Article
Biology
Ann Louise Hunter, Charlotte E. Pelekanou, Nichola J. Barron, Rebecca C. Northeast, Magdalena Grudzien, Antony D. Adamson, Polly Downton, Thomas Cornfield, Peter S. Cunningham, Jean-Noel Billaud, Leanne Hodson, Andrew S. Loudon, Richard D. Unwin, Mudassar Iqbal, David W. Ray, David A. Bechtold
Summary: The circadian clock component NR1D1 plays a crucial role in regulating lipid metabolism and can drive dysregulation of white adipose tissue (WAT) lipogenesis and obesity when globally deleted. However, adipocyte-selective deletion does not lead to the same phenotype. Under high-fat diet conditions, NR1D1 in adipocytes controls metabolic processes and plays a critical role in obesity-related WAT pathology and insulin resistance.
Article
Biochemical Research Methods
Lirong Zhang, Yanchao Yang, Lu Chai, Qianzhong Li, Junjie Liu, Hao Lin, Li Liu
Summary: This study quantitatively analyzed the correlation between transcription factors (TFs) and gene expression and identified TF modules associated with gene expression. A convolutional neural network model, TFCNN, was constructed to predict gene expression levels based on the enrichment characteristics of TFs. Results showed that TFCNN achieved high prediction performance and outperformed other models by better extracting combinatorial interactions among TFs.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biotechnology & Applied Microbiology
Soonkyu Hwang, Namil Lee, Donghui Choe, Yongjae Lee, Woori Kim, Ji Hun Kim, Gahyeon Kim, Hyeseong Kim, Neung-Ho Ahn, Byoung-Hee Lee, Bernhard O. Palsson, Byung-Kwan Cho
Summary: In this study, the regulatory elements of transcription and translation in Streptomyces griseus were analyzed using multiple "omics" datasets. Several important regulators and elements were identified, providing a foundation for genetic engineering to improve secondary metabolite production in Streptomyces.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Yameng Xu, Xinglong Wang, Chenyang Zhang, Xuan Zhou, Xianhao Xu, Luyao Han, Xueqin Lv, Yanfeng Liu, Song Liu, Jianghua Li, Guocheng Du, Jian Chen, Rodrigo Ledesma-Amaro, Long Liu
Summary: This study reports the engineering of Saccharomyces cerevisiae to produce rubusoside and rebaudiosides, which are considered as the next generation of sugar substitutes. Through a modular engineering approach, the authors were able to overcome several limitations and achieve high titers of these molecules. This research provides a sustainable and scalable solution for the production of diverse rebaudiosides.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
S. Kalra, R. Peyser, J. Ho, C. Babbin, N. Bohan, A. Cortes, J. Erley, M. Fatima, J. Flinn, E. Horwitz, R. Hsu, W. Lee, V. Lu, A. Narch, D. Navas, I. Kalu, E. Ouanemalay, S. Ross, F. Sowole, E. Specht, J. Woo, K. Yu, J. D. Coolon
Summary: Precise regulation of transcription is crucial for normal organism form and function, and minor alterations in gene expression can lead to phenotypic variation and disease. In this study, we investigated the response of target genes to systematic reduction of RAP1 expression in Saccharomyces cerevisiae. Our results revealed that Rap1 acts as an activator for more target genes than as a repressor and functions differently in different gene groups. These findings expand our understanding of this important transcriptional regulator.
Article
Plant Sciences
Fan Qi, Fu Wang, Chunxiao Xiaoyang, Zhenhui Wang, Yujie Lin, Zhanwu Peng, Jun Zhang, Ningning Wang, Jian Zhang
Summary: This study conducted transcriptome analysis to analyze the gene expression profiles of different organs in flax. The results identified differentially expressed genes and organ-specific expression patterns. Gene ontology enrichment analysis revealed the biological processes and molecular functions associated with organ growth. The study also investigated the role of AP2 transcription factors in regulating flax organ development and stress response. Overall, this research provides valuable insights into the molecular mechanisms of flax organ development and has implications for genetic improvement of flax crops.
Article
Veterinary Sciences
Dawei Wei, Sayed Haidar Abbas Raza, Xingping Wang, Rajwali Khan, Zhaoxiong Lei, Guijie Zhang, Jiupan Zhang, Zhuoma Luoreng, Yun Ma, Muna O. Alamoudi, Bandar Hamad Aloufi, Ahmed Mohajja Alshammari, Ayman Hassan Abd El-Aziz, Majid Alhomrani, Abdulhakeem S. Alamri
Summary: This study investigated the tissue expression patterns and functional promoter of bovine LATS1, and identified the key transcription factors in the core promoter region. It revealed the regulatory mechanisms of bovine LATS1 transcription in mediating skeletal muscle growth. Bovine LATS1 was highly expressed in the longissimus thoracis and upregulated in infancy muscle.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Changyang Linghu, Bobae An, Monika Shpokayte, Orhan T. Celiker, Nava Shmoel, Ruihan Zhang, Chi Zhang, Demian Park, Won Min Park, Steve Ramirez, Edward S. Boyden
Summary: Observing cellular physiological histories is crucial for understanding normal and disease-related processes. Researchers have developed a fully genetically encoded method called expression recording islands, which allows continuous digital recording of biological information within cells and high-throughput readout in fixed cells. This method stores information in growing intracellular protein chains and enables the reading of physiological history along the ordered subunits of protein chains using conventional optical microscopy. The researchers successfully used this method to record gene expression timecourse downstream of specific pharmacological and physiological stimuli in cultured neurons and living mouse brain, with a time resolution of a fraction of a day over periods of days to weeks.
NATURE BIOTECHNOLOGY
(2023)
Article
Plant Sciences
Zhenlu Zhang, Xiuxiu Zhao, Zhengqun Zhang, Xiaoqin Huang, Lixia Zhang, Ping Sun
Summary: Cellulose accumulation in the new shoots of tea plants negatively affects the tenderness of the leaves, especially in the secondary cell walls. The study also showed the importance of cellulose synthase enzymes in this process.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Biology
Pramila Pal, Mohd Younus Khan, Shivani Sharma, Yashwant Kumar, Nikita Mangla, Prem S. Kaushal, Nisheeth Agarwal
Summary: The transcription regulator ResR/McdR plays a crucial role in the survival and drug resilience of Mycobacterium tuberculosis. It directly regulates ribosomal gene expression and protein synthesis, contributing to bacterial proliferation and important metabolic activities. Chemical inhibitors targeting ResR/McdR may be effective as adjunctive therapy to shorten the duration of tuberculosis treatment.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Matthieu Dos Santos, Stephanie Backer, Frederic Aurade, Matthew Man-Kin Wong, Maud Wurmser, Remi Pierre, Francina Langa, Marcio Do Cruzeiro, Alain Schmitt, Jean-Paul Concordet, Athanassia Sotiropoulos, F. Jeffrey Dilworth, Daan Noordermeer, Frederic Relaix, Iori Sakakibara, Pascal Maire
Summary: The contractile properties of adult myofibers are influenced by the isoform content of their Myosin heavy chain. This study identifies a super-enhancer that interacts with fast Myosin promoters to activate the expression of adult fast Myosin genes. Deletion of this super-enhancer demonstrates its important role in controlling the associated fast Myosin genes. Disruption of the organization of fast Myosin reveals positional heterogeneity within limb skeletal muscles, which may contribute to selective muscle susceptibility in certain myopathies.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Yun-Xin Luo, Shou-Kun Chen, Peng-Dan Wang, De Peng, Xu Zhang, Hai-Feng Li, Cui-Zhu Feng
Summary: In this study, researchers identified 26 RAV genes in the wheat genome, which were classified into three classes. Among them, TaRAV1 gene was found to be expressed in multiple tissues of wheat and its expression was regulated by heat, salt, ABA, and GA. The TaRAV1 protein was localized in the nucleus and showed DNA binding and transcriptional activation activities. Overexpressing TaRAV1 enhanced salt tolerance in Arabidopsis and upregulated the expression of SOS genes and other stress response genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Yang Wu, Zheqi Li, Abdalla M. Wedn, Allison N. Casey, Daniel Brown, Shalini Rao, Soleilmane Omarjee, Jagmohan Hooda, Jason S. Carroll, Jason Gertz, Jennifer M. Atkinson, Adrian Lee, Steffi Oesterreich
Summary: Estrogen receptor alpha (ER/ESR1) mutations are common in endocrine resistant ER-positive breast cancer. Forkhead box A1 (FOXA1) plays a role in ER-chromatin interactions and endocrine response, but its role in ESR1-mutant breast cancer is unclear. This study shows that FOXA1 redistribution is associated with transcriptomic alterations caused by ESR1 mutations and suggests targeting the retinoid X receptor (RXR) pathway as a therapeutic strategy for breast tumors with ESR1 mutation.
MOLECULAR CANCER RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Kai Liu, Xiaolei Han, Zhaolin Liang, Jiadi Yan, Peihua Cong, Caixia Zhang
Summary: This study detected 48 MdHDZ genes in apples and categorized them into three subfamilies. Analysis of chromosomal locations, gene/protein structures, and physiological and biochemical properties revealed the key role of segmental duplications in the expansion of the apple HD-Zip family. MdHDZ genes may be involved in the regulation of apple growth and tolerance to environmental stresses. Additionally, this research suggests the potential involvement of apple HD-Zip genes in the response to fungal infection and adventitious bud regeneration.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Narjes Kmeli, Inchirah Bettaieb, Jihen Hamdi, Rania Mlouka, Sonia Gaaied, Khaled Chatti, Dhia Bouktila
Summary: This study extensively investigated the characteristics of the WRKY gene complement in the common fig, revealing its significant roles in plant development and fruit quality.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Biophysics
Md Zulfikar Ali, Sandeep Choubey, Dipjyoti Das, Robert C. Brewster
BIOPHYSICAL JOURNAL
(2020)
Article
Multidisciplinary Sciences
Nicholas C. Lammers, Vahe Galstyan, Armando Reimer, Sean A. Medin, Chris H. Wiggins, Hernan G. Garcia
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biology
Md Zulfikar Ali, Vinuselvi Parisutham, Sandeep Choubey, Robert C. Brewster
Review
Cell Biology
Nicholas C. Lammers, Yang Joon Kim, Jiaxi Zhao, Hernan G. Garcia
CURRENT OPINION IN CELL BIOLOGY
(2020)
Article
Biology
Augusto Berrocal, Nicholas C. Lammers, Hernan G. Garcia, Michael B. Eisen
Article
Biochemical Research Methods
Jonathan Liu, Donald Hansen, Elizabeth Eck, Yang Joon Kim, Meghan Turner, Simon Alamos, Hernan Garcia
Summary: This study presents a novel approach to study the effective parameters of the eukaryotic transcription cycle in real time and at the single-cell level, using the developing fruit fly embryo as a case study. The method allows for detailed investigations into cell-to-cell variability in transcription-cycle parameters as well as single-cell correlations between these parameters. It also reveals a substantial variability in the elongation rate of individual RNA polymerase molecules and uncovers a novel mechanistic connection between RNA polymerase density and nascent RNA cleavage efficiency.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biology
Myron Barber Child, Jack R. Bateman, Amir Jahangiri, Armando Reimer, Nicholas C. Lammers, Nica Sabouni, Diego Villamarin, Grace C. McKenzie-Smith, Justine E. Johnson, Daniel Jost, Hernan G. Garcia
Summary: Research suggests that somatic homolog pairing in fruit fly may be driven by specifically interacting 'buttons' encoded along chromosomes, and a quantitative biophysical model has been proposed to demonstrate this hypothesis.
Review
Biochemistry & Molecular Biology
Nathan M. Belliveau, Griffin Chure, Christina L. Hueschen, Hernan G. Garcia, Jane Kondev, Daniel S. Fisher, Julie A. Theriot, Rob Phillips
Summary: By analyzing Escherichia coli proteomic data, this study estimates the basic requirements and physical constraints of steady-state growth, suggesting that cells are predominantly tuned for the task of cell doubling across a continuum of growth rates. The research proposes a model of proteomic regulation as a function of nutrient supply, highlighting the theoretical inability to parallelize ribosomal synthesis as a firm limit on achievable growth rate.
Article
Cell Biology
Sunil Guharajan, Shivani Chhabra, Vinuselvi Parisutham, Robert C. Brewster
Summary: By designing synthetic target genes, the fundamental regulatory interactions of transcription factors in E. coli are isolated, revealing that the contribution of each mechanism depends on the characteristics of the transcription factors and their binding positions. Additionally, it is shown that regulatory actions may occur through different mechanisms.
Article
Biochemical Research Methods
Md Zulfikar Ali, Robert C. Brewster
Summary: Studied how gene expression timing is encoded in gene networks, and found that network size and binding affinity have significant impact on response time and accuracy of gene expression.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Plant Sciences
Eduardo Gonzalez-Grandio, Simon Alamos, Yu Zhang, Jutta Dalton-Roesler, Krishna K. Niyogi, Hernan G. Garcia, Peter H. Quail
Summary: This study identifies rapidly light-responsive genes and their relationship with chromatin modifications, suggesting that light-induced transcriptional and chromatin-remodeling processes may be mechanistically intertwined.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Vinuselvi Parisutham, Shivani Chhabra, Md Zulfikar Ali, Robert C. Brewster
Summary: Through experimental studies controlling the concentration of transcription factors, the important role of transcription factors in physiology and regulation has been revealed, aiding in the understanding of regulatory mechanisms in gene networks. The research findings demonstrate that zinc and the concentration of paralogous transcription factors can influence regulatory functions, further highlighting the complexity of transcription factor concentration regulation in gene regulation.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Article
Biology
Yang Joon Kim, Kaitlin Rhee, Jonathan Liu, Selene Jeammet, Meghan A. Turner, Stephen J. Small, Hernan G. Garcia
Summary: A challenge in quantitative biology is to predict gene expression patterns using knowledge of transcription factor patterns and binding sites on regulatory DNA. By studying transcriptional repression in early fruit fly embryos, researchers found that higher-order cooperativity between multiple molecular players is required, which cannot be determined from simpler regulatory architectures. This highlights the challenges in understanding transcriptional regulation in eukaryotes and calls for quantitative approaches to dissect their molecular nature.
Article
Biochemistry & Molecular Biology
Jiaxi Zhao, Mindy Liu Perkins, Matthew Norstad, Hernan G. Garcia
Summary: This study combines in vivo live imaging with mathematical modeling to dissect the binary cell fate dynamics of fruit fly gene ftz. They found that the autoregulatory module of ftz is indeed bistable, and the early element transiently determines the content of the binary cell fate decision. This work confirms the hypothesis that autoregulation can establish developmental fates through bistability.
Article
Plant Sciences
Simon Alamos, Armando Reimer, Krishna K. Niyogi, Hernan G. Garcia
Summary: RNA-labelling technologies were used to image RNA polymerase II activity in single cells of living tobacco and Arabidopsis plants, revealing a switch-like behavior in response to external signals. The results showed that cellular heterogeneity in transcriptional dynamics mainly originates from stochasticity in individual alleles, enabling quantitative studies of transcriptional programs in single plant cells.