Review
Genetics & Heredity
Scott E. Devine
Summary: Three mobile element classes, Alu, LINE-1 (L1), and SVA elements, are actively mobile in human genomes and continue to produce new mobile element insertions (MEIs). Traditional methods of MEI discovery, such as Southern blots, PCR, and detection of MEI copies, are being replaced by whole genome sequencing and bioinformatics analysis. The expanding resources of sequenced human genomes will provide unprecedented opportunities to discover and study MEIs and their impact on human traits and diseases, as well as the source elements that produce these new MEIs. Understanding MEI mutagenesis and its impact on human biology will be greatly enhanced.
Article
Geriatrics & Gerontology
Hui-Hui Fan, Jing Zheng, Xiao-Ya Huang, Ke-Yun Wu, Lei Cui, Hao-Jia Dong, Zhen Wang, Xiong Zhang, Jian-Hong Zhu
Summary: This study reveals a significant association between the antisense Alu element insertion/deletion polymorphism of ALDH1A1 and Parkinson's disease susceptibility, suggesting that this polymorphism may have an impact on the pathogenesis of PD by suppressing gene transcription.
Article
Biology
Yulan Wang, Jian Zhao, Jing Wu, Jingjing Liu, Yixuan Wang, Tianyi Xu, Meng Zhang, Minhui Zhuang, Lingxiao Zou, Wei Sun, Ping Han, Xiaofeng Song
Summary: This study identifies dysregulated RNA editing events in circRNAs in cervical cancer and reveals a decrease in A-to-I RNA editing levels compared to normal tissues. The findings suggest that editing may influence circRNA biogenesis and the back-splicing process through structural modifications of Alu elements. Furthermore, RNA editing is shown to modulate circRNA expression and coding potential, and three potential RNA editing sites are identified as biomarkers.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Medicine, General & Internal
Zhi-Hui Yang, Xin Cai, Zhong-Li Ding, Wei Li, Chu-Yi Zhang, Jin-Hua Huo, Yue Zhang, Lu Wang, Lin-Ming Zhang, Shi-Wu Li, Ming Li, Chen Zhang, Hong Chang, Xiao Xiao
Summary: This study discovered a psychiatric risk gene (NISCH) at the 3p21.1 GWAS locus that influences dendritic spine morphogenesis and cognitive function. It was found that a risk variant (rs71052682) associated with schizophrenia and bipolar disorder affects the expression of NISCH.
Article
Biochemistry & Molecular Biology
Yubo Cheng, Luke Saville, Babita Gollen, Ana Alvarez Veronesi, Majid Mohajerani, Jeffrey T. Joseph, Athanasios Zovoilis
Summary: Research has shown that non-coding RNAs produced by SINE elements play a significant role in the pathogenesis of Alzheimer's disease, controlling gene expression and exhibiting a pattern of deregulation in the brains of AD patients.
Article
Microbiology
Jo-Ann McClure, Sahreena Lakhundi, Amani Niazy, George Dong, Osahon Obasuyi, Paul Gordon, Sidong Chen, John M. Conly, Kunyan Zhang
Summary: Detailed genetic analysis was conducted on the Staphylococcus aureus (SA) sequence type ST59, revealing the concurrent but separate evolution of North American and East Asian lineages, with extensive diversification observed in the East Asian lineage and the presence of mobile element structure (MES) as a major difference between the two continental lineages.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Evolutionary Biology
Maria Stitz, Cristian Chaparro, Zhigang Lu, V. Janett Olzog, Christina E. Weinberg, Jochen Blom, Alexander Goesmann, Christoph Grunau, Christoph G. Grevelding
Summary: The study focuses on satellite-DNA elements of the blood fluke Schistosoma mansoni, revealing new insights into the classification and transcription of W-elements in different stages, sexes, pairings, gonads, and strains. Additionally, structural analyses suggest a potential role as a source of noncoding RNA-like hammerhead ribozymes. The variable occurrence of W-element families in different schistosome species indicates potential genetic factors influencing the variability and evolution of the Schistosomatidae family.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Ching-Ting Huang, Shu-Ting Cho, Yu-Chen Lin, Choon-Meng Tan, Yi-Ching Chiu, Jun-Yi Yang, Chih-Horng Kuo
Summary: This study obtained the complete genome sequence of a phytoplasma associated with witches' broom disease of loofah and found that the genome has remarkably high repetitiveness. The study also classified the phytoplasma-specific mobile genetic elements into three types and showed their significance in phytoplasma genome variability.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Matias Autio, Talal Bin Amin, Arnaud Perrin, Jen Yi Wong, Roger S-Y Foo, Shyam Prabhakar
Summary: A novel statistical test was developed to identify 20 high-confidence recently mobile transposable element subfamilies, which play important roles in human genetic disorders and diverse cancers. The study provides insights into TE mobility and regulatory potential, serving as a valuable resource for human disease genetics and population history studies.
Review
Biology
James P. J. Hall, Joao Botelho, Adrian Cazares, David A. Baltrus
Summary: This article provides an overview of the distribution, diversity, biology, and gene content of megaplasmids, emphasizing their widespread existence and often overlooked importance as mobile genetic elements.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Genetics & Heredity
Jessica M. Storer, Jerilyn A. Walker, Jasmine N. Baker, Shifat Hossain, Christian Roos, Travis J. Wheeler, Mark A. Batzer
Summary: The history of Alu retroposons can be divided into different subfamilies, each with a distinct nucleotide consensus sequence. AluJ is the oldest subfamily, followed by AluS, AluY, and AluTa. The expansion of Alu in platyrrhines is mainly driven by AluTa15.
Article
Oncology
Christian Thomas, Kathrin Oehl-Huber, Susanne Bens, Patrick Soschinski, Arend Koch, Karolina Nemes, Florian Oyen, Uwe Kordes, Marcel Kool, Michael C. Fruehwald, Martin Hasselblatt, Reiner Siebert
Summary: AT/RT is a malignant brain tumor predominantly occurring in infants, caused by SMARCB1 mutations, with some cases lacking biallelic mutations. A case report found SMARCB1 loss due to Alu element insertion resulting in frame-shift truncation, a mechanism not widely recognized in AT/RT.
GENES CHROMOSOMES & CANCER
(2021)
Article
Multidisciplinary Sciences
Mikhail A. Moldovan, Zoe S. Chervontseva, Daria S. Nogina, Mikhail S. Gelfand
Summary: RNA editing is a common phenomenon, particularly in soft-bodied cephalopods, where thousands of editing sites have been identified. These editing sites tend to cluster and contribute significantly to transcriptome diversity. Different types of editing site clusters have been identified, and their formation may be influenced by RNA structural features and mechanisms.
SCIENTIFIC REPORTS
(2022)
Review
Microbiology
Catherine Badel, Violette Da Cunha, Jacques Oberto
Summary: Archaeal integrases play a crucial role in shaping evolution by catalyzing recombination reactions beyond site-specific recombination. These enzymes, active in extreme environments, can generate deep rearrangements of host genomes and are termed "suicidal" due to their ability to disrupt their own gene upon integration. The presence of novel mechanisms for evolution is implied by the paradoxical maintenance of integrases that disrupt their gene upon integration.
FEMS MICROBIOLOGY REVIEWS
(2021)
Article
Microbiology
Maria L. Bonatelli, Thore Rohwerder, Denny Popp, Yu Liu, Caglar Akay, Carolyn Schultz, Kuan-Po Liao, Chang Ding, Thorsten Reemtsma, Lorenz Adrian, Sabine Kleinsteuber
Summary: In this study, the metabolism of acesulfame by microbial degraders was investigated, leading to the identification of two gene clusters involved in the degradation pathway. Transposition of these gene clusters between chromosome and plasmid was observed. The global evolution and spread of the acesulfame degradation pathway was also elucidated, highlighting the importance of this research in understanding microbial degradation of harmful substances and environmental remediation.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Yue-Qiu Tan, Chaofeng Tu, Lanlan Meng, Shimin Yuan, Calvin Sjaarda, Aixiang Luo, Juan Du, Wen Li, Fei Gong, Changgao Zhong, Han-Xiang Deng, Guangxiu Lu, Ping Liang, Ge Lin
GENETICS IN MEDICINE
(2019)
Article
Plant Sciences
Ayelign M. Adal, Lukman S. Sarker, Radesh P. N. Malli, Ping Liang, Soheil S. Mahmoud
Article
Biochemistry & Molecular Biology
Wooseok Lee, Minhoon Choi, Songmi Kim, Wanxiangfu Tang, Dong Hee Kim, Heui-Soo Kim, Ping Liang, Kyudong Han
Article
Genetics & Heredity
Daniel Benjamin Callaghan, Sanja Rogic, Powell Patrick Cheng Tan, Kristina Calli, Ying Qiao, Robert Baldwin, Matthew Jacobson, Manuel Belmadani, Nathan Holmes, Chang Yu, Yanchen Li, Yingrui Li, Franz-Edward Kurtzke, Boris Kuzeljevic, An Yi Yu, Melissa Hudson, Amy J. M. Mcaughton, Yuchen Xu, Alexandre Dionne-Laporte, Simon Girard, Ping Liang, Evica Rajcan Separovic, Xudong Liu, Guy Rouleau, Paul Pavlidis, M. E. Suzanne Lewis
Article
Genetics & Heredity
Sunyoung Lee, Wanxiangfu Tang, Ping Liang, Kyudong Han
Article
Evolutionary Biology
Wanxiangfu Tang, Ping Liang
GENOME BIOLOGY AND EVOLUTION
(2019)
Article
Biotechnology & Applied Microbiology
Yuanyuan Li, Hongyan Pan, Yaowen Chang, Na Dong, Lei Zou, Ping Liang, Wei Tian, Zunxue Chang
ENZYME AND MICROBIAL TECHNOLOGY
(2020)
Article
Multidisciplinary Sciences
Roshane Francis, Haiyang Guo, Catherine Streutker, Musaddeque Ahmed, Theodora Yung, Peter B. Dirks, Housheng Hansen He, Tae-Hee Kim
Article
Immunology
Conglei Li, Evelyn Lam, Christian Perez-Shibayama, Lesley A. Ward, Jianbo Zhang, Dennis Lee, Albert Nguyen, Musaddeque Ahmed, Emma Brownlie, Kirill Korneev, Olga Rojas, Tian Sun, William Navarre, Housheng Hansen He, Shan Liao, Alberto Martin, Burkhard Ludewig, Jennifer L. Gommerman
SCIENCE IMMUNOLOGY
(2019)
Article
Biochemical Research Methods
Wanxiangfu Tang, Ping Liang
ANALYTICAL BIOCHEMISTRY
(2020)
Article
Endocrinology & Metabolism
Weijuan Shao, Wenjuan Liu, Ping Liang, Zhuolun Song, Odisho Israel, Gerald J. Prud'homme, Qinghua Wang, Tianru Jin
JOURNAL OF ENDOCRINOLOGY
(2020)
Article
Multidisciplinary Sciences
Sung-Yeon Hwang, Hyunchul Jung, Seyoung Mun, Sungwon Lee, Kiwon Park, S. Chan Baek, Hyungseok C. Moon, Hyewon Kim, Baekgyu Kim, Yongkuk Choi, Young-Hyun Go, Wanxiangfu Tang, Jongsu Choi, Jung Kyoon Choi, Hyuk-Jin Cha, Hye Yoon Park, Ping Liang, V. Narry Kim, Kyudong Han, Kwangseog Ahn
Summary: The study reveals that m(6)A modifications on L1 RNA enhance translation efficiency and retrotransposition in human cells. M(6)A motifs are more enriched in evolutionary young L1s.
NATURE COMMUNICATIONS
(2021)
Review
Biology
Arsala Ali, Kyudong Han, Ping Liang
Summary: Transposable elements (TEs), also known as mobile elements (MEs), are interspersed repeats that constitute a major fraction of genomes, contributing to gene regulation by providing cis-regulatory sequences and encoding regulatory RNAs. These TE-derived regulatory mechanisms play crucial roles in gene regulation, providing evolutionary novelty and tissue-specific functions.
Review
Cell Biology
Ricardo Alva, Georgina L. Gardner, Ping Liang, Jeffrey A. Stuart
Summary: Most conventional incubators used in cell culture do not regulate O-2 levels, which leads to a higher oxygen concentration compared to the physiological conditions in human tissues. This review discusses the effects of supraphysiological O-2 levels on various biological processes and emphasizes the importance of maintaining physiological oxygen levels in cell culture to better replicate in vivo-like tissue physiology and pathology and to avoid artifacts in research involving cell culture.
Article
Biochemistry & Molecular Biology
Ricardo Alva, Fereshteh Moradi, Ping Liang, Jeffrey A. Stuart
Summary: The oxygen level in cell culture can significantly affect gene expression, metabolism, mitochondrial networks, and response to drugs and hormones. This study investigated the transcriptional response to different oxygen levels in four human cancer cell lines and found that oxygen levels affected the transcript abundance of thousands of genes, with little overlap between cell lines. The study also observed differential transcription of mitochondria-encoded genes in response to oxygen levels. These findings emphasize the importance of regulating oxygen levels in cell culture.