Review
Biochemistry & Molecular Biology
Seungsoo Kim, Joanna Wysocka
Summary: Uncovering the cis-regulatory code that governs gene transcription in a given genome and cellular state remains a central goal of biology. This review discusses the different layers of regulation that influence transcriptional outputs, including the binding of transcription factors to specific DNA sequences, the role of cofactors in facilitating their function, and the complex interplay within regulatory landscapes. The authors propose that a quantitative, mechanistically informed model of transcriptional regulation is essential for ultimately understanding the cis-regulatory code.
Article
Cell Biology
Yiqun Zhang, Fengju Chen, Erin Pleasance, Laura Williamson, Cameron J. Grisdale, Emma Titmuss, Janessa Laskin, Steven J. M. Jones, Isidro Cortes-Ciriano, Marco A. Marra, Chad J. Creighton
Summary: The study found that somatic structural variants (SVs) have an impact on gene regulation in advanced tumors, leading to altered expression of hundreds of genes near SV breakpoints. Some of these SV-expression associations are correlated with patient survival rates, while a high overall SV burden is associated with treatment using specific drugs.
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
Genetics & Heredity
Steven K. Reilly, Sager J. Gosai, Alan Gutierrez, Ava Mackay-Smith, Jacob C. Ulirsch, Masahiro Kanai, Kousuke Mouri, Daniel Berenzy, Susan Kales, Gina M. Butler, Adrianne Gladden-Young, Redwan M. Bhuiyan, Michael L. Stitzel, Hilary K. Finucane, Pardis C. Sabeti, Ryan Tewhey
Summary: HCR-FlowFISH is a new approach for characterizing CRISPR-perturbed cis-regulatory elements (CREs) by accurately quantifying native transcripts and using CASA for analysis. The study found that CREs can regulate multiple genes and exhibit activating and/or silencing effects. At the FADS locus, endogenous screens combined with reporter assays successfully identified target genes for multiple genome-wide association signals.
Review
Biochemical Research Methods
Meng Zhang, Cangzhi Jia, Fuyi Li, Chen Li, Yan Zhu, Tatsuya Akutsu, Geoffrey Webb, Quan Zou, Lachlan J. M. Coin, Jiangning Song
Summary: This study provides benchmark datasets for promoter prediction in 58 different species, and finds that deep learning and traditional machine learning-based approaches generally outperform scoring function-based approaches.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Genetics & Heredity
Debajyoti Chowdhury, Chao Wang, Aiping Lu, Hailong Zhu
Summary: The gene transcription process is random and influences temporal fluctuations in mRNA and protein abundance through generating distinct transcriptional variations known as noise. Promoter architecture and remote interference of regulatory elements are crucial determinants of noise, which is reflected in phenotypic heterogeneity.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Wei Su, Meng-Lu Liu, Yu-He Yang, Jia-Shu Wang, Shi-Hao Li, Hao Lv, Fu-Ying Dao, Hui Yang, Hao Lin
Summary: This study established a Prokaryotic Promoter Database (PPD) which manually extracted 129,148 experimentally validated promoters across 63 prokaryotic species from published papers, providing users with a user-friendly interface for browsing, searching, visualizing, submitting, and downloading data.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biology
Luca Livraghi, Joseph J. Hanly, Steven M. Van Bellghem, Gabriela Montejo-Kovacevich, Eva S. M. van Der Heijden, Ling Sheng Loh, Anna Ren, Ian A. Warren, James J. Lewis, Carolina Concha, Laura Hebberecht, Charlotte J. Wright, Jonah M. Walker, Jessica Foley, Zachary H. Goldberg, Henry Arenas-Castro, Camilo Salazar, Michael W. Perry, Riccardo Papa, Arnaud Martin, W. Owen McMillan, Chris D. Jiggins
Summary: In Heliconius butterflies, wing color pattern diversity and scale types are controlled by a few genes of large effect, which regulate color pattern switches between morphs and species. The gene cortex is identified as a major determinant of scale cell identity through CRISPR knockouts in multiple Heliconius species. Chromatin accessibility profiling and introgression scans reveal cis-regulatory regions associated with discrete phenotypic switches.
Article
Multidisciplinary Sciences
Huaxing Huang, Jiafeng Liu, Mingsen Li, Huizhen Guo, Jin Zhu, Liqiong Zhu, Siqi Wu, Kunlun Mo, Ying Huang, Jieying Tan, Chaoqun Chen, Bofeng Wang, Yankun Yu, Li Wang, Yizhi Liu, Hong Ouyang
Summary: This study investigates the regulatory network involved in the acquisition of cell fate, focusing on the induction of surface epithelium from human embryonic stem cells. By analyzing changes in morphology-related genes and the remodeling of the cytoskeleton, the study identifies grainyhead-like 3 (GRHL3) as an initiation factor that drives the commitment to surface epithelium fate. Furthermore, the study uncovers a positive feedback loop between GRHL3 and bone morphogenetic protein 4 in regulating surface epithelium fate decisions.
Article
Multidisciplinary Sciences
I. Cody MacDonald, Travis R. Seamons, Jonathan C. Emmons, Shwan B. Javdan, Tara L. Deans
Summary: Expansion of genetic toolkits for prokaryotic synthetic biology can enhance gene expression dynamics. Integrating the eukaryotic transcription factor QF into E. coli allows for the construction of genetic devices with complex functions.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Zhan Qi, Christophe Jung, Peter Bandilla, Claudia Ludwig, Mark Heron, Anja Sophie Kiesel, Mariam Museridze, Julia Philippou-Massier, Miroslav Nikolov, Alessio Renna Max Schnepf, Ulrich Unnerstall, Stefano Ceolin, Bettina Muhlig, Nicolas Gompel, Johannes Soeding, Ulrike Gaul
Summary: Through a comprehensive structure-function analysis, it was found that the activity of the core promoter is influenced by different types of mutations, including knockout of individual sequence motifs and motif combinations, variations of motif strength, nucleosome positioning, and flanking sequences. A linear combination of the individual motif features largely explains the combinatorial effects on core promoter activity.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Article
Genetics & Heredity
Clara Poupault, Diane Choi, Khanh Lam-Kamath, Deepshe Dewett, Ansa Razzaq, Joseph Bunker, Alexis Perry, Irene Cho, Jens Rister
Summary: This study investigates the regulation of color-sensing Rhodopsin proteins in Drosophila photoreceptors, suggesting that both distal and proximal core promoter regions play a role in generating unique expression patterns. The proximal core promoter regions are not only involved in general activation but also contribute to generating non-overlapping expression patterns. Combinatorial cis-regulatory motifs in both promoter regions recruit transcription factors to generate the distinct rhodopsin patterns.
Article
Biotechnology & Applied Microbiology
Colin K. W. Lim, Tristan X. McCallister, Christian Saporito-Magrina, Garrett D. McPheron, Ramya Krishnan, M. Alejandra Zeballos, Jackson E. Powell, Lindsay Clark, Pablo Perez-Pinera, Thomas Gaj
Summary: The study demonstrates the broad application potential of CRISPR base editing technology in modulating gene expression through editing non-coding regulatory elements. It shows the specific effectiveness of base editors in perturbing gene expression.
Article
Biotechnology & Applied Microbiology
Xiao Liu, Yuqiao Xu, Yachuan Luo, Li Teng
Summary: This study utilized transfer learning in deep neural networks to improve the promoter prediction performance by reducing the dependence on large amounts of data. The experimental results demonstrated a significant increase in the prediction accuracy of ResNet after transfer learning, indicating the effectiveness of this approach.
BIOPROCESS AND BIOSYSTEMS ENGINEERING
(2022)
Article
Multidisciplinary Sciences
Pallavi Singh, Sean R. Stevenson, Patrick J. Dickinson, Ivan Reyna-Llorens, Anoop Tripathi, Gregory Reeves, Tina B. Schreier, Julian M. Hibberd
Summary: C4 photosynthesis has evolved by repurposing enzymes found in C3 plants. Compared with the ancestral C3 state, accumulation of C4 cycle proteins is enhanced. The coordination of C4 gene expression and chloroplast biogenesis in Gynandropsis gynandra supports the rapid increase in transcripts of C4 genes, which are more strongly induced than orthologs from Arabidopsis thaliana. The binding of transcription factors and light-responsive elements further contributes to the high expression of C4 genes.
Article
Chemistry, Multidisciplinary
Lijing Zhu, Teng Yang, Yunlei Zhong, Zhitong Jin, Xingxing Zhang, Cheng Hu, Ziqiang Wang, Zhenghan Wu, Zhidong Zhang, Zhiwen Shi, Jing Kong, Xu Zhang, Lin Zhou
Summary: This study presents a general damage-free transfer method for sensitive 2D materials, along with a TEM sample preparation technique for recycling materials on TEM grids with high fidelity.
Article
Polymer Science
Zi-Qiang Wang, Yue-Fei Zhang, Yan Li, Jin-Rong Zhong
Summary: A novel composite filler SL/CaCO3 prepared by dry ball milling exhibited improved thermal properties and nucleation ability for isotactic polypropylene, resulting in enhanced mechanical properties.
Article
Engineering, Electrical & Electronic
Haosen Yang, Xin Shi, Robert C. Qiu, Xing He, Qian Ai, Ziqiang Wang
Summary: The increasing integration of renewable energy sources in power grids has created uncertainties that challenge traditional deterministic approaches for voltage stability assessment. This paper proposes a high-dimensional spatial-temporal matrix factorization approach to separate the deterministic part and uncertain elements caused by renewable energy sources, and presents a probabilistic index for online evaluation of voltage stability. The proposed method uses an adaptive and analytical model to describe the eigenvalue distribution of random components, and has been proven effective in various scenarios.
IEEE TRANSACTIONS ON SMART GRID
(2022)
Article
Materials Science, Multidisciplinary
Ziqiang Wang, Miaosen Yu, Chen Yang, Xuehao Long, Ning Gao, Zhongwen Yao, Limin Dong, Xuelin Wang
Summary: This study investigated the influence of radiation defects on the thermo-mechanical properties of UO2 using molecular dynamics method, finding that Frenkel pairs and antisite defects lead to reduced thermal expansion coefficient and linear decrease in elastic modulus at finite temperatures.
Article
Materials Science, Multidisciplinary
Ziqiang Wang, Miaosen Yu, Xuehao Long, Chen Yang, Ning Gao, Zhongwen Yao, Xuelin Wang
Summary: In this study, molecular dynamics simulations were used to investigate the interaction mechanisms between dislocations and radiation defects in irradiated metals. Three new kinetic mechanisms were proposed, and it was found that the specific characteristics of the dislocation loops determine the dominant mechanism for the interaction with dislocation lines. The results also showed that the critical stress for the dislocation to cross the loop varied due to the interactions involved in these new mechanisms.
RESULTS IN PHYSICS
(2022)
Article
Engineering, Electrical & Electronic
Haosen Yang, Xing He, Ziqiang Wang, Robert C. Qiu, Qian Ai
Summary: This paper proposes a blind FDIA approach against the state estimation of power grids based on matrix reconstruction and subspace estimation. It overcomes the shortcoming of previous methods in handling measurement noise with limited data. The proposed method demonstrates high successful rate of FDIA and great robustness to large-scale power grids and high-level measurement noise.
IEEE TRANSACTIONS ON SMART GRID
(2022)
Article
Engineering, Electrical & Electronic
Ziqiang Wang, Meiling Ma, Quan Zhou, Linyun Xiong, Lingling Wang, Jinming Wang, Jie Wang
Summary: This paper proposes a novel integrated privacy-preserving distributed fixed-time secondary control method for islanded AC microgrids, which achieves privacy protection through state decomposition and the use of additional virtual proportional coefficients. Real-time simulations validate the effectiveness and advantages of the proposed method.
IEEE TRANSACTIONS ON SMART GRID
(2022)
Article
Materials Science, Multidisciplinary
Wenxue Ma, Yibin Dong, Miaosen Yu, Ziqiang Wang, Yong Liu, Ning Gao, Limin Dong, Xuelin Wang
Summary: This study investigates the evolution of atomic structures and related changes in energy state, atomic displacement, and free volume of symmetrical grain boundaries in body-centered cubic iron under external strain using molecular dynamics method. The results show that complete MD relaxations at high temperatures are necessary to obtain lower energy states of grain boundaries. Under external strain, two mechanisms for the failure of these grain boundaries are explored, including slip system activation, dislocation nucleation, and dislocation network formation induced by the external strain field or phase transformation from bcc to fcc structure under the effects of external strain.
Article
Materials Science, Multidisciplinary
Miaosen Yu, Ziqiang Wang, Fei Wang, Wahyu Setyawan, Xuehao Long, Yong Liu, Limin Dong, Ning Gao, Fei Gao, Xuelin Wang
Summary: The segregation behavior of Cr and Al atoms to a prismatic dislocation loop in a Fe-Cr-Al alloy is investigated using molecular dynamics method and ab initio energy calculation. The results show that Cr can segregate to the loops, while Al atoms cannot segregate by themselves. However, the presence of segregated Cr atoms can promote Al segregation, resulting in a coupled segregation of Cr and Al. Furthermore, the pinning behavior of the dislocation loop to an edge dislocation motion can be affected by Al segregation through the coupled segregation process.
Article
Engineering, Electrical & Electronic
Haosen Yang, Xing He, Ziqiang Wang, Fan Yang, Robert C. Qiu
Summary: This paper proposes a data-driven approach to estimate the power flow Jacobian matrix online with limited data collected by PMU. By analyzing the cross-variance matrix and using random matrix theory, uncertainties are quantified and mitigated. Experimental results show that the proposed method can obtain more accurate estimation results and provide additional information for power system monitoring.
INTERNATIONAL JOURNAL OF ELECTRICAL POWER & ENERGY SYSTEMS
(2023)
Article
Chemistry, Organic
Ziqiang Wang, Chenyang Chang, Yasu Chen, Xinxin Wu, Jie Li, Chen Zhu
Summary: We describe a novel reaction mode involving functional group migration, which is utilized for the radical-mediated remote desaturation of hexenenitriles. The reaction proceeds through consecutive alkene sulfonylation, intramolecular cyano migration, and single-electron oxidation of benzyl radical to cation followed by deprotonation, resulting in various densely functionalized alkenes. The protocol offers mild photocatalytic conditions, broad functional group tolerance, and high product diversity.
Article
Chemistry, Multidisciplinary
Zepeng Liu, Ziqiang Wang, Yu Meng, Yongchang Song, Linfan Li, Ming Yu, Jingye Li
Summary: In this study, a new method utilizing electron beam irradiation to immobilize zinc-imidazolate MOF (ZIF-8) onto cotton fabric was reported, resulting in antimicrobial textiles with excellent durability.
Letter
Engineering, Electrical & Electronic
Jiawei Wang, Hao Xu, Ziqiang Wang, Haikun Jia, Hanjun Jiang, Chun Zhang, Zhihua Wang
Summary: This article introduces a 4-level Pulse Amplitude Modulation (PAM-4) Feed Forward Equaliser (FFE) with a novel Internal Node Charge Controlled 1-Unit Interval Pulse Generator (INCC 1UIPG). Partially segmented architecture and tailless 1-stage front end are used to reduce load capacitance for better bandwidth and power performance. The proposed INCC 1UIPG adopts a stacking-reduced structure and precise control of internal nodes, demonstrating advantages in speed, power, and jitter, showing better potential for working at ultra-high baud rates. The wider bandwidth and faster transition edge enable the equalizer to operate at 128Gbps with an area of 0.014 mm2 in 65 nm CMOS.
IET CIRCUITS DEVICES & SYSTEMS
(2023)
Article
Chemistry, Multidisciplinary
Wei Liu, Ziqiang Wang, Tayyab Gulzar, Xiaodong Zhang, Guoping Ding, Peng Xu, Biao Yu
Summary: We have revealed that EPP glycosides can be utilized as glycosylation donors through an unprecedented activation mechanism. We further report that EPP glycosides without the 3,5-dimethyl groups, previously installed to prevent side reactions, can also undergo effective glycosylation. By employing an EPP 2-azidoglucoside as a donor, we have successfully constructed the challenging alpha-GlcN-(1 -> 4)-GlcA linkage, leading to a heparin tri-saccharides precursor.
PURE AND APPLIED CHEMISTRY
(2023)
Article
Chemistry, Physical
Juntian Qu, Qiangjing Yuan, Zhenkun Li, Ziqiang Wang, Feng Xu, Qigao Fan, Min Zhang, Xiang Qian, Xueqian Wang, Xiaohao Wang, Minyi Xu
Summary: In this work, an environment-friendly high-performance ionic hydrogel with fracture toughness capable of strain and triboelectric sensing is developed. The developed strain-triboelectric sensors have demonstrated great potentials in enhancing the actively perceiving capabilities during underwater soft robotic grasping.
