Transcriptional events play a crucial role in major cellular processes that specify the activity of an individual cells and influences cell population behavior in response to environment. Active (ON) and an inactive (OFF) states controls the transcriptional burst. Yet, the mechanism and kinetics of ON/OFF-state across the different growth phases of Escherichia coli remains elusive. Here, we have used a single mRNA detection method in live-cells to comprehend the ON/OFF mechanism of the first transcriptional (T) and consecutive events (T) controlled by lactose promoters, P and P. We determined that the duration of T ON/OFF has different modes, exhibiting a close to inverse behavior to that of T ON/OFF. Dynamics of ON/OFF states in fast and slow-dividing cells were affected by the promoter region during the initiation of transcription. Period of T ON-state defines the behavior of T by altering the number and the frequency of mRNAs formed. Furthermore, we have shown that delayed OFF-time in T affects the dynamics of T in both states which is mainly determined by the upstream promoter region. Furthermore, using elongation arrest experiments, we independently validate that mRNA noise in T is governed by the delayed OFF-period in T. We have identified the position of the regulatory regions that plays a crucial role in noise (Fano) modulation. Taken together, our results suggest that the dynamics of the first transcriptional event, T, pre-defines the diversity of the population.
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http://dx.doi.org/10.1016/j.ijbiomac.2024.132457 | DOI Listing |
Nat Commun
December 2024
School of Data Science, The Chinese University of Hong Kong-Shenzhen, Shenzhen, China.
Recently, RNA velocity has driven a paradigmatic change in single-cell RNA sequencing (scRNA-seq) studies, allowing the reconstruction and prediction of directed trajectories in cell differentiation and state transitions. Most existing methods of dynamic modeling use ordinary differential equations (ODE) for individual genes without applying multivariate approaches. However, this modeling strategy inadequately captures the intrinsically stochastic nature of transcriptional dynamics governed by a cell-specific latent time across multiple genes, potentially leading to erroneous results.
View Article and Find Full Text PDFNat Commun
December 2024
Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.
Short tandem repeats (STRs) have emerged as important and hypermutable sites where genetic variation correlates with gene expression in plant and animal systems. Recently, it has been shown that a broad range of transcription factors (TFs) are affected by STRs near or in the DNA target binding site. Despite this, the distribution of STR motif repetitiveness in eukaryote genomes is still largely unknown.
View Article and Find Full Text PDFJ Biomol Struct Dyn
February 2025
Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, India.
The P53 protein, a cancer-associated transcriptional factor and tumor suppressor, houses a Zn ion in its DNA-binding domain (DBD), essential for sequence-specific DNA binding. However, common mutations at position 273, specifically from Arginine to Histidine and Cysteine, lead to a loss of function as a tumor suppressor, also called DNA contact mutations. The mutant (MT) P53 structure cannot stabilize DNA due to inadequate interaction.
View Article and Find Full Text PDFJ Agric Food Chem
December 2024
Agronomy College, Guizhou University, Huaxi, 550025 Guiyang, Guizhou, P. R. China.
Safflower ( L.) is a valuable oil crop due to its bioactive ingredients and high linoleic acid content, which contribute to its antioxidant properties and potential for preventing atherosclerosis. Current research on safflower focuses on understanding the biosynthesis of seed oil through omics strategies, yet there is a lack of comprehensive knowledge of the dynamic changes in lipids and the regulatory mechanisms during seed development.
View Article and Find Full Text PDFJ Adv Res
December 2024
College of Animal Science, Shandong Provincial Key Laboratory for Livestock Germplasm Innovation & Utilization, Shandong Agricultural University, Taian, China; College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China. Electronic address:
Brown adipose tissue (BAT) is responsible for non-shivering thermogenesis, but it is absent in some mammals, including pigs. During development, BAT progenitors are derived from paired box 7 (Pax7)-expressing somitic mesodermal stem cells, which also give rise to skeletal muscle. However, the intrinsic mechanisms underlying the fate decisions between brown fat and muscle progenitors remain elusive.
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