Article
Plant Sciences
Baoyi Zhang, Yuhan Fei, Jiejie Feng, Xueai Zhu, Rui Wang, Hanqing Xiao, Hongsheng Zhang, Ji Huang
Summary: This study constructed a comprehensive rice ncRNA co-expression atlas, RiceNCexp, which provides expression information and co-expression analysis tools for rice ncRNAs in multiple tissues/organs.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Oncology
Radhika Manukonda, Vengala Rao Yenuganti, Nupur Nagar, Pankaj Singh Dholaniya, Shivani Malpotra, Jyothi Attem, Mamatha M. Reddy, Saumya Jakati, Dilip K. Mishra, Pallu Reddanna, Krishna Mohan Poluri, Geeta K. Vemuganti, Swathi Kaliki
Summary: This study provides a comprehensive overview of the sEV RNAs in retinoblastoma (RB) and their regulatory interactions. The results show that sEVs in RB and non-RB serum have similar exosome properties, and RB-related miRNAs, lncRNAs, and their target mRNAs are involved in cell cycle, metabolism, and tumor-associated signaling pathways. Network analysis reveals that hub ncRNAs regulate cell cycle-specific genes, and DE mRNAs related to the eye are involved in retinal cell differentiation and metabolism. These findings contribute to the identification of serum prognostic biomarkers for RB.
Article
Biochemistry & Molecular Biology
Fabio A. Simoes, Greig Joilin, Oliver Peters, Luisa-Sophie Schneider, Josef Priller, Eike Jakob Spruth, Ina Vogt, Okka Kimmich, Annika Spottke, Daniel C. Hoffmann, Bjoern Falkenburger, Moritz Brandt, Johannes Prudlo, Kathrin Brockmann, Franca Laura Fries, James B. Rowe, Alistair Church, Gesine Respondek, Sarah F. Newbury, P. Nigel Leigh, Huw R. Morris, Guenter U. Hoeglinger, Majid Hafezparast
Summary: This study identified dysregulated ncRNA in serum and CSF samples of patients with PSP, suggesting their potential as diagnostic biomarkers for PSP. Further research is needed to explore this possibility.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Lin Yu, Tengda Huang, Xinyu Qi, Jingsu Yu, Tian Wu, Zupeng Luo, Lei Zhou, Yixing Li
Summary: lncRNAs involved in nodule senescence were identified in Medicago truncatula, and were found to be associated with transposable elements and play a key role in substance transport.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Xin Liu, Jing Zhang, Danyao Nie, Kun Zeng, Huiling Hu, Jinjun Tie, Liangnan Sun, Ling Peng, Xinhua Liu, Jiantao Wang
Summary: Transcriptome analysis of pterygium tissues identified differential expression of 579 mRNAs, 275 lncRNAs, and 21 circRNAs, which are associated with extracellular matrix organization, blood vessel morphogenesis, and focal adhesion. Key genes such as FN1, VCAM1, and MMP2, as well as lncRNAs like MIR4435-2HG and LINC00968, were identified to potentially play a role in the pathogenesis of pterygium. Additionally, circRNAs such as hsa_circ_0007482 and hsa_circ_001730 were found to be involved in the development of pterygium.
FRONTIERS IN GENETICS
(2021)
Review
Cell Biology
Melissa M. M. Rowe, Klaus H. H. Kaestner
Summary: Non-coding RNAs (ncRNAs) play important roles in liver disease and regeneration. This review focuses on key microRNAs (miRs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in the liver. Specifically, it highlights the role of miR-122, miR-21, the let-7 family of miRs, miR-451a, miR-144, and MALAT1.
Article
Biotechnology & Applied Microbiology
Biao Li, Jinzeng Yang, Jun He, Xing Peng, Qinghua Zeng, Yukun Song, Kang Xu, Haiming Ma
Summary: This study comprehensively analyzed the whole transcriptome of Ningxiang pig spleens at different developmental stages, identifying potential non-coding RNAs related to immunomodulation such as miRNAs and circRNAs. The results suggest that miRNAs and circRNAs may play a key role in regulating spleen function and biological processes related to immunity and disease resistance, providing new insights into the phenotypic formation of immunity and disease resistances in Chinese indigenous pig breeds.
Article
Agronomy
Li-Wei Meng, Guo-Rui Yuan, Meng-Ling Chen, Wei Dou, Tian-Xing Jing, Li-Sha Zheng, Meng-Lan Peng, Wen-Jie Bai, Jin-Jun Wang
Summary: This study identified lncRNAs potentially related to malathion resistance in Bactrocera dorsalis, with two lncRNAs possibly influencing resistance by modulating the structure or components of the cuticle.
PEST MANAGEMENT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Tanya Cross, Kari Bente Foss Haug, Berit Sletbakk Brusletto, Stine Kamilla Ommundsen, Anne-Marie Siebke Troseid, Trude Aspelin, Ole Kristoffer Olstad, Hans Christian Dalsbotten Aass, Hilde Kanli Galtung, Tor Paaske Utheim, Janicke Liaaen Jensen, Reidun Ovstebo
Summary: Sjogren's syndrome is an autoimmune rheumatic disease that causes inflammation in the salivary and lacrimal glands, leading to dry mouth and dry eyes. This study examines the RNA content of salivary extracellular vesicles (EVs) in patients with primary Sjogren's syndrome (pSS) and identifies potential biomarkers, including downregulated tRNAs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Jennifer Stiens, Kristine B. Arnvig, Sharon L. Kendall, Irene Nobeli
Summary: A definitive transcriptome atlas for non-coding expressed elements of Mycobacterium tuberculosis complex members is lacking. Incomplete lists of non-coding transcripts can be found for some reference genomes, but their homologues in related species or strains are unclear. This review highlights the disparities in non-coding RNA information across commonly used databases and discusses combining computational solutions with experiments to predict and confirm the non-coding transcriptome.
MOLECULAR MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Feng Shang, Bi-Yue Ding, Yong-Te Zhang, Jin-Jin Wu, Si-Tong Pan, Jin-Jun Wang
Summary: Long non-coding RNAs (lncRNAs) play crucial roles in insect physiological processes, with limited information on those related to wing development. In this study, lncRNAs associated with wing development were identified in the brown citrus aphid Aphis citricidus through RNA-seq comparisons. The up-regulation of lncRNA Ac_lnc54106.1 during the transition from winged nymphs to winged adults highlighted its critical role in regulating wing development, as confirmed by RNA interference leading to malformed wings.
INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2021)
Article
Genetics & Heredity
David A. Morales-Vicente, Lu Zhao, Gilbert O. Silveira, Ana C. Tahira, Murilo S. Amaral, James J. Collins III, Sergio Verjovski-Almeida
Summary: This study reanalyzed single-cell RNA-sequencing data from adult Schistosoma mansoni to identify the lncRNA signature of adult schistosome cell types. The results suggest tissue-specific expression and a regulated expression program of lncRNAs in S. mansoni, providing a basis for further exploration of lncRNA genes as potential therapeutic targets.
FRONTIERS IN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Gobong Choi, Jongbum Jeon, Hyunjun Lee, Shenxian Zhou, Yong-Hwan Lee
Summary: This study identified novel lncRNAs during host infection of the model pathogenic fungus Magnaporthe oryzae and revealed their potential roles in pathogenesis-related gene regulation.
Article
Plant Sciences
Dongfeng Qiu, Yan Wu, Kuaifei Xia, Mingyong Zhang, Zaijun Zhang, Zhihong Tian
Summary: In this study, researchers identified a group of lncRNAs that are potentially involved in the regulation of nitrogen use efficiency in rice. One specific lncRNA, named lncRNA24320.6, was found to positively regulate the expression of a gene related to growth and nitrogen absorption. These findings provide valuable insights into the role of lncRNAs in the response of rice to nitrogen starvation.
Article
Medicine, General & Internal
Greig Joilin, Elizabeth Gray, Alexander G. Thompson, Kevin Talbot, P. Nigel Leigh, Sarah F. Newbury, Martin R. Turner, Majid Hafezparast
Summary: In this study, we investigated the expression of non-coding RNA transcripts in the cerebrospinal fluid of ALS patients compared to healthy controls. RNA-seq identified dysregulated non-coding RNA transcripts, but these were not validated with RT-qPCR. We conclude that cerebrospinal fluid is not a suitable source of diagnostic biomarkers.
ANNALS OF MEDICINE
(2022)
Review
Biochemistry & Molecular Biology
Claire Hill, Elizabeth R. Dellar, Luis Alberto Baena-Lopez
Summary: Cell-cell communication is crucial for multicellular organisms, regulating cell proliferation, growth, and death. Recent studies have revealed novel roles of caspases in intercellular signaling mediated by extracellular vesicles, influencing vesicle biogenesis, cargo selection, and function in recipient cells.
Article
Multidisciplinary Sciences
Franz Wendler, Sangbin Park, Claire Hill, Alessia Galasso, Kathleen R. Chang, Iman Awan, Yulia Sudarikova, Mar Bustamante-Sequeiros, Sichen Liu, Ethan Y-H Sung, Gabrielle Aisa-Bonoko, Seung K. Kim, Luis A. Baena-Lopez
Summary: The existence of three independent binary systems for conditional gene expression in Drosophila melanogaster has greatly expanded versatile genetic analyses. However, the limitation of needing multiple collections of noninterchangeable transgenic fly strains for each inducible gene expression system hinders their experimental application. To overcome this, researchers have developed a modular vector that combines the regulatory elements from all three binary systems, allowing for Gal4-, LexA-, or QF-dependent expression of transgenes. Their methods also enable site-specific recombination and elimination of regulatory modules with spatial and temporal control, offering unprecedented possibilities for in vivo genetic modulation and efficient interconversion of overexpression transgenic fly lines.
SCIENTIFIC REPORTS
(2022)
Article
Infectious Diseases
Emily Robb, Erin M. McCammick, Duncan Wells, Paul McVeigh, Erica Gardiner, Rebecca Armstrong, Paul McCusker, Angela Mousley, Nathan Clarke, Nikki J. Marks, Aaron G. Maule
Summary: Liver flukes of the Fasciola spp. have significant impacts in veterinary and human medicine. This study reveals that there are commonalities in core biological functioning among juveniles of Fasciola hepatica maintained under in vitro and in vivo conditions. However, in vivo juveniles exhibit higher cell proliferation and growth rates, suggesting the involvement of neuronal signaling in regulating growth and development. Differences in miRNA expression and neuronal gene expression between in vitro and in vivo juveniles further highlight the importance of neuronal targets in controlling parasite growth and development.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Cell Biology
Ruby White, Javier Sotillo, Maria Eugenia Ancarola, Anne Borup, Anders Toftegaard Boysen, Paul J. Brindley, Edit Buzas, Serena Cavallero, Sujittra Chaiyadet, Iain W. Chalmers, Marcela A. Cucher, Maude Dagenais, Chelsea N. Davis, Eileen Devaney, Maria A. Duque-Correa, Ramon Marc Eichenberger, Santiago Fontenla, Thomas A. Gasan, Cornelis H. Hokke, Maja Kosanovic, Marije E. Kuipers, Thewarach Laha, Alex Loukas, Rick M. Maizels, Antonio Marcilla, Hynek Mazanec, Russell M. Morphew, Kyriaki Neophytou, Linh Thuy Nguyen, Esther Nolte-'t Hoen, Michael Povelones, Mark W. Robinson, Alicia Rojas, Irma Schabussova, Hermelijn H. Smits, Sivapong Sungpradit, Lucienne Tritten, Bradley Whitehead, Amin Zakeri, Peter Nejsum, Amy H. Buck, Karl F. Hoffmann
Summary: Over the past decade, there has been a growing research interest in studying how extracellular vesicles (EVs) shape cross-species communication. In particular, helminths, which are parasitic worm species, have been found to manipulate the immune function and physiology of their hosts. This article highlights the challenges and best practices for studying helminth-derived EVs, complementing existing guidelines for mammalian EV research.
JOURNAL OF EXTRACELLULAR VESICLES
(2023)
Article
Infectious Diseases
Victor Cana-Bozada, Mark W. Robinson, David Hernandez-Mena, Francisco N. Morales-Serna
Summary: This study examined the phylogenetic relationships within Neodermata using putative orthologous groups of proteins (OGPs) from 11 species of Monogenea, Trematoda, and Cestoda. The analysis showed that monopisthocotylean monogeneans are sister-group to cestodes, and polyopisthocotylean monogeneans are sister-group to trematodes. However, the sister-group relationship between Monopisthocotylea and Cestoda was not statistically supported. The study also revealed a cluster formed by polyopisthocotyleans and trematodes.
TROPICAL MEDICINE AND INFECTIOUS DISEASE
(2023)
Article
Biochemistry & Molecular Biology
Alessia Galasso, Derek Cui Xu, Claire Hill, Daria Iakovleva, Maria Irina Stefana, Luis Alberto Baena-Lopez
Summary: Current evidence suggests that non-apoptotic caspase activation is associated with the regulation of basic cellular functions and may contribute to certain diseases. In this study, non-apoptotic caspase activation was shown to prevent the accumulation of the Patched receptor in autophagosomes, inhibiting autophagy induction. These findings reveal a pro-survival role of caspases under specific cellular conditions.
Article
Multidisciplinary Sciences
Wael Osman, Mira Mousa, Mohammed Albreiki, Zahrah Baalfaqih, Hinda Daggag, Claire Hill, Amy Jayne McKnight, Alexander P. Maxwell, Habiba Al Safar
Summary: Diabetic kidney disease (DKD), or diabetic nephropathy, is a major cause of renal impairment and end-stage renal disease. This study conducted a genome-wide association study to investigate genetic factors associated with the development and progression of DKD in the Emirati population. The CNR2 gene was found to be significantly associated with the development of DKD in individuals with type 2 diabetes mellitus (T2DM).
SCIENTIFIC REPORTS
(2023)
Article
Genetics & Heredity
Claire Hill, Seamus M. Duffy, Laura Kettyle, Liane McGlynn, Niina M. Sandholm, Rany Salem, Alex J. Thompson, Elizabeth Swan, Jill Kilner, Peter G. Rossing, Paul Shiels, Maria Lajer, Per-Henrik Groop, Alexander Peter Maxwell, Amy Jayne McKnight, GENIE Consortium
Summary: Diabetic kidney disease (DKD) is a major global health problem characterized by accelerated aging. This study explored features affecting telomere biology and methylation dysregulation in DKD using multi-omics approaches, which may provide useful biomarkers or therapeutic targets.
Review
Genetics & Heredity
Claire Hill, Seamus Duffy, Tiernan Coulter, Alexander Peter Maxwell, Amy Jayne McKnight
Summary: The global prevalence of diabetes is increasing and research is needed to find new ways to manage it. Diabetes can lead to kidney disease, which is a burden to patients and healthcare services. This review highlights studies on genomic and functional prediction tools that have identified genes and pathways associated with diabetic kidney disease, particularly focusing on the regulation of telomere length. The potential to use therapeutics that modulate telomere length for the treatment of diabetic kidney disease is discussed in the review.
Article
Endocrinology & Metabolism
Nicoline Uglebjerg, Fariba Ahmadizar, Dina M. Aly, Marisa Canadas-Garre, Claire Hill, Annemieke Naber, Asmundur Oddsson, Sunny S. Singh, Laura Smyth, David-Alexandre Tregouet, Layal Chaker, Mohsen Ghanbari, Valgerdur Steinthorsdottir, Emma Ahlqvist, Samy Hadjadj, Mandy Van Hoek, Maryam Kavousi, Amy Jayne McKnight, Eric J. Sijbrands, Kari Stefansson, Matias Simons, Peter Rossing, Tarunveer S. Ahluwalia
Summary: This study aims to explore the association between four missense variants in the CUBN gene and estimated glomerular filtration rate (eGFR) and investigate their effects on kidney-related traits. The results show significant positive associations between these variants and eGFR in individuals without diabetes.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Medicine, General & Internal
Alysha S. Thompson, Anna Tresserra-Rimbau, Nena Karavasiloglou, Amy Jennings, Marie Cantwell, Claire Hill, Aurora Perez-Cornago, Nicola P. Bondonno, Neil Murphy, Sabine Rohrmann, Aedin Cassidy, Tilman Kuehn
Summary: This cohort study in middle-aged UK adults found that a diet rich in high-quality plant-based foods and low in animal products is associated with lower risks of mortality, cardiovascular disease, and cancer, regardless of other chronic disease risk factors and genetic predisposition.