Article
Biotechnology & Applied Microbiology
Galen F. Gao, Peng Li, Warren J. Leonard
Summary: This study investigates the correlation between TAD rearrangements and gene expression changes in TCR-induced CD4(+) T cells using Hi-C and RNA-seq data. The findings suggest a significant relationship between TAD rearrangements and changes in local gene expression, and provide new insights into the global mechanisms that regulate gene expression.
Article
Plant Sciences
Huiyun Yu, Leiyun Yang, Zhan Li, Feng Sun, Bo Li, Shengsong Guo, Yong-Fei Wang, Tong Zhou, Jian Hua
Summary: In situ deletion series generated by CRISPR/Cas9 genome editing identified cis-regulatory elements and potential transcription factors for the expression of the intracellular immune receptor NLR gene SNC1, and revealed the critical role of SNC1 in NLR gene co-expression.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Plant Sciences
Huiyun Yu, Leiyun Yang, Zhan Li, Feng Sun, Bo Li, Shengsong Guo, Yong-Fei Wang, Tong Zhou, Jian Hua
Summary: The transcriptional and post-transcriptional regulation of intracellular immune receptor nucleotide-binding leucine-rich repeats (NLRs) is complex and involves multiple cis-acting elements. The NLR gene SNC1 is a critical regulator of gene expression in the same gene cluster, and its expression is under complex local regulation.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Huiqi Zhao, Hong Liao, Shuixian Li, Rui Zhang, Jing Dai, Pengrui Ma, Tianpeng Wang, Meimei Wang, Yi Yuan, Xuehao Fu, Jie Cheng, Xiaoshan Duan, Yanru Xie, Peng Zhang, Hongzhi Kong, Hongyan Shan
Summary: By conducting extensive studies, including phylogenetic analysis, comparative transcriptomics, and functional studies, the evolutionary histories, expression patterns, and functions of floral organ identity and symmetry genes in Delphinieae were clarified. It was found that the duplication and diversification of APETALA3-3 (AP3-3), AGAMOUS-LIKE6 (AGL6), CYCLOIDEA (CYC), and DIVARICATA (DIV) lineage genes were closely associated with the origin of Delphinieae flowers. Therefore, the duplication and diversification of floral symmetry genes, as well as their integration into the preexisting floral regulatory network, played a key role in the development of Delphinieae flowers.
Article
Biochemistry & Molecular Biology
Linhua Sun, Yuxin Cao, Zhu Li, Yi Liu, Xiaochang Yin, Xing Wang Deng, Hang He, Weiqiang Qian
Summary: Higher-order chromatin organization plays important roles in transcriptional regulation and genome functions. This study identified and characterized long-range chromatin loops in the Arabidopsis 3D genome and found their association with H3K27me3 modifications. These chromatin loops are dependent on Polycomb group proteins and are involved in tissue-specific and dynamically regulated gene expression. The conservation of these chromatin loops in other plant species suggests their importance in genome evolution and transcriptional coregulation.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Colin Farrell, Maria Vaquero-Sedas, Maria D. Cubiles, Michael Thompson, Alejandro Vega-Vaquero, Matteo Pellegrini, Miguel A. Vega-Palas
Summary: DNA methylation modulates telomere function in Arabidopsis thaliana, where subtelomeric DNA methylation extends from Interstitial Telomeric Sequences (ITSs) near telomeres. However, it drops at the telomeric side and disappears at the inner part of telomeres.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
David Sere, Oceane Cassan, Fanny Bellegarde, Cecile Fizames, Jossia Boucherez, Geoffrey Schivre, Jacinthe Azevedo, Thierry Lagrange, Alain Gojon, Antoine Martin
Summary: Polycomb-group (PcG) proteins play a crucial role in gene expression regulation, mainly by keeping genes in a transcriptionally silent state during development. Recent studies have shown that PcG proteins may have additional functions, including targeting active genes or acting independently of gene expression regulation. This study reveals that mutations in two Arabidopsis PcG proteins, CURLY LEAF (CLF) and LIKE HETEROCHROMATIN PROTEIN1 (LHP1), result in deregulation of active genes targeted by PcG proteins or enriched in associated chromatin marks. The deregulation is associated with the accumulation of small RNAs, leading to the degradation of active gene transcripts. It is concluded that PcG protein function is essential for maintaining the accurate degradation of RNA and ensuring proper gene expression levels.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Thomas Depuydt, Klaas Vandepoele
Summary: This study introduces a novel automated function prediction method that leverages complementary information from gene co-expression networks to successfully predict biological process annotations for Arabidopsis thaliana genes. Using experimental data validation, high-confidence functional annotations were obtained for unknown genes and genes with computational annotations, shedding light on a variety of developmental processes and molecular responses in Arabidopsis.
Article
Plant Sciences
Chaokun Huang, Ken-ichi Kurotani, Ryo Tabata, Nobutaka Mitsuda, Ryohei Sugita, Keitaro Tanoi, Michitaka Notaguchi
Summary: Grafting is a widely used plant propagation technique in agriculture. A recent discovery in Nicotiana suggests the potential of interfamily grafting. This study reveals the importance of xylem connection in interfamily grafting and investigates the molecular basis of xylem formation at the graft junction.
HORTICULTURE RESEARCH
(2023)
Article
Biology
Diogo M. Ribeiro, Chaymae Ziyani, Olivier Delaneau
Summary: This study utilizes single-cell datasets to identify gene co-expression in different human cell types. The results show that many co-expressed genes are functionally related and their co-expression is maintained at the protein level. Additionally, the study reveals that co-expressed gene pairs share regulatory elements, suggesting the importance of studying shared regulatory architecture between genes in understanding disease comorbidity.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Doron Stupp, Elad Sharon, Idit Bloch, Marinka Zitnik, Or Zuk, Yuval Tabach
Summary: This study developed a machine-learning approach to predict functional interactions between human genes using phylogenetic profiles across 1154 eukaryotic species. The method showed a 14% performance increase compared to previous methods, enabling better annotation of less studied genes, particularly in the field of DNA repair.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Tobias Strunz, Martin Kellner, Christina Kiel, Bernhard H. F. Weber
Summary: This study identified clusters of co-regulated genes across multiple tissues using eQTL analysis and colocalization studies, highlighting the importance of understanding common effects on biological pathways and treatment implications when targeting co-regulated disease genes.
Article
Multidisciplinary Sciences
Satoyo Oya, Mayumi Takahashi, Kazuya Takashima, Tetsuji Kakutani, Soichi Inagaki
Summary: This study identifies three Arabidopsis methyltransferases that direct H3K4me1 and suggests that one methyltransferase functions co-transcriptionally while the others are associated with specific histone modifications and DNA sequences.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Xingjie Ren, Mengchi Wang, Bingkun Li, Kirsty Jamieson, Lina Zheng, Ian R. Jones, Bin Li, Maya Asami Takagi, Jerry Lee, Lenka Maliskova, Tsz Wai Tam, Miao Yu, Rong Hu, Lindsay Lee, Armen Abnousi, Gang Li, Yun Li, Ming Hu, Bing Ren, Wei Wang, Yin Shen
Summary: The study introduces a screening strategy called CRISPRpath for characterizing CREs of genes linked to the same biological pathway and converging phenotypes in parallel. It demonstrates the ability of CRISPRpath to identify functional enhancers of six genes in the 6-thioguanine-induced DNA mismatch repair pathway simultaneously.
Article
Biochemistry & Molecular Biology
Heng Deng, Yao Chen, Ziyu Liu, Zhaoqiao Liu, Peng Shu, Ruochen Wang, Yanwei Hao, Dan Su, Julien Pirrello, Yongsheng Liu, Zhengguo Li, Don Grierson, James J. Giovannoni, Mondher Bouzayen, Mingchun Liu
Summary: This study reveals that SlERF.F12, an ethylene response factor, negatively regulates the initiation of tomato fruit ripening by recruiting a co-repressor and histone deacetylases. SlERF.F12 interacts with the co-repressor and recruits histone deacetylases to form a complex, which decreases the acetylation level at the promoter regions of ripening genes, thus repressing their transcription.
Article
Biochemistry & Molecular Biology
Margarita Takou, Tuomas Hamala, Evan M. Koch, Kim A. Steige, Hannes Dittberner, Levi Yant, Mathieu Genete, Shamil Sunyaev, Vincent Castric, Xavier Vekemans, Outi Savolainen, Juliette de Meaux
Summary: The study found that in the populations of the European subspecies Arabidopsis lyrata ssp. petraea, edge populations faced a decline in effective population size and an increase in derived nonsynonymous variants, indicating an increase in the genomic burden of deleterious mutations but a decrease in rare deleterious variants. While the demographic history predicted a slight decrease in per-individual fitness for the range-edge population, it performed well in terms of growth and survival, showing strong resilience to the effect of range expansion.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Book Review
Multidisciplinary Sciences
Itai Yanai, Martin J. Lercher
Article
Genetics & Heredity
Benedict Wieters, Kim A. Steige, Fei He, Evan M. Koch, Sebastian E. Ramos-Onsins, Hongya Gu, Ya-Long Guo, Shamil Sunyaev, Juliette de Meaux
Summary: The rate of plant growth is a major functional trait in plant ecology, with little known about its genetic variation in natural populations. Environmental plasticity is a predominant source of variation to adapt plant size to prevailing light conditions, while significant genetic variation exists in growth rate and plasticity. Adaptive processes have played a more important role in shaping regional differences in rosette growth, with Spanish genotypes tending to reach a significantly larger size than Northern European genotypes.
Article
Multidisciplinary Sciences
F. He, K. A. Steige, V Kovacova, U. Goebel, M. Bouzid, P. D. Keightley, A. Beyer, J. de Meaux
Summary: The study suggests that gene expression differences in response to dehydration stress are influenced by genetic regulation, with the direction of plasticity affecting the effects of gene variants. Evolution of gene expression in Arabidopsis lyrata tends to amplify stress response, while in Arabidopsis halleri it tends to mitigate stress response.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Esther M. Sundermann, Martin J. Lercher, David Heckmann
Summary: The regulation of resource allocation in biological systems today is a result of natural selection in ancestral and recent environments. Research suggests that C-4 plants require more nitrogen re-allocation between photosynthetic components to adapt to new environments, indicating that resource distribution patterns still reflect optimality in ancestral environments.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Jacob Moe-Lange, Nicoline M. Gappel, Mackenzie Machado, Michael M. Wudick, Cosima S. A. Sies, Stephan N. Schott-Verdugo, Michele Bonus, Swastik Mishra, Thomas Hartwig, Margaret Bezrutczyk, Debarati Basu, Edward E. Farmer, Holger Gohlke, Andrey Malkovskiy, Elizabeth S. Haswell, Martin J. Lercher, David W. Ehrhardt, Wolf B. Frommer, Thomas J. Kleist
Summary: Glutamate plays dual roles in metabolism and signaling, with low-glutamate domains at synapses indicating distinct signaling functions. In plants, wound-induced electrical and calcium signaling involve homologs of mammalian glutamate receptors. The stretch-activated anion channel MSL10 is identified as necessary for proper wound-induced signaling and acts in the same pathway as glutamate receptor-like proteins (GLRs). This study provides a molecular genetic basis for mechanical signal perception and long-distance electrical and calcium signal transmission in plants.
Article
Biochemistry & Molecular Biology
Hannes Dittberner, Aurelien Tellier, Juliette de Meaux
Summary: Contemporary gene flow can have crucial consequences for endangered species, as shown by the study on Arabis nemorensis and A. sagittata. The research used genetic sequencing to determine the history of gene flow between these two plant species and found that low levels of gene flow persisted long after speciation. Eventually, a hotspot of contemporary hybridization was formed in a unique sympatric population. This occasional sympatry may have helped protect these lineages from extinction despite their low diversity.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
S. Andreas Angermayr, Tin Yau Pang, Guillaume Chevereau, Karin Mitosch, Martin J. Lercher, Tobias Bollenbach
Summary: Dose-response relationships play a crucial role in understanding biological systems and can have significant implications in treatment and drug resistance. This study investigates the mechanisms shaping the dose-response curve of antibiotics and identifies a negative growth-mediated feedback loop as a key factor. Specifically, the antibiotic trimethoprim slows down bacterial growth and weakens its own effectiveness. The upregulation of the drug target, dihydrofolate reductase, is found to be the molecular basis for this feedback loop. The study suggests that growth-mediated feedback loops may have broader implications in drug responses and could be utilized to prevent drug resistance.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Article
Plant Sciences
Manuel Balparda, Jessica Schmitz, Martin Duemmel, Isabell C. Wuthenow, Marc Schmidt, Saleh Alseekh, Alisdair R. Fernie, Martin J. Lercher, Veronica G. Maurino
Summary: Plants have two different GLX systems of different origins and functions to metabolize 2-keto-D-glucose and protect cells from the toxicity of reactive carbonyl species. The first system is shared by all eukaryotes and mainly scavenges methylglyoxal and glyoxal, while the second system, acquired through horizontal gene transfer, metabolizes keto-D-glucose and features a different type of GLXI protein.
Letter
Biotechnology & Applied Microbiology
Itai Yanai, Martin J. Lercher
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Alexander Kroll, Sahasra Ranjan, Martin K. M. Engqvist, Martin J. Lercher
Summary: For most proteins annotated as enzymes, it is unknown which primary and/or secondary reactions they catalyze. Machine learning predictions could provide an efficient alternative, but are hampered by a lack of information regarding enzyme non-substrates, as available training data comprises mainly positive examples. Here, we present ESP, a general machine-learning model for the prediction of enzyme-substrate pairs with an accuracy of over 91% on independent and diverse test data.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Tin Yau Pang, Martin Lercher
Summary: A considerable amount of bacterial cytosol is filled with catalysts and their substrates. The optimal cytosolic volume occupancy depends on the allocation of resources and the balance between metabolic enzymes and ribosomes. The variation in cytosolic density in bacterial cells follows an optimality principle of cellular efficiency.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Hugo Dourado, Wolfram Liebermeister, Oliver Ebenhoeh, Martin Lercher
Summary: This study extends the growth balance analysis (GBA) framework to investigate the optimality of each biochemical reaction and determine the mathematical conditions for the activation of a reaction at optimal growth. It provides a method to identify the economic values of biochemical reactions and relate them to proteome allocation costs and benefits. The study also generalizes the concept of Metabolic Control Analysis to growing cell models.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Alexander Kroll, Yvan Rousset, Xiao-Pan Hu, Nina A. Liebrand, Martin J. Lercher
Summary: Researchers developed a general model that can predict turnover numbers of enzyme-catalyzed reactions, even for dissimilar enzymes. This model outperforms existing models and provides a valuable tool for understanding enzyme efficiency and cellular physiology. The development of accurate computational prediction methods for turnover numbers is highly desirable due to the lack of experimental estimates.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Xiao-Pan Hu, Stefan Schroeder, Martin J. Lercher
Summary: Understanding the allocation of the cellular proteome to different cellular processes is crucial for unraveling the organizing principles of bacterial physiology. This study systematically analyzes the proteome efficiency of metabolic pathways in Escherichia coli, revealing that the most costly biosynthesis pathways are regulated for near-optimal efficiency. In contrast, proteins involved in nutrient uptake and central metabolism tend to be highly over-abundant.
