Article
Multidisciplinary Sciences
Deepak Khatri, Audrey Putoux, Audric Cologne, Sophie Kaltenbach, Alicia Besson, Eloise Bertiaux, Justine Guguin, Adele Fendler, Marie A. Dupont, Clara Benoit-Pilven, Leila Qebibo, Samira Ahmed-Elie, Severine Audebert-Bellanger, Pierre Blanc, Thomas Rambaud, Martin Castelle, Gaelle Cornen, Sarah Grotto, Agnes Guet, Laurent Guibaud, Caroline Michot, Sylvie Odent, Lyse Ruaud, Elise Sacaze, Virginie Hamel, Remy Bordonne, Anne -Louise Leutenegger, Patrick Edery, Lydie Burglen, Tania Attie-Bitach, Sylvie Mazoyer, Marion Delous
Summary: In the human genome, 750 genes contain one intron excised by the minor spliceosome. Mutations in the noncoding gene RNU4ATAC have been found in several syndromes. This study reveals bi-allelic RNU4ATAC mutations in patients with Joubert syndrome, expanding the spectrum of RNU4ATAC-associated disorders and suggesting ciliary dysfunction as a downstream mechanism of minor splicing defects.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biology
Davia Blake, Caleb M. Radens, Max B. Ferretti, Matthew R. Gazzara, Kristen W. Lynch
Summary: The study investigates the impact of CD28 costimulation on alternative splicing in T cells activated through the T cell receptor (TCR). It is found that CD28 signaling has minimal impact on splicing alone but enhances the extent of change in TCR-induced alternative splicing events. Interestingly, enhanced splicing events occur within genes encoding key components of the apoptotic signaling pathway. Experimental evidence shows that isoforms induced by CD3/CD28 costimulation promote resistance to apoptosis and changes in these genes function combinatorially to further promote cell viability. The JNK signaling pathway is also found to be required for these splicing events, highlighting their co-regulation.
Article
Genetics & Heredity
Anna Grandchamp, Katrin Berk, Elias Dohmen, Erich Bornberg-Bauer
Summary: De novo genes are novel genes that emerge from non-coding DNA. This study investigates the properties of these genes, such as intron presence and position, regulatory motifs, untranslated regions (UTRs), and protein domains. The findings suggest that introns may have been captured by a significant portion of de novo genes, and the emergence mechanism impacts the enrichment of certain motifs. Additionally, the stability of mRNA structures and the acquisition of new protein domains with age are observed. Overall, the genomic position of de novo genes strongly influences their properties.
Article
Engineering, Chemical
Shuai Zhang, Feilong Rong, Shunjiang Huang, Shuangrun Zhao, Minghua Wang, Linghao He, Zhihong Zhang, Miao Du
Summary: A series of mesoporous carbon nanotube networks loaded with trace atomic Fe sites (Fe-CNTs) were constructed and used as efficient catalysts for the photodegradation of tetracycline compounds under visible-light irradiation. Fe-CNT-900, synthesized at 900°C, demonstrated multifunctionality and superior performance in terms of porosity, specific surface area, and magnetic properties.
SEPARATION AND PURIFICATION TECHNOLOGY
(2022)
Review
Developmental Biology
Anouk M. Olthof, Alisa K. White, Rahul N. Kanadia
Summary: Splicing is a crucial regulatory mechanism for gene expression that expands the proteome from a limited number of genes. Changes in splicing during vertebrate evolution may have played a role in neural, neural crest, and skeletal development. Mutations in spliceosome subunits are linked to developmental disorders, and inhibiting splicing can lead to tissue-specific phenotypes. Further research is needed to explore these mechanisms and address gaps in our knowledge.
Article
Genetics & Heredity
Pavel Dvorak, Vojtech Hanicinec, Pavel Soucek
Summary: Evidence shows that introns play a role in regulating the transfer of genetic information, with longer first introns found to be common in eukaryotic gene structure and containing conserved sequences and functional elements. Our study provides more precise information on the position of the longest introns in human protein-coding genes and their possible connection to biological function and gene expression. Results indicate that the longest introns are mainly located in the first and second thirds of introns, with peaks at the middle and last introns, and the median length decreases with increasing distance from the start of the gene.
FRONTIERS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Karan Bedi, Brian Magnuson, Ishwarya Venkata Narayanan, Michelle T. Paulsen, Thomas E. Wilson, Mats Ljungman
Summary: This study investigated cotranscriptional splicing efficiencies of 17,000 introns expressed across six human cell lines using Bru-seq and BruChase-seq. Less than half of all introns were found to be cotranscriptionally spliced. The efficiency of splicing varied across cell lines and within genes, and was not correlated with gene length, intron position, splice site strengths, or GC content. Binding signals from RNA-binding proteins were found to correlate with splicing efficiency, suggesting their important roles in determining splicing outcomes in a cell type- and intron-specific manner.
Article
Chemistry, Physical
Yuping Wang, Yanan Shi, Xiao Zhang, Feng Yan, Jianzhong Zhang, Xitian Zhang, Yujin Chen, Chunling Zhu
Summary: In this study, atomically dispersed Mn sites were introduced into N-doped carbon nanotubes to fabricate Mn-N-x/NCNT with tubular morphology and large surface area. This material exhibited excellent EMW absorption property at low filler ratio and matching thickness. Experimental and theoretical results demonstrated that the atomically dispersed Mn sites adjusted the electronic structure and polarizability of NCNTs, leading to enhanced conductivity and polarization losses, and thus improved EMW property.
Article
Multidisciplinary Sciences
Kelsey C. North, Andrew A. Shaw, Anna N. Bukiya, Alex M. Dopico
Summary: Progesterone activates BK channels in mouse cerebrovascular myocytes by binding to the regulatory subunits, with a high-affinity site enabling steroid binding at a low-affinity site to activate the channel. Mutation of the high-affinity site weakens channel activation by progesterone, indicating its permissive role.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Vita Setrajcic Dragos, Ksenija Strojnik, Gasper Klancar, Petra Skerl, Vida Stegel, Ana Blatnik, Marta Banjac, Mateja Krajc, Srdjan Novakovic
Summary: In this study, we performed functional characterization of pathogenic/likely pathogenic variants in susceptibility genes that disrupt RNA splicing using RNAseq analysis. We successfully reclassified 50% of the investigated variants, leading to improved clinical management of the patient and the family members.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Computer Science, Information Systems
Waseem Ullah, Khan Muhammad, Ijaz Ul Haq, Amin Ullah, Saeed Ullah Khattak, Muhammad Sajjad
Summary: Accurate splice site prediction is crucial in medical sciences and biochemistry as mutations can lead to genetic diseases and cancer. The study utilized machine learning algorithms and a composite features-based model to improve the accuracy of splice site prediction. The results showed high accuracy rates for donor and acceptor sites datasets using SVM classifier.
MULTIMEDIA TOOLS AND APPLICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Jirayu Nuadthaisong, Tanaporn Phetruen, Chanakan Techawisutthinan, Sittinan Chanarat
Summary: Stentor coeruleus, a ciliate with regenerative ability, has exceptionally small introns in its genome. Analysis of the spliceosomal components in the organism revealed the presence of all snRNAs but a reduction in size for many proteins. Interestingly, some regulators, such as Serine/Arginine-rich proteins, were not detected. Furthermore, while most parts of spliceosomal proteins were conserved, regions of branching factors projecting to the active site were different. This suggests that steric-clash avoidance and unique splicing regulation may be occurring in Stentor coeruleus.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Karla Alejandra Ruiz-Ceja, Dalila Capasso, Michele Pinelli, Eugenio Del Prete, Diego Carrella, Diego di Bernardo, Sandro Banfi
Summary: This study explores the transcript composition of inherited retinal disease genes in the human retina through a meta-analysis of publicly available RNA-seq datasets. It identifies many previously unreported transcripts and examines their potential impact on the protein level. The findings contribute to understanding the missing heritability in inherited retinal diseases.
Review
Microbiology
Suraya Muzafar, Ravi Datta Sharma, Neeraj Chauhan, Rajendra Prasad
Summary: Spliceosomal introns are noncoding sequences spliced from pre-mRNA, and alternative splicing is a common mode of posttranscriptional regulation in eukaryotes. Fungi exhibit diverse intron numbers and alternative splicing, which play important roles in growth, development, protein localization, and adaptability to changing environments. The role of alternative splicing in pathogenicity and drug resistance in fungi is gaining attention, suggesting potential for new therapeutic development.
FEMS MICROBIOLOGY LETTERS
(2021)
Article
Microbiology
Ronald Muryellison Oliveira da Silva Gomes, Kassia Jessica Galdino da Silva, Leonardo Capistrano Ferreira, Thales Domingos Arantes, Raquel Cordeiro Theodoro
Summary: This study evaluated the presence of group I introns in the mitochondrial genes cob and cox1 in different Cryptococcus isolates. The results showed that C. neoformans complex has fewer introns compared to C. gattii complex and there is significant polymorphism in the presence and size of these elements. It was possible to differentiate among genotypes within each species complex by combining PCRs of mtLSU and cox1 introns for C. neoformans species, and mtLSU and cob introns for C. gattii species.
Article
Biochemistry & Molecular Biology
Philipp Michl-Holzinger, Simon Obermeyer, Hanna Markusch, Alexander Pfab, Andreas Ettner, Astrid Bruckmann, Sabrina Babl, Gernot Laengst, Uwe Schwartz, Andrey Tvardovskiy, Ole N. Jensen, Akihisa Osakabe, Frederic Berger, Klaus D. Grasser
Summary: The heterodimeric histone chaperone FACT, composed of SSRP1 and SPT16, is involved in dynamic nucleosome rearrangements during DNA-dependent processes. In this study, post-translational modifications of SSRP1 and SPT16 were investigated in Arabidopsis cells. Acetylation of lysine residues in SSRP1's C-terminal region and phosphorylation of serine/threonine residues in SPT16's acidic C-terminal region were identified. Mutational analysis showed that acetylation of SSRP1 had minimal effects, but phosphorylation of SPT16 by protein kinase CK2 was crucial for histone interactions. Plants expressing a non-phosphorylatable version of SPT16 had reduced histone binding and exhibited growth and developmental defects. These findings suggest that phosphorylation of SPT16 is required for proper nucleosome occupancy at the transcriptional start sites of active genes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Natasa Josipovic, Karoline K. Ebbesen, Anne Zirkel, Adi Danieli-Mackay, Christoph Dieterich, Leo Kurian, Thomas B. Hansen, Argyris Papantonis
Summary: In this study, we cataloged nascent RNA-enriched circRNAs from primary human cells and identified circRAB3IP as a crucial player in maintaining cellular homeostasis. Depletion of circRAB3IP disrupted gene expression, suppressed cell cycle progression, and induced changes in gene expression associated with senescence. Conversely, excess circRAB3IP delivered to endothelial cells through extracellular vesicles accelerated their division. These effects were attributed to the interplay between circRAB3IP and the splicing factor SF3B1, which affects transcript variant expression levels of cell cycle-related genes.
Article
Pharmacology & Pharmacy
David Peterhoff, Stefanie Thalhauser, Patrick Neckermann, Clara Barbey, Kristina Straub, Julian Nazet, Rainer Merkl, Gernot Laengst, Miriam Breunig, Ralf Wagner
Summary: Selective targeting of germline B cells with specifically designed germline-targeting HIV-1 envelope immunogens presented on the surface of silica nanoparticles can enhance the affinity to B cells and induce the generation of broadly neutralizing antibodies. Covalent conjugation of GT-Env exhibits better binding capability to structure-dependent bnAbs compared to non-specifically adsorbed GT-Env. The use of nanoparticle delivery allows activation of B cells at lower concentrations, likely due to avidity effects.
EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS
(2022)
Article
Evolutionary Biology
Elizabeth H. J. Robbins, Steven Kelly
Summary: The chloroplast, evolved from endosymbiosis, has a highly conserved genome organization and a slow rate of molecular evolution. Through analysis of angiosperm plastid genomes, it was found that the distance from the replication origin, amino acid composition, and mRNA abundance are key factors influencing the rate of molecular evolution in plastid genes. These factors account for over 50% of the variation in evolution rate and have constrained the adaptive evolution and evolvability of the chloroplast.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Cell Biology
Helen Hoffmeister, Simon Holzinger, Marie-Sofie Duerr, Astrid Bruckmann, Susanne Schindler, Regina Groebner-Ferreira, Reinhard Depping, Gernot Laengst
Summary: Chromatin remodeling enzymes are essential for genome regulation, and the nuclear import of the human CHD4 protein is characterized in this study. It is shown that CHD4 enters the nucleus through importin-alpha proteins (1, 5, 6 and 7) independently of importin beta 1. Importin alpha 1 directly interacts with a specific motif in CHD4, but mutating this motif only leads to a partial reduction in nuclear localization, suggesting the existence of additional import mechanisms. Furthermore, CHD4 is associated with NuRD core subunits in the cytoplasm, indicating assembly of the NuRD complex before nuclear import. We propose that CHD4 is dragged into the nucleus through a 'piggyback' mechanism using the import signals of the associated NuRD subunits.
JOURNAL OF CELL SCIENCE
(2023)
Article
Plant Sciences
Jacques W. Bouvier, Steven Kelly
Summary: In this article, the authors respond to criticisms regarding the rubisco kinetic traits and show that these criticisms are unfounded. They demonstrate that phylogenetic constraints have a greater impact on rubisco adaptation than catalytic trade-offs.
JOURNAL OF PLANT PHYSIOLOGY
(2023)
Article
Genetics & Heredity
Shu Zhang, Nadine Uebelmesser, Mariano Barbieri, Argyris Papantonis
Summary: High-resolution Micro-C is used to study the effect of RNA polymerase II (RNAPII) loss on chromosome looping. The formation of enhancer-promoter loops depends on RNAPII binding to their anchors. RNAPII plays a role in transcription as well as in setting up regulatory three-dimensional chromatin contacts, including cohesin loop extrusion.
Article
Biology
Federico Nebuloni, Joseph Morgan, Edmond J. Walsh, Peter R. Cook
Summary: Organoids grown in vitro need refreshing flows to avoid necrosis, and we have developed a platform for culturing micro-organoids using an immiscible fluorocarbon to provide nutrients. Through this platform, clonal growth of human embryonic kidney cells can be achieved, even with a distance from the surrounding fluid walls.
Article
Multidisciplinary Sciences
Deniz Bartsch, Kaustubh Kalamkar, Gaurav Ahuja, Jan-Wilm Lackmann, Juergen Hescheler, Timm Weber, Hisham Bazzi, Massimiliano Clamer, Sasha Mendjan, Argyris Papantonis, Leo Kurian
Summary: Research shows that the fate of forming the heart is preset in pluripotency by a specialized mRNA translation circuit controlled by RBPMS in hESCs. Loss of RBPMS leads to patterning and morphogenetic defects in the cardiac mesoderm. This study reveals how specialized mRNA translation programs future fate trajectories during embryogenesis.
Review
Biochemistry & Molecular Biology
Rodrigo Maldonado, Gernot Laengst
Summary: Mammalian genomes are transcribed extensively, producing numerous coding and non-coding transcripts. These transcripts are physically associated with chromatin and play roles in gene regulation and genome organization. This review focuses on the sequence-specific targeting of RNA to DNA by forming triple helical structures and discusses the importance of nucleosome positioning and histone modifications in stabilizing these structures.
BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Uwe Schwartz, Tetsuro Komatsu, Claudia Huber, Floriane Lagadec, Conradin Baumgartl, Elisabeth Silberhorn, Margit Nuetzel, Fabienne Rayne, Eugenia Basyuk, Edouard Bertrand, Michael Rehli, Harald Wodrich, Gernot Laengst
Summary: Through various techniques, such as RNA-seq, MNase-seq, and ChIP-seq, the study investigated the dynamics of viral chromatin structure changes during adenovirus infection and their correlation with gene transcription. The adenoviral genome was found to be arranged in nucleoprotein particles called adenosomes, which are positioned by a DNA sequence code and protect a specific portion of DNA. The viral nucleoprotein architecture, specifically the replacement of protamine-like protein pVII by histone H3.3, plays a central role in the structural changes and nucleosome assembly during early infection.
Editorial Material
Biology
Steven Kelly
Letter
Genetics & Heredity
Antonios Papadakis, Akos Gyenis, Joris Pothof, Jan Hoeijmakers, Argyris Papantonis, Andreas Beyer
Article
Cell Biology
Giada Forte, Lora Boteva, Filippo Conforto, Nick Gilbert, Peter R. Cook, Davide Marenduzzo
Summary: Forte et al. conducted simulations to demonstrate the importance of bridging condensins in condensing chromosomes into mitotic cylinders. These findings highlight the significance of the bridging and looping activities of condensins, and propose a mechanistic model for chromatin structure at chromosome fragile sites.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
David Mark Emms, Steven Kelly
Summary: Determining evolutionary relationships between genes is crucial in comparative biological research. SHOOT is introduced as a fast and accurate tool for phylogenetic analysis of novel query sequences. It performs the analysis with comparable speed to BLAST and can accurately identify orthologs.