Article
Cell Biology
Dawei Meng, Qian Zheng, Xue Zhang, Xuejiao Piao, Li Luo, Yichang Jia
Summary: Emerging evidence suggests that intron-detaining transcripts (IDTs) play a crucial role in cellular response to environmental stimuli and stress. This study proposes a mechanism for the splicing of detained introns (DIs) involving the interaction between Smad Nuclear Interacting Protein 1 (SNIP1) and RNPS1. The misregulation of this mechanism may contribute to neurodegeneration.
Article
Multidisciplinary Sciences
Jonas Tholen, Michal Razew, Felix Weis, Wojciech P. Galej
Summary: Recognition of intron branch site by U2 snRNP is a critical event during spliceosome assembly. The stability of BS:U2 snRNA duplex, aided by SF3B6, is important for binding introns with poor sequence complementarity. ATP-dependent remodeling captures U2 snRNA in a conformation that competes with BS recognition, providing a mechanism based on branch helix stability.
Article
Biochemistry & Molecular Biology
Kirsten A. Reimer, Claudia A. Mimoso, Karen Adelman, Karla M. Neugebauer
Summary: The study revealed tight coordination between co-transcriptional splicing and transcription elongation and 3' end formation in mammalian cells, with splicing delays possibly taking place between the two catalytic steps. Additionally, inefficient 3' end cleavage was associated with intron retention, highlighting the functional coupling between these co-transcriptional processes.
Review
Cell Biology
Zhan Ding, Yan-Ran Meng, Yu-Jie Fan, Yong-Zhen Xu
Summary: RNA splicing is a process catalyzed by spliceosomes in the nucleus, which removes intronic sequences from precursor RNAs and generates mature RNA. This process increases proteome complexity and fine-tunes gene expression. The major spliceosome and the minor spliceosome are the two coexisting spliceosomes in most metazoans. The major spliceosome removes the majority of introns, while the minor spliceosome removes fewer introns. Understanding the dynamic assembly, catalysis, and protein composition of the minor spliceosome is still limited. The recognition and processing of minor introns, which are rare and usually flanked by major introns, are also poorly understood.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2023)
Article
Plant Sciences
Takamasa Suzuki, Tomomi Shinagawa, Tomoko Niwa, Hibiki Akeda, Satoki Hashimoto, Hideki Tanaka, Yoko Hiroaki, Fumiya Yamasaki, Hiroyuki Mishima, Tsutae Kawai, Tetsuya Higashiyama, Kenzo Nakamura
Summary: The study identified the specific role of DROL1 in regulating the splicing of minor introns with AT-AC termini in Arabidopsis, which plays a crucial role in plant growth and development. The reduced splicing of AT-AC-type introns in drol1 mutants led to retarded growth of seedlings, possibly affecting important genes involved in stress responses and cell proliferation.
Article
Agronomy
Lei Liu, Depeng Wu, Yujuan Gu, Fuxia Liu, Bin Liu, Feng Mao, Xin Yi, Tang Tang, Xiangxiang Zhao
Summary: The study found that alternative splicing changes can lead to an increase in transcriptomic diversity during secondary dormancy induction, with intron retention being the dominant splicing type. The global isoform expression percentage variations in alternative splicing are more significant in differentially expressed genes (DEGs) than in non-DEGs. Spliceosome components are overrepresented among the differently spliced genes associated with secondary dormancy.
MOLECULAR BREEDING
(2022)
Article
Biochemical Research Methods
Morgan Shine, Chengxin Zhang, Anna Marie Pyle
Summary: AMIGOS III is a PyMOL plugin that calculates pseudo-torsion angles for both DNA and RNA structures and performs motif searching based on these angles. It offers improved visualization and faster database generation compared to the previous version, and also introduces support for DNA structures.
Article
Biochemistry & Molecular Biology
Yi Zeng, Benjamin J. Fair, Huilin Zeng, Aiswarya Krishnamohan, Yichen Hou, Johnathon M. Hall, Alexander J. Ruthenburg, Yang Li, Jonathan P. Staley
Summary: Previous studies suggested that most vertebrate genes require exon definition for splicing, where spliceosome assembly occurs on exons rather than introns. However, our research found that 90% of introns, including long introns, can splice before the transcription of a downstream exon, indicating that exon definition is not necessary for most human introns. Additionally, splicing timing varies greatly among introns and is influenced by various genetic elements.
Article
Biochemistry & Molecular Biology
Sandra M. Fernandez-Moya, Janina Ehses, Karl E. Bauer, Rico Schieweck, Anob M. Chakrabarti, Flora C. Y. Lee, Christin Illig, Nicholas M. Luscombe, Max Harner, Jernej Ule, Michael A. Kiebler
Summary: RNA secondary structures play a crucial role in regulating the assembly, localization, and translation of RNA granules, with different effects in neurons. Disrupting RNA hairpins impairs the observed effects of RNA localization and assembly.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Jessica S. Y. Ho, Federico Di Tullio, Megan Schwarz, Diana Low, Danny Incarnato, Florence Gay, Tommaso Tabaglio, JingXian Zhang, Heike Wollmann, Leilei Chen, Omer An, Tim Hon Man Chan, Alexander Hall Hickman, Simin Zheng, Vladimir Roudko, Sujun Chen, Alcida Karz, Musaddeque Ahmed, Housheng Hansen He, Benjamin D. Greenbaum, Salvatore Oliviero, Michela Serresi, Gaetano Gargiulo, Karen M. Mann, Eva Hernando, David Mulholland, Ivan Marazzi, Dave Keng Boon Wee, Ernesto Guccione
Summary: The study indicates that the dependency of cancer cells on heterogeneous nuclear ribonucleoprotein M (HNRNPM) is due to its role in mis-splicing of key homeostatic genes, mimicking HNRNPM-dependent splicing events can inhibit the growth of prostate cancer cells.
Article
Biochemical Research Methods
Michael Uhl, Dominik Rabsch, Florian Eggenhofer, Rolf Backofen
Summary: This article introduces Peakhood, the first tool that utilizes CLIP-seq peak regions, CLIP-seq read information, and genomic annotations to determine the context for each peak region and determine the most probable splice variant, resulting in a comprehensive collection of transcript context binding sites.
Article
Multidisciplinary Sciences
Rui Bai, Ruixue Wan, Lin Wang, Kui Xu, Qiangfeng Zhang, Jianlin Lei, Yigong Shi
Summary: The study reveals the atomic features of the activated human minor spliceosome and the proteins that stabilize its conformation, providing a framework for understanding the mechanism of the minor spliceosome function.
Article
Biochemistry & Molecular Biology
Pingwei Gao, Yujie Zhong, Chengfu Sun
Summary: This study identifies spliceosomal components in the protist Euglena gracilis and reveals the sequence-level sensitivity to splicing modulators. The prevalence of SL RNA-mediated trans-splicing is estimated to be high in this species. Furthermore, a comparison of splicing proteomes between E. gracilis and its evolutionary cousins provides insights for further exploration of splicing mechanisms.
ACTA BIOCHIMICA ET BIOPHYSICA SINICA
(2023)
Review
Genetics & Heredity
Kaitlin N. Girardini, Anouk M. Olthof, Rahul N. Kanadia
Summary: This article focuses on the role of introns in eukaryotic gene expression by using an intron-centric approach. It discusses how intron architecture influences splicing mechanisms and the impact of spliceosomal snRNAs and their variants on intron splicing. Additionally, the article explores how the presence of introns and the need for splicing affect transcription regulation. Despite the abundant presence of introns in the eukaryotic genome and their emerging role in gene expression regulation, there are still many unexplored areas. Therefore, the article refers to introns as the "dark matter" of the eukaryotic genome and discusses some unresolved questions in the field.
FRONTIERS IN GENETICS
(2023)
Article
Multidisciplinary Sciences
Rui Bai, Ruixue Wan, Chuangye Yan, Qi Jia, Jianlin Lei, Yigong Shi
Summary: Prp2, together with its coactivator Spp2, plays a crucial role in coupling spliceosome remodeling to pre-mRNA splicing. The ATPase/helicase Prp2 loads pre-mRNA into a featured channel between the N and C halves, preventing backward sliding towards the 5'-end, and triggers unidirectional stepwise translocation towards the 3'-end through ATP binding and hydrolysis. This mechanism explains the precise regulation of spliceosome activity during pre-mRNA splicing.
Review
Medicine, Research & Experimental
Sandro Michelini, Maurizio Ricci, Roberta Serrani, Liborio Stuppia, Tommaso Beccari, Dominika Veselenyiova, Sercan Kenanoglu, Shila Barati, Danjela Kurti, Mirko Baglivo, Syed Hussain Basha, Juraj Krajcovic, Munis Dundar, Matteo Bertelli
Summary: The study demonstrates the importance of RORC gene in normal lymphatic system function, and rare variants of RORC may predispose individuals to lymphedema.
LYMPHATIC RESEARCH AND BIOLOGY
(2021)
Review
Genetics & Heredity
Sandro Michelini, Maurizio Ricci, Roberta Serrani, Shila Barati, Sercan Kenanoglu, Dominika Veselenyiova, Danjela Kurti, Mirko Baglivo, Syed Hussain Basha, Sasi Priya, Astrit Dautaj, Munis Dundar, Juraj Krajcovic, Matteo Bertelli
Summary: Researchers developed a Next-Generation-Sequencing protocol to screen genetic variants related to lymphedema in 246 Italian patients. Seven out of 235 patients were found to carry rare missense variants in the NOTCH1 gene, suggesting its potential role as a novel candidate for genetic predisposition to lymphedema. The study highlights the importance of genetic analysis in understanding the causes of lymphedema.
MOLECULAR GENETICS & GENOMIC MEDICINE
(2021)
Article
Cell Biology
Friedrich Hans Kleiner, Matej Vesteg, Juergen Michael Steiner
Summary: In this study, a novel cytochrome c(6)-like protein called PetJ2 was identified in the nuclear genome of Cyanophora paradoxa, a member of the glaucophytes. It is proposed that the glaucophyte PetJ2 protein is related to cyanobacterial c(6B) and c(6C) cytochromes, and that green algal and land plant cytochromes c(6A) may have evolved from an ancestral PetJ2 protein. Import experiments showed that PetJ2 is imported into plastids using the Sec pathway instead of the Tat import pathway.
JOURNAL OF CELL SCIENCE
(2021)
Article
Genetics & Heredity
Leonardo Gatticchi, Dominika Veselenyiova, Jan Miertus, Paolo Enrico Maltese, Elena Manara, Alisia Costantini, Sabrina Benedetti, Darina Durovcikova, Juraj Krajcovic, Matteo Bertelli
Summary: This study identified two sisters in a family with rare genetic disorders using next-generation sequencing and Sanger sequencing, confirming the genetic mutations responsible for their conditions and further verifying the carrier status of their parents. The findings suggest that the detection of multilocus genomic variations can provide accurate diagnosis even in cases with high phenotypic complexity. A targeted sequencing approach can be useful for clinical management by uncovering the relationships between observed phenotypes and underlying genotypes.
MOLECULAR GENETICS & GENOMIC MEDICINE
(2021)
Review
Chemistry, Multidisciplinary
Alexandra Lukacova, Matej Vesteg
Summary: Multiple independent losses of photosynthesis have occurred among several unrelated eukaryotic lineages. Non-photosynthetic plastids are often involved in essential metabolic pathways such as fatty acid synthesis and heme synthesis.
Article
Biotechnology & Applied Microbiology
Alexandra Lukacova, Terezia Beck, Katarina Trnkova, Miriam Trnikova, Juraj Krajcovic, Matej Vesteg
Summary: MALDI-TOF MS is a suitable, accurate and rapid method for discrimination of different strains of E. gracilis.
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Alexandra Lukacova, Terezia Beck, Lenka Koptasikova, Ales Benda, Lucia Tomeckova, Miriam Trnikova, Diana Lihanova, Juergen Michael Steiner, Juraj Krajcovic, Matej Vesteg
Summary: Euglena gracilis, a freshwater protist, has various biotechnological applications and can be used for biofuel production, pharmaceuticals, and water remediation. However, its large-scale cultivation is limited by the high cost of adding vitamins B1 and B12 to the media. This study demonstrates that E. gracilis can be grown for long periods without the need for added vitamins B1 and B12 in a co-culture system involving the filamentous fungus Cladosporium westerdijkiae and the bacteria Lysinibacillus boronitolerans and Pseudobacillus badius. This finding significantly reduces the cultivation costs and the fungus C. westerdijkiae can be used for effective harvesting of E. gracilis through bioflocculation.
JOURNAL OF BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Dominika Veselenyiova, Lenka Hutarova, Alexandra Lukacova, Maria Schneiderova, Matej Vesteg, Juraj Krajcovic
Summary: In this study, the presence of calpains in selected cyanobacterial species was investigated using in silico analyses. Calpains defined by possessing CysPC core domain were found in several cyanobacterial genera. Putative interaction partners for the identified cyanobacterial calpains were predicted based on in silico protein interaction analysis. The phylogenetic analysis divided bacterial and eukaryotic calpains into two separate monophyletic clusters, and two possible evolutionary scenarios were proposed to explain this tree topology.
SCIENTIFIC REPORTS
(2022)
Review
Biotechnology & Applied Microbiology
Diana Lihanova, Alexandra Lukacova, Terezia Beck, Andrej Jedlicka, Dominika Veselenyiova, Juraj Krajcovic, Matej Vesteg
Summary: Euglena gracilis, a freshwater protist, has secondary chloroplasts derived from green algae and can undergo bleaching due to various physical and chemical factors. It can be used as a model organism to study the effects of pollutants and for bioremediation. Genetic modifications have been successfully applied to E. gracilis for the synthesis of biotechnological compounds. Large-scale cultivation is limited by the inability to synthesize essential B-vitamins, but co-cultivation with other microorganisms can overcome this disadvantage.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2023)
Article
Oncology
Michal Konecny, Klaudia Kosova, Petra Tilandyova, Lenka Wachsmannova, Marian Baldovic, Juraj Krajcovic, Andrea Patlevicova, Jan Markus, Sona Ciernikova
Summary: This study conducted multigene panel testing on Slovak HBOC families, revealing that nearly one-third of pathogenic mutations are located in susceptibility genes other than BRCA1/2, offering valuable data for clinical management.
Article
Immunology
S. Michelini, B. Amato, M. Ricci, R. Serrani, D. Veselenyiova, S. Kenanoglu, D. Kurti, A. Dautaj, M. Baglivo, R. Compagna, J. Krajcovic, M. Dundar, S. H. Basha, S. Priya, J. P. Belgrado, M. Bertelli
Summary: This study found rare heterozygous missense single-nucleotide variants in the SVEP1 gene in patients with lymphedema. Healthy family members carrying the same variants reported some subclinical edema. SVEP1 is proposed as a candidate gene to be sequenced in patients with lymphatic malformations to investigate its possible involvement in the development of lymphedema.
Review
Genetics & Heredity
Sandro Michelini, Maurizio Ricci, Roberta Serrani, Shila Barati, Sercan Kenanoglu, Dominika Veselenyiova, Danjela Kurti, Mirko Baglivo, Syed Hussain Basha, Sasi Priya, Astrit Dautaj, Munis Dundar, Juraj Krajcovic, Matteo Bertelli
Summary: A Next-Generation-Sequencing protocol was developed to screen genetic variants related to lymphedema, with results suggesting NOTCH1 as a novel candidate gene for lymphedema predisposition.
MOLECULAR GENETICS & GENOMIC MEDICINE
(2021)
