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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
Francesco Nicola Carelli, Chiara Cerrato, Yan Dong, Alex Appert, Abby Dernburg, Julie Ahringer
Summary: The movement of selfish DNA elements can lead to widespread genomic alterations and rewiring of germline transcriptional regulation. This study found that transposon expansions in Caenorhabditis nematodes led to the acquisition of germline-specific promoters from miniature inverted repeat transposable elements (TEs). These promoters are regulated by a transcription factor related to a transposase. Comparative analyses revealed evolutionary conservation and species-specificity of the co-opted promoters.
Article
Biochemistry & Molecular Biology
Anushua Biswas, Leelavati Narlikar
Summary: cisDIVERSITY is a new statistical framework that analyzes various gene regulation activities by modeling regions as diverse modules characterized by combinations of motifs while simultaneously learning the motifs themselves.
Review
Biochemical Research Methods
Shuangquan Zhang, Anjun Ma, Jing Zhao, Dong Xu, Qin Ma, Yan Wang
Summary: Identifying cis-regulatory motifs from genomic sequencing data is crucial for understanding gene regulatory mechanisms. Deep learning methods have been widely used for this purpose, but a systematic evaluation is lacking. In this study, 20 deep learning methods were assessed using different datasets, revealing their high complementarity and the need to choose the most suitable method based on data characteristics and desired outputs.
BRIEFINGS IN BIOINFORMATICS
(2022)
Editorial Material
Genetics & Heredity
Emily R. Miraldi, Xiaoting Chen, Matthew T. Weirauch
Summary: A new study introduces a novel deep-learning approach to decode the syntax of transcription-factor binding from high-resolution ChIP-nexus data. In silico simulations confirmed complex sequence-based predictions, including helical periodicity and directional cooperativity between transcription factors.
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
Cell Biology
Lauren Winkler, Maria Jimenez, Joshua T. Zimmer, Adam Williams, Matthew D. Simon, Nadya Dimitrova
Summary: The study shows that the full transcription, splicing, and accumulation of lincRNA-p21 are not crucial for gene regulation, but the production of lincRNA-p21 through specific exon regions can promote cis-activation of the gene.
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
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.
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.
Review
Biochemistry & Molecular Biology
Robert J. Schmitz, Erich Grotewold, Maike Stam
Summary: This review discusses the characteristics, identification technologies, and role of cis-regulatory sequences in plant biology. Despite advances in sequence assembly and genome annotation, there are still challenges in identifying and understanding cis-regulatory modules.
Article
Multidisciplinary Sciences
Zheng Wei, Kui Hua, Lei Wei, Shining Ma, Rui Jiang, Xuegong Zhang, Yanda Li, Wing H. Wong, Xiaowo Wang
Summary: Discovering DNA regulatory sequence motifs and their relative positions is crucial for understanding gene expression regulation. However, it has been challenging to discover motifs and their combinations from deep convolutional neural networks (CNNs) due to multifaceted neurons. This paper proposes the NeuronMotif algorithm to interpret CNs and successfully uncovers sequence motifs and their combination patterns. NeuronMotif enhances the utility of CNN in genome interpretation by enabling the deciphering of cis-regulatory codes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
Dania Machlab, Lukas Burger, Charlotte Soneson, Filippo M. Rijli, Dirk Schuebeler, Michael B. Stadler
Summary: Proteins binding to specific nucleotide sequences, such as transcription factors, have significant roles in regulating gene expression. The monaLisa package, an R/Bioconductor package, provides methods to identify relevant transcription factors from experimental data. It allows seamless motif analyses without relying on software outside of R.
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)
Review
Biochemistry & Molecular Biology
Stephen P. Long, Amy Marshall-Colon, Xin-Guang Zhu
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Plant Sciences
Saber Hamdani, Mingnan Qu, Chang-Peng Xin, Ming Li, Chengcai Chu, Govindjee, Xin-Guang Zhu
JOURNAL OF PLANT PHYSIOLOGY
(2015)
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Agronomy
Qingfeng Song, Han Xiao, Xianglin Xiao, Xin-Guang Zhu
AGRICULTURAL AND FOREST METEOROLOGY
(2016)
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Agronomy
Xiurong Jiao, Kirsten Korup, Mathias Neumann Andersen, Erik J. Sacks, Xin-Guang Zhu, Poul Erik Laerke, Uffe Jorgensen
GLOBAL CHANGE BIOLOGY BIOENERGY
(2017)
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Plant Sciences
Shuyue Wang, Danny Tholen, Xin-Guang Zhu
PLANT CELL AND ENVIRONMENT
(2017)
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Biochemistry & Molecular Biology
Yimin Tao, Ming-Ju Amy Lyu, Xin-Guang Zhu
PLANT MOLECULAR BIOLOGY
(2016)
Article
Multidisciplinary Sciences
Xin Wang, Wei Liu, Changpeng Xin, Yi Zheng, Yanbing Cheng, Su Sun, Runze Li, Xin-Guang Zhu, Susie Y. Dai, Peter M. Rentzepis, Joshua S. Yuan
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Review
Plant Sciences
Tian-Gen Chang, Xin-Guang Zhu
JOURNAL OF EXPERIMENTAL BOTANY
(2017)
Review
Genetics & Heredity
Chensi Cao, Feng Liu, Hai Tan, Deshou Song, Wenjie Shu, Weizhong Li, Yiming Zhou, Xiaochen Bo, Zhi Xie
GENOMICS PROTEOMICS & BIOINFORMATICS
(2018)
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Plant Sciences
Yu Wang, Andrea Braeutigam, Andreas P. M. Weber, Xin-Guang Zhu
JOURNAL OF EXPERIMENTAL BOTANY
(2014)
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Plant Sciences
Chang-Peng Xin, Danny Tholen, Vincent Devloo, Xin-Guang Zhu
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Plant Sciences
Xianbin Yu, Guangyong Zheng, Lanlan Shan, Guofeng Meng, Martin Vingron, Qi Liu, Xin-Guang Zhu
FRONTIERS IN PLANT SCIENCE
(2014)
Article
Plant Sciences
Erik van den Bergh, Canan Kuelahoglu, Andrea Braeutigam, Julian M. Hibberd, Andreas P. M. Weber, Xin-Guang Zhu, M. Eric Schranz
CURRENT PLANT BIOLOGY
(2014)