Article
Multidisciplinary Sciences
Landen Gozashti, Scott W. Roy, Bryan Thornlow, Alexander Kramer, Manuel Ares, Russell Corbett-Detig
Summary: There is significant variation in intron numbers across eukaryotic genomes, and the major drivers of intron content during evolution remain unclear. This study identified 27,563 introns derived from specialized transposons called Introners in 175 eukaryotic genomes, indicating that Introners may explain the episodic nature of intron gain across the eukaryotic tree of life. Species with Introners span diverse phylogenetic backgrounds, and aquatic organisms are more likely to contain Introners. The mechanistic diversity of Introners suggests convergent evolution from nonautonomous transposable elements.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Genetics & Heredity
Jennifer E. Hurtig, Ambro van Hoof
Summary: Through yeast genetics, it is discovered that TSEN not only participates in tRNA splicing but also has other functions, including degradation of a subset of mRNA encoding mitochondrial proteins and an unknown essential function. Overexpression of SEN54 can suppress sen2 mutants, indicating its general suppressive effect on sen2, regardless of tRNA-dependent or tRNA-independent functions. Mutations in the intron-debranching enzyme Dbr1 can also serve as tRNA splicing-independent suppressors. These findings provide insights into the essential function(s) of TSEN.
Review
Cell Biology
John G. Conboy
Summary: Deep intron elements play crucial roles in regulating splicing processes, such as recursive splicing exons, decoy splice sites, and RNA:RNA bridges, with mutations potentially leading to human diseases. Understanding these noncanonical splicing pathways and regulatory signals in deep introns is important for medical applications and uncovering new disease mechanisms.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2021)
Article
Genetics & Heredity
Scout R. L. Thompson, Dong Kyung Lee, Marc-Andre Lachance, David Roy Smith
Summary: Studying homologous recombination with self-splicing introns in Metschnikowia yeasts' mitochondrial genomes sheds light on the mutational effects of these introns, revealing a higher density of polymorphisms near the insertion sites. This suggests that carrying self-splicing introns may come with fitness costs.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Daofeng Li, Deepak Purushotham, Jessica K. Harrison, Silas Hsu, Xiaoyu Zhuo, Changxu Fan, Shane Liu, Vincent Xu, Samuel Chen, Jason Xu, Shinyi Ouyang, Angela S. Wu, Ting Wang
Summary: WashU Epigenome Browser is a web-based tool for exploring, visualizing, and analyzing genomic data. It has a renovated user interface and functions that allow users to interact with data of different dimensions in a single web page. The browser supports displaying three-dimensional chromatin structures and animated time-series data, as well as viewing imaging data from microscopy experiments. In addition to software development, the browser serves and expands data hubs for large consortia.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Cell Biology
Jigeesha Mukhopadhyay, Georg Hausner
Summary: Introns in organellar genomes play important roles in encoding proteins and participating in non-canonical splicing. Different types of introns show diverse distribution patterns in fungi, plants, and algae.
Article
Biochemistry & Molecular Biology
Francesco Cicconardi, James J. Lewis, Simon H. Martin, Robert D. Reed, Charles G. Danko, Stephen H. Montgomery
Summary: The study reveals that multiple chromosome fusions in Heliconius butterflies have significant impacts on population evolution and genetic diversity, altering the characteristics of fused and unfused chromosomes, reducing diversity, and affecting turnover rates of functional loci. The findings further support the notion that chromosome fusion in Heliconius has dramatic effects on rates of neutral and adaptive divergence, potentially influencing patterns of diversification in these butterflies, a classic example of adaptive radiation.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Biochemistry & Molecular Biology
Xuemei Wang, Jingyi Wang, Simin Li, Congming Lu, Na Sui
Summary: RNA splicing is a process of removing introns and joining exons together in pre-mRNA. Chloroplast introns have lost their self-splicing ability and now rely on nuclear-encoded splicing factors. These splicing factors may form ribonucleoprotein particles to facilitate intron splicing. Although some chloroplast intron splicing factors have been identified, their precise roles in the splicing process remain unclear.
Article
Multidisciplinary Sciences
Samoil Sekulovski, Pascal Devant, Silvia Panizza, Tasos Gogakos, Anda Pitiriciu, Katharina Heitmeier, Ewan Phillip Ramsay, Marie Barth, Carla Schmidt, Thomas Tuschl, Frank Baas, Stefan Weitzer, Javier Martinez, Simon Trowitzsch
Summary: Mutations within subunits of the tRNA splicing endonuclease complex are associated with pontocerebellar hypoplasia, and modulation of TSEN stability may contribute to the disease phenotype.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Chloe Ambroset, Aurelie Peticca, Agnes Tricot, Florence Tardy
Summary: Researchers provide three new complete M. bovis genomes and compare them, finding differences in the content of mobile genetic elements, which may impact the structure of the genomes. Whole-genome comparison of these genomes provides valuable resources for future studies combining epidemiology, phylogenetic data, and phylodynamic methods.
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.
Review
Biochemistry & Molecular Biology
Elena McBeath, Keigi Fujiwara, Marie-Claude Hofmann
Summary: Until recently, the methods for generating floxed mice have been challenging, expensive, error-prone, or time-consuming. To overcome these issues, some labs have successfully used a small artificial intron to conditionally knockout a gene of interest in mice. However, others have encountered difficulties with the technique, primarily due to incorrect splicing or insufficient knockout of the gene's protein. This article presents a guide on selecting the appropriate exon and placing the recombinase-regulated artificial intron to prevent splicing disruption and maximize mRNA degradation. Following these recommendations should increase the success rate of producing tissue-specific knockout mice using this alternative technique.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Plant Sciences
Marjorie Chery, Laurence Drouard
Summary: This review article highlights the additional functions of tRNA in plants, apart from its role in protein synthesis, such as priming reverse transcription, mRNA transportation, and small RNA production. Additionally, tRNA has been found to play roles in tetrapyrrole biosynthesis, mRNA stabilization and transport, reverse transcription of viral RNAs, and the formation of tRNA-like structures in RNA viral genomes. The cleavage of tRNA also plays an important role in regulating gene expression and producing small non-coding RNAs known as tRNA-derived RNAs. Here, the biogenesis of tRNA-derived RNAs and their emerging functions in plants are examined in more detail.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biotechnology & Applied Microbiology
Julianne K. David, Sean K. Maden, Mary A. Wood, Reid F. Thompson, Abhinav Nellore
Summary: Short-read tools for detecting intron retention have poor performance and often result in false positives and false negatives, calling into question the completeness and validity of putatively retained introns called by commonly used methods.
Article
Biology
Alena Kroupova, Fabian Ackle, Igor Asanovic, Stefan Weitzer, Franziska M. Boneberg, Marco Faini, Alexander Leitner, Alessia Chui, Ruedi Aebersold, Javier Martinez, Martin Jinek
Summary: RtcB enzymes are RNA ligases that are essential for various cellular processes, including tRNA splicing and RNA repair. In metazoa, RtcB functions as part of a larger tRNA ligase complex, with different subunits playing crucial roles in maintaining complex integrity. The crystal structures of key subunits provide insights into the catalytic mechanism and molecular architecture of the human tRNA ligase complex, shedding light on its functions in cellular RNA metabolism.
Article
Biochemistry & Molecular Biology
Lennart Randau
DNA HABITATS AND THEIR RNA INHABITANTS
(2015)
Article
Biotechnology & Applied Microbiology
Patrick P. Dennis, Vanessa Tripp, Lauren Lui, Todd Lowe, Lennart Randau
Article
Biochemical Research Methods
Kundan Sharma, Ajla Hrle, Katharina Kramer, Timo Sachsenberg, Raymond H. J. Staals, Lennart Randau, Anita Marchfelder, John van der Oost, Oliver Kohlbacher, Elena Conti, Henning Urlaub
Article
Biology
Andre Plagens, Michael Daume, Julia Wiegel, Lennart Randau
Article
Biochemistry & Molecular Biology
Vanessa Tripp, Roman Martin, Alvaro Orell, Omer S. Alkhnbashi, Rolf Backofen, Lennart Randau
MOLECULAR MICROBIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Daniel Gleditzsch, Hanna Mueller-Esparza, Patrick Pausch, Kundan Sharma, Srivatsa Dwarakanath, Henning Urlaub, Gert Bange, Lennart Randau
NUCLEIC ACIDS RESEARCH
(2016)
Article
Biochemistry & Molecular Biology
Yaming Shao, Hagen Richter, Shengfang Sun, Kundan Sharma, Henning Urlaub, Lennart Randau, Hong Li
Article
Biochemistry & Molecular Biology
Patrick Pausch, Hanna Mueller-Esparza, Daniel Gleditzsch, Florian Altegoer, Lennart Randau, Gert Bange
Article
Microbiology
Michael Daume, Michael Uhl, Rolf Backofen, Lennart Randau
Editorial Material
Microbiology
Hanna Mueller-Esparza, Lennart Randau
FRONTIERS IN MICROBIOLOGY
(2017)
Editorial Material
Microbiology
Lennart Randau
NATURE MICROBIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Alvaro Orell, Vanessa Tripp, Victor Aliaga-Tobar, Sonja-Verena Albers, Vinicius Maracaja-Coutinho, Lennart Randau
NUCLEIC ACIDS RESEARCH
(2018)
Review
Biochemistry & Molecular Biology
Daniel Gleditzsch, Patrick Pausch, Hanna Mueller-Esparza, Ahsen Oezcan, Xiaohan Guo, Gert Bange, Lennart Randau
Article
Biochemistry & Molecular Biology
Hagen Richter, Judith Rompf, Julia Wiegel, Kristina Rau, Lennart Randau
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2017)
Review
Microbiology
Andre Plagens, Hagen Richter, Emmanuelle Charpentier, Lennart Randau
FEMS MICROBIOLOGY REVIEWS
(2015)
