Article
Biochemistry & Molecular Biology
Forrest Hurley, Christine Heitsch
Summary: RNAprofiling 2.0 identifies dominant helices/stems and organizes them into profiles based on suboptimal sampling data. It enhances profile selection and visualizes relationships in a decision tree, allowing a greater understanding of trade-offs among different possible base pairing combinations. This analysis is made accessible to experimental researchers in a portable format as an interactive webpage.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Makiha Fukuda, Jitong Cai, Joel S. Bader, Jef D. Boeke
Summary: A synthetic biology approach to constructing an RNA-based genome expands our understanding of living things and opens avenues for technological advancement. Understanding the structure-function relationships of RNA sequences is critical for the precise design of an artificial RNA replicon.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Virology
Simon Poblete, Horacio V. Guzman
Summary: Studying the three-dimensional reconstruction of RNA is crucial for understanding the functions of proteinaceus capsids, but RNA self-association remains an open question. Recent chemical probing reports provide reliable secondary structures of diverse RNA ensembles. The proposed method combines a coarse-grained model with a subdomain composition scheme to reconstruct the complete 3D structure of RNA genomes based on experimental techniques.
Article
Chemistry, Multidisciplinary
Sandro Bottaro, Giovanni Bussi, Kresten Lindorff-Larsen
Summary: This study predicted the structure and dynamics of RNA stem loops in the 5'UTR of the SARS-CoV-2 genome using extensive molecular dynamics simulations, revealing rich dynamics and specific structural rearrangements. These findings could provide insights into the structural features and functional roles of RNA molecules.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Review
Biochemistry & Molecular Biology
Lulu Yu, Vladimir Majerciak, Zhi-Ming Zheng
Summary: Human papillomaviruses (HPV) are a group of viruses that cause cancer, with HPV16 and HPV18 being the most common types responsible for majority of cases. The expression of their genome is regulated by alternative RNA splicing, and epigenetic modifications also play a role in HPV infections and carcinogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Automation & Control Systems
Hanyuan Hang, Zhouchen Lin, Xiaoyu Liu, Hongwei Wen
Summary: In this paper, a novel algorithm named Histogram Transform Ensembles (HTE) is proposed for large-scale regression problems. The algorithm utilizes random rotations, stretchings, and translations, along with histogram transformed partition and constant functions or SVMs to obtain individual regression estimates. The theoretical properties and application of NHT and KHT in different spaces are investigated, with experiments confirming the superiority of ensemble NHT and the effectiveness of KHT in predicting smoother regression functions.
JOURNAL OF MACHINE LEARNING RESEARCH
(2021)
Article
Biochemical Research Methods
Juan A. Ferrer-Bonsoms, Xabier Morales, Pegah T. Afshar, Wing H. Wong, Angel Rubio
Summary: It is still unclear whether gene structure and isoform concentration can be uniquely inferred given paired-end reads, and no objective method to select the fragment length has been found. We propose a method to determine the identifiability of the deconvolution problem and find that the optimal average fragment length and read length for the human transcriptome are 400-600 nt and 150-200 nt, respectively.
Article
Multidisciplinary Sciences
Mark A. Boerneke, Nandan S. Gokhale, Stacy M. Horner, Kevin M. Weeks
Summary: The genomes of RNA viruses contain functional structural elements critical to viral fitness. A study identified 22 structure-similar motifs in the coding sequences of dengue virus RNA genomes, with at least 10 of them modulating viral fitness. These viral RNA structures promote compact genome architecture, interact with proteins, and regulate the viral replication cycle.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Virology
Liqing Ye, Uddhav B. Ambi, Marco Olguin-Nava, Anne-Sophie Gribling-Burrer, Shazeb Ahmad, Patrick Bohn, Melanie M. Weber, Redmond P. Smyth
Summary: The generation of infectious viral particles involves the specific selection of genomic RNA from a complex mixture of cellular and non-genomic viral RNAs. This process is influenced by viral encoded RNA structures, packaging signals constructed from base pairings within viral genomes, and the biophysical properties of RNA. Additionally, the impact of RNA packaging signals on viral evolution is examined.
Article
Multidisciplinary Sciences
Ryan J. Andrews, Warren B. Rouse, Collin A. O'Leary, Nicholas J. Booher, Walter N. Moss
Summary: The identification of RNA elements in genomes and transcriptomes is a major challenge in target discovery for research and intervention. ScanFold 2.0, a revised version of the original algorithm, uses machine learning to estimate folding energy and significantly improves prediction speeds for large sequences. Comparative tests demonstrate the consistency and efficiency of ScanFold 2.0 compared to the original version.
Article
Biotechnology & Applied Microbiology
Emilie Derisoud, Luc Jouneau, Cedric Dubois, Catherine Archilla, Yan Jaszczyszyn, Rachel Legendre, Nathalie Daniel, Nathalie Peynot, Michele Dahirel, Juliette Auclair-Ronzaud, Laurence Wimel, Veronique Duranthon, Pascale Chavatte-Palmer
Summary: This study found that maternal age affects gene expression in equine blastocysts. As mares age, gene expression related to mitochondria and protein metabolism is disrupted, leading to impaired embryo development and decreased fertility.
Article
Microbiology
Kieran Tebben, Aliou Dia, David Serre
Summary: This study evaluates a reference data set that can be used to estimate the proportions of different stages of malaria parasites in infected human blood samples. This allows for accurate gene expression analysis and correction of biases caused by differences in cell composition.
Article
Infectious Diseases
Minyu Zhou, Lian Xu, Dahua Xu, Wen Chen, Jehangir Khan, Yue Hu, Hui Huang, Hang Wei, Yiqing Zhang, Phiraphol Chusongsang, Kanthi Tanasarnprasert, Xiang Hu, Yanin Limpanont, Zhiyue Lv
Summary: This study presents a high-quality, chromosome-scale reference genome of Schistosoma mekongi, which provides valuable insights into its biology, evolutionary relationships, and parasite-host interactions. The findings also contribute to drug discovery, vaccine development, and intervention strategies for schistosomiasis.
INFECTIOUS DISEASES OF POVERTY
(2023)
Article
Mechanics
Chao Zhang, Zelong Yuan, Yunpeng Wang, Ruibo Zhang, Jianchun Wang
Summary: This study investigates the density-unweighted subgrid-scale (SGS) closure problem in large-eddy simulations (LES) of compressible isotropic turbulence. Different SGS models, including the gradient model (GM), approximate deconvolution model (ADM), dynamic Smagorinsky model (DSM), dynamic mixed model (DMM), and the dynamic iterative approximate deconvolution (DIAD) model, are used to reconstruct the unclosed SGS terms. The DIAD model shows great advantages over other SGS models in predicting the various statistics and structures of compressible turbulence. The results of this study provide insights into the application of density-unweighted methods in LES of turbulence.
Article
Computer Science, Artificial Intelligence
Juan E. Arco, Andres Ortiz, Javier Ramirez, Francisco J. Martinez-Murcia, Yu-Dong Zhang, Juan M. Gorriz
Summary: The use of automatic systems based on artificial intelligence for medical image classification has greatly improved the diagnosis of various diseases. This study proposes a multi-level ensemble classification system based on Bayesian Deep Learning to maximize performance while also providing uncertainty of each classification decision. The system demonstrates high accuracy in different real scenarios, making it an applicable tool for clinicians.
INFORMATION FUSION
(2023)
Review
Biochemistry & Molecular Biology
Ilaria Manfredonia, Danny Incarnato
Summary: Coronaviruses are positive-sense single-stranded RNA viruses with the largest viral RNA genomes known to date. In addition to encoding viral proteins, certain regions of CoV genomes fold into stable structures that control various aspects of the virus life cycle. Recent discoveries from analyzing the SARS-CoV-2 genome have contributed to our understanding of CoV RNA structures.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2021)
Article
Biochemistry & Molecular Biology
Tycho Marinus, Adam B. Fessler, Craig A. Ogle, Danny Incarnato
Summary: 2A3 is a general probe for RNA structure interrogation in living cells, showing better performance than NAI in vivo, especially in bacteria. When used as a restraint for RNA structure prediction, data derived by 2A3 yields more accurate predictions compared to NAI-derived data.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Cell Biology
Fatemeh Mirzadeh Azad, Isabelle Laurence Polignano, Valentina Proserpio, Salvatore Oliviero
Summary: Long noncoding RNAs play a crucial role in stem cell maintenance and differentiation, exhibiting diverse functions through interactions with proteins, DNA, and RNA. This heterogeneity in function enhances the capabilities of the lncRNome toolkit but also poses challenges in predicting the functions of novel lncRNAs.
TRENDS IN CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Afsaneh Malekzadeh Shafaroudi, Ali Sharifi-Zarchi, Saeid Rahmani, Nahid Nafissi, Seyed Javad Mowla, Andrea Lauria, Salvatore Oliviero, Maryam M. Matin
Summary: Studies have revealed the significant downregulation of the C1orf132 long transcript in breast cancer, along with the identification of its promoter that has a notable impact on the expression of miR-29c, subsequently influencing cell migration ability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Carla Liaci, Lucia Prandi, Lisa Pavinato, Alfredo Brusco, Mara Maldotti, Ivan Molineris, Salvatore Oliviero, Giorgio R. Merlo
Summary: Long non-coding RNAs (lncRNAs) are widely expressed in the human brain, and may play a role in normal brain development and the molecular pathology of neurodevelopmental disorders. However, their involvement in intellectual disability (ID) and neurodevelopmental disorders is still poorly understood, and only a few genomic alterations have been causally linked to the disease endophenotype. Further investigation into the non-coding genome may uncover novel pathogenic mechanisms and translational opportunities.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Sharon Aviran, Danny Incarnato
Summary: RNA structure probing experiments are a straightforward way to determine RNA molecule structures. However, the dynamic nature of RNA poses challenges in interpreting the experimental data. Recent efforts have focused on developing computational methods to reconstruct alternative RNA conformations, enabling the study of RNA structure ensembles even in living cells.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Edoardo Morandi, Martijn J. van Hemert, Danny Incarnato
Summary: The popularity of RNA structure probing methods has led to a large amount of available RNA structure information. This study introduces SHAPEwarp, a sequence-agnostic SHAPE-guided algorithm, for the identification of structurally-similar regions in RNA molecules. The analysis of Dengue, Zika, and coronavirus genomes reveals known and novel conserved structural features. This work represents a preliminary step towards the search and identification of shared and conserved RNA structural features within transcriptomes.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Elena Astanina, Gabriella Doronzo, Davide Cora, Francesco Neri, Salvatore Oliviero, Tullio Genova, Federico Mussano, Emanuele Middonti, Edoardo Vallariello, Chiara Cencioni, Donatella Valdembri, Guido Serini, Federica Limana, Eleonora Foglio, Andrea Ballabio, Federico Bussolino
Summary: This study investigates how the transcription factor EB (TFEB) regulates epithelial-mesenchymal transition (EMT) during heart development by tuning sensitivity to transforming growth factor (TGF) beta signaling. The authors find that TFEB activates the transcription of TGFβ/Smad pathway repressor Tgif1, promoting EMT. Furthermore, TFEB overexpression inhibits TGFβ-induced EMT, while loss of TFEB function enhances cellular sensitivity to TGFβ, leading to EMT.
NATURE COMMUNICATIONS
(2022)
Review
Genetics & Heredity
Robert C. Spitale, Danny Incarnato
Summary: RNA is a crucial regulator of cellular processes, and understanding its structure is important for its function. Advances in high-throughput sequencing-based RNA structure mapping methods have allowed researchers to study the structural organization of the entire cellular transcriptome. Recent analyses have revealed the dynamic nature of RNA ensembles and their role in regulating cellular processes.
NATURE REVIEWS GENETICS
(2023)
Article
Multidisciplinary Sciences
Andrea Lauria, Guohua Meng, Valentina Proserpio, Stefania Rapelli, Mara Maldotti, Isabelle Laurence Polignano, Francesca Anselmi, Danny Incarnato, Anna Krepelova, Daniela Donna, Chiara Levra Levron, Giacomo Donati, Ivan Molineris, Francesco Neri, Salvatore Oliviero
Summary: The establishment of DNA methylation patterns during mouse early development is crucial for cell fate determination. However, the specific molecular targets and mechanisms of de novo methylation machinery during differentiation are not fully understood. In this study, the researchers identified DNMT3B-dependent regulatory elements that play a critical role in cell fate determination. They found that DNMT3B-dependent DNA methylation is essential for proper differentiation and lineage determination, and ectopic expression of DNMT3B can restore normal gene expression and cell fate. This study provides important insights into the role of DNA methylation in early development and cell fate determination.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Sara Bonzano, Eleonora Dallorto, Ivan Molineris, Filippo Michelon, Isabella Crisci, Giovanna Gambarotta, Francesco Neri, Salvatore Oliviero, Ruth Beckervordersandforth, Dieter Chichung Lie, Paolo Peretto, Serena Bovetti, Michele Studer, Silvia De Marchis
Summary: The nuclear receptor NR2F1 is a strong transcriptional regulator in neural cells. Mutations in the NR2F1 gene cause BBSOAS, a rare neurodevelopmental disorder characterized by vision impairment, intellectual disability, and autistic traits. In this study, the researchers identified a set of nuclear-encoded mitochondrial genes as potential targets under direct NR2F1 control. They demonstrated that NR2F1 loss of function in mice resulted in reduced mitochondrial mass, fragmentation, and downregulation of key mitochondrial proteins in newborn neurons, impairing their generation, survival, and integration. Similar dysregulation was also observed in a BBSOAS mouse model. These findings highlight the role of NR2F1 in the mitochondrial gene expression network in neurons and suggest a connection between mitochondrial dysfunction and BBSOAS pathogenesis.
DISEASE MODELS & MECHANISMS
(2023)
Editorial Material
Medicine, Research & Experimental
Salvatore Oliviero
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Biochemistry & Molecular Biology
Guohua Meng, Andrea Lauria, Mara Maldotti, Francesca Anselmi, Isabelle Laurence Polignano, Stefania Rapelli, Daniela Donna, Salvatore Oliviero
Summary: Smad7 functions as a general transcription factor in ESCs, regulating both TGF-beta unrelated genes and key stemness regulators. Loss of Smad7 results in the downregulation of stemness master regulators and the upregulation of developmental genes, leading to loss of the stem phenotype. Integrative analysis reveals that Smad7 co-occupies promoters of highly expressed key stemness regulators by binding to a specific consensus response element.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
