Article
Biochemistry & Molecular Biology
Misbah Khan, Shuai Hou, Sikandar Azam, Haixin Lei
Summary: The study identified a cytoplasmic accumulation region (CAR-N) in intronless lncRNA NKILA that is crucial for its export by facilitating TREX recruitment. Depletion of TREX-TAP pathway components resulted in strong nuclear retention of NKILA, highlighting the importance of this pathway in mRNA export. The binding of SRSF1/7 to clustered motifs in CAR-N plays a key role in promoting the export of NKILA and is essential for its function in inhibiting breast cancer cell migration.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Pedro G. Nachtigall, Luiz A. Bovolenta, James G. Patton, Bastian Fromm, Ney Lemke, Danillo Pinhal
Summary: Despite the differences in heart development among different vertebrate groups, both conserved and group-specific miRNAs play crucial roles in modulating the core and peripheral genes of heart GRNs. Conserved miRNAs have higher expression levels and more targets, while group-specific miRNAs have lower expression levels and fewer targets.
Article
Multidisciplinary Sciences
Shady Younis, Alice Jouneau, Marten Larsson, Jean-Francois Oudin, Pierre Adenot, Jihad Omar, Vincent Brochard, Leif Andersson
Summary: Zc3h11a is crucial for embryonic viability and survival, as well as involved in metabolic regulation of embryonic cells. Inactivation of Zc3h11a expression in adult tissues does not lead to obvious phenotypic defects.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
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)
Article
Biochemistry & Molecular Biology
Robert M. Martin, Madalena R. de Almeida, Eduardo Gameiro, Sergio F. de Almeida
Summary: We developed RHINO, a genetically encoded sensor that can selectively bind RNA:DNA hybrids for live-cell imaging of cellular R-loops. With the help of RHINO, we investigated the dynamics of R-loops at nucleoli, telomeres, and protein-coding genes, and found significant variations across these regions.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Thomas Kehrer, Anastasija Cupic, Chengjin Ye, Soner Yildiz, Mehdi Bouhaddou, Nicholas A. Crossland, Erika A. Barrall, Phillip Cohen, Anna Tseng, Tolga Cagatay, Raveen Rathnasinghe, Daniel Flores, Sonia Jangra, Fahmida Alam, Ignacio Mena, Sadaf Aslam, Anjali Saqi, Magdalena Rutkowska, Manisha R. Ummadi, Giuseppe Pisanelli, R. Blake Richardson, Ethan C. Veit, Jacqueline M. Fabius, Margaret Soucheray, Benjamin J. Polacco, Baran Ak, Arturo Marin, Matthew J. Evans, Danielle L. Swaney, Ana S. Gonzalez-Reiche, Emilia M. Sordillo, Harm van Bakel, Viviana Simon, Lorena Zuliani-Alvarez, Beatriz M. A. Fontoura, Brad R. Rosenberg, Nevan J. Krogan, Luis Martinez-Sobrido, Adolfo Garcia-Sastre, Lisa Miorin
Summary: The ORF6 protein of SARS-CoV-2 plays a crucial role in antagonizing the host's innate immunity by disrupting nuclear import and inhibiting cellular mRNA export. It also regulates viral protein expression. Mutations in ORF6 affect its interactions with host components and impair immune evasion in certain variants.
CELL HOST & MICROBE
(2023)
Article
Multidisciplinary Sciences
Xiaopan Gao, Huabin Tian, Kaixiang Zhu, Qing Li, Wei Hao, Linyue Wang, Bo Qin, Hongyu Deng, Sheng Cui
Summary: This study reveals the molecular basis for the antagonistic function of Sarbecovirus ORF6 and suggests a potential strategy for immunosuppressive drug development using ORF6 CTT-derived peptides.
NATURE COMMUNICATIONS
(2022)
Article
Dermatology
Yinggai Song, Nickolas Menezes da Silva, Vania A. Vicente, Yu Quan, Marcus Teixeira, Jie Gong, Sybren de Hoog, Ruoyu Li
Summary: The study sequenced genomes of six species within the Phialophora verrucosa complex, finding a higher prevalence of Phialophora species in patients with CARD9-related immunodeficiency. Different mutations in the CARD9 gene appear to increase susceptibility to infection by various species.
Article
Cell Biology
Tae Yeon Yoo, Timothy J. Mitchison
Summary: Macromolecular transport across the nuclear envelope is dependent on facilitated diffusion through nuclear pore complexes (NPCs), with O-GlcNAc modification accelerating nucleocytoplasmic transport by enhancing the nonspecific permeability of the FG-repeat barrier. Through high-throughput assays and superresolution imaging, it was found that increasing O-GlcNAc modification of NPCs accelerated NTR-facilitated transport of proteins in both directions.
JOURNAL OF CELL BIOLOGY
(2021)
Review
Plant Sciences
Sara Shakir, Syed Shan-e-Ali Zaidi, Farahnaz Sadat Golestan Hashemi, Chantal Nyirakanani, Herve Vanderschuren
Summary: Recent metagenomic studies have revealed a diverse range of viruses in plants, and high-throughput methods are needed to study their functions. The development of viral infectious clones is a preferred method to understand virus biology and their role in plant ecosystems. This review discusses efficient approaches for characterizing plant viruses, technological advances in high-throughput sequencing and synthetic biology to assemble viral infectious clones, applications of plant viral vectors in research, and proposals for safer field applications.
TRENDS IN PLANT SCIENCE
(2023)
Article
Microbiology
Yingying Huang, Chenglong Yang, Istvan Molnar, Shen Chen
Summary: In this study, a comparative transcriptomic analysis was performed on high and low citrinin-producing Monascus purpureus strains using RNA-Seq and qRT-PCR. A total of 2518 differentially expressed genes were identified, with 1141 downregulated and 1377 upregulated genes in the low citrinin producer strain. Many upregulated genes were associated with energy metabolism and carbohydrate metabolism, potentially providing more biosynthetic precursors for Monascus pigments synthesis. Additionally, several potentially interesting genes encoding transcription factors were also identified. This study provides valuable insights into metabolic adaptations and safer Monascus pigments production.
Article
Virology
Margarita Valdes Aleman, Luca D. Bertzbach, Thomas Speiseder, Wing Hang Ip, Ramon A. Gonzalez, Thomas Dobner
Summary: During human adenovirus infection, the late phase of viral replication results in a significant increase in viral late mRNA abundance, which outcompetes cellular mRNA biogenesis rather than selectively exporting viral mRNA.
Article
Biochemistry & Molecular Biology
Eun Seon Kim, Chang Geon Chung, Jeong Hyang Park, Byung Su Ko, Sung Soon Park, Yoon Ha Kim, In Jun Cha, Jaekwang Kim, Chang Man Ha, Hyung-Jun Kim, Sung Bae Lee
Summary: It has been found in a Drosophila model that nuclear accumulation of the RNA-binding protein Staufen may be a crucial pathological feature contributing to ALS/FTD. The nuclear accumulation of Staufen could potentially enhance the toxicity of certain proteins, and regulating the levels of Fibrillarin may affect the degree of cellular toxicity caused by protein aggregates.
HUMAN MOLECULAR GENETICS
(2021)
Article
Multidisciplinary Sciences
Bo Yu, Pan Li, Qiangfeng Cliff Zhang, Lin Hou
Summary: DiffScan is a computational framework for normalization and differential analysis of RNA structure probing data, which can accurately identify SVRs at nucleotide resolution, demonstrating its compatibility with various structure probing platforms.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Hang Yang, Yunlong Wang, Yunlu Tian, Xuan Teng, Zehui Lv, Jie Lei, Erchao Duan, Hui Dong, Xue Yang, Yuanyan Zhang, Yinglun Sun, Xiaoli Chen, Xiuhao Bao, Rongbo Chen, Chuanwei Gu, Yipeng Zhang, Xiaokang Jiang, Wenyu Ma, Pengcheng Zhang, Yi Ji, Yu Zhang, Yihua Wang, Jianmin Wan
Summary: A mutant rice flo22 showed delayed amyloplast development in endosperm cells, affecting mitochondrial morphology and function. Flo22, encoding a mitochondrion-localized P-type PPR protein, mutations led to defective trans-splicing of mitochondrial nad1 intron 1 and affected complex I assembly and activity. Additionally, FLO22 interacted with DYW3 and participated in mitochondrial RNA editing.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Physiology
Angela Fago, Chandrasekhar Natarajan, Martin Pettinati, Federico G. Hoffmann, Tobias Wang, Roy E. Weber, Salvador Drusin, Federico Issoglio, Marcelo A. Marti, Dario Estrin, Jay F. Storz
AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY
(2020)
Article
Biology
Jay F. Storz, Chandrasekhar Natarajan, Magnus K. Grouleff, Michael Vandewege, Federico G. Hoffmann, Xinxin You, Byrappa Venkatesh, Angela Fago
JOURNAL OF EXPERIMENTAL BIOLOGY
(2020)
Article
Mycology
Phillip L. Vines, Federico G. Hoffmann, Florencia Meyer, Thomas W. Allen, Jing Luo, Ning Zhang, Maria Tomaso-Peterson
Article
Evolutionary Biology
Yue Hao, Hyuk Jin Lee, Michael Baraboo, Katherine Burch, Taylor Maurer, Jason A. Somarelli, Gavin C. Conant
GENOME BIOLOGY AND EVOLUTION
(2020)
Article
Biochemical Research Methods
Adam Thrash, Federico Hoffmann, Andy Perkins
BMC BIOINFORMATICS
(2020)
Article
Genetics & Heredity
Andreas Prothmann, Federico G. Hoffmann, Juan C. Opazo, Peter Herbener, Jay F. Storz, Thorsten Burmester, Thomas Hankeln
FRONTIERS IN GENETICS
(2020)
Article
Ecology
Jennifer Fenner, Caleb Benson, Luis Rodriguez-Caro, Anna Ren, Riccardo Papa, Arnaud Martin, Federico Hoffmann, Ryan Range, Brian A. Counterman
FRONTIERS IN ECOLOGY AND EVOLUTION
(2020)
Article
Biotechnology & Applied Microbiology
Matias Preza, Javier Calvelo, Mauricio Langleib, Federico Hoffmann, Estela Castillo, Uriel Koziol, Andres Iriarte
Summary: The study revealed massive transcriptomic changes in the lifecycle of the tapeworm Hymenolepis microstoma, with key gene families contributing substantially to the expression load in each stage. Members of the cestode-specific hydrophobic ligand-binding protein (HLBP) family were found to be highly expressed in each lifecycle stage, with major metabolic changes during the transition from cysticercoids to adult worms. This research contributes to understanding the gene expression changes during the development of this important cestode species, representing the first transcriptomic study with robust replicates spanning all main lifecycle stages of a tapeworm.
Article
Multidisciplinary Sciences
Anthony Signore, Michael S. Tift, Federico G. Hoffmann, Todd L. Schmitt, Hideaki Moriyama, Jay F. Storz
Summary: Penguins have evolved increased hemoglobin-oxygen affinity and a significantly enhanced Bohr effect, allowing for more efficient oxygen extraction from the lungs and oxygen unloading in acidified tissues. This evolutionary adaptation enables penguins to fully utilize onboard oxygen stores and maximize underwater foraging time.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Evolutionary Biology
Federico G. Hoffmann, Jay F. Storz, Shigehiro Kuraku, Michael W. Vandewege, Juan C. Opazo
Summary: Globin-X (GbX) is a mysterious member of the vertebrate globin gene family, with potential roles in cellular signaling or protection against lipid oxidation. Research integrates bioinformatics, synteny, and phylogenetic analyses to study the diversity of GbX genes in different species and the impact of whole-genome duplications on vertebrate genomes.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Mycology
Phillip L. Vines, Federico G. Hoffmann, Florencia Meyer, Thomas W. Allen, Maria Tomaso-Peterson
Summary: This study identified a new species within the genus Gaeumannomyces and demonstrated its pathogenicity and ability to infect the roots of ultradwarf bermudagrass.
Article
Developmental Biology
Juan C. Opazo, Federico G. Hoffmann, Kattina Zavala, Scott Edwards
Summary: The DAN gene family plays fundamental roles in development and is associated with diseases in adulthood. This study investigates the evolutionary history of the DAN gene family in vertebrates, identifying two new gene lineages and reconstructing the ancestral repertoire of DAN genes in gnathostomes.
DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Michael W. Vandewege, Roy N. I. I. I. I. Patt, Dana K. Merriman, David A. Ray, Federico G. Hoffmann
Summary: The PIWI/piRNA defense system against transposable elements (TEs) is less effective in the absence of actively mobilizing TEs. The study on the 13-lined ground squirrel reveals that while there is no active TE insertion, TEs are still actively transcribed. The Piwi genes are not expressed until after a certain stage of testis development, and there is little change in TE expression with the onset of Piwi expression. This suggests that the PIWI/piRNA system is less efficient in suppressing TE transcription in squirrels compared to mice and rabbits.
Article
Evolutionary Biology
William Joyce, Daniel M. Ripley, Todd Gillis, Amanda Coward Black, Holly A. Shiels, Federico G. Hoffmann
Summary: The troponin complex, responsible for muscle activation, is composed of three interacting protein subunits: TnC, TnI, and TnT. Through phylogenetic and synteny analysis, we have identified five distinct TNNI classes (TNNI1-5) and four TNNT classes (TNNT1-4) in a diverse array of vertebrates.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Juan C. Opazo, Michael W. Vandewege, Federico G. Hoffmann, Kattina Zavala, Catalina Melendez, Charlotte Luchsinger, Viviana A. Cavieres, Luis Vargas-Chacoff, Francisco J. Morera, Patricia Burgos, Cheril Tapia-Rojas, Gonzalo A. Mardones
Summary: Studying the evolutionary history of gene families is important for understanding gene origin, evolution, and their implications for functional studies. The sirtuin gene family, involved in aging-related functions, has a complex duplicative history, but our results provide a well-resolved phylogeny and shed light on the repertoire of sirtuin genes among vertebrates. We identified a new member (SIRT3.2) that was lost in amniotes but retained in other jawed vertebrates, and its experimental analysis revealed its mitochondrial location and deacetylase activity similar to mammalian SIRT3.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)