Article
Microbiology
Perumal Arumugam Desingu, K. Nagarajan, Nagalingam R. Sundaresan
Summary: Different groups of MPXVs contain unique tandem repeats in the ITR regions, which may play a role in the genetic diversity of the virus. These repeats are only found in MPXVs and are different from the tandem repeats in human and rodent genomes.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemical Research Methods
Piotr Wlodzimierz, Michael Hong, Ian R. Henderson
Summary: The advent of long-read DNA sequencing enables the complete assembly of highly repetitive genomic regions, including centromeric satellite repeat arrays in eukaryotes. To annotate these repetitive regions, a method called TRASH is developed for de novo annotation of tandem repeats without prior knowledge of repeat composition. TRASH precisely maps the repeats and their higher order structures in fasta assembly files.
Article
Agronomy
Zhiguo Wu, Wei Xi, Zixuan Han, Yanhua Wu, Yongzhuo Guan, Yuxian Zhu
Summary: In this study, a method called matrix-TE was used to comprehensively investigate the differentiation of LTR/TEs in plant genomes. The results showed that there were six LTR/TE superfamilies in Indica and Japonica rice genomes, and the divergence between the two genomes was mainly caused by Ty3/Gypsy insertion events.
Review
Cell Biology
Elisa Balzano, Franca Pelliccia, Simona Giunta
Summary: Repeated sequences make up more than half of the human genome and play a significant role in various physiological and pathological conditions. Tandem repeats, a major category of repetitive DNA in the human genome, have a higher mutation rate and are prone to aberrant recombination, leading to associations with a variety of diseases.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Nadezhda G. Ivanova, Dmitrii Ostromyshenskii, Olga Podgornaya
Summary: Constitutive heterochromatin, containing tandem repeats, poses challenges in assembly, annotation, and mapping due to its specific organization. In this study, specific probes for pig and Chinese hamster genomes were designed and used to trace the centromeric region assembly. Observations in spermatogenic cells of both species supported the loop model with loop sizes around 50 kb.
CYTOGENETIC AND GENOME RESEARCH
(2021)
Review
Genetics & Heredity
Jessica M. Storer, Robert Hubley, Jeb Rosen, Arian F. A. Smit
Summary: In this review, we discuss established methods and recent developments in de novo transposable element (TE) analysis, and explore opportunities for further advancement in this field.
Review
Medicine, Research & Experimental
Jack N. G. Marshall, Ana Illera Lopez, Abigail L. Pfaff, Sulev Koks, John P. Quinn, Vivien J. Bubb
Summary: Understanding the mechanisms regulating tissue-specific and stimulus-inducible regulation is crucial for understanding human biology and its implications for health, aging, and disease progression. Polymorphic DNA variations add an additional layer of complexity, shaping individuality and influencing personalized medicine. This review highlights the role of repetitive DNA, particularly variable number tandem repeats and SINE-VNTR-Alu domains, in modifying gene structure and expression, as well as their impact on disease risk and progression. These elements, previously under-reported in genomic analysis, have the potential to significantly contribute to normal physiological function and disease mechanisms, and recent advances in sequencing methods are expected to enhance our understanding of their roles.
EXPERIMENTAL BIOLOGY AND MEDICINE
(2021)
Review
Cell Biology
Lori L. Wallrath, Felipe Rodriguez-Tirado, Pamela K. Geyer
Summary: Heterochromatin, the dark side of the genome, is concentrated in regions repressive to nuclear functions such as DNA replication and transcription. Recent research has revealed the complexities and significance of heterochromatin.
Article
Biochemistry & Molecular Biology
Pablo Mier, Miguel A. Andrade-Navarro
Summary: Tandem repeats in proteins are patterns of adjacent repeated residues. The evolution of these repeats can be analyzed using homologous sequences, which can point to duplication or deletion events. The variability of certain types of repeats in a protein family might suggest their function. This study proposes a method to calculate protein short tandem repeats (pSTRs) and assess their variability within a protein family, and the results suggest that families with more changes in their repeat patterns may have specific functions requiring adaptability.
Article
Biochemistry & Molecular Biology
Igor Bychkov, Galina Baydakova, Alexandra Filatova, Ochir Migiaev, Andrey Marakhonov, Nataliya Pechatnikova, Ekaterina Pomerantseva, Fedor Konovalov, Maria Ampleeva, Vladimir Kaimonov, Mikhail Skoblov, Ekaterina Zakharova
Summary: Pompe disease is an autosomal recessive lysosomal storage disorder caused by mutations in the GAA gene, with over 679 pathogenic variants identified in GAA. A novel molecular genetic cause of Pompe disease involving a complex mobile genetic element insertion in intron 15 of the GAA gene was discovered through whole genome sequencing and comprehensive functional analysis, highlighting the limitations of routine molecular genetic analysis in detecting such complex genetic causes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Alexander Miguel Monzon, Paula Nazarena Arrias, Arne Elofsson, Pablo Mier, Miguel A. Andrade-Navarro, Martina Bevilacqua, Damiano Clementel, Alex Bateman, Layla Hirsh, Maria Silvina Fornasari, Gustavo Parisi, Damiano Piovesan, Andrey V. Kajava, Silvio C. E. Tosatto
Summary: The article attempts to rationalize the existing knowledge on Tandem Repeat Proteins (TRPs) by pointing out several dichotomies, and proposes an operational definition for Structural Tandem Repeat Proteins (STRPs) - a subclass with distinctive features.
JOURNAL OF STRUCTURAL BIOLOGY
(2023)
Review
Biology
Xingyu Liao, Wufei Zhu, Juexiao Zhou, Haoyang Li, Xiaopeng Xu, Bin Zhang, Xin Gao
Summary: This review explores the characteristics of DNA repeats, their functional impacts, and available tools for their analysis.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Emma Price, Olympia Gianfrancesco, Patrick T. Harrison, Bernhard Frank, Vivien J. Bubb, John P. Quinn
Summary: In this study, SVA retrotransposons were shown to have cis-regulatory activity through CRISPR deletion, affecting the expression of TRPV1 and TRPV3 genes. The human-specific SVA insertion between TRPV1 and TRPV3 was found to disrupt their co-expression, highlighting the role of SVA retrotransposons in species-specific gene expression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Peter Ebert, Peter A. Audano, Qihui Zhu, Bernardo Rodriguez-Martin, David Porubsky, Marc Jan Bonder, Arvis Sulovari, Jana Ebler, Weichen Zhou, Rebecca Serra Mari, Feyza Yilmaz, Xuefang Zhao, PingHsun Hsieh, Joyce Lee, Sushant Kumar, Jiadong Lin, Tobias Rausch, Yu Chen, Jingwen Ren, Martin Santamarina, Wolfram Hops, Hufsah Ashraf, Nelson T. Chuang, Xiaofei Yang, Katherine M. Munson, Alexandra P. Lewis, Susan Fairley, Luke J. Tallon, Wayne E. Clarke, Anna O. Basile, Marta Byrska-Bishop, Andre Corvelo, Uday S. Evani, Tsung-Yu Lu, Mark J. P. Chaisson, Junjie Chen, Chong Li, Harrison Brand, Aaron M. Wenger, Maryam Ghareghani, William T. Harvey, Benjamin Raeder, Patrick Hasenfeld, Allison A. Regier, Haley J. Abel, Ira M. Hall, Paul Flicek, Oliver Stegle, Mark B. Gerstein, Jose M. C. Tubio, Zepeng Mu, Yang Li, Xinghua Shi, Alex R. Hastie, Kai Ye, Zechen Chong, Ashley D. Sanders, Michael C. Zody, Michael E. Talkowski, Ryan E. Mills, Scott E. Devine, Charles Lee, Jan O. Korbel, Tobias Marschall, Evan E. Eichler
Summary: Through the use of long-read and strand-specific sequencing technologies, this study has achieved the de novo assembly of high-quality haplotype-resolved human genomes without the need for parent-child trio data. The research identified various forms of genetic variation, including structural variants and SV hotspots, and revealed the mechanisms of SV formation while providing SV candidates for adaptive selection within the human population.
Article
Biotechnology & Applied Microbiology
Jian-Wei Zheng, Yang Lu, Yu-Feng Yang, Dan Huang, Da-Wei Li, Xiang Wang, Yang Gao, Wei-Dong Yang, Yuanfang Guan, Hong-Ye Li
Summary: This study analyzed the transcriptomes of 34 Conus species and identified conotoxin genes, revealing that some of these genes underwent positive natural selection. The genome of C. betulinus was also reassembled and annotated, uncovering 221 conotoxin-encoding genes. The presence of transposon elements in the flanking regions and adjacent introns of conotoxin genes may contribute to the extensive variability observed in conotoxins.