Article
Plant Sciences
Peirong Li, Tongbing Su, Deshuang Zhang, Weihong Wang, Xiaoyun Xin, Yangjun Yu, Xiuyun Zhao, Shuancang Yu, Fenglan Zhang
Summary: The study characterized heterosis in Chinese cabbage F-1 hybrid and its parental lines, showing marked heterosis in leaf weight and biomass yield. Analysis of small RNA sequencing revealed differentially expressed microRNAs at different growth stages, with majority of miRNA clusters in F-1 hybrid showing lower expression levels compared to mid-parent values. Furthermore, transcriptome analysis demonstrated differential expression of genes related to photosynthesis and chlorophyll synthesis in the F-1 hybrid, resulting in increased photosynthesis capacity and chlorophyll content. These findings provide new insights into the regulation of target genes and miRNA expression patterns in leaf size and heterosis for biomass of B. rapa.
HORTICULTURE RESEARCH
(2021)
Article
Microbiology
Xiaohui Ju, Fang Li, Jingrui Li, Chunyan Wu, Guangtao Xiang, Xiaomin Zhao, Yuchen Nan, Dongming Zhao, Qiang Ding
Summary: The study suggests that ASFV infection causes a strong suppression of host immune responses, leading to dysregulation of host chemokine axis and metabolic pathways in porcine alveolar macrophages.
VETERINARY MICROBIOLOGY
(2021)
Article
Cell Biology
Guo Li, Xiaoning Zhu, Yihan Wang, Hongru Ma, Yuzhe Wang, Hanyu Wu, Xiangyang Li, Yiling Wang, Jianen Gao, Xuexin Chen, Xingxu Huang, Yuan Yao, Xiaoxiang Hu
Summary: RNA base editing is a promising tool for precise molecular therapy, and currently there are two widely used RNA base editors, REPAIR and RESCUE. REPAIR only facilitates A-to-I conversions, while RESCUE performs both A-to-I and C-to-U conversions, and can generate twice the number of mutations compared to REPAIR. However, the transcription-wide impact caused by RESCUE-induced off-target single-nucleotide variants (SNVs) is not fully understood. Therefore, this study used transcription-wide sequencing to determine the off-target effects of RESCUE-mediated editing and found different off-target effects on various RNA types.
JOURNAL OF MOLECULAR CELL BIOLOGY
(2023)
Article
Cell Biology
Lijie Wang, Wei Xue, Hongxia Zhang, Runze Gao, Houyuan Qiu, Jia Wei, Lina Zhou, Yun-Ni Lei, Xiaocheng Wu, Xiao Li, Chengfang Liu, Jing Wu, Qiubing Chen, Hanhui Ma, Xingxu Huang, Cheguo Cai, Ying Zhang, Bei Yang, Hao Yin, Li Yang, Jia Chen
Summary: The study introduces a novel base editor system, tBE, which efficiently performs C-to-T editing by fusing a cleavable dCDI domain, reducing off-target mutations. The tBE system remains inactive at off-target sites, preventing unintended mutations, and activates for precise base editing at on-target sites.
NATURE CELL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Sukhen Das Mandal, Partho Sarothi Ray
Summary: m(6)A-modified mRNAs are more targeted by miRNAs and RBPs, with miRNA target sites and RBP-binding sites located close to m(6)A sites, indicating a three-way interplay between m(6)A, microRNA, and RBP binding.
Review
Biochemistry & Molecular Biology
Amrutha Menon, Noraini Abd-Aziz, Kanwal Khalid, Chit Laa Poh, Rakesh Naidu
Summary: This review focuses on the role of miRNA in cancer, therapeutic approaches with miRNAs, and effective delivery into the system. Patents and ongoing clinical trials for miRNA therapy are also summarized.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Forestry
Jiangtao Du, Qianqian Shi, Yu Liu, Guozhao Shi, Xi Li, Xingang Li
Summary: This study investigates the regulatory network of jujube embryo abortion using correlation analysis, artificial pollination, sugar content measurements, and multi-omics analysis. The results reveal that embryo abortion is a major factor contributing to the low kernel rate of cultivated jujube, and 21 days after pollination is a critical period for embryo abortion. Transcriptome, miRNA, and degradome sequencing identified differentially expressed genes and miRNA-target gene pairs involved in the regulation of embryo abortion during kernel development.
Article
Oncology
Pouria Samadi, Meysam Soleimani, Fatemeh Nouri, Fatemeh Rahbarizadeh, Rezvan Najafi, Akram Jalali
Summary: This study using a systems biology approach investigated potential molecular biomarkers and therapeutic targets related to the progression of colorectal cancer (CRC) from early stages to metastasis. The results identified several potential therapeutic targets and biomarkers, with lncRNA LINC00974 found to be an important and novel biomarker.
Article
Cell Biology
Anjali Bhat, Haritz Irizar, Johan Hilge Thygesen, Karoline Kuchenbaecker, Oliver Pain, Rick A. Adams, Eirini Zartaloudi, Jasmine Harju-Seppanen, Isabelle Austin-Zimmerman, Baihan Wang, Rebecca Muir, Ann Summerfelt, Xiaoming Michael Du, Heather Bruce, Patricio O'Donnell, Deepak P. Srivastava, Karl Friston, L. Elliot Hong, Mei-Hua Hall, Elvira Bramon
Summary: A study identified two genes associated with MMN, which are overexpressed in the frontal cortex during prenatal development but significantly downregulated in adulthood. MMN was found to be a considerably superior psychosis endophenotype compared to three other candidate endophenotypes.
Article
Multidisciplinary Sciences
Shaoyi Ji, Ze Yang, Leonardi Gozali, Thomas Kenney, Arif Kocabas, Carolyn Jinsook Park, Mary Hynes
Summary: Recent studies have revealed that isolated 3'UTRs may play a significant role in gene regulation, although their specific mechanisms are not well understood. Researchers have found that the expression ratio between 3'UTRs and CDS can vary across tissues, development stages, and cell states, potentially influencing cell-specific gene expression and regulation.
Article
Immunology
Ibrahim A. Akkouh, Timothy Hughes, Vidar M. Steen, Joel C. Glover, Ole A. Andreassen, Srdjan Djurovic, Attila Szabo
Summary: Despite the high heritability of schizophrenia, the detailed pathophysiology and etiology are still unknown. Recent findings suggest that abnormal inflammatory regulation and miRNAs are involved. Comparative analysis of miRNome in SCZ astrocytes revealed four differentially expressed miRNAs with lower baseline expression compared to healthy controls. Peripheral blood analysis also showed significantly lower expression of specific target genes in SCZ patients, further enhancing the understanding of SCZ pathobiology.
BRAIN BEHAVIOR AND IMMUNITY
(2021)
Article
Biotechnology & Applied Microbiology
Vaishnovi Sekar, Emilio Marmol-Sanchez, Panagiotis Kalogeropoulos, Laura Stanicek, Eduardo A. Sagredo, Albin Widmark, Evangelos Doukoumopoulos, Franziska Bonath, Inna Biryukova, Marc R. Friedlander
Summary: In this study, a new method called agoTRIBE is developed to comprehensively detect miRNA targets at the single-cell level. By fusing Argonaute2 protein with the RNA editing domain of ADAR2, the method allows sensitive single-cell RNA sequencing to identify miRNA targets. The results show that agoTRIBE can identify functional miRNA targets and obtain transcriptome-wide measurements of RNA abundance.
NATURE BIOTECHNOLOGY
(2023)
Article
Chemistry, Applied
Chen Chen, Lijia Shi, Yuqi Bin, Chenghui Liu, Mixia Tian, Aili Jiang
Summary: This study investigates the molecular mechanism of early browning response in fresh-cut apple and identifies genes related to respiratory, energy, antioxidant, lipid, and secondary metabolism activation in the early stage of browning.
Article
Plant Sciences
Juan He, Chi Xu, Chenjiang You, Beixin Mo, Xuemei Chen, Lei Gao, Lin Liu
Summary: This study conducted a comprehensive identification of miRNA target genes in maize using the PARE analysis method. A total of 246 target genes, including transcription factors and other genes, were identified. The study also revealed tissue-specific target transcript cleavage guided by miRNAs. Additionally, miRNA-target gene pairs involved in seed germination were identified.
Article
Biochemical Research Methods
Steven M. Blue, Brian A. Yee, Gabriel A. Pratt, Jasmine R. Mueller, Samuel S. Park, Alexander A. Shishkin, Anne C. Starner, Eric L. Van Nostrand, Gene W. Yeo
Summary: The discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets is crucial for understanding the regulation of RNA processing. In this study, a method called seCLIP is presented, which allows for efficient and high-resolution analysis of these interactions, along with a comprehensive bioinformatics pipeline.
Article
Biochemistry & Molecular Biology
Stefan E. Seemann, Aashiq H. Mirza, Claus H. Bang-Berthelsen, Christian Garde, Mikkel Christensen-Dalsgaard, Christopher T. Workman, Flemming Pociot, Niels Tommerup, Jan Gorodkin, Walter L. Ruzzo
Summary: The accelerated evolution of RNA structures in vertebrates, though rare, does not preclude the conservation of their functions, as shown in the study.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Matilda Rehn, Anne Wenzel, Anne-Katrine Frank, Mikkel Bruhn Schuster, Sachin Pundhir, Nanna Jorgensen, Kristoffer Vitting-Seerup, Ying Ge, Johan Jendholm, Magali Michaut, Erwin M. Schoof, Tanja Lyholm Jensen, Nicolas Rapin, Russell T. Sapio, Kasper Langebjerg Andersen, Anders H. Lund, Michele Solimena, Martin Holzenberger, Dimitri G. Pestov, Bo Torben Porse
Summary: Ribosomopathies are a range of disorders that affect protein synthesis and primarily impact hematopoietic stem cells and erythroid development. This study demonstrates that the deletion of poly-pyrimidine-tract-binding protein 1 (PTBP1) in the hematopoietic compartment leads to a condition resembling ribosomopathy. The loss of PTBP1 results in reduced HSC self-renewal, erythroid differentiation, and protein synthesis, along with defects in splicing and ribosome biogenesis.
Article
Biochemical Research Methods
Christian Anthon, Giulia Ilaria Corsi, Jan Gorodkin
Summary: The effectiveness of CRISPR/Cas9-mediated genome editing experiments relies on the careful selection of guide RNA (gRNA) for target recognition and cleavage activation. This study presents a user-friendly webserver that incorporates both on- and off-target prediction tools, CRISPRon and CRISPRoff, to facilitate gRNA selection.
Article
Genetics & Heredity
Enrique Gonzalez-Tortuero, Christian Anthon, Jakob H. Havgaard, Adrian S. Geissler, Anne Breuner, Carsten Hjort, Jan Gorodkin, Stefan E. Seemann
Summary: Non-coding RNAs play important regulatory roles in bacteria, but many predicted non-coding RNAs lack functional associations. The study finds that Bacillaceae-1 RNA motif is conserved in non-pathogenic strains of the genus Bacillus, with different structural and genomic context characteristics. Furthermore, it is observed that the motif has different expression patterns and structural features depending on its location upstream of the ribosomal RNA cluster or between coding genes.
Article
Biochemistry & Molecular Biology
Zubairul Islam, Bharath Saravanan, Kaivalya Walavalkar, Umer Farooq, Anurag Kumar Singh, Radhakrishnan Sabarinathan, Jitendra Thakur, Awadhesh Pandit, Steven Henikoff, Dimple Notani
Summary: Vertebrate genomes are divided into chromatin domains called topologically associating domains (TADs), which are typically bound by pairs of CTCF binding sites. Transcription at domain boundaries is correlated with better insulation, and this study shows that boundary-associated RNAs aid in the recruitment and clustering of CTCF at TAD borders. These boundary-associated RNAs enhance TAD insulation, enhancer-promoter interactions, and gene expression within the TAD.
Article
Biochemistry & Molecular Biology
Reza Yarani, Oana Palasca, Nadezhda T. Doncheva, Christian Anthon, Bartosz Pilecki, Cecilie A. S. Svane, Aashiq H. Mirza, Thomas Litman, Uffe Holmskov, Claus H. Bang-Berthelsen, Mogens Vilien, Lars J. Jensen, Jan Gorodkin, Flemming Pociot
Summary: This study identified common conserved pathological UC-related gene expression signatures between humans and mice by comparing gene expression data. These signatures can be used as treatment targets or biomarker candidates. Less known genes with importance in disease pathogenesis were identified and validated in different samples. The findings contribute to disease phenotyping, treatment decisions, drug discovery, and clinical trial design.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Oncology
Rahul Kumar, Bhavya Dhaka, Sarthak Sahoo, Mohit Kumar Jolly, Radhakrishnan Sabarinathan
Summary: Induction of immunoproteasome expression in tumour cells can improve antigen presentation and immune response. However, the association between IP expression and overall prognosis and response to ICB therapy varies among different solid tumours and is influenced by immune cell infiltration patterns.
MOLECULAR ONCOLOGY
(2023)
Article
Neurosciences
Giulia I. Corsi, Veerendra P. Gadekar, Henriette Haukedal, Nadezhda T. Doncheva, Christian Anthon, Sheetal Ambardar, Dasaradhi Palakodeti, Poul Hyttel, Kristine Freude, Stefan E. Seemann, Jan Gorodkin
Summary: Alzheimer's disease (AD) is a progressive and irreversible brain disorder caused by complex factors. This study investigates the gene expression changes in neurons with fAD mutations in the PSEN1 gene using hiPSCs. The analysis reveals significant alterations in genes related to extracellular matrix, calcium homeostasis, mitochondrial oxidative stress, and circular RNA. These findings contribute to a better understanding of the cellular mechanisms in AD neurons.
NEUROBIOLOGY OF DISEASE
(2023)
Article
Neurosciences
Henriette Haukedal, Giulia I. Corsi, Veerendra P. Gadekar, Nadezhda T. Doncheva, Shekhar Kedia, Noortje de Haan, Abinaya Chandrasekaran, Pia Jensen, Pernille Schionning, Sarah Vallin, Frederik Ravnkilde Marlet, Anna Poon, Carlota Pires, Fawzi Khoder Agha, Hans H. Wandall, Susanna Cirera, Anja Hviid Simonsen, Troels Tolstrup Nielsen, Jorgen Erik Nielsen, Poul Hyttel, Ravi Muddashetty, Blanca I. Aldana, Jan Gorodkin, Deepak Nair, Morten Meyer, Martin Rossel Larsen, Kristine Freude
Summary: Alzheimer's disease is a common cause of dementia with no cure. This study investigated specific disease phenotypes in glutamatergic forebrain neurons and identified Golgi fragmentation as one of the earliest AD phenotypes. The study also found that genetic variants in SORL1 could aggravate Golgi fragmentation and glycosylation changes.
FRONTIERS IN NEUROSCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Jacopo Vegni, Ying Sun, Stefan E. Seemann, Martina Zappaterra, Roberta Davoli, Stefania Dall'Olio, Jan Gorodkin, Paolo Zambonelli
Summary: Dietary intake of omega-3 polyunsaturated fatty acids and antioxidants in humans has anti-inflammatory and antioxidant effects. However, the use of omega-3 polyunsaturated fatty acids in pig diet has been less studied. This study aimed to investigate gene expression differences in the muscle tissue of pigs fed with different diets. The results showed that adding omega-3 polyunsaturated fatty acids and antioxidants to the diet improved the lipid composition and anti-inflammatory potential of the muscle tissue.
Article
Immunology
Henriette Haukedal, Signe Syshoj Lorenzen, Emil Winther Westi, Giulia I. Corsi, Veerendra P. Gadekar, Amanda McQuade, Hayk Davtyan, Nadezhda T. Doncheva, Benjamin Schmid, Abinaya Chandrasekaran, Stefan E. Seemann, Susanna Cirera, Mathew Blurton-Jones, Morten Meyer, Jan Gorodkin, Blanca I. Aldana, Kristine Freude
Summary: FTD is a common form of early-onset dementia with no current treatment options. FTD3 is a rare subtype of the disease caused by a mutation in the CHMP2B gene. This study explores the role of glial cells, specifically microglia, in FTD3 pathogenesis and identifies different inflammatory profiles and behaviors based on the CHMP2B mutation status.
BRAIN BEHAVIOR AND IMMUNITY
(2023)
Article
Biotechnology & Applied Microbiology
Rania Velissari, Mirolyuba Ilieva, James Dao, Henry E. Miller, Jens Hedelund Madsen, Jan Gorodkin, Masanori Aikawa, Hideshi Ishii, Shizuka Uchida
Summary: The cases of inflammatory bowel disease (IBD) are increasing rapidly worldwide. High-throughput techniques are being used to understand the molecular changes associated with IBD, including genetic mutations, microbiome environments, transcriptome, and proteome. However, non-coding RNAs (ncRNAs), particularly long non-coding RNAs (lncRNAs), have been largely unexplored in IBD research. This study re-analyzed RNA-seq data and conducted loss-of-function experiments to study the expression profiles and functional relevance of lncRNAs in IBD. A web database, IBDB, was also developed to facilitate further research on lncRNAs in IBD.
BRIEFINGS IN FUNCTIONAL GENOMICS
(2023)
Article
Multidisciplinary Sciences
Elizabeth Heyes, Anna S. Wilhelmson, Anne Wenzel, Gabriele Manhart, Thomas Eder, Mikkel B. Schuster, Edwin Rzepa, Sachin Pundhir, Teresa DAltri, Anne-Katrine Frank, Coline Gentil, Jakob Woessmann, Erwin M. Schoof, Manja Meggendorfer, Jurg Schwaller, Torsten Haferlach, Florian Grebien, Bo T. Porse
Summary: The myeloid transcription factor CEBPA is frequently mutated in acute myeloid leukemia, and its co-mutation with GATA2 and TET2 is common. This study reveals the molecular mechanisms of these co-mutations, showing that CEBPA(NT) enhances GATA2 expression while loss of TET2 increases Gata2 promoter methylation in CEBPA(DM) AML, leading to balanced GATA2 levels. Demethylating treatment can restore Gata2 levels and prolong disease latency in CEBPA-TET2 co-mutated AML.
NATURE COMMUNICATIONS
(2023)
Letter
Biochemical Research Methods
Giulia Ilaria Corsi, Christian Anthon, Jan Gorodkin
Article
Oncology
Anurag Kumar Singh, Kaivalya Walavalkar, Daniele Tavernari, Giovanni Ciriello, Dimple Notani, Radhakrishnan Sabarinathan
Summary: The integration of human papillomavirus (HPV) into the host genome affects the expression of adjacent genes, and this study reveals that the effects differ depending on the chromatin state at the integration site. The integration of HPV leads to the upregulation of nearby genes within the same topologically associating domains (TADs), but does not affect genes in adjacent TADs. Recurrent HPV integration in specific TADs results in the overexpression of oncogenes.
MOLECULAR ONCOLOGY
(2023)
