Article
Computer Science, Artificial Intelligence
Yongqing Zhang, Shaojie Qiao, Yuanqi Zeng, Dongrui Gao, Nan Han, Jiliu Zhou
Summary: A new method is proposed that combines a convolutional autoencoder with a convolutional neural network to predict transcription factor binding sites using positive DNA nucleotide samples, outperforming existing methods in accuracy and performance.
EXPERT SYSTEMS WITH APPLICATIONS
(2021)
Article
Genetics & Heredity
Kevin W. Currin, Chael R. Erdos, Narisu Narisu, Vivek Rai, Swarooparani Vadlamudi, Hannah J. Perrin, Jacqueline R. Idol, Tingfen Yan, Ricardo D'Oliveira Albanus, K. Alaine Broadaway, Amy S. Etheridge, Lori L. Bonnycastle, Peter Orchard, John P. Didion, Amarjit S. Chaudhry, Federico Innocenti, Erin G. Schuetz, Laura J. Scott, Stephen C. J. Parker, Francis S. Collins, Karen L. Mohlke
Summary: This study mapped caQTLs in human liver tissue and identified thousands of caQTL variants enriched in liver tissue promoter and enhancer states. We predicted target genes for hundreds of caQTL peaks and identified dozens of colocalized caQTLs and GWAS signals. Validation at the LITAF LDL-cholesterol GWAS locus showed allelic differences in protein binding and transcriptional activity for a caQTL variant.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Irene M. Kaplow, Abhimanyu Banerjee, Chuan Sheng Foo
Summary: In this study, the researchers developed a new approach to identify the binding motifs of individual DNA binding domains (DBDs) of a transcription factor (TF). By analyzing chromatin immunoprecipitation sequencing (ChIP-seq) data, they trained a deep convolutional neural network to predict the preservation of wild-type TF binding sites in mutant TF datasets. They applied this approach to mouse CTCF ChIP-seq data and successfully identified the binding preferences of CTCF ZFs 3-11 as well as a putative GAG binding motif for ZF 1. Their findings provide new insights into the binding preferences of CTCF's DBDs.
Review
Biochemistry & Molecular Biology
Arina O. Degtyareva, Elena Antontseva, Tatiana Merkulova
Summary: Many genetic variants affecting gene expression are found in the noncoding part of the genome, mainly through alterations in transcription factor binding. Advanced methods such as eQTL analysis and searching for allele-specific events in various sequencing data are used to identify regulatory variants and understand their functionality.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Erik K. Zhivkoplias, Oleg Vavulov, Thomas Hillerton, Erik L. L. Sonnhammer
Summary: The regulatory relationships between genes and proteins in a cell form a gene regulatory network (GRN) that controls cellular response. Methods have been developed to reverse engineer GRNs from expression data, but realistic simulations are necessary due to the lack of ground-truth GRNs. Analysis shows that the feed-forward loop (FFL) motif is significantly enriched in real GRNs, leading to the development of a novel preferential attachment algorithm, FFLatt, for network generation.
FRONTIERS IN GENETICS
(2022)
Article
Green & Sustainable Science & Technology
Naveenarani Murugan, Ravinder Kumar, Shashi Kant Pandey, Pooja Dhansu, Mahadevaiah Chennappa, Saranya Nallusamy, Hemaprabha Govindakurup, Appunu Chinnaswamy
Summary: This study investigated the characteristics and regulatory mechanisms of phosphate transporter gene promoters through computer analysis. It found that one of the gene promoters can enhance gene expression under salt stress conditions, which is of great significance for the development of salt-tolerant transgenic crops.
Article
Biochemistry & Molecular Biology
Jun Yuan, Xiaomei He, Yinsheng Wang
Summary: High-order chromatin organization is crucial for biological processes and disease development. This study investigated the role of guanine quadruplex (G4) structures in RNA polymerase II (RNAPII)-mediated DNA interactions and transcription activity. Data analysis revealed a strong positive correlation between RNAPII-linked DNA loops and G4 structures in chromatin. Treatment with PDS, a G4-binding ligand, was found to diminish RNAPII-linked long-range DNA contacts, especially those involving G4 structure loci, leading to changes in gene expression.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Bahareh Nikparvar, Margarita Andreevskaya, Ilhan C. Duru, Florentina I. Bucur, Leontina Grigore-Gurgu, Daniela Borda, Anca I. Nicolau, Christian U. Riedel, Petri Auvinen, Nadav Bar
Summary: The pathogen Listeria (L.) monocytogenes exhibits different gene regulation modes in response to high pressure processing, including survival mode, repair mode, and re-growth mode. This allows for the timely activation of transcription factors associated with immediate stress response, followed by repair and re-growth to survive and recover from extreme conditions. The findings provide insights for potential design of specific strategies to target genes or mechanisms to prevent L. monocytogenes recovery during food storage under high pressure conditions.
Article
Biochemical Research Methods
Yongqing Zhang, Zixuan Wang, Yuanqi Zeng, Jiliu Zhou, Quan Zou
Summary: Research has shown that deep learning models can predict TFBSs at the base-pair level, but there is a need for improvement to integrate information more effectively for increased accuracy.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Microbiology
Heungyun Moon, Mi-Kyung Lee, Ilhan Bok, Jin Woo Bok, Nancy P. Keller, Jae-Hyuk Yu
Summary: This study reveals the gene regulatory networks governed by VeA and LaeA in Aspergillus nidulans, shedding light on the understanding of fungal biology and genetics. The findings demonstrate the vital roles of these global regulators in developmental and metabolic processes.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemical Research Methods
Wei Liu, Xingen Sun, Li Yang, Kaiwen Li, Yu Yang, Xiangzheng Fu
Summary: Accurately inferring gene regulatory networks is crucial for understanding pathogenesis and curing diseases. However, identifying redundant regulations remains a challenge in existing methods. In this study, we propose a network structure control method that specifies the specific forms and cooperation mode of both global and local topology. Experimental results demonstrate the unique advantages of our method in gene regulatory network inference.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biology
Selina Klees, Felix Heinrich, Armin Otto Schmitt, Mehmet Gueltas
Summary: This study introduces agReg-SNPdb-Plants, a database storing regulatory SNPs for agriculturally important plant species, and provides a web interface for querying. The identification of regulatory SNPs is valuable for interpreting GWAS results and uncovering biologically causative variants. The researchers extended their previous work by storing regulatory SNPs and their predicted effects on transcription factor binding in agReg-SNPdb-Plants, including 13 agriculturally important plant species and subspecies.
Article
Biochemical Research Methods
Zhen Gao, Jin Tang, Junfeng Xia, Chun-Hou Zheng, Pi-Jing Wei
Summary: This study proposes a supervised model called CNNGRN, which uses a convolutional neural network to reconstruct gene regulatory networks from gene expression data. The model integrates gene expression data and network structure information, and uses the extracted complex features to infer regulatory relationships. Experimental results show that CNNGRN achieves competitive performance on benchmark datasets and confirms key genes involved in biological processes.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Xiusheng Zhu, Qitong Huang, Lei Huang, Jing Luo, Qing Li, Dashuai Kong, Biao Deng, Yi Gu, Xueyan Wang, Chenying Li, Siyuan Kong, Yubo Zhang
Summary: Proper cell fate determination relies on precise spatial and temporal genome-wide cooperation between regulatory elements and their targeted genes. A method called MAE-seq was developed to experimentally identify functional regulatory elements at a 25-bp scale. Using this method, a large number of 25-bp enhancers were identified in mouse embryonic stem cells, C2C12, and HEK 293T. These 25-bp sequences were shown to act as functional units and contribute to gene regulation and genomic landscape exploration.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Dabin Jeong, Sangsoo Lim, Sangseon Lee, Minsik Oh, Changyun Cho, Hyeju Seong, Woosuk Jung, Sun Kim
Summary: This paper presents a novel computational method for constructing condition-specific transcriptional networks, focusing on the complex multiple-to-multiple regulatory interactions between transcription factors and target genes. By applying kernel canonical correlation analysis, the method identifies these relationships and was demonstrated on responses to high fat diet in humans and cold/heat stress in arabidopsis. The method not only detected known regulatory interactions but also uncovered novel TF-TG relations in response to specific stress.
FRONTIERS IN GENETICS
(2021)
