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Specifying cellular context of transcription factor regulons for exploring context-specific gene regulation programs.
NAR Genom Bioinform
March 2025
Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Tomtebodavägen 23A, 17165 Solna, Sweden.
Understanding the role of transcription and transcription factors (TFs) in cellular identity and disease, such as cancer, is essential. However, comprehensive data resources for cell line-specific TF-to-target gene annotations are currently limited. To address this, we employed a straightforward method to define regulons that capture the cell-specific aspects of TF binding and transcript expression levels.
View Article and Find Full Text PDFAdaptation of Archaeal Communities to Summer Hypoxia in the Sediment of Bohai Sea.
Ecol Evol
January 2025
Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Science Tianjin Normal University Tianjin China.
Understanding the adaptation of archaea to hypoxia is essential for deciphering the functions and mechanisms of microbes when suffering environmental changes. However, the dynamics and responses of archaea to the sedimentary hypoxia in Bohai Sea are still unclear. In this study, the diversity, composition, and distribution of archaeal community in sediment along an inshore-offshore transect across the oxygen-depleted area in the Bohai Sea were investigated in June, July, and August of 2021 by employing high-throughput sequencing of 16S rRNA gene.
View Article and Find Full Text PDFDeciphering the δ-Lactam Formation and lron-Reducing Activity of Spinactins from .
Org Lett
January 2025
Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
The cyclic structure of non-ribosomal peptides (NRPs) is critical for enhancing their stability and bioactivity, which highlights the importance of exploring NRP cyclization enzymes for natural product discovery. Thioesterases (TEs) are crucial enzymes that catalyze the formation of various lactams, including macrolactams, β-lactams, and γ-lactams; however, their potential to produce other lactam types remains largely unexplored. In this study, we identified spinactin A () and novel derivatives, spinactin B-E (-), from NRRL 18395 and characterized the biosynthetic enzymes involved, particularly a unique TE SncF, responsible for δ-lactam formation.
View Article and Find Full Text PDFDeciphering progressive lesion areas in breast cancer spatial transcriptomics via TGR-NMF.
Brief Bioinform
November 2024
School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, 200240 Shanghai, China.
Identifying spatial domains is critical for understanding breast cancer tissue heterogeneity and providing insights into tumor progression. However, dropout events introduces computational challenges and the lack of transparency in methods such as graph neural networks limits their interpretability. This study aimed to decipher disease progression-related spatial domains in breast cancer spatial transcriptomics by developing the three graph regularized non-negative matrix factorization (TGR-NMF).
View Article and Find Full Text PDFDeciphering the Coupling State-Dependent Transcription Termination in the Escherichia coli Galactose Operon.
Mol Microbiol
January 2025
Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, Republic of Korea.
The distance between the ribosome and the RNA polymerase active centers, known as the mRNA loop length, is crucial for transcription-translation coupling. Despite the existence of multiple expressomes with varying mRNA loop lengths, their in vivo roles remain largely unexplored. This study examines the mechanisms governing transcription termination in the Escherichia coli galactose operon, revealing a crucial role in the transcription and translation coupling state.
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