Article
Plant Sciences
Jingxiong Zhang, Yuxing Xu, Jing Xie, Huifu Zhuang, Hui Liu, Guojing Shen, Jianqiang Wu
Summary: Dodder is a parasitic plant that can transfer nitrogen systemic signals between hosts with different nitrogen levels, regulating transcriptome and methylome changes in the recipient hosts. This study also found that under nitrogen stress conditions, dodder facilitates bilateral nitrogen systemic signaling between different hosts, impacting inter-plant mobile mRNAs.
Article
Chemistry, Multidisciplinary
Xiao-Meng Tang, Tian -Tian Ye, Xue-Jiao You, Xiao-Ming Yin, Jiang -Hui Ding, Wen-Xuan Shao, Meng -Yuan Chen, Bi-Feng Yuan, Yu-Qi Feng
Summary: In this study, a method for purifying plant ribosomal RNA (rRNA) was proposed and modifications in plant 18S rRNA and 25S rRNA were characterized using LC-ESI-MS/MS. The study revealed the presence of new modifications in plant rRNAs, including 2 modifications in 18S rRNA and 4 modifications in 25S rRNA. Exposure to cadmium induced significant changes in rRNA modifications, highlighting the importance of rRNA modifications in response to environmental stress. The discovery of new modifications expands our understanding of plant rRNA modifications and enhances the investigation of the functional roles of plant ribosomes in gene expression regulation.
CHINESE CHEMICAL LETTERS
(2023)
Article
Plant Sciences
Yue Zhao, Jingnan Miao, Jinqiu He, Xuejun Tian, Kaili Gao, Chao Ma, Xiubin Tian, Wenqiang Men, Huanhuan Li, Huihui Bi, Wenxuan Liu
Summary: The heat shock factor TaHsfA2d plays a crucial role in mediating plant responses to Pi deficiency stress, with its overexpression leading to increased sensitivity to Pi deficiency and regulation of stress response and flavonoid biosynthesis genes.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Article
Plant Sciences
Qing Zhang, Aiwen Deng, Min Xiang, Qiuyan Lan, Xiaokun Li, Shuai Yuan, Xin Gou, Shuang Hao, Juan Du, Chaowen Xiao
Summary: Pectin, cellulose, and hemicellulose are important components of the primary cell wall in eudicots and play a vital role in plant development. This study found that PGX2 is involved in regulating root hair development, and its activation tagging affects cell wall remodeling, auxin signaling, and actin microfilament orientation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Hsin-Yen Larry Wu, Polly Yingshan Hsu
Summary: This study describes a custom library construction method for super-resolution Ribo-seq in Arabidopsis, which can be applied to study genome-wide mRNA translation.
Article
Biochemistry & Molecular Biology
Yong-Soon Park, Jong-Seok Park, Soohyun Lee, Sung-Hee Jung, Seon-Kyu Kim, Choong-Min Ryu
Summary: The study revealed a complex interaction between the marine bacterial pathogen V. vulnificus and the land plant Arabidopsis thaliana. The pathogen actively modulates its virulence factors and potential host immune regulators.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Ranju Chutia, Sarah Scharfenberg, Steffen Neumann, Steffen Abel, Joerg Ziegler
Summary: The research reveals the important roles of iron and phosphate in plant growth and metabolic regulation, showing their interdependency and interaction which affect plant growth and development under different nutrient conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Ahmet Bakirbas, Elsbeth L. Walker
Summary: This study identified an iron-regulated lncRNA, COS, in Arabidopsis that is involved in leaf and seed iron levels, chlorophyll levels, root length, and singlet oxygen accumulation during iron deficiency.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Yuxin Cao, Jiayin Wang, Songlin Wu, Xiaochang Yin, Jia Shu, Xing Dai, Yannan Liu, Linhua Sun, Danmeng Zhu, Xing Wang Deng, Keqiong Ye, Weiqiang Qian
Summary: This study identified box C/D SnoR28.1s as crucial regulators of plant growth and development using a CRISPR/Cas9-generated ncRNA deletion mutant library. SnoR28.1s guide the 2'-O-ribose methylation of 25S rRNA at G2396, and their deletion results in impaired ribosome assembly and function, leading to growth defects in plants.
Article
Plant Sciences
Chang-Yi Chiu, Hui-Fang Lung, Wen-Chun Chou, Li-Yen Lin, Hong-Xuan Chow, Yu-Hao Kuo, Pei-Shan Chien, Tzyy-Jen Chiou, Tzu-Yin Liu
Summary: Autophagy in plants is regulated by different signaling cascades in response to environmental changes. Fine-tuning of its activity is critical for cellular homeostasis. This study observed that Pi deficiency moderately upregulates most ATG genes and increases autophagic structures in the root of Arabidopsis, but does not significantly alter autophagic flux in the whole roots. At the organismal level, mutants of ATG exhibited decreased shoot Pi concentrations and smaller meristem sizes under Pi sufficiency.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Oncology
Bo Zhou, Huan Yang, Chuan Yang, Yu-lu Bao, Shi-ming Yang, Jiao Liu, Yu-feng Xiao
Summary: This article summarizes the importance of noncoding RNAs (ncRNAs) and their encoded peptides/proteins in cancer research, introduces the methods, tools, and databases for identifying and validating these peptides/proteins, and discusses the future application prospects and challenges.
Article
Biochemistry & Molecular Biology
Hongyu Chen, Yang Lv, Xinxin Yin, Xi Chen, Qinjie Chu, Qian-Hao Zhu, Longjiang Fan, Longbiao Guo
Summary: The study evaluated the impact of sample size on single-cell transcriptome analysis outcomes, finding that the most significant principal components can be achieved with 20,000-30,000 cells sampled, and relatively high reliability of cell clustering can be achieved with 20,000 cells.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Bin Li, Donghao Li, Linjun Cai, Qiting Zhou, Cong Liu, Jianzhong Lin, Yixing Li, Xiaoying Zhao, Li Li, Xuanming Liu, Chongsheng He
Summary: Acetylation of N4-cytidine (ac4C) is a recently discovered mRNA modification that plays a key regulatory role in RNA stability, translation, and thermal stress response. This study confirms the presence of ac4C in both Arabidopsis thaliana and rice mRNAs and provides transcriptome-wide atlases of RNA ac4C modification. The results show that ac4C is enriched near translation start and end sites in mRNA and is positively correlated with RNA half-life, splicing variants, and translation efficiency.
Article
Plant Sciences
Liping Che, Han Meng, Junxiang Ruan, Lianwei Peng, Lin Zhang
Summary: RBD1 is crucial for PSII assembly in higher plants, as it not only contributes to the formation of functional PSII core complex, but also participates in the translation of D1 protein.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biology
Chao Ma, Qiuju Chen, Shiping Wang, Amnon Lers
Summary: The microRNA miR827 and the transcription regulator GPL alpha are functionally involved in both senescence and phosphate homeostasis, with miR827 playing a role in regulating the expression of GPL alpha. The expression of GPL alpha is induced by phosphate deficiency and overexpression of GPL alpha leads to reduced expression of phosphate transporter genes. The close interactions between senescence and phosphate homeostasis are further emphasized by the functional involvement of miR827 and GPL alpha in both processes.
Review
Allergy
Elena Della Bella, Jana Koch, Katja Baerenfaller
Summary: Regulatory non-coding RNAs have received considerable attention in recent years due to their condition- and tissue-specific expression and various modes of action. Translation of short open reading frames is an important mechanism for these RNAs to regulate gene expression. However, the study of translational regulation through regulatory RNAs is still limited.
Article
Multidisciplinary Sciences
Klemens Froehlich, Eva Brombacher, Matthias Fahrner, Daniel Vogele, Lucas Kook, Niko Pinter, Peter Bronsert, Sylvia Timme-Bronsert, Alexander Schmidt, Katja Baerenfaller, Clemens Kreutz, Oliver Schilling
Summary: This study presents a benchmark dataset for evaluating DIA data analysis workflows in clinical settings, using real-world inter-patient heterogeneity. The results demonstrate the effectiveness of gas-phase fractionated spectral libraries and non-parametric permutation-based statistical tests for correctly identifying differentially abundant proteins in DIA analysis.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Haroon Butt, Jeremie Bazin, Kasavajhala V. S. K. Prasad, Nourelislam Awad, Martin Crespi, Anireddy S. N. Reddy, Magdy M. Mahfouz
Summary: Abiotic stresses have significant impacts on plant growth, development, and crop productivity. The plant-specific splicing factor RS33 plays an important role in regulating pre-mRNA splicing and abiotic stress responses in rice.
Article
Plant Sciences
Sombir Rao, Sarita Jha, Chandni Bansal, Apoorva Gupta, Celine Sorin, Martin Crespi
Summary: Heat stress transcription factors (HSFs) and microRNAs (miRNAs) play a critical role in the regulation of heat stress response in plants by regulating different stress and developmental networks through regulatory feedback mechanisms.
Review
Biochemistry & Molecular Biology
Pablo A. Manavella, Micaela A. Godoy Herz, Alberto R. Kornblihtt, Reed Sorenson, Leslie E. Sieburth, Kentaro Nakaminami, Motoaki Seki, Yiliang Ding, Qianwen Sun, Hunseung Kang, Federico D. Ariel, Martin Crespi, Axel J. Giudicatti, Qiang Cai, Hailing Jin, Xiaoqi Feng, Yijun Qi, Craig S. Pikaard
Summary: This article presents and discusses new and long-standing open questions in plant RNA biology, covering topics such as alternative splicing, dynamics, translation, structures, epitranscriptomics, long non-coding RNAs, small RNA production and functions, and more. It provides insights into the current state-of-the-art in the field and aims to provoke future discoveries and reflections.
Article
Multidisciplinary Sciences
Ying Huang, Jing An, Sanchari Sircar, Clara Bergis, Chloe Dias Lopes, Xiaoning He, Barbara Da Costa, Feng-Quan Tan, Jeremie Bazin, Javier Antunez-Sanchez, Maria Florencia Mammarella, Ravi-sureshbhai Devani, Rim Brik-Chaouche, Abdelhafid Bendahmane, Florian Frugier, Chongjing Xia, Christophe Rothan, Aline V. Probst, Zouine Mohamed, Catherine Bergounioux, Marianne Delarue, Yijing Zhang, Shaojian Zheng, Martin Crespi, Sotirios Fragkostefanakis, Magdy M. Mahfouz, Federico Ariel, Jose Gutierrez-Marcos, Cecile Raynaud, David Latrasse, Moussa Benhamed
Summary: This study examines the changes in chromatin and gene expression in response to heat stress in tomato. They found that heat stress rapidly alters chromatin structure and leads to the formation of temporary contacts between promoters and enhancers, which drive the expression of genes responsive to heat stress. The researchers also discovered that this spatial reorganization of chromatin requires the transcription factor HSFA1a.
NATURE COMMUNICATIONS
(2023)
Article
Infectious Diseases
Filip Styrzynski, Damir Zhakparov, Marco Schmid, Damian Roqueiro, Zuzanna Lukasik, Julia Solek, Jakub Nowicki, Milosz Dobrogowski, Joanna Makowska, Milena Sokolowska, Katja Baerenfaller
Summary: This study provides a set of easily obtainable parameters that can be used to rapidly identify SARS-CoV-2 positive patients, assess the risk of death during hospitalization, and predict the disease outcome.
INFECTIOUS DISEASES AND THERAPY
(2023)
Article
Allergy
Yasutaka Mitamura, Matthias Reiger, Juno Kim, Yi Xiao, Damir Zhakparov, Ge Tan, Beate Ruckert, Arturo O. Rinaldi, Katja Baerenfaller, Mubeccel Akdis, Marie-Charlotte Bruggen, Kari C. Nadeau, Patrick M. Brunner, Damian Roqueiro, Claudia Traidl-Hoffmann, Cezmi A. Akdis
Summary: This study reveals the cellular crosstalk in the leukocyte-infiltrated area of AD skin through single-cell analysis and spatial transcriptomics. The results demonstrate unique distribution patterns and interactions among fibroblasts, dendritic cells, and macrophages in the skin lesions. Additionally, the expression levels of TNC and CCL18 are correlated with disease severity. These findings provide valuable insights for the development of improved treatments.
Article
Biochemistry & Molecular Biology
Jeremie Bazin, Emilie Elvira-Matelot, Thomas Blein, Vincent Jauvion, Nathalie Bouteiller, Jun Cao, Martin D. Crespi, Herve Vaucheret
Summary: In addition to regulating splicing, the spliceosome components SmD1 and PRP39 also promote posttranscriptional gene silencing in Arabidopsis thaliana. However, their actions are distinct in both splicing and gene silencing. The double mutant analysis suggests that PRP39 and SmD1 work together to limit degradation of transgene-derived aberrant RNAs, thus promoting the initiation of posttranscriptional gene silencing in the cytoplasm.
Article
Plant Sciences
Li Liu, Michel Heidecker, Thomas Depuydt, Nicolas Manosalva Perez, Martin Crespi, Thomas Blein, Klaas Vandepoele
Summary: A study identified 6599 high-confidence lincRNA loci in Arabidopsis and constructed a TF-lincRNA regulatory network containing 2659 lincRNAs and 15686 interactions. Experimental validation confirmed the role of three transcription factors in controlling root-specific lincRNA expression.
Article
Biochemistry & Molecular Biology
Thomas Roule, Maria Florencia Legascue, Andana Barrios, Nicolas Gaggion, Martin Crespi, Federico Ariel, Thomas Blein
Summary: Long noncoding RNAs (lncRNAs) play a crucial role in regulating gene expression in plants, including various molecular mechanisms. In Arabidopsis, lncRNAs have been identified and associated with plant development and environmental response. This study identified a lncRNA called ARES downstream of the key gene IAA14/SOLITARYROOT (SLR) involved in root development. Knockdown and knockout experiments revealed that ARES affects the induction of the neighboring gene NF-YB3 in response to exogenous auxin and leads to a root developmental phenotype. Transcriptomic analysis showed deregulation of ARF7-dependent genes. These findings suggest that ARES functions as a novel regulator of auxin response and lateral root development.
Article
Biochemistry & Molecular Biology
Wil Prall, Arsheed H. Sheikh, Jeremie Bazin, Jean Bigeard, Marilia Almeida-Trapp, Martin Crespi, Heribert Hirt, Brian D. Gregory
Summary: Posttranscriptional regulation of mRNA mediated by m6A has significant impacts on transcriptome regulation in plants. This study provides a comprehensive understanding of the effects of m6A on both short-term and long-term responses to pathogen signaling in Arabidopsis. The results show that m6A-deficient plants exhibit enhanced resistance to bacterial and fungal pathogen infections with altered immune responses. Furthermore, m6A deposition on defense and immunity-related transcripts is specifically coordinated prior to and during pathogen signal flagellin, and correlates with changes in transcript abundance and cleavage.
Article
Microbiology
Damir Zhakparov, Yves Quirin, Yi Xiao, Nicole Battaglia, Michael Holzer, Martin Buehler, Walter Kistler, Doortje Engel, Jon Paulin Zumthor, Alexa Caduff, Katja Baerenfaller
Summary: Sequencing SARS-CoV-2 RNA in wastewater is an unbiased method to detect the spread of emerging variants and track regional infection dynamics. Major international events promote the spread of new variants in the respective host region.
Proceedings Paper
Computer Science, Artificial Intelligence
Damir Zhakparov, Kathleen Moriarty, Nonhlanhla Lunjani, Marco Schmid, Carol Hlela, Michael Levin, Avumile Mankahla, Cezmi Akdis, Liam O'Mahony, Katja Baerenfaller, Damian Roqueiro
Summary: High throughput RNA sequencing (RNA-Seq) allows for profiling of transcripts in multiple samples. Standard methods are limited by high dimensionality and imbalanced sample-to-feature ratio. Machine learning-based feature selection methods can address these limitations.
MACHINE LEARNING AND PRINCIPLES AND PRACTICE OF KNOWLEDGE DISCOVERY IN DATABASES, ECML PKDD 2022, PT II
(2023)
Article
Biochemistry & Molecular Biology
Maria Florencia Mammarella, Leandro Lucero, Nosheen Hussain, Aitor Munoz-Lopez, Ying Huang, Lucia Ferrero, Guadalupe L. Fernandez-Milmanda, Pablo Manavella, Moussa Benhamed, Martin Crespi, Carlos L. Ballare, Jose Gutierrez Marcos, Pilar Cubas, Federico Ariel
Summary: The long noncoding RNA APOLO regulates the shade avoidance syndrome in Arabidopsis thaliana by dynamically modulating expression of key factors. APOLO deregulation leads to the repression of the BRC1 gene and an increase in shoot branching. It also plays a role in leaf hyponasty and influences auxin homeostasis by modulating auxin synthesis and efflux genes.