Article
Cell Biology
Dan Lei, Wen-Ting Yang, Peng-Sheng Zheng
Summary: HOXB4 suppresses cervical cancer cell proliferation and tumorigenesis by inhibiting the activity of the Wnt/beta-catenin signaling pathway.
CELL DEATH & DISEASE
(2021)
Review
Obstetrics & Gynecology
Yujun Liu, Michal M. Masternak, Augusto Schneider, Xu Zhi
Summary: Dwarf mice have unique characteristics such as long lifespan, delayed ovarian aging, altered metabolism, lower oxidative damage, and lower cancer incidence rate. They are commonly used models to study aging and metabolism. In addition to these aspects, the reproductive features of female dwarf mice have also attracted interest. This review summarizes the research progress on dwarf mice as models in the field of reproductive aging, highlighting their larger ovarian reserve and delayed ovarian aging compared to normal mice, as well as distinctive gene expression patterns.
REPRODUCTIVE BIOMEDICINE ONLINE
(2022)
Article
Genetics & Heredity
Victor Gourain, Isabelle Duluc, Claire Domon-Dell, Jean-Noel Freund
Summary: The study focuses on whether a gene involved in distinct tissue or cell functions exerts a core of common molecular activities, specifically looking at the transcription factor and regulator of chromatin accessibility encoded by the Cdx2 homeobox gene. By integrating RNAseq data in mouse embryogenesis and analyzing ChIPseq data, a core set of common genes responsive to CDX2 during developmental processes were identified. The relevance of these findings was highlighted by demonstrating altered expression of human orthologous genes to the CDX2-responsive genes in human malignancies.
FRONTIERS IN GENETICS
(2021)
Article
Geriatrics & Gerontology
Joseph M. Dhahbi, Joe W. Chen, Supriya Bhupathy, Hani Atamna, Marcelo B. Cavalcante, Tatiana D. Saccon, Allancer D. C. Nunes, Jeffrey B. Mason, Augusto Schneider, Michal M. Masternak
Summary: This study identified unique responses in ovarian tissues regarding aging and dwarfism, with specific tRF-piRNAs potentially targeting and decreasing the expression of BCAR3 gene, and certain piLRNAs potentially de-repressing transposable elements to have a beneficial impact on ovarian aging in df/df mice. The findings highlight the complexity of aging effects on gene expression and suggest that piRNAs, piLRNAs, tRF-piRNAs, and their targets could play crucial roles in maintaining a younger ovarian phenotype in df/df mice, in addition to miRNAs.
JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Ni Han, Rui Tang, Xueqian Chen, Zhixuan Xu, Zhonghai Ren, Lina Wang
Summary: In this study, a total of 11 WOX transcription factor family members were identified in the cucumber genome and classified into three clades with nine subclades based on phylogenetic analysis results. All WOX members in cucumber contain the typical homeodomain structure, and gene duplication event analysis revealed possible segment duplication affecting the number of WOX members. Expression profiles of CsWOX genes in different tissues show that some members are constitutively expressed at higher levels compared to others, with cis-element analysis suggesting involvement in phytohormone pathways and stress responses, supported by RNA-seq data.
Article
Biochemistry & Molecular Biology
Lingli Tang, Yuhua He, Bin Liu, Yongyang Xu, Guangwei Zhao
Summary: This study identified and characterized 11 CmWOX genes that play significant roles in melon development and response to abiotic stresses. Evolutionary analysis revealed protein variations among the CmWOX family members in Arabidopsis, tomato, cucumber, melon, and rice. Cis-element analysis suggested that CmWOX genes may respond to abiotic stresses. RNA-seq and qRT-PCR results demonstrated that the expression of some CmWOX genes is associated with cold and drought.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Geriatrics & Gerontology
Rachana Trivedi, Bailey Knopf, Jitendra Kumar Tripathi, Shar Rakoczy, Gunjan D. Manocha, Holly Brown-Borg, Donald A. Jurivich
Summary: Aging leads to changes in the heat shock axis, with old dwarf mice showing preserved and enhanced activating elements compared to old wild-type mice. This suggests that exceptional longevity may be associated with compensatory and enhanced HSF1 regulation in response to age-dependent forces that downregulate the heat shock axis.
Article
Multidisciplinary Sciences
Mehmet Neset Ozel, Claudia Skok Gibbs, Isabel Holguera, Mennah Soliman, Richard Bonneau, Claude Desplan
Summary: The study reveals that the Drosophila visual system contains nearly 200 distinct types of neurons, each defined by unique combinations of about 10 continuously expressed transcription factors. Modifying the terminal selector code can predictably convert neuronal fates and these conversions are morphologically and transcriptionally complete. Additionally, the study identifies one gene that is linked to an upstream patterning factor, which specifies neuronal fates in stem cells.
Article
Biochemistry & Molecular Biology
Feng-Quan Tan, Wentao Wang, Junjie Li, Yue Lu, Bo Zhu, Fangfang Hu, Qi Li, Yu Zhao, Dao-Xiu Zhou
Summary: Rice PACP interacts with TALE transcription factors to establish and maintain Polycomb Repressive Complex 2-mediated silencing of cell differentiation-promoting genes during shoot meristem development. PACP is required for the repression of cell differentiation-promoting genes targeted by a rice KNOX1 protein in the shoot apical meristem (SAM), and it is involved in the recruitment or stabilization of PRC2 to genes targeted by KNOX/BELL transcription factors to maintain H3K27me3 and gene repression in dividing cells of the SAM.
Article
Plant Sciences
Wenshuang Xie, Dee Marie Marty, Junhuan Xu, Nitika Khatri, Kristen Willie, Wanderson Bucker Moraes, Lucy R. Stewart
Summary: The results demonstrate that MDMV-based vector can be used as a tool for simultaneous gene expression and multi-gene silencing in maize.
Article
Multidisciplinary Sciences
Sandra Ampuero, Guillermo Bahamonde, Fabian Tempio, Maria Luisa Garmendia, Mauricio Ruiz, Rolando Pizarro, Patricio Rossi, Lucia Huenchur, Luis Lizama, Mercedes Lopez, Luis F. Avendano, Vivian Luchsinger
Summary: Community-acquired pneumonia (CAP) is a leading cause of death worldwide. This study explores the involvement of the IL-7/IL7R alpha axis in the severity of adult CAP for the first time. Specific genotypes and levels of IL7R gene are associated with the prognosis of CAP. Increased plasmatic sIL7R could help identify CAP cases at risk of death.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Nils Kloecker, Florian P. Weissenboeck, Melissa van Dulmen, Petr Spacek, Sabine Huewel, Andrea Rentmeister
Summary: Translation of mRNA is a crucial process in gene expression, and a new study introduces FlashCaps, cap analogues with photo-cleavable groups, that can regulate translation of mRNA effectively. These compounds inhibit translation in vitro and in mammalian cells, but can be restored through irradiation for efficient translation. FlashCaps present a promising approach for controlling mRNA expression and dosing mRNA therapeutics with spatial and temporal control.
Article
Biochemistry & Molecular Biology
Tianzhen Liu, Xin Zhang, Huan Zhang, Zhijun Cheng, Jun Liu, Chunlei Zhou, Sheng Luo, Weifeng Luo, Shuai Li, Xinxin Xing, Yanqi Chang, Cuilan Shi, Yulong Ren, Shanshan Zhu, Cailin Lei, Xiuping Guo, Jie Wang, Zhichao Zhao, Haiyang Wang, Huqu Zhai, Qibing Lin, Jianmin Wan
Summary: Research has identified a rice mutant, dht1, which exhibits pleiotropic phenotypes similar to mutants defective in strigolactone (SL) signaling. The DHT1 protein plays a role in intron splicing and is crucial for the proper functioning of SL signaling in regulating plant development.
Article
Biochemistry & Molecular Biology
Boris Slobodin, Urmila Sehrawat, Anastasia Lev, Daniel Hayat, Binyamin Zuckerman, Davide Fraticelli, Ariel Ogran, Amir Ben-Shmuel, Elad Bar-David, Haim Levy, Igor Ulitsky, Rivka Dikstein
Summary: Translation of SARS-CoV-2-encoded mRNAs is crucial for its propagation. The viral protein NSP1 inhibits translation and induces mRNA degradation, while viral mRNAs remain stable. A conserved RNA element in viral mRNAs confers resistance to NSP1-mediated translation inhibition. The 5' UTR of SARS-CoV-2 promotes cap-independent translation and expression of NSP1. These findings provide insights into the virus's propagation mechanism and potential therapeutic targets.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
T. Lohoff, S. Ghazanfar, A. Missarova, N. Koulena, N. Pierson, J. A. Griffiths, E. S. Bardot, C. -H. L. Eng, R. C. V. Tyser, R. Argelaguet, C. Guibentif, S. Srinivas, J. Briscoe, B. D. Simons, A. -K. Hadjantonakis, B. Gottgens, W. Reik, J. Nichols, L. Cai, J. C. Marioni
Summary: Improved integration of spatial and single-cell transcriptomic data through the seqFISH method provides insights into mouse development, revealing cell types across the embryo and uncovering axes of cell differentiation that are not apparent from scRNA-seq data. This approach offers a high-resolution spatial map for studying cell fate decisions in complex tissues and development.
NATURE BIOTECHNOLOGY
(2022)
Article
Physics, Multidisciplinary
Debashis Ghosh
Summary: In this article, an approach to interpreting SDR techniques using information theory is developed, leading to a less assumption-lean understanding of what SDR methods do and allowing for connections to results in the information theory literature.
Article
Medicine, Research & Experimental
Paola Valentini, Bianca Pierattini, Elsa Zacco, Damiano Mangoni, Stefano Espinoza, Natalie A. Webster, Byron Andrews, Piero Carninci, Gian Gaetano Tartaglia, Luca Pandolfini, Stefano Gustincich
Summary: SINEUPs are a novel class of natural and synthetic non-coding antisense RNA molecules that can increase the translation of a target mRNA, with a modular organization. Through chemical modifications, SINEUP activity can be realized, with the m6A and psi combination showing the best performance and improved stability.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2022)
Article
Biochemistry & Molecular Biology
Giovanni Pascarella, Chung Chau Hon, Kosuke Hashimoto, Annika Busch, Joachim Luginbuhl, Callum Parr, Wing Hin Yip, Kazumi Abe, Anton Kratz, Alessandro Bonetti, Federico Agostini, Jessica Severin, Shigeo Murayama, Yutaka Suzuki, Stefano Gustincich, Martin Frith, Piero Carninci
Summary: This study reveals the somatic recombination of repeat elements, such as Alu and L1, in the human genome. It also identifies tissue-specific non-allelic homologous recombination hallmarks and retroelements as potential recombination hotspots. The study further shows that neuron-specific recombination of repeat elements accompanies chromatin changes during cell-fate determination. Moreover, somatic recombination profiles are altered in Parkinson's and Alzheimer's disease, indicating a link between retroelement recombination and genomic instability in neurodegeneration.
Article
Biochemistry & Molecular Biology
Michiel de Hoon, Alessandro Bonetti, Charles Plessy, Yoshinari Ando, Chung-Chau Hon, Yuri Ishizu, Masayoshi Itoh, Sachi Kato, Dongyan Lin, Sho Maekawa, Mitsuyoshi Murata, Hiromi Nishiyori, Jay W. Shin, Jens Stolte, Ana Maria Suzuki, Michihira Tagami, Hazuki Takahashi, Alistair R. R. Forrest, Yoshihide Hayashizaki, Juha Kere, Piero Carninci, Supat Thongjuea
Summary: In eukaryotes, capped RNAs can be categorized into long transcripts like messenger RNAs and long noncoding RNAs, as well as shorter transcripts like spliceosomal RNAs, small nucleolar RNAs, and enhancer RNAs. Deep sequencing of short capped RNAs reveals new families of noncoding RNAs and elucidates the diversity of transcripts generated at known and novel promoters and enhancers, showing a strong preference for specific 3' ends and enrichment for disease-associated SNPs.
Article
Biochemistry & Molecular Biology
Hironori Bando, Michelle L. Brinkmeier, Frederic Castinetti, Qing Fang, Mi-Sun Lee, Alexandru Saveanu, Frederique Albarel, Clementine Dupuis, Thierry Brue, Sally A. Camper
Summary: Congenital hypopituitarism is a genetically heterogeneous condition that may be associated with holoprosencephaly. This study identified rare genetic variants in SIX3 and POU1F1 as the cause of neonatal hypopituitarism in two children. Mouse models were used to investigate the mechanism, and it was found that both SIX3 and POU1F1 are required for normal pituitary development. The findings suggest the possibility of a digenic basis for pituitary diseases.
HUMAN MOLECULAR GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Caterina Gasperini, Kiril Tuntevski, Silvia Beatini, Roberta Pelizzoli, Amanda Lo Van, Damiano Mangoni, Rosa M. Cossu, Giovanni Pascarella, Paolo Bianchini, Pascal Bielefeld, Margherita Scarpato, Meritxell Pons-Espinal, Remo Sanges, Alberto Diaspro, Carlos P. Fitzsimons, Piero Carninci, Stefano Gustincich, Davide De Pietri Tonelli
Summary: Piwil2 is crucial for neurogenesis in the adult hippocampus, and its expression is related to the dynamic expression of piRNAs. Depletion of Mili and piRNAs affects aNPCs differentiation, induces senescence, and generates reactive glia in the adult hippocampus. Mili depletion results in the modulation of transcripts with sequences complementary or homologous to piRNAs, including repetitive elements and mRNAs encoding essential proteins for proper neurogenesis.
Review
Cell Biology
John S. S. Mattick, Paulo P. P. Amaral, Piero Carninci, Susan Carpenter, Howard Y. Y. Chang, Ling-Ling Chen, Runsheng Chen, Caroline Dean, Marcel E. E. Dinger, Katherine A. A. Fitzgerald, Thomas R. R. Gingeras, Mitchell Guttman, Tetsuro Hirose, Maite Huarte, Rory Johnson, Chandrasekhar Kanduri, Philipp Kapranov, Jeanne B. B. Lawrence, Jeannie T. T. Lee, Joshua T. T. Mendell, Timothy R. R. Mercer, Kathryn J. J. Moore, Shinichi Nakagawa, John L. L. Rinn, David L. L. Spector, Igor Ulitsky, Yue Wan, Jeremy E. E. Wilusz, Mian Wu
Summary: Genes encoding lncRNAs are abundant in complex organisms and are transcribed by RNA polymerase I, II, and III, as well as processed introns. The classification and annotation of lncRNAs are challenging due to their various functions, isoforms, and interactions with other genes. These lncRNAs evolve rapidly, are cell type-specific, and regulate multiple cellular processes, including gene expression and translation control.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Engineering, Biomedical
Masaru Koido, Chung-Chau Hon, Satoshi Koyama, Hideya Kawaji, Yasuhiro Murakawa, Kazuyoshi Ishigaki, Kaoru Ito, Jun Sese, Nicholas F. Parrish, Yoichiro Kamatani, Piero Carninci, Chikashi Terao
Summary: A machine-learning model called MENTR has been developed to link genome sequence and non-coding RNA expression at the cell type level. This model can predict the effects of RNA transcription and identify genetic variants associated with complex traits.
NATURE BIOMEDICAL ENGINEERING
(2023)
Article
Multidisciplinary Sciences
Yonghua Zhuang, Fuyong Xing, Debashis Ghosh, Brian D. D. Hobbs, Craig P. P. Hersh, Farnoush Banaei-Kashani, Russell P. P. Bowler, Katerina Kechris
Summary: Network approaches have been used to study the complex mechanisms of diseases like COPD. However, integrating protein-protein interaction (PPI) network information with omics data for disease prediction is still limited. This study uses a deep learning method called ConvGNN to integrate COPD-associated PPI, proteomics, and transcriptomics data and improve the accuracy of COPD classification. The updated COPD-associated network developed using AhGlasso algorithm further enhances prediction accuracy. Gene Ontology enrichment analysis identifies important gene/proteins and signaling pathways for COPD classifications.
Article
Medicine, General & Internal
Eric W. Prince, Debashis Ghosh, Carsten Gorg, Todd C. Hankinson
Summary: Diagnosis of ACP mainly relies on invasive pathological examination, although clinical experts can distinguish it from MRI with an accuracy of 86%. Deep learning classification provides a potential non-invasive diagnostic solution, but its implementation is limited due to the lack of predictive uncertainty representation.
Editorial Material
Oncology
Giovanni Pascarella, Martin Frith, Piero Carninci
CLINICAL AND TRANSLATIONAL MEDICINE
(2023)
Article
Endocrinology & Metabolism
Randi K. Johnson, Amanda J. Ireton, Patrick M. Carry, Lauren A. Vanderlinden, Fran Dong, Alex Romero, David R. Johnson, Debashis Ghosh, Fan Yang, Brigitte Frohnert, Ivana V. Yang, Katerina Kechris, Marian Rewers, Jill M. Norris
Summary: This study examined the association between T1D family history and T1D risk mediated by methylation near the DLGAP2 gene. The results showed a significant interaction between T1D family history and methylation at DLGAP2 region CpGs on T1D risk. The increased risk of T1D for children with affected mothers compared to those with no family history was mediated through differences in methylation at two CpGs in the DLGAP2 region, while DNA methylation changes did not explain the increased risk for children with an affected father or sibling. Additionally, DNA methylation in the DLGAP2 region was associated with gene expression of nearby protein-coding genes.
PEDIATRIC DIABETES
(2023)
Article
Genetics & Heredity
Souvik Seal, Benjamin G. Bitler, Debashis Ghosh
Summary: This article introduces a non-parametric method called SMASH for detecting spatially variable genes in high-throughput spatial transcriptomics studies. Compared with other methods, SMASH has superior statistical power and robustness, and can be applied to datasets from different platforms, helping to uncover the structural and functional characteristics of tissues.
Article
Statistics & Probability
Youngjoo Cho, Paul L. Auer, Debashis Ghosh
Summary: Mendelian Randomization is a popular method used in genomic studies to estimate causal effects. This paper focuses on IV selection and introduces nonparametric variable selection approaches, comparing linear and nonlinear instrumental variable selection methods. Simulation studies demonstrate the good performance of the proposed methods, which are also applied to the UKBiobank data for Mendelian Randomization.
SANKHYA-SERIES B-APPLIED AND INTERDISCIPLINARY STATISTICS
(2023)
Article
Endocrinology & Metabolism
Amanda H. Winningham, Sally A. Camper
Summary: Epithelial to mesenchymal transition (EMT) plays a crucial role in the development of organs, wound healing, fibrosis, and cancer. The study focused on the genetic hierarchy and signaling pathways involved in the EMT process of pituitary stem cells. It was found that Prop1 mutant stem cells showed altered gene expression, including reduced BMP and TGF-beta family gene expression and elevated Elf5 expression. Manipulating gene expression confirmed that the EMT inducer Zeb2 is necessary for BMP signaling and repression of Elf5. Overall, the study established the genetic hierarchy and pathways involved in the transition of pituitary stem cells.
