Article
Cell Biology
Eric Cornes, Loan Bourdon, Meetali Singh, Florian Mueller, Piergiuseppe Quarato, Erik Wernersson, Magda Bienko, Blaise Li, Germano Cecere
Summary: Our study identifies piRNAs as direct regulators of endogenous transcriptional programs during germline development and gamete differentiation in C. elegans, triggering the transcriptional silencing of hundreds of spermatogenic genes and promoting sperm differentiation and function. This silencing signal requires piRNA-dependent small RNA biogenesis and loading into downstream nuclear effectors.
DEVELOPMENTAL CELL
(2022)
Review
Oncology
Zahra Sadat Razavi, Vida Tajiknia, Shahab Majidi, Maryam Ghandali, Hamid Reza Mirzaei, Neda Rahimian, Michael R. Hamblin, Hamed Mirzaei
Summary: Gynecologic cancers involve female genital organs and are influenced by personal lifestyle, exposure history, genetics, and other factors. Research has shown that non-coding RNAs play a significant role in the regulation of cellular function in gynecological cancer, potentially leading to new avenues for diagnosis and treatment.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2021)
Article
Cell Biology
Salam Salloum-Asfar, Sara A. A. Abdulla, Rowaida Z. Z. Taha, I. Richard Thompson, Mohamed M. M. Emara
Summary: Somatic cells can be reprogrammed to iPSCs using reprogramming factors, and the addition of miRNAs has been shown to increase iPSC formation. This study identified potential regulomics and regulatory networks of miRNA-mRNA interactions and other ncRNAs in enhancing iPSC generation, pluripotency, and differentiation.
Review
Genetics & Heredity
Xiang-feng Bai, Rui-ze Niu, Jia Liu, Xu-dong Pan, Feng Wang, Wei Yang, Lu-qiao Wang, Li-zhong Sun
Summary: This review focuses on the current research of different types of noncoding RNAs (ncRNAs) in myocardial ischemia-reperfusion injury (MIRI), outlining their important features in pathological initiation and development, and summarizing related studies. Clarifying the roles of ncRNAs in MIRI and their associated networks further elucidates their crucial involvement in the disease.
Article
Biochemical Research Methods
Yu-Jian Kang, Jing-Yi Li, Lan Ke, Shuai Jiang, De-Chang Yang, Mei Hou, Ge Gao
Summary: This study introduces the ribosome calculator, which quantitatively models the coding ability of RNAs in the human genome, and successfully predicts transcripts with different coding abilities in various cell types. This suggests that the coding ability of transcripts should be modeled as a continuous spectrum with context-dependent nature.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Cell Biology
Wentao Ma, Weihong Zhang, Bing Cui, Jing Gao, Qiuhong Liu, Mengying Yao, Hanbing Ning, Lihua Xing
Summary: This study reveals that EPCs derived EVs transmit TUG1 to alleviate sepsis by promoting macrophage M2 polarization. Additionally, TUG1 can competitively bind to miR-9-5p to upregulate SIRT1 expression, leading to the inhibition of miR-9-5p-mediated SIRT1 inhibition, which contributes to a more comprehensive understanding of the pathogenesis of sepsis.
CELL DEATH & DISEASE
(2021)
Article
Biotechnology & Applied Microbiology
Owen T. Watson, Gabriele Buchmann, Paul Young, Kitty Lo, Emily J. Remnant, Boris Yagound, Mitch Shambrook, Andrew F. Hill, Benjamin P. Oldroyd, Alyson Ashe
Summary: This study characterized small RNAs present in honey bee reproductive tissues and showed that they may play an important role in honey bee gametogenesis and reproduction. Small RNAs can potentially explain the parent-of-origin effects on gene expression and reproductive physiology observed in honey bees.
Article
Multidisciplinary Sciences
Kristen P. Rodgers, Alicia Hulbert, Hamza Khan, Maria Shishikura, Shun Ishiyama, Malcolm V. Brock, Yuping Mei
Summary: A new method called TFP, using TRIzol for the extraction of 30-60 nt sncRNAs from plasma, is reported in this study. The TFP method yields more sncRNAs compared to commercial kits and shows lower CT values in plasma samples from different races.
SCIENTIFIC REPORTS
(2022)
Article
Biology
Hemakumar M. Reddy, Rupa Bhattacharya, Shrish Tiwari, Kankadeb Mishra, Pranatharthi Annapurna, Zeenath Jehan, Nissankararao Mary Praveena, Jomini Liza Alex, Vishnu M. Dhople, Lalji Singh, Mahadevan Sivaramakrishnan, Anurag Chaturvedi, Nandini Rangaraj, Thomas Michael Shiju, Badanapuram Sreedevi, Sachin Kumar, Ram Reddy Dereddi, Sunayana M. Rayabandla, Rachel A. Jesudasan
Summary: A study identified novel male-specific Y long arm-derived noncoding RNAs in mice, which may regulate the expression of several autosomal genes through piRNAs. The sperm phenotypes of Yq-deleted mice are similar to those reported in inter-specific male-sterile hybrids, suggesting a potential role of these noncoding RNAs in male sterility and speciation.
Article
Biology
Jordana Inacio Nascimento Oliveira, Adauto Lima Cardoso, Ivan Rodrigo Wolf, Rogerio Antonio de Oliveira, Cesar Martins
Summary: This study characterized PIWI-interacting RNA (piRNA) clusters and pathways responsible for silencing the mobilization of transposable elements (TEs) in the gonads of the cichlid fish Astatotilapia latifasciata carrying the B chromosome. The study predicted and annotated piRNA clusters in the A. latifasciata genome for the first time and observed biased expression related to sex and the presence of the B chromosome. The study also identified three piRNA clusters in the B chromosome, with two of them exclusively expressed in gonads of samples with the B chromosome. The study suggests that the B chromosome has its own genomic guardians to prevent uncontrolled TE mobilization.
Editorial Material
Biochemistry & Molecular Biology
Peiwei Chen, Alexei A. Aravin
Summary: Mutations in piRNA pathway protein components can lead to transposon activation and fertility defects in fruit flies, but deleting three large germline piRNA clusters does not affect transposon silencing or fertility.
Review
Oncology
Lidia Chellini, Ramona Palombo, Veronica Riccioni, Maria Paola Paronetto
Summary: This review summarizes the functions of different classes of RNA molecules in body fluids and discusses their potential as biomarkers for sarcoma diagnosis and prognosis. However, the lack of standardized assessment methods limits their adoption in clinical practice.
Article
Biochemistry & Molecular Biology
Zhenjun Yu, Yuhan Li, Shuai Shao, Beichen Guo, Mengxia Zhang, Lina Zheng, Kun Zhang, Feng Zhou, Li Zhang, Chiyi Chen, Wentao Jiang, Wei Hong, Tao Han
Summary: Chinese researchers have discovered that a long non-coding RNA called Mir122hg plays a protective role in promoting the growth of new healthy cells after liver injury. By activating signaling pathways and promoting gene transcription, Mir122hg encourages hepatocyte proliferation, suggesting its potential use in new therapies.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2022)
Review
Biochemistry & Molecular Biology
Pietro Laneve, Paolo Tollis, Elisa Caffarelli
Summary: RNA metabolism is crucial to cellular physiopathology, with ncRNAs playing a key role in maintaining neural system homeostasis and potentially contributing to neurodegenerative diseases like ALS. Research explores the link between ncRNA dysregulation and ALS, presenting the possibility of using them as diagnostic biomarkers and therapeutic targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Na Zhao, Lei Jia, Qiuxia Deng, Chunhua Zhu, Bo Zhang
Summary: This study characterized the sperm piwi-interacting RNAs profiles of Cynoglossus semilaevis and identified differential piRNAs associated with sex development and methylation. Five of the piRNAs showed sex bias and could be used as male-specific molecular biomarkers for C. semilaevis. Additionally, the study implied the possibility of transgenerational inheritance of sex-biased piRNAs in sperm.
MARINE BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Joshua L. Wetzel, Mona Singh
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Shilpa Nadimpalli Kobren, Bernard Chazelle, Mona Singh
Article
Biochemistry & Molecular Biology
Borislav H. Hristov, Bernard Chazelle, Mona Singh
Article
Biochemical Research Methods
Daniel Munro, Mona Singh
Article
Cell Biology
Robert A. Marmion, Liu Yang, Yogesh Goyal, Granton A. Jindal, Joshua L. Wetzel, Mona Singh, Trudi Schupbach, Stanislav Y. Shvartsman
Summary: Terminal patterning in Drosophila embryos is regulated by ERK signaling, with recent studies focusing on gain-of-function variants of human MEK1, revealing both signal-independent kinase activity and signal-dependent activation mechanisms.
MOLECULAR BIOLOGY OF THE CELL
(2021)
Article
Biochemistry & Molecular Biology
Yuri Pritykin, Joris van der Veeken, Allison R. Pine, Yi Zhong, Merve Sahin, Linas Mazutis, Dana Pe'er, Alexander Y. Rudensky, Christina S. Leslie
Summary: CD8 T cells are crucial in defending against viral and bacterial infections as well as tumor immunity, but their loss of functionality is complex due to the heterogeneity of states described in experimental and clinical settings. By analyzing a unified dataset of over 300 experiments, a shared trajectory of differentiation towards dysfunction was defined, revealing an early bifurcation of functional and dysfunctional T cell states across models. Experimental dissection of acute and chronic viral infections identified state-specific drivers and progenitor-like populations at an early branch point, aiding in mechanistic studies and translational efforts.
Article
Biochemistry & Molecular Biology
Anat Etzion-Fuchs, David A. Todd, Mona Singh
Summary: A novel machine learning method dSPRINT has been introduced to predict whether a protein domain binds DNA, RNA, small molecules, ions or peptides, and the positions within it that participate in these interactions. Through stringent cross-validation testing, it has shown excellent performance in uncovering ligand-binding positions and domains.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Chaitanya Aluru, Mona Singh
Summary: The study introduces a reconciliation-based framework that considers the relative positions of protein domains within extant sequences to uncover tandem domain duplications accurately. By developing an integer linear programming approach and a heuristic algorithm, the researchers are able to identify single and tandem domain duplication events with high accuracy. Through extensive simulation studies and testing on an orthogroup with complex domain duplication patterns, the effectiveness of the approach is demonstrated.
Article
Cell Biology
Minggang Zhang, Zeguo Zhao, Yuri Pritykin, Margaret Hannum, Andrew C. Scott, Fengshen Kuo, Viraj Sanghvi, Timothy A. Chan, Venkatraman Seshan, Hans-Guido Wendel, Andrea Schietinger, Michel Sadelain, Morgan Huse
Summary: The study showed that ectopic expression of miR-200c enhanced the antitumor activity of CD8(+) cytotoxic T lymphocytes during adoptive T cell therapy (ACT) in mouse models, leading to reduced apoptosis, increased in vivo persistence, and up-regulation of certain genes. These genetic perturbations resulted in phenotypically distinct T cells with advantageous therapeutic properties, highlighting the potential of the miR-200c-EpCAM axis in improving ACT outcomes.
SCIENCE TRANSLATIONAL MEDICINE
(2021)
Article
Immunology
Yi Zhong, Sarah K. Walker, Yuri Pritykin, Christina S. Leslie, Alexander Y. Rudensky, Joris van der Veeken
Summary: Zhong et al. studied the transcriptional regulation of T cell gene expression upon viral challenge using B6/Cast F1 hybrid mice. They found that members of Ets, Runx, and TCF/Lef transcription factor families play key roles in maintaining or increasing chromatin accessibility during T cell activation. Some highly induced immune response genes exhibit a noncanonical TF recruitment pattern.
Article
Biochemical Research Methods
Li Chen, Wenyun Lu, Lin Wang, Xi Xing, Ziyang Chen, Xin Teng, Xianfeng Zeng, Antonio D. Muscarella, Yihui Shen, Alexis Cowan, Melanie R. McReynolds, Brandon J. Kennedy, Ashley M. Lato, Shawn R. Campagna, Mona Singh, Joshua D. Rabinowitz
Summary: NetID is a novel global network optimization approach for annotating untargeted LC-MS metabolomics data. By combining known biochemical and metabolomic principles, it significantly enhances annotation coverage and accuracy, facilitating the discovery of metabolites.
Article
Multidisciplinary Sciences
Prakriti Paul Chacha, Ryoko Horie, Takehiro G. Kusakabe, Yasunori Sasakura, Mona Singh, Takeo Horie, Michael Levine
Summary: The study found that the lateral regions of the neural plate in the protovertebrate Ciona intestinalis type A exhibit characteristics of vertebrate placodes and neural crest, and can generate sensory cell types. Misexpression of the POU IV gene was found to cause epidermal cells to transform into hybrid sensory cell types, which exhibit properties of both palp sensory cells (PSCs) and bipolar tail neurons (BTNs).
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Sean B. King, Mona Singh
Summary: The study suggests that rodents and primates may have had ancient exposures to viruses similar to SARS-CoV-2 and HCoV-229E, respectively, leading to adaptive amino acid substitutions in the ACE2 receptor. This indicates that some rodent species may have acquired tolerance or resistance to SARS-like coronaviruses, while non-adapted mammals and primates may be more susceptible to symptomatic disease.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Immunology
Joris van der Veeken, Clarissa Campbell, Yuri Pritykin, Michail Schizas, Jacob Verter, Wei Hu, Zhong-Min Wang, Fanny Matheis, Daniel Mucida, Louis-Marie Charbonnier, Talal A. Chatila, Alexander Y. Rudensky
Summary: The role of Foxp3 in peripheral pTreg cells and the mechanisms supporting their differentiation remain poorly understood. This study used genetic tracing to identify microbiota-induced pTreg cells and found that many of their distinguishing features were Foxp3 independent. While Foxp3 was critical for the suppression of certain diseases, pTreg cells could suppress colonic effector T cell expansion in a Foxp3-independent manner. Thus, Foxp3 and the tolerogenic signals preceding and promoting its expression confer distinct facets of pTreg functionality.
Article
Biochemical Research Methods
Sean B. B. King, Mona Singh
Summary: This study constructed a structural database of protein-ligand interactions in 18 primate species and found that ligand-binding sites are more conserved than other sites, particularly those binding with DNA and RNA. The study also revealed that variable ligand-binding sites are enriched in gene regulatory pathways, and identified amino acid variations in several transcription factors specific to humans. These findings suggest that ligand-binding sites in primates have undergone selective pressure and may play a significant role in phenotypic variation through pleiotropic effects on gene regulation.
PLOS COMPUTATIONAL BIOLOGY
(2023)