Article
Biochemical Research Methods
Dimitris Grigoriadis, Nikos Perdikopanis, Georgios K. Georgakilas, Artemis G. Hatzigeorgiou
Summary: This study presents DeepTSS, a novel computational method for processing CAGE samples, that combines genomic signal processing (GSP), DNA features, evolutionary conservation evidence and Deep Learning (DL) to provide accurate TSS predictions. Experimental results show that DeepTSS outperforms existing algorithms on all benchmarks.
BMC BIOINFORMATICS
(2022)
Review
Microbiology
Thi Tuong Vi Dang, Jessie Colin, Guilhem Janbon
Summary: Pathogenic fungi require delicate gene regulation mechanisms to adapt and survive in different environments. The usage of alternative transcription start sites (aTSS) in fungi plays a crucial role in fine-tuning gene expression, and disrupted control of aTSS can severely affect fungal growth and infectious capacity.
Article
Biochemistry & Molecular Biology
Christopher Hennecker, Lynn Yamout, Chuyang Zhang, Chenzhi Zhao, David Hiraki, Nicolas Moitessier, Anthony Mittermaier
Summary: This study provides new evidence linking G4 polymorphism to biological function. The analysis of G4-containing regions in human gene promoter regions revealed that G4CRs with higher degrees of polymorphism are more tightly clustered near transcription sites and tend to contain G4s with shorter loops and bulges. Furthermore, G4CRs with well-characterized biological functions tended to be longer and more polymorphic than genome-wide averages.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Christopher S. Juerges, Lars Doelken, Florian Erhard
Summary: The study introduces a comprehensive approach called iTiSS for accurately identifying TSS in any eukaryotic TSS profiling experiment, reducing false positives by jointly analyzing multiple complementary datasets.
Article
Biochemical Research Methods
Jose Antonio Barbero-Aparicio, Santiago Cuesta-Lopez, Cesar Ignacio Garcia-Osorio, Javier Perez-Rodriguez, Nicolas Garcia-Pedrajas
Summary: This article explores the use of a physical model as an additional information source to improve the prediction of transcription start sites. The study shows that the physical model can accurately predict these sites and opens up new possibilities for research at the intersection of statistical mechanics and machine learning.
BMC BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Hongbin Li, Vishaal Rajani, Lu Han, Danielle Chung, James E. Cooke, Ameet S. Sengar, Michael W. Salter
Summary: NMDA receptors (NMDARs) are a principal subtype of excitatory neurotransmitter receptor, composed of two GluN1 and two GluN2 subunits. Alternative splicing of GluN1 can affect the signaling of glycine, which is crucial for the nonionotropic signaling by NMDARs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Genetics & Heredity
Natalia Savytska, Peter Heutink, Vikas Bansal
Summary: The transcriptional activity of Transposable Elements (TEs) is involved in various pathological processes, but analyzing TE expression using short-read sequencing technologies is challenging. Several tools and quantification strategies have been developed, but their performance at the individual loci level has not been fully evaluated. This study compared different tools and strategies and found a high number of false positives, suggesting an improvement strategy.
FRONTIERS IN GENETICS
(2022)
Editorial Material
Biochemistry & Molecular Biology
Alexandra Bergfort, Karla M. Neugebauer
Summary: Alfonso-Gonzalez et al. present an innovative combination of long-read sequencing approaches that reveal coupling between alternative transcription start sites and alternative polyadenylation site usage at a global level.
Article
Genetics & Heredity
Xinping Chen, Tao Wu, Lingguo Li, Yu Lin, Zhichao Ma, Jinjin Xu, Hui Li, Fanjun Cheng, Ruoyan Chen, Kun Sun, Yuxue Luo, Chen Zhang, Fang Chen, Jiao Wang, Tingyu Kuo, Xiaojuan Li, Chunyu Geng, Feng Lin, Chaojie Huang, Junjie Hu, Jianhua Yin, Ming Liu, Ye Tao, Jiye Zhang, Rijing Ou, Fang Zheng, Yan Jin, Huanming Yang, Jian Wang, Xun Xu, Shengmiao Fu, Hongyan Jiang, Xin Jin, Haiqiang Zhang
Summary: The study highlights the importance of understanding biological characteristics in severe COVID-19 patients, and demonstrates the potential of cfDNA in assessing disease progression. Upregulated and downregulated genes in the plasma of severe patients are closely related to the affected biological processes and functions. Furthermore, transcriptome analysis reveals viral and antiviral activity in blood cells of severe patients, illustrating the intense viral replication and immune system response.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Sofia Papanikolaou, George K. Bertsias, Christoforos Nikolaou
Summary: Alternative RNA splicing can lead to reduced mRNA translation or production of non-functional proteins, playing a vital role in gene regulation. In patients with Systemic Lupus Erythematosus, extensive changes in transcription dynamics were identified, predominantly involving intron retention events. Functional analysis of alternatively spliced genes revealed associations with metabolism and histone acetylation.
Article
Biochemistry & Molecular Biology
Simone Bach, Jana-Christin Demper, Nadine Biedenkopf, Stephan Becker, Roland K. Hartmann
Summary: The study reveals that hairpin structures formed by Ebola virus RNA at transcription start sequence and internal genes may impact the activity of the viral polymerase, thus influencing viral transcription and replication processes. Viral RNA synthesis shows high tolerance to a certain range of spacer lengths, but activity declines beyond a specific length limit. Minor enhancements of hairpin structures could rapidly inhibit viral polymerase activity, suggesting a new strategy for inhibiting viral RNA synthesis.
Article
Cell Biology
Fengyan Han, Beibei Yang, Mingyue Zhou, Qiong Huang, Minglang Mai, Zhaohui Huang, Maode Lai, Enping Xu, Honghe Zhang
Summary: This study reveals the co-regulatory mechanism of alternative splicing and transcription elongation in tumors. The researchers found that GLTSCR1 decreases the transcription elongation rate of the ZO1 gene, promoting the binding of a specific splicing factor and the splicing of an exon, which suppresses the migration and invasion of colorectal cancer cells.
JOURNAL OF MOLECULAR CELL BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
A. Gallo, D. Dolfini, A. Bernardini, N. Gnesutta, R. Mantovani
Summary: NF-YA, the regulatory subunit of the trimeric CCAAT-binding transcription factor NF-Y, has multiple alternative spliced isoforms, and NF-YAx and NF-YAg are enriched in Aves and play a major role in early chicken embryo development. In addition, the absence of exon-5 in NF-YAg leads to a global reduction of beta-stranded elements, while removal of the disordered exon-3 sequence has limited effects on TAD architecture.
Article
Biochemistry & Molecular Biology
Francisco Carranza, Hossein Shenasa, Klemens J. Hertel
Summary: Alternative splicing is a highly combinatorial mechanism that allows higher eukaryotes to increase mRNA diversity. The selection of alternative splice sites is influenced by sequence, cis-regulatory elements, exon and intron length, and RNA secondary structures. The study showed that the mode of splice site recognition, either intron or exon definition, plays a role in alternative splicing decisions.
Article
Plant Sciences
Bing He, Lin Meng, Lina Tang, Weicong Qi, Fengqin Hu, Yuanda Lv, Wenjing Song
Summary: This study investigated the transcriptome changes in roots and shoots of allopolyploid Nicotiana tabacum under K+ deficiency, revealing significant alterations in root architecture and IAA content. Analysis of alternative splicing (AS) events showed a tissue-specific response to K+ deficiency, with differentially alternatively spliced genes playing a unique regulatory role in plants' adaptation to low potassium conditions. The study also identified DAS transcription factors that were involved in response to auxin signaling, highlighting the functional significance of AS events in regulating root growth and architecture.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Andreas J. Forstner, Swapnil Awasthi, Christiane Wolf, Eduard Maron, Angelika Erhardt, Darina Czamara, Elias Eriksson, Catharina Lavebratt, Christer Allgulander, Nina Friedrich, Jessica Becker, Julian Hecker, Stefanie Rambau, Rupert Conrad, Franziska Geiser, Francis J. McMahon, Susanne Moebus, Timo Hess, Benedikt C. Buerfent, Per Hoffmann, Stefan Herms, Stefanie Heilmann-Heimbach, Ingrid Kockum, Tomas Olsson, Lars Alfredsson, Heike Weber, Georg W. Alpers, Volker Arolt, Lydia Fehm, Thomas Fydrich, Alexander L. Gerlach, Alfons Hamm, Tilo Kircher, Christiane A. Pane-Farre, Paul Pauli, Winfried Rief, Andreas Strohle, Jens Plag, Thomas Lang, Hans-Ulrich Wittchen, Manuel Mattheisen, Sandra Meier, Andres Metspalu, Katharina Domschke, Andreas Reif, Iiris Hovatta, Nils Lindefors, Evelyn Andersson, Martin Schalling, Hamdi Mbarek, Yuri Milaneschi, Eco J. C. de Geus, Dorret Boomsma, Brenda W. J. H. Penninx, Thorgeir E. Thorgeirsson, Stacy Steinberg, Kari Stefansson, Hreinn Stefansson, Bertram Muller-Myhsok, Thomas Folkmann Hansen, Anders D. Borglum, Thomas Werge, Preben Bo Mortensen, Merete Nordentoft, David M. Hougaard, Christina M. Hultman, Patrick F. Sullivan, Markus M. Nothen, David P. D. Woldbye, Ole Mors, Elisabeth B. Binder, Christian Rueck, Stephan Ripke, Juergen Deckert, Johannes Schumacher
Summary: The study describes the largest genome-wide association study of PD to date, identifying no significant loci but significant genetic correlations between PD and major depressive disorder, depressive symptoms, and neuroticism. The findings represent a major step towards elucidating the genetic susceptibility to PD.
MOLECULAR PSYCHIATRY
(2021)
Article
Psychology, Developmental
Elena Raffetti, Anton Jonatan Landgren, Filip Andersson, Francesco Donato, Catharina Lavebratt, Yvonne Forsell, Maria Rosaria Galanti
Summary: The study found that higher levels of morning cortisol and cortisol area under the curve were associated with an increased risk of tobacco use initiation in adolescents, while there were no significant associations with afternoon cortisol concentration.
JOURNAL OF ADOLESCENT HEALTH
(2021)
Review
Biochemistry & Molecular Biology
Philippe A. Melas, Maria Scherma, Walter Fratta, Carlo Cifani, Paola Fadda
Summary: CBD, as the most abundant non-psychoactive component of cannabis, has received attention for its anxiolytic and antidepressant properties. Even though the exact molecular mechanism of action of CBD remains unknown, preclinical animal studies support its potential as an anxiolytic- and antidepressant-like compound. Additionally, evidence linking the neuropharmacological effects of CBD to its behavioral effects suggests a promising role in treating anxiety and mood disorders.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Obstetrics & Gynecology
Xinxia Chen, Emilia Koivuaho, Terhi T. Piltonen, Mika Gissler, Catharina Lavebratt
Summary: The study indicated that maternal PCOS/anovulatory infertility may lead to an increased risk of offspring obesity at early age and diabetes in female offspring during late adolescence. It also suggested that children of mothers with PCOS have an increased risk of subtle signs of cardiometabolic alterations.
HUMAN REPRODUCTION
(2021)
Article
Psychiatry
Elena Raffetti, Philippe Anastasios Melas, Anton Jonatan Landgren, Filip Andersson, Yvonne Forsell, Catharina Lavebratt, Maria Rosaria Galanti
Summary: Early life stress is associated with increased methylation of the NR3C1 gene, and this hypermethylation can predict substance use in middle adolescence, particularly recent use and use duration. Additional longitudinal studies are needed to confirm these findings.
TRANSLATIONAL PSYCHIATRY
(2021)
Letter
Obstetrics & Gynecology
Xinxia Chen, Emilia Koivuaho, Terhi T. Piltonen, Mika Gissler, Catharina Lavebratt
HUMAN REPRODUCTION
(2022)
Article
Obstetrics & Gynecology
Xinxia Chen, Mika Gissler, Catharina Lavebratt
Summary: The presence of PCOS is associated with higher risks of total and spontaneous preterm birth in mothers with non-insulin-treated type 2 diabetes and GDM, while lower risk of offspring being LGA in mothers with insulin-treated diabetes.
HUMAN REPRODUCTION
(2022)
Article
Biochemistry & Molecular Biology
George Hunt, Ann Boija, Mattias Mannervik
Summary: Maintenance of appropriate cell states involves epigenetic mechanisms, including Polycomb-group (PcG)-mediated transcriptional repression. This study reveals the association between the p300/CREB-binding protein (CBP) co-activator and PcG regions in Drosophila and mouse cells. CBP stabilizes Pol II at PcG-bound repressive sites and promotes Pol II pausing, which are necessary for R-loop formation and nucleosome depletion at Polycomb Response Elements (PREs), thereby supporting PcG-mediated silencing.
Article
Clinical Neurology
Katja Ponzer, Vincent Millischer, Martin Schalling, Mika Gissler, Catharina Lavebratt, Lena Backlund
Summary: Using nationwide registers, this study found that long-term lithium treatment is associated with a lower risk of cardiovascular and cerebrovascular diseases, but no significant effect on dementia. However, it also showed an increased risk of pulmonary embolism, Parkinson's disease, and kidney disease in individuals prescribed lithium compared to the general population and psychiatric subcohort.
Article
Biochemistry & Molecular Biology
Johanna S. Qvist, Maria Scherma, Nitya Jayaram-Lindstrom, Walter Fratta, Denise B. Kandel, Eric R. Kandel, Paola Fadda, Philippe A. Melas
Summary: The regular use of cannabis during adolescence has been associated with negative life outcomes, but the exact molecular mechanisms are not well understood. This study found that exposure to a synthetic cannabinoid in adolescent rats led to changes in the expression of proteins related to the gamma-aminobutyric acid (GABA)-ergic neurotransmitter system in the prefrontal cortex (PFC). The synaptic protein SYNGAP1 was upregulated in the PFC following prolonged drug abstinence, and this change was specific to adolescent exposure and not seen in adulthood. Similar changes in SYNGAP1 levels were also observed in rats exposed to a natural cannabinoid. The findings suggest a link between cannabinoid exposure and SYNGAP1 changes that are spatio-temporal and developmental in nature.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Psychiatry
Liu L. Yang, Miranda Stiernborg, Elin Skott, Therese Gillberg, Rikard Landberg, MaiBritt Giacobini, Catharina Lavebratt
Summary: This study found lower plasma concentrations of short-chain fatty acids (SCFAs) in children and adults with ADHD compared to healthy family members. Antibiotic medication, age, and stimulant medication were identified as factors influencing SCFA levels.
JOURNAL OF PSYCHIATRIC RESEARCH
(2022)
Article
Immunology
Miranda Stiernborg, J. W. Debelius, Liu L. Yang, Elin Skott, Vincent Millischer, MaiBritt Giacobini, Philippe A. Melas, Fredrik Boulund, Catharina Lavebratt
Summary: Recent evidence suggests that there is a link between neurodevelopmental disorders, such as ADHD, and the gut microbiome. A study was conducted with 147 well-characterized adult and child ADHD patients to investigate the impact of psychostimulant medication on the gut microbiome. The findings showed significant differences in bacterial strains, bacterial genes, inflammatory markers, and short-chain fatty acids between ADHD patients and controls, as well as between medicated and non-medicated children with ADHD.
BRAIN BEHAVIOR AND IMMUNITY
(2023)
Article
Oncology
Alexander Pfab, Sergey Belikov, Michaela Keuper, Martin Jastroch, Mattias Mannervik
Summary: This study found that the neurotoxin symbolscript can trigger cell death of dopamine neurons, leading to Parkinson's disease symptoms. Additionally, the neurotoxin directly affects mitochondrial function and transcription, resulting in reduced ATP production. These findings reveal the direct effects of symbolscript on cellular processes, while other gene expression or epigenetic changes are secondary effects reflecting cellular adaptation.
EXPERIMENTAL CELL RESEARCH
(2023)
Article
Psychology, Clinical
Judit Ozsvar, Mika Gissler, Catharina Lavebratt, Ida A. K. Nilsson
Summary: This study identified various prenatal and at birth exposures associated with offspring eating disorders, some of which are specific to certain types of eating disorders and show sex-specific associations. Confounding by maternal BMI cannot be excluded, however, highlighting the importance of subtype- and sex-stratified analyses.
INTERNATIONAL JOURNAL OF EATING DISORDERS
(2023)
Article
Genetics & Heredity
Lisa Bornscheuer, Andreas Lundin, Yvonne Forsell, Catharina Lavebratt, Philippe A. Melas
Summary: This study explores the relationship between fatty acid amide hydrolase (FAAH) and subjective well-being, and found a functional polymorphism in the FAAH gene to be associated with decreased well-being and increased alcohol dependence. The findings suggest that chronically elevated levels of anandamide may disrupt the well-being system, leading to increased alcohol intake.
Article
Biochemistry & Molecular Biology
Giovanni Pacini, Bo Ahren
Summary: Tirzepatide stimulates both insulin secretion and glucose effectiveness, with stimulation of glucose effectiveness being the prominent process to reduce glucose.
Article
Biochemistry & Molecular Biology
Si -yu Wang, Yu-zhe Zhang, Xiao-han Liu, Xue-ci Guo, Xiao-fang Wang, Feng-tong Han, Yao Zhang, Chang -lin Wang
Summary: In the formalin pain test, the EM-2 analogs EM-2-Me, EM-2-Et, and EM-2-Bu showed significant analgesic effects with reduced tolerance and gastrointestinal side effects. These effects were mediated through central opioid mechanisms, with EM-2-Me possibly involving dynorphin A release and EM-2-Bu directly activating multiple opioid receptors.
