Article
Biochemistry & Molecular Biology
Ari Loytynoja
Summary: This study reanalyzed genome sequence data from 25 human populations and found thousands of complex mutation clusters caused by template switching mutations in the human genome. Computational tools were developed for detecting template switching mutations, and it was discovered that commonly used analysis pipelines for short-read sequencing data cannot accurately identify these mutations.
Article
Biochemistry & Molecular Biology
Lu-Yu Zhou, Shuang Zhang, Li-Yun Li, Guo-Yu Yang, Lei Zeng
Summary: The regulation of gene expression in mammalian cells by combining various cis-regulatory features was studied using expression vectors containing different combinations of regulatory elements. The results showed that protein expression can be regulated by optimizing the combination of cis-acting elements. Additionally, it was found that not all combinations of multiple regulatory elements exhibit synergistic effects to enhance expression further.
MOLECULAR GENETICS AND GENOMICS
(2023)
Article
Biotechnology & Applied Microbiology
Georg Back, Dirk Walther
Summary: This study identified a set of novel sequence motifs located in the first introns of genes in the plant Arabidopsis thaliana that may play a role in inducing high and correlated gene expression of the genes harboring them. The study confirmed the regulatory role of first introns on gene expression and characterized their conservation within the species, using deep sequencing and broad gene expression information on a genome-wide scale.
Article
Multidisciplinary Sciences
Wenlin Xu, Haoran Qi, Tengfei Shen, Meiqi Zhao, Zihe Song, Na Ran, Jiali Wang, Mengli Xi, Meng Xu
Summary: Poplar coma, also known as seed hairs, is a cluster of trichomes attached to the seed coat that aids in seed dispersal. However, it can also cause health issues for humans, such as sneezing, difficulty breathing, and skin irritation. Despite efforts to understand the regulatory mechanism of herbaceous trichome formation, the development of poplar coma is still poorly understood. In this study, we investigated the origin of poplar coma and constructed a miRNA regulatory network, providing insights into its molecular mechanisms.
Article
Biotechnology & Applied Microbiology
Yongil Yang, Jun Hyung Lee, Magen R. Poindexter, Yuanhua Shao, Wusheng Liu, Scott C. Lenaghan, Amir H. Ahkami, Eduardo Blumwald, Charles Neal Stewart
Summary: Researchers identified five synthetic promoters in hybrid poplar that showed better inducibility under abiotic stress conditions compared to native promoters, demonstrating the potential of synthetic biology in producing transgenic plants with improved stress resistance traits.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Biology
Carly Weiss, Lana Harshman, Fumitaka Inoue, Hunter B. Fraser, Dmitri A. Petrov, Nadav Ahituv, David Gokhman
Summary: The study utilized massively parallel reporter assays to investigate the regulatory effects of modern human-specific variants, revealing that a portion of these variants drove differential gene expression between human populations, particularly in genes related to vocal tract and brain anatomy and function.
Article
Biochemistry & Molecular Biology
Mohannad Dardiry, Gabi W. Eberhard, Hanh J. Witte, Christian Roedelsperger, James Lightfoot, Ralf Sommer
Summary: This study reveals the genetic mechanism underlying the phenotypic plasticity in the predatory nematode Pristionchus pacificus. It identifies a core developmental gene and a QTL that control the expression of cannibalistic morph, which is composed of several cis-regulatory elements. The comparisons of other predatory nematodes further support the rapid evolution of these cis-regulatory elements, demonstrating their important roles in plastic trait expression and control of nematode cannibalism.
Article
Plant Sciences
Weijie Xu, Yue Wang, Jianbo Xie, Shuxian Tan, Haofei Wang, Yiyang Zhao, Qing Liu, Yousry A. El-Kassaby, Deqiang Zhang
Summary: Soil salinity affects crop productivity and triggers salt stress in plants. This study found that the growth-regulating factor 15 (PagGRF15) and its target gene high-affinity K+ transporter 6 (PagHAK6) play important roles in the salt stress response. Overexpression of PagGRF15 and PagHAK6 improved salt tolerance in poplar by enhancing Na+ transport and regulating H2O2 accumulation.
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)
Review
Developmental Biology
Jihyun Irizarry, Angelike Stathopoulos
Summary: Morphogen concentrations in space and time during development are important for specifying cell fate. Bicoid and Dorsal are two morphogens that directly regulate target genes in Drosophila embryos, providing insights into how morphogens interact and change roles over time. In addition to these factors, there are other inputs working together to control spatiotemporal gene expression in embryos.
Article
Cell Biology
Ulrich Dobramysl, Iris Katharina Jarsch, Yoshiko Inoue, Hanae Shimo, Benjamin Richier, Jonathan R. Gadsby, Julia Mason, Pantelis Savvas Ioannou, Guilherme Pereira Correia, Astrid Walrant, Richard Butler, Edouard Hannezo, Benjamin D. Simons, Jennifer L. Gallop
Summary: Research has shown that the composition of the regulatory protein complex in the filopodial tip is heterogeneous, with the presence of functional subcomplexes. This supports a theoretical framework where multiple subcomplexes can randomly join to drive filopodia formation.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Plant Sciences
Maria A. Lujan, Angel Soria-Garcia, Ana Claver, Patricia Lorente, Maria C. Rubio, Rafael Picorel, Miguel Alfonso
Summary: Trienoic fatty acids are crucial for biomembranes and plant defense responses. AtFAD7 and AtFAD8 are essential enzymes for synthesizing trienoic fatty acids in the plastid.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Xiaowei Wu, Yan Liang, Hengbin Gao, Jiyao Wang, Yan Zhao, Lekai Hua, Yundong Yuan, Ahong Wang, Xiaohui Zhang, Jiafan Liu, Jie Zhou, Xiangbing Meng, Dahan Zhang, Shaoyang Lin, Xuehui Huang, Bin Han, Jiayang Li, Yonghong Wang
Summary: The study identified a previously unrecognized regulatory gene OsREM20 that controls grain number per panicle (GNP) in rice, and revealed that genetic variation in the IR sequence of the OsREM20 promoter affects its expression level and contributes to GNP variation among rice varieties. The findings suggest a promising strategy for improving rice production by manipulating the cis-regulatory element-containing IR sequence in the OsREM20 promoter.
Article
Genetics & Heredity
Damir Baranasic, Matthias Hortenhuber, Piotr J. Balwierz, Tobias Zehnder, Abdul Kadir Mukarram, Chirag Nepal, Csilla Varnai, Yavor Hadzhiev, Ada Jimenez-Gonzalez, Nan Li, Joseph Wragg, Fabio M. D'Orazio, Dorde Relic, Mikhail Pachkov, Noelia Diaz, Benjamin Hernandez-Rodriguez, Zelin Chen, Marcus Stoiber, Michael Dong, Irene Stevens, Samuel E. Ross, Anne Eagle, Ryan Martin, Oluwapelumi Obasaju, Sepand Rastegar, Alison C. McGarvey, Wolfgang Kopp, Emily Chambers, Dennis Wang, Hyejeong R. Kim, Rafael D. Acemel, Silvia Naranjo, Maciej Lapinski, Vanessa Chong, Sinnakaruppan Mathavan, Bernard Peers, Tatjana Sauka-Spengler, Martin Vingron, Piero Carninci, Uwe Ohler, Scott Allen Lacadie, Shawn M. Burgess, Cecilia Winata, Freek van Eeden, Juan M. Vaquerizas, Jose Luis Gomez-Skarmeta, Daria Onichtchouk, Ben James Brown, Ozren Bogdanovic, Erik van Nimwegen, Monte Westerfield, Fiona C. Wardle, Carsten O. Daub, Boris Lenhard, Ferenc Muller
Summary: Zebrafish, an important model organism for studying embryonic development and human diseases, lacks a systematic functional annotation program. The international DANIO-CODE consortium addressed this issue by creating a central repository to store and process zebrafish developmental functional genomic data. They improved existing annotations and identified over 140,000 cis-regulatory elements throughout development. They also compared regulatory elements and epigenomic landscapes between zebrafish and mouse, predicting functional relationships between them. This study extends the utility of zebrafish developmental genomics to mammals.
Article
Biochemistry & Molecular Biology
Peng Zhou, Tara A. Enders, Zachary A. Myers, Erika Magnusson, Peter A. Crisp, Jaclyn M. Noshay, Fabio Gomez-Cano, Zhikai Liang, Erich Grotewold, Kathleen Greenham, Nathan M. Springer
Summary: Changes in gene expression are crucial for responses to abiotic stress. Transcriptome profiling of heat- or cold-stressed maize genotypes reveals many alterations in transcript abundance. By analyzing expression responses in multiple genotypes and identifying cis- or trans-regulatory variation, predictive models of gene expression responses for thermal stress-responsive genes can be developed. Models focusing on unmethylated regions near the transcription start sites (TSSs) show improved accuracy, suggesting that different genes may have varying response dynamics to stress.
Article
Biochemistry & Molecular Biology
Jun Ding, Chieh Lin, Ziv Bar-Joseph
NUCLEIC ACIDS RESEARCH
(2019)
Article
Cell Biology
Honghai Liu, Cheng-Hai Zhang, Niyatie Ammanamanchi, Sangita Suresh, Christopher Lewarchik, Krithika Rao, Gerrida M. Uys, Lu Han, Maryline Abrial, Dean Yimlamai, Balakrishnan Ganapathy, Christelle Guillermier, Nathalie Chen, Mugdha Khaladkar, Jennifer Spaethling, James H. Eberwine, Junhyong Kim, Stuart Walsh, Sangita Choudhury, Kathryn Little, Kimberly Francis, Mahesh Sharma, Melita Viegas, Abha Bais, Dennis Kostka, Jun Ding, Ziv Bar-Joseph, Yijen Wu, Vijay Yechoor, Mousumi Moulik, Jennifer Johnson, Jacqueline Weinberg, Miguel Reyes-Mugica, Matthew L. Steinhauser, Bernhard Kuhn
SCIENCE TRANSLATIONAL MEDICINE
(2019)
Article
Cell & Tissue Engineering
Killian Hurley, Jun Ding, Carlos Villacorta-Martin, Michael J. Herriges, Anjali Jacob, Marall Vedaie, Konstantinos D. Alysandratos, Yuliang L. Sun, Chieh Lin, Rhiannon B. Werder, Jessie Huang, Andrew A. Wilson, Aditya Mithal, Gustavo Mostoslavsky, Irene Oglesby, Ignacio S. Caballero, Susan H. Guttentag, Farida Ahangari, Naftali Kaminski, Alejo Rodriguez-Fraticelli, Fernando Camargo, Ziv Bar-Joseph, Darrell N. Kotton
Article
Biochemical Research Methods
Chieh Lin, Jun Ding, Ziv Bar-Joseph
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Biochemical Research Methods
Dongshunyi Li, Jun Ding, Ziv Bar-Joseph
Summary: The study presents a method called MESSI that accurately predicts active signaling genes within and between cells, and divides them into different subtypes. By utilizing information from neighboring cells through multi-task learning, the prediction of response genes within cells is improved.
Article
Biochemistry & Molecular Biology
Necola Guerrina, Hussein Traboulsi, Angela Rico de Souza, Yohan Bosse, Thomas H. Thatcher, Annette Robichaud, Jun Ding, Pei Z. Li, Leora Simon, Swati Pareek, Jean Bourbeau, Wan C. Tan, Andrea Benedetti, Ma'en Obeidat, Don D. Sin, Corry-Anke Brandsma, David C. Nickle, Patricia J. Sime, Richard P. Phipps, Parameswaran Nair, Michela Zago, Qutayba Hamid, Benjamin M. Smith, David H. Eidelman, Carolyn J. Baglole
Summary: Emphysema, a component of COPD, is characterized by irreversible alveolar destruction caused by cigarette smoke. The aryl hydrocarbon receptor (AHR) is proposed as a new susceptibility factor in COPD pathogenesis. Research shows that Ahr-deficient mice exposed to cigarette smoke develop airspace enlargement and decreased lung function, while COPD patients exhibit reduced expression of pulmonary and systemic AHR, with systemic AHR levels correlating with lung function.
Article
Biochemical Research Methods
Jun Ding, David Earl Hostallero, Mohamed Reda El Khili, Gregory Joseph Fonseca, Simon Milette, Nuzha Noorah, Myriam Guay-Belzile, Jonathan Spicer, Noriko Daneshtalab, Martin Sirois, Karine Tremblay, Amin Emad, Simon Rousseau
Summary: Through computational analysis, the study suggests that the release of Neutrophils Extracellular Traps (NETs) may contribute to the severe coagulation problems in COVID-19, and identifies potential factors that increase the risk of severe complications in COVID-19.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Cell Biology
Noof Aloufi, Zahraa Haidar, Jun Ding, Parameswaran Nair, Andrea Benedetti, David H. Eidelman, Imed-Eddine Gallouzi, Sergio Di Marco, Sabah N. Hussain, Carolyn J. Baglole
Summary: Patients with COPD may face a higher risk of severe COVID-19 due to upregulation of ACE2. Our study found a significant positive correlation between HuR and ACE2 in COPD cells, but knocking out HuR did not change ACE2 protein levels. Further investigation is needed to understand the regulatory mechanisms of ACE2 expression.
Article
Multidisciplinary Sciences
Euxhen Hasanaj, Jingtao Wang, Arjun Sarathi, Jun Ding, Ziv Bar-Joseph
Summary: Cell type assignment is a major challenge in high throughput single cell data analysis. To address this issue, researchers have developed Cellar, a software tool that provides interactive support for cell type assignment and dataset comparison.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Dongshunyi Li, Jun Ding, Ziv Bar-Joseph
Summary: UNIFAN is a neural network method that simultaneously clusters and annotates cells using known gene sets, improving the cell type classification of single-cell RNA sequencing data. By leveraging knowledge about gene sets, UNIFAN provides strong evidence for annotations of the clustering results.
Review
Biochemical Research Methods
Jun Ding, Amir Alavi, Mo R. Ebrahimkhani, Ziv Bar-Joseph
Summary: This review focuses on computational approaches for analyzing single-cell omics and imaging data to address challenges in the development, validation, and usage of cells obtained from pluripotent cell differentiation.
CELL REPORTS METHODS
(2021)
Article
Biochemistry & Molecular Biology
Jun Ding, Ziv Bar-Joseph
CURRENT OPINION IN SYSTEMS BIOLOGY
(2020)
Article
Medicine, Research & Experimental
John E. McDonough, Farida Ahangari, Qin Li, Siddhartha Jain, Stijn E. Verleden, Jose Herazo-Maya, Milica Vukmirovic, Giuseppe DeIuliis, Argyrios Tzouvelekis, Naoya Tanabe, Fanny Chu, Xiting Yan, Johny Verschakelen, Robert J. Homer, Dimitris Manatakis, Junke Zhang, Jun Ding, Karen Maes, Laurens De Sadeleer, Robin Vos, Arne Neyrinck, Panayiotis Benos, Ziv Bar-Joseph, Dean Tantin, James C. Hogg, Bart M. Vanaudenaerde, Wim A. Wuyts, Naftali Kaminski
Meeting Abstract
Critical Care Medicine
K. J. Hurley, A. Jacob, J. Ding, C. Lin, F. J. Hawkins, C. Villacorta-Martin, Z. Bar-Joseph, D. N. Kotton
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2019)
Article
Physiology
Noof Aloufi, Hussein Traboulsi, Jun Ding, Gregory J. Fonseca, Parameswaran Nair, Steven K. Huang, Sabah N. A. Hussain, David H. Eidelman, Carolyn J. Baglole
Summary: This study found that lung fibroblasts derived from idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD) express higher levels of ACE2, which may make these patients more susceptible to SARS-CoV-2 infection. This discovery could help further understand the mechanisms of COVID-19 complications.
AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY
(2021)