D/maT and DD39D/GT families within the Tc1/mariner transposons, shedding light on their role in the evolution of eukaryotic genomes. The findings revealed different distributions of maTs and GTs, with potential horizontal transfer events between kingdoms and phyla of eukaryotes. The intact transposases and target site duplications suggest that these families may still be active in influencing genome evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Kevin H-C Wei, Dat Mai, Kamalakar Chatla, Doris Bachtrog
Summary: TE insertion frequency is negatively associated with nearby gene expression. Recent amplification of TE families is strongly associated with high expression in the expanded species.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Review
Plant Sciences
Nathan S. Catlin, Emily B. Josephs
Summary: TEs play a significant role in genomic variation in plants. New approaches have allowed us to quantify TE polymorphisms and understand their evolutionary dynamics, revealing their important but underappreciated contribution to intraspecific phenotypic variation.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
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
Philippine Garret, Martin Chevarin, Antonio Vitobello, Simon Verdez, Cyril Fournier, Alain Verloes, Emilie Tisserant, Pierre Vabres, Orlane Prevel, Christophe Philippe, Anne-Sophie Denomme-Pichon, Ange-Line Bruel, Frederic Tran Mau-Them, Hana Safraou, Aicha Boughalem, Jean-Marc Costa, Detlef Trost, Christel Thauvin-Robinet, Laurence Faivre, Yannis Duffourd
Summary: This study identified two de novo mobile element insertions (MEIs) in patients with developmental and neurological abnormalities, highlighting the importance of incorporating ME detection in exome sequencing for improved diagnostic rate.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Review
Oncology
Emanuela Felley-Bosco
Summary: Endogenous retroviruses (ERVs) make up 8% of the human genome, but were previously considered junk DNA. However, recent research has shown that their expression is important in cancer, particularly in mesothelioma. This review highlights the potential of investigating ERV expression for prognosis and immunotherapy, with a focus on mesothelioma.
Article
Biochemistry & Molecular Biology
Katarzyna Siudeja, Marius van den Beek, Nick Riddiford, Benjamin Boumard, Annabelle Wurmser, Marine Stefanutti, Sonia Lameiras, Allison J. Bardin
Summary: This study using Drosophila midgut as a model, revealed the prevalence of somatic transposition in somatic tissue, finding that retrotransposon insertions are associated with inactivation of the tumor suppressor Notch and tissue-specific differences in retrotransposition. The research also showed that somatic TE insertions in the adult fly intestine are enriched in genic regions and in transcriptionally active chromatin, providing new insights into somatic TE mobility in vivo.
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)
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.
Article
Biochemistry & Molecular Biology
Iskander Said, Michael P. McGurk, Andrew G. Clark, Daniel A. Barbash
Summary: Competition between transposable elements (TEs) may lead to the emergence of new variants, with hosts preferentially producing antisense piRNAs to silence these emerging variants.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)