scholarly journals G-Quadruplex in Gene Encoding Large Subunit of Plant RNA Polymerase II: A Billion-Year-Old Story

2021 ◽  
Vol 22 (14) ◽  
pp. 7381
Author(s):  
Adriana Volná ◽  
Martin Bartas ◽  
Václav Karlický ◽  
Jakub Nezval ◽  
Kristýna Kundrátová ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Gene Expression Regulation ◽  
Uv Light ◽  
Large Subunit ◽  
Expression Regulation ◽  
Gene Encoding ◽  
Additional Layer ◽  
G Quadruplex

G-quadruplexes have long been perceived as rare and physiologically unimportant nucleic acid structures. However, several studies have revealed their importance in molecular processes, suggesting their possible role in replication and gene expression regulation. Pathways involving G-quadruplexes are intensively studied, especially in the context of human diseases, while their involvement in gene expression regulation in plants remains largely unexplored. Here, we conducted a bioinformatic study and performed a complex circular dichroism measurement to identify a stable G-quadruplex in the gene RPB1, coding for the RNA polymerase II large subunit. We found that this G-quadruplex-forming locus is highly evolutionarily conserved amongst plants sensu lato (Archaeplastida) that share a common ancestor more than one billion years old. Finally, we discussed a new hypothesis regarding G-quadruplexes interacting with UV light in plants to potentially form an additional layer of the regulatory network.

Heterobasidion amyloideopsis sp. nov. (Basidiomycota, Russulales) evidenced by morphological characteristics and phylogenetic analysis

Phytotaxa ◽  
2017 ◽  
Vol 317 (3) ◽  
pp. 199 ◽  
Author(s):  
CHANG-LIN ZHAO ◽  
MALKA SABA ◽  
ABDUL NASIR KHALID ◽  
JIE SONG ◽  
DONALD H. PFISTER
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Morphological Characteristics ◽  
Molecular Evidence ◽  
Gene Encoding ◽  
Annual Habit

Heterobasidion amyloideopsis sp. nov., a new poroid wood-inhabiting species from Pakistan, is introduced based on a combination of molecular evidence and morphological characteristics. We generated sequences from the nuclear internal transcribed spacer regions (ITS) and the large subunit ribosomal RNA gene (LSU), the gene encoding the largest subunit of RNA polymerase II (RPB1) and the second subunit of RNA polymerase II (RPB2), focusing on two specimens from Pakistan. We performed phylogenetic analyses with maximum likelihood, maximum parsimony, and bayesian inference methods on two datasets (RPB1+RPB2 and ITS+nLSU+RPB1+RPB2). Both analyses supported the existence of the new species and showed that it formed a monophyletic group within the H. insulare complex as a sister to H. amyloideum. In addition to assessing the origin and divergence of this new species, we focused on the RPB1+RPB2 dataset to perform maximum likelihood based estimation and Bayesian binary analyses. Heterobasidion amyloideopsis is characterized by an annual habit, pileate basidiomata with a rust colored pileal surface, white, obtuse margin, a dimitic hyphal system with simple septate generative hyphae in the trama and clamp connections present on the contextual hyphae, amyloid skeletal hyphae and broadly ellipsoid, hyaline, fairly thick-walled, and asperulate basidiospores.

scholarly journals The gene encoding the large subunit of human RNA polymerase II.

1985 ◽  
Vol 260 (28) ◽  
pp. 15204-15210
Author(s):  
K W Cho ◽  
K Khalili ◽  
R Zandomeni ◽  
R Weinmann
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Large Subunit ◽  
Gene Encoding

Nutrient-regulated gene expression in eukaryotes

2006 ◽  
Vol 73 ◽  
pp. 85-96 ◽  
Author(s):  
Richard J. Reece ◽  
Laila Beynon ◽  
Stacey Holden ◽  
Amanda D. Hughes ◽  
Karine Rébora ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Direct Interaction ◽  
Signalling Pathways ◽  
A Cell ◽  
One Step ◽  
Higher Eukaryotes ◽  
Regulated Gene Expression

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

Gerea: Prediction Of Gene Expression Regulators From Transcriptome Profiling Data To Transition Networks

2021 ◽  
Vol 16 ◽  
Author(s):  
Min Yao ◽  
Caiyun Jiang ◽  
Chenglong Li ◽  
Yongxia Li ◽  
Shan Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Networks ◽  
Target Gene ◽  
Gene Expression Regulation ◽  
Transcriptome Profiling ◽  
Expression Regulation ◽  
Mouse Gene ◽  
Mouse Gene Expression ◽  
Causality Inference ◽  
Identify Gene Expression

Background: Mammalian genes are regulated at the transcriptional and post-transcriptional levels. These mechanisms may involve the direct promotion or inhibition of transcription via a regulator or post-transcriptional regulation through factors such as micro (mi)RNAs. Objective: This study aimed to construct gene regulation relationships modulated by causality inference-based miRNA-(transition factor)-(target gene) networks and analyze gene expression data to identify gene expression regulators. Methods: Mouse gene expression regulation relationships were manually curated from literature using a text mining method which was then employed to generate miRNA-(transition factor)-(target gene) networks. An algorithm was then introduced to identify gene expression regulators from transcriptome profiling data by applying enrichment analysis to these networks. Results: A total of 22,271 mouse gene expression regulation relationships were curated for 4,018 genes and 242 miRNAs. GEREA software was developed to perform the integrated analyses. We applied the algorithm to transcriptome data for synthetic miR-155 oligo-treated mouse CD4+ T-cells and confirmed that miR-155 is an important network regulator. The software was also tested on publicly available transcriptional profiling data for Salmonella infection, resulting in the identification of miR-125b as an important regulator. Conclusion: The causality inference-based miRNA-(transition factor)-(target gene) networks serve as a novel resource for gene expression regulation research, and GEREA is an effective and useful adjunct to the currently available methods. The regulatory networks and the algorithm implemented in the GEREA software package are available under a free academic license at website : http://www.thua45.cn/gerea.

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