Article
Multidisciplinary Sciences
Ashley N. Hall, Tychele N. Turner, Christine Queitsch
Summary: The study investigated copy number variation of ribosomal RNA genes (rDNA) and found no differences in probands with autism spectrum disorder and unaffected siblings. Validation results suggest that the previously reported concerted copy number variation between 45S and 5S arrays may be due to variable data quality, and meaningful correlation between 45S and 5S copy numbers was not detected in various datasets.
SCIENTIFIC REPORTS
(2021)
Article
Environmental Sciences
Jianlin Lou, Shoukai Yu, Lingfang Feng, Xinnian Guo, Meng Wang, Alan T. Branco, Tao Li, Bernardo Lemos
Summary: Exposure to hexavalent chromium induces instability in the rDNA of human cells, leading to rapid amplification and contraction of the array. Environmental exposure and drinking habits, but not age, influence the natural variation in rDNA copy number in human populations exposed to Cr (VI).
ENVIRONMENT INTERNATIONAL
(2021)
Article
Biotechnology & Applied Microbiology
Hongbiao Li, Song Gao, Siqi Zhang, Weizhu Zeng, Jingwen Zhou
Summary: Flavonoids have notable biological activities and are widely used in various industries. This study successfully integrated multiple flavonoid pathway genes in a single-step integration method in yeast, significantly improving the production of naringenin. Optimizing the supply of donor DNA and utilizing a high titer p-coumaric acid strain as a chassis were key factors in enhancing flavonoid production.
JOURNAL OF BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jun He, Sisi Lin, Zhongyu Yu, Aiping Song, Zhiyong Guan, Weimin Fang, Sumei Chen, Fei Zhang, Jiafu Jiang, Fadi Chen, Haibin Wang
Summary: Using rDNA as a FISH probe, researchers found that 5S rDNA sites are mainly located in subterminal chromosome regions, while the number and intensity of 45S rDNA sites differ from previously studied Chrysanthemum resources. These findings offer insight into the chromosomal structural variations in Chrysanthemum and its related species.
MOLECULAR BIOLOGY REPORTS
(2021)
Review
Cell Biology
Evgeny Smirnov, Nikola Chmurciakova, Frantisek Liska, Pavla Bazantova, Dusan Cmarko
Summary: The review discusses the causes and types of human rDNA instability, the methods of detection, its distribution within the locus, and its biological significance. Literature data suggests that the variability of rDNA is not only a potential cause of pathology, but also an important but poorly understood aspect of normal cell physiology.
Article
Neurosciences
Vandre C. Figueiredo, Yuan Wen, Bjorn Alkner, Rodrigo Fernandez-Gonzalo, Jessica Norrbom, Ivan J. Vechetti, Taylor Valentino, C. Brooks Mobley, Gabriel E. Zentner, Charlotte A. Peterson, John J. McCarthy, Kevin A. Murach, Ferdinand von Walden
Summary: The study reveals the genetic and rDNA gene-wide epigenetic regulation of ribosome biogenesis in response to exercise, highlighting the roles of rDNA dosage and CpG methylation in skeletal muscle. This indicates a genetic predisposition for hypertrophic responsiveness and preferential up-regulation of ribosome biogenesis with resistance exercise. The findings expand our understanding of the genetic and epigenetic factors involved in exercise-induced changes in ribosome biogenesis.
JOURNAL OF PHYSIOLOGY-LONDON
(2021)
Review
Cell Biology
Selina M. Kindelay, Keith A. Maggert
Summary: The ribosomal DNA (rDNA) in Drosophila exists as two independent clusters of individual 35 S cistmns. The multiplicity of rDNA is crucial for ensuring proper translational demands, but the tandem arrays are susceptible to copy number variation within and between populations. This article discusses how cells respond to insufficient rDNA copy number, including the historical concept of rDNA magnification and recent discoveries of rDNA loss and potential mechanisms of magnification.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Article
Plant Sciences
Xiaoxia Ding, Jieting Chen, Chunyan Dai, Peiqi Shi, Hengyu Pan, Yanqi Lin, Yikang Chen, Lu Gong, Linming Chen, Wenguang Wu, Xiaohui Qiu, Jiang Xu, Zhihai Huang, Baosheng Liao
Summary: This study characterized the ribosomal DNA (rDNA) of Artemisia annua and identified rich polymorphisms in rDNA copy number and sequence in A. annua populations. The study also found significant differences in the haplotype composition of the internal transcribed spacer 2 (ITS2) region among A. annua strains. These findings suggest that ITS2 haplotype analysis is an ideal tool for A. annua strain identification and population genetic homogeneity assessment.
Article
Biochemistry & Molecular Biology
Aleem Razzaq, Yosra Bejaoui, Tanvir Alam, Mohamad Saad, Nady El Hajj
Summary: The analysis of human ribosomal DNA (rDNA) copy number has been challenging due to its repetitive nature. However, studying rDNA variations is important for understanding its role in human health and disease. In this study, whole-genome bisulphite sequencing was used to quantify rDNA copy number and measure DNA methylation at the 45S rDNA locus. The results showed high inter-individual variation in rDNA copy number, but no significant differences were found in autism spectrum disorder (ASD) or schizophrenia brains. However, a strong positive correlation between copy number and DNA methylation was observed in multiple tissues, suggesting a possible dosage compensation mechanism.
Review
Soil Science
Nicolas Romillac, Lucia Santorufo
Summary: The paper discusses the growing interest and difficulties in using functional trait approaches to study soil bacterial communities. The authors propose to identify functional traits based on bacterial fitness rather than their relationship to ecosystem functions, and suggest a framework including growth rate, survival, and dispersion as components of bacterial fitness.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Review
Health Care Sciences & Services
Lev N. Porokhovnik
Summary: Copy number variation of ribosomal DNA and pericentromeric satellite repeats can modulate the stress response and have phenotypic manifestations, indicating the importance of individual data measurement.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Review
Cell Biology
Evgeny Smirnov, Nikola Chmurciakova, Dusan Cmarko
Summary: The rDNA locus in human cells is a fragile site of the genome with high risk of instability leading to cancer, characterized by repetitive and highly transcribed nature. It contains functional regions producing non-coding RNAs that participate in activity regulation and stress reactions, showing potential as therapeutic targets for cancer treatment. Variability in the structure of the locus may contribute to malignant transformation, highlighting the importance of rDNA in carcinogenesis.
Article
Genetics & Heredity
Anna Samelak-Czajka, Pawel Wojciechowski, Malgorzata Marszalek-Zenczak, Marek Figlerowicz, Agnieszka Zmienko
Summary: MicroRNAs (miRNAs) regulate gene expression through the RNA interference mechanism. Conserved MIRs are involved in developmental and physiological processes, while nonconserved MIRs participate in stress responses. Copy number variations of Arabidopsis MIRs are related to their age, function, and genomic localization.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
Article
Plant Sciences
Gigi Y. Wong, Anthony A. Millar
Summary: In plants, the relationships between microRNAs (miRNAs) and their target genes are complex, with predictions indicating numerous and diverse targets based on complementarity. However, there is also a hypothesis suggesting that miRNA specificity is constrained and limited to a few targets with compatible expression. To explore these opposing views, a bioinformatic pipeline was used to identify highly conserved miRNA targets across species. The results supported the constrained hypothesis, showing that the majority of miRNA targets belong to conserved target gene families, with a minority of secondary families or non-conserved targets.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Plant Sciences
Preston Hurst, James C. Schnable, David R. Holding
Summary: Tandem duplication can lead to copy number variation and functional novelty in genes, as well as diversity between individuals in a species. In maize, the alpha-zein gene family copies show conservation in both gene sequence and gene regulation patterns between different inbreds, even though there may be differences in overall expression levels.
Article
Cell Biology
Sona Legartova, Paolo Fagherazzi, Lenka Stixova, Ales Kovarik, Ivan Raska, Eva Bartova
Summary: The study found that DNA damaging agents and inhibitors of RNA polymerases cause DNA damage and increase the level of SC-35 protein, while PARP inhibitors and A-type lamin depletion can lead to the formation of nuclear blebs and affect the spliceosome component SRRM2. Additionally, SC-35 protein displays different localization patterns during cell mitosis, indicating the establishment of nuclear speckles and the occurrence of splicing factors. In conclusion, splicing is shown to occur transcriptionally and is dependent on A-type lamin.
Article
Plant Sciences
Josep A. Rossello, Alexis J. Maravilla, Marcela Rosato, Nestor Torres, P. Pablo Ferrer-Gallego
Summary: The lectotype of Dactylis ibizensis is based on a specimen at W, consisting exclusively of diploid plants according to anatomical and macromorphological data from karyologically verified individuals. This helps preserve the name currently used for Balearic cocksfoot on the islands of Formentera and Ibiza.
Article
Genetics & Heredity
Roman Matyasek, Katerina Rehurkova, Kristyna Berta Marosiova, Ales Kovarik
Summary: Analysis of over 95,000 virus genomes reveals that C>U and G>U mutations are the most common, comprising the majority of variations. While there is a significant excess of substitutions between hydrophobic and hydrophilic amino acids, mutations in the S-protein predominantly lead to hydrophilic amino acids, contrary to the global trend.
Review
Biology
Judit E. Sponer, Jiri Sponer, Ales Kovarik, Ondrej Sedo, Zbynek Zdrahal, Giovanna Costanzo, Ernesto Di Mauro
Summary: The review summarizes the recent progress in template-free nonenzymatic polymerization of 3 ',5' cyclic nucleotides, aiming to address the most frequently raised questions among scientists in the field of prebiotic chemistry, covering topics such as detection and characterization of oligomeric products, as well as the geological context of this chemistry.
Article
Chemistry, Multidisciplinary
Sreekar Wunnava, Christina F. Dirscherl, Jakub Vyravsky, Ales Kovarik, Roman Matyasek, Jiri Sponer, Dieter Braun, Judit E. Sponer
Summary: The study demonstrates that the dry polymerization of 3',5'-cyclic guanosine monophosphate (3',5'-cGMP) is not sensitive to the presence of cations when conducted in an acidic environment, contrary to previous reports suggesting optimal conditions at pH 9.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Jana Sochorova, Francisco Galvez, Roman Matyasek, Sonia Garcia, Ales Kovarik
Summary: The study reveals a high variability in 5S and 45S rDNA loci numbers in animals, with rare occurrences of karyotypes with extremely high loci numbers, generally converging to two 5S sites and two 45S rDNA sites per diploid genome. The position of 45S rDNA on sex chromosomes is relatively common, especially in arthropods, and is predominantly located in microchromosomes in birds and reptiles. Additionally, as the number of 45S rDNA loci increases, the proportion of active NORs progressively decreases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Zuzana Tulpova, Ales Kovarik, Helena Toegelova, Pavla Navratilova, Veronika Kapustova, Eva Hribova, Jan Vrana, Jiri Macas, Jaroslav Dolezel, Hana Simkova
Summary: This study deciphered the genomic organization and tissue-specific expression of rDNA loci in hexaploid bread wheat, revealing the significant contribution of the 1B and 6B loci to rRNA transcription and the differential cytosine methylation level in the 5D locus. This provides insights into wheat evolution and transcriptional regulation.
Article
Plant Sciences
Laszlo Bartha, Terezie Mandakova, Ales Kovarik, Paul-Adrian Bulzu, Nathalie Rodde, Vaclav Mahelka, Martin A. Lysak, Margaux-Alison Fustier, Jan Safar, Petr Capal, Lujza Keresztes, Horia L. Banciu
Summary: This study provides evidence supporting the integration hypothesis of alien ribosomal DNA (rDNA) from eudicots into the genome of the monocot genus Erythronium. The transferred eudicot-type rDNA is still active in the monocot host, adding a new example of nuclear-to-nuclear DNA transfer between eudicots and monocots.
Article
Plant Sciences
F. Lara, R. D. Porley, I. Draper, M. Aleffi, C. Garcia, R. Garilleti
Summary: This study identified five species of Ulota inhabiting the southernmost Mediterranean localities. The distribution of these species was found to be irregular, with notable discoveries in southern Portugal, Italy, and the central Mediterranean.
Review
Plant Sciences
Josep A. Rossello, Alexis J. Maravilla, Marcela Rosato
Summary: This article discusses the issue of applying 35S rDNA in plant taxonomy and phylogenetics. The correct interpretation of this marker is limited by the instability of the genetic architecture, the diversity of molecular changes, and the evolutionary dynamics of rDNA units in hybrids and polyploid species. In addition, the use of different terminology by different authors complicates comparisons.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Radka Vozarova, Wencai Wang, Jana Lunerova, Fengqing Shao, Jaume Pellicer, Ilia J. Leitch, Andrew R. Leitch, Ales Kovarik
Summary: This study analyzed the abundance and homogeneity of telomeric repeats in a wide range of plant species and found a positive correlation between repeat abundance and intragenomic sequence heterogeneity. The research revealed unique patterns of telomeric repeat diversity in different plant taxa.
Article
Plant Sciences
Nikolay Matanov, Francisco Lara, Isabel Draper, Juan A. A. Calleja, Belen Albertos, Ricardo Garilleti
Summary: A recent study identified a previously unnoticed endemic genus in New Zealand called Rehubryum, based on the species Ulota bellii. The study examined specimens from 80 localities in New Zealand and concluded that our recent collections correspond to the original concept of Ulota bellii, now classified as Rehubryum bellii. The study also discussed the similarities and differences between Rehubryum and its sister genus Atlantichella, as well as its distinction from Australasian species of Orthotrichaceae.
JOURNAL OF BRYOLOGY
(2023)
Article
Plant Sciences
Kristel van Zuijlen, Michael P. Nobis, Lars Hedenaes, Nick Hodgetts, Juan A. Calleja Alarcon, Belen Albertos, Markus Bernhardt-Roemermann, Rosalina Gabriel, Ricardo Garilleti, Francisco Lara, Chris D. Preston, Josef Simmel, Edi Urmi, Irene Bisang, Ariel Bergamini
Summary: Building on recent publications and previous compilations, the Bryophytes of Europe Traits (BET) data set includes a comprehensive collection of biological and ecological traits of bryophytes, as well as bioclimatic variables based on European distribution. With 65 traits and 25 bioclimatic variables, this data set provides valuable information for future studies in bryophyte biology, ecology, and conservation.
JOURNAL OF VEGETATION SCIENCE
(2023)
Correction
Ecology
Wencai Wang, Xianzhi Zhang, Sonia Garcia, Andrew R. Leitch, Ales Kovarik
Review
Ecology
Wencai Wang, Xianzhi Zhang, Sonia Garcia, Andrew R. Leitch, Ales Kovarik
Summary: The classical model of concerted evolution states that rDNA units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected. However, advanced sequencing techniques have revealed that rDNA homogenization in many organisms is not complete. This work summarizes the variation in rDNAs across different taxa and discusses the factors contributing to this incomplete concerted evolution.