Article
Plant Sciences
Hongtao Song, Qi Wang, Zhonghua Zhang, Kui Lin, Erli Pang
Summary: This study presents a computational approach to predict putative cis-regulatory elements in the Cucurbitaceae genomes. The researchers identified a large number of cis-regulatory elements using whole-genome alignment and validated their predictions using various datasets. The results provide valuable resources for functionally annotating conserved non-coding sequences and studying their regulatory roles in Cucurbitaceae genomes.
HORTICULTURE RESEARCH
(2023)
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
Plant Sciences
Julien Roziere, Cecile Guichard, Veronique Brunaud, Marie-Laure Martin, Sylvie Coursol
Summary: This study explores preferentially located motifs (PLMs) in the cis-regulatory regions of Arabidopsis thaliana and Zea mays genes using a genome-wide de novo approach. The study identifies three groups of PLMs, with a focus on conserved PLMs in both species, particularly in the 3'-gene-proximal region. Comparison with transcription factor and microRNA binding sites reveals that a significant portion of the identified PLMs are unassigned and show functional predictions that differ from known binding sites.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Kurtis Stefan, Artem Barski
Summary: Cis-regulatory elements (CRE) are essential for coordinating gene expression programs in specific cells. The STARR-Seq technique has been used to annotate functional CREs, but is mostly limited to cell lines. In this study, Lenti-STARR-Seq was successfully implemented in human CD4+ T cells, providing a genome-wide analysis of CRE function in primary cells. The study identified thousands of enhancers and negative regulatory elements (NREs) in CD4+ T cells, and revealed differences in nucleosome organization between enhancers and NREs. The findings also support the concept of silencer repurposing as enhancers in alternate cell types.
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
Genetics & Heredity
Jianfei Wu, Fan Gao, Tongtong Li, Haixia Guo, Li Zhang, Yijie Fan, Aiyun Chen, Jianjun Wang, Fengjuan Shi, Guangyao Shan, Huihui Guo, Fanchang Zeng
Summary: Auxin, a hormone, plays a crucial role in various aspects of plant development. This study proposes a method to identify genes responsive to auxin in the model plant Arabidopsis thaliana. By analyzing specific regulatory elements in gene promoters, the researchers were able to predict candidate genes with an accuracy rate of 65.2%. The results provide valuable insights into the understanding of auxin-responsive genes and improve gene annotation.
Article
Plant Sciences
Wenxiu Ye, Shota Koya, Yuki Hayashi, Huimin Jiang, Takaya Oishi, Kyohei Kato, Kohei Fukatsu, Toshinori Kinoshita
Summary: Stomatal guard cells are specialized cells that respond to stimuli such as blue light and abscisic acid for regulating stomatal aperture. Several GC-specific genes, including ALMT6, were identified to play important roles in stomatal movement, particularly in the opening process. The study highlights the significance of GC-specific genes in stomatal regulation and provides new insights into the molecular mechanisms involved.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Plant Sciences
Alexandre P. Marand, Robert J. Schmitz
Summary: Plant tissues and organs are composed of different cell types with variations in cell identity and function. Single-cell profiling has emerged as a powerful tool to study the relationship between cellular phenotypic variation and cis-regulatory mechanisms in plants.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
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
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
Genetics & Heredity
Daniel S. Kim, Viviana I. Risca, David L. Reynolds, James Chappell, Adam J. Rubin, Namyoung Jung, Laura K. H. Donohue, Vanessa Lopez-Pajares, Arwa Kathiria, Minyi Shi, Zhixin Zhao, Harsh Deep, Mahfuza Sharmin, Deepti Rao, Shin Lin, Howard Y. Chang, Michael P. Snyder, William J. Greenleaf, Anshul Kundaje, Paul A. Khavari
Summary: By analyzing multiomic data and using a deep learning framework, cooperative DNA sequence rules that regulate gene modules during epidermal differentiation were identified. The temporal dynamics and cis-regulatory logic were validated through massively parallel reporter assay analysis.
Article
Multidisciplinary Sciences
Hongchun Lin, Hui Peng, Yuxiang Sun, Meijun Si, Jiao Wu, Yanlin Wang, Sandhya S. Thomas, Zheng Sun, Zhaoyong Hu
Summary: This study presents an atlas of accessible chromatin regions in skeletal muscles and identifies cell-type-specific cis-regulatory networks. It explores the reprogramming of these networks in response to denervation and uncovers a hierarchical structure of transcription factors in atrophic muscle. The study also highlights the role of ELK4 as a key transcription factor in muscle atrophy.
NATURE COMMUNICATIONS
(2023)
Review
Plant Sciences
Alexandre P. Marand, Andrea L. Eveland, Kerstin Kaufmann, Nathan M. Springer
Summary: This article discusses the functions and identification methods of various classes of cis-regulatory elements in plant development and response to the environment. It also highlights the opportunities to exploit cis-regulatory variants for crop improvement efforts.
ANNUAL REVIEW OF PLANT BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Jaime Alvarez-Benayas, Nikolaos Trasanidis, Alexia Katsarou, Kanagaraju Ponnusamy, Aristeidis Chaidos, Philippa C. May, Xiaolin Xiao, Marco Bua, Maria Atta, Irene A. G. Roberts, Holger W. Auner, Evdoxia Hatjiharissi, Maria Papaioannou, Valentina S. Caputo, Ian M. Sudbery, Anastasios Karadimitris
Summary: Multiple myeloma is a genetically heterogeneous cancer driven by overexpression of specific oncogenes. By analyzing chromatin accessibility and transcriptome profiles, researchers have identified distinct genetic subgroups within multiple myeloma and uncovered unique gene regulatory networks that contribute to the disease. This study highlights the importance of understanding the transcriptional landscape in driving multiple myeloma progression and identifying potential therapeutic targets.
NATURE COMMUNICATIONS
(2021)
Article
Engineering, Electrical & Electronic
Charles A. Guo, Y. Jay Guo, He Zhu, Wei Ni, Jinhong Yuan
Summary: Currently, there is a growing interest in analog multibeam antennas that can steer beams in any direction. The previous paper introduced a theoretical framework for synthesizing individually steerable multiple beams using generalized joined coupler (GJC) matrices. In this article, a more robust optimization method is presented to directly optimize the multibeams and control various characteristics. The proposed method is validated through numerical examples and experimental results.
IEEE TRANSACTIONS ON ANTENNAS AND PROPAGATION
(2023)
Article
Engineering, Electrical & Electronic
Ying Ju, Haoyu Wang, Yuchao Chen, Tong-Xing Zheng, Qingqi Pei, Jinhong Yuan, Naofal Al-Dhahir
Summary: In this paper, a deep reinforcement learning-based joint beam allocation and relay selection (JoBARS) scheme is proposed to mitigate blocking effects and optimize the total transmission rate in vehicular communication networks.
IEEE TRANSACTIONS ON COMMUNICATIONS
(2023)
Article
Engineering, Electrical & Electronic
Qingya Lu, Shuangyang Li, Baoming Bai, Jinhong Yuan
Summary: In this paper, the reduced-complexity detection and code design issues in faster-than-Nyquist (FTN) signaling are jointly investigated. A scheme is proposed to increase the minimum squared Euclidean distance by employing repetition coding, at the cost of increased complexity. The concept of spatially-coupling from coding theory is adopted to reduce the rate loss, resulting in spatially-coupled faster-than-Nyquist (SC-FTN) signaling. These findings provide insights into the error-floor, decoding threshold, and complexity of detection and decoding in FTN systems.
IEEE TRANSACTIONS ON COMMUNICATIONS
(2023)
Article
Engineering, Electrical & Electronic
Tianle Liu, Jun Tong, Jinhong Yuan, Jiangtao Xi, Haiquan Wang, Lou Zhao
Summary: This paper investigates the performance of uplink massive MIMO systems with low-resolution ADCs operating over Rician fading channels. Zero-forcing group successive interference cancellation receivers are studied and the spectrum efficiency is analyzed for general power allocation under both perfect and imperfect CSI. The optimal power allocation for a given QoS is derived for the GSIC receivers. Based on random matrix theory, the asymptotic approximations of SINR for the system and the power allocation are derived. The results show that power allocation improves the overall EE and GSIC receiver yields high EE with a small number of groups. Additionally, the system EE can be improved with intermediate-resolution ADCs and ordered SIC.
IEEE TRANSACTIONS ON VEHICULAR TECHNOLOGY
(2023)
Article
Engineering, Electrical & Electronic
Zongming Yuan, Meng Tang, Jianhua Chen, Taibin Fang, Hao Wang, Jinhong Yuan
Summary: This article proposes a novel low-complexity parallel message passing (PMP) detection scheme for orthogonal time-frequency space (OTFS) modulation technology. The PMP scheme optimizes the structure of the symbol detection algorithm and significantly shortens the detection time compared to the traditional message passing (MP) scheme. A non-sparse channel coefficient matrix representation is used for parallel detection. The performance of the PMP algorithm is more prominent in continuous multi-frame data transmission.
IEEE TRANSACTIONS ON VEHICULAR TECHNOLOGY
(2023)
Article
Engineering, Electrical & Electronic
Longfei Yan, Chong Han, Nan Yang, Jinhong Yuan
Summary: In this paper, an energy-efficient dynamic-subarray with fixed phase shifters (DS-FPS) architecture is proposed for terahertz hybrid beamforming, which compensates for the spectral efficiency loss caused by the fixed phase of FPS through a switch network and designs the hybrid beamforming matrices using a row-successive-decomposition (RSD) algorithm. A row-by-row (RBR) algorithm is further proposed to reduce computational complexity. Extensive simulation results show that the proposed DS-FPS architecture with the RSD and RBR algorithms achieves higher energy efficiency and robustness to CSI error compared to existing architectures.
IEEE TRANSACTIONS ON WIRELESS COMMUNICATIONS
(2023)
Article
Engineering, Electrical & Electronic
Xingyu Zhou, Keke Ying, Zhen Gao, Yongpeng Wu, Zhenyu Xiao, Symeon Chatzinotas, Jinhong Yuan, Bjorn Ottersten
Summary: This paper investigates the integration of grant-free non-orthogonal multiple access (GF-NOMA) paradigm with orthogonal time frequency space (OTFS) modulation for low Earth orbit (LEO) satellite-based Internet of Things (IoT) to address challenges such as long round-trip latency and severe Doppler effect. The proposed two-stage successive active terminal identification and channel estimation scheme along with a low-complexity multi-user signal detection method demonstrate superior performance compared to existing solutions in terms of ATI, CE, and SD under the mentioned challenges.
IEEE TRANSACTIONS ON WIRELESS COMMUNICATIONS
(2023)
Article
Computer Science, Information Systems
Yiyan Ma, Guoyu Ma, Ning Wang, Zhangdui Zhong, Jinhong Yuan, Bo Ai
Summary: This article proposes a grant-free orthogonal time-frequency space-based tandem spreading multiple access (OTFS-TSMA) scheme for machine-type communications (mMTC) in smart railways environmental sensing. By using differential Doppler shift, the proposed scheme achieves high resource efficiency and provides service continuity and controllable multiuser interference.
IEEE INTERNET OF THINGS JOURNAL
(2023)
Article
Telecommunications
Ziwei Liu, Wen Chen, Zhendong Li, Jinhong Yuan, Qingqing Wu, Kunlun Wang
Summary: In this study, a cognitive radio network (CRN) with a transmissive reconfigurable intelligent surface (TRIS) transmitter is investigated for downlink transmission. Time-modulated arrays (TMA) and rate splitting multiple access (RSMA) are implemented for low power consumption and high-rate multi-stream communication. The joint optimization algorithm based on difference-of-convex (DC) programming and successive convex approximation (SCA) is proposed to improve and balance the energy efficiency (EE) and spectral efficiency (SE) of the network.
IEEE COMMUNICATIONS LETTERS
(2023)
Article
Telecommunications
Yihuan Liao, Min Qiu, Jinhong Yuan
Summary: This letter investigates the design of self-connected spatially coupled low-density parity-check (SC-LDPC) codes. First, a termination method is proposed to reduce rate loss. We introduce a single-side open SC-LDPC ensemble to halve the rate loss of conventional terminated SC-LDPC codes by reducing the number of check nodes. Moreover, a self-connection method is proposed to improve the decoding threshold by allowing reliable information propagation from multiple directions. The proposed codes exhibit better trade-off, threshold saturation behavior, and superior error performance compared to existing protograph SC-LDPC codes.
IEEE COMMUNICATIONS LETTERS
(2023)
Article
Engineering, Electrical & Electronic
Min Qiu, Yu-Chih Huang, Jinhong Yuan
Summary: This study investigates the design of downlink transmission schemes for supporting heterogeneous ultra-reliable low-latency communications (URLLC) and/or other types of services. The broadcast channel is considered, where the base station sends superimposed signals to multiple users. Due to heterogeneous blocklength constraints and stringent latency requirements, a practical downlink transmission scheme with discrete signaling and single-user decoding (SUD) is proposed. The proposed scheme achieves a high achievable rate under short blocklength, operating close to the benchmark schemes that assume perfect successive interference cancellation (SIC) with Gaussian signaling.
IEEE JOURNAL ON SELECTED AREAS IN COMMUNICATIONS
(2023)
Article
Engineering, Electrical & Electronic
Zijun Qin, Zesong Fei, Jingxuan Huang, Yeliang Wang, Ming Xiao, Jinhong Yuan
Summary: In this paper, we investigate the application of reinforcement learning (RL) in online fountain codes and propose two schemes to reduce the overhead of full recovery with limited feedback. The first scheme, RL-based degree determination (RL-DD), uses RL to determine the optimal degree of coded symbols based on theoretical analysis. The second scheme, online fountain codes with no build-up phase using sectioned distribution (OFCNB-SD), eliminates the build-up phase and improves the decoder to utilize non-immediately decodable coded symbols. The simulation results demonstrate that our proposed schemes achieve lower full-recovery overhead compared to existing schemes.
IEEE TRANSACTIONS ON COMMUNICATIONS
(2023)
Article
Computer Science, Information Systems
Qiang Sun, Hongwu Liu, Shen Yan, Theodoros A. Tsiftsis, Jinhong Yuan
Summary: In this letter, the joint optimization of transmit power allocation and receive/passive beamforming in a RIS-assisted uplink RSMA system is investigated. An AO algorithm is proposed to optimize the receive/passive beamforming and transmit power allocation. Simulation results demonstrate that the proposed AO algorithm achieves a higher achievable rate than existing benchmark schemes.
IEEE WIRELESS COMMUNICATIONS LETTERS
(2023)
Article
Telecommunications
Weijie Yuan, Zhiqing Wei, Jiamo Jiang, Shun Zhang, Jinhong Yuan, Pingzhi Fan
CHINA COMMUNICATIONS
(2023)
Article
Engineering, Electrical & Electronic
Boyu Ning, Zhongbao Tian, Weidong Mei, Zhi Chen, Chong Han, Shaoqian Li, Jinhong Yuan, Rui Zhang
Summary: This paper provides a review of beamforming technologies for terahertz ultra-massive multiple-input-multiple-output (UM-MIMO) systems. It presents the system model, channel parameters, and discusses the far-field and near-field assumptions in terahertz UM-MIMO. The beam training strategy in terahertz band is introduced, along with codebook design approaches. The paper also explores intelligent-reflecting-surface (IRS)-assisted joint beamforming and multi-user beamforming in terahertz UM-MIMO systems.
IEEE OPEN JOURNAL OF THE COMMUNICATIONS SOCIETY
(2023)
