Contribution of structural accessibility to the cooperative relationship of TF-lncRNA in myopia

2021 ◽  
Author(s):  
Hong Wang ◽  
Jing Li ◽  
Siyu Wang ◽  
Xiaoyan Lu ◽  
Guosi Zhang ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Molecular Mechanisms ◽  
Systematic Research ◽  
Regulation Of Transcription ◽  
Molecular Binding ◽  
Binding Force ◽  
Cooperative Relationship ◽  
Relationship Of ◽  
Spatial Architecture ◽  
Candidate Set

Abstract Transcriptional regulation is associated with complicated mechanisms including multiple molecular interactions and collaborative drive. Long noncoding RNAs (lncRNAs) have highly structured characteristics and play vital roles in the regulation of transcription in organisms. However, the specific contributions of conformation feature and underlying molecular mechanisms are still unclear. In the present paper, a hypothesis regarding molecular structure effect is presented, which proposes that lncRNAs fold into a complex spatial architecture and act as a skeleton to recruit transcription factors (TF) targeted binding, and which is involved in cooperative regulation. A candidate set of TF-lncRNA coregulation was constructed, and it was found that structural accessibility affected molecular binding force. In addition, transcription factor binding site (TFBS) regions of myopia-related lncRNA transcripts were disturbed, and it was discovered that base mutations affected the occurrence of significant molecular allosteric changes in important elements and variable splicing regions, mediating the onset and development of myopia. The results originated from structureomics and interactionomics and created conditions for systematic research on the mechanisms of structure-mediated TF-lncRNA coregulation in transcriptional regulation. Finally, these findings will help further the understanding of key regulatory roles of molecular allostery in cell physiological and pathological processes.

Triiodothyronine-mediated myosin heavy chain gene transcription in the heart

2003 ◽  
Vol 284 (6) ◽  
pp. H2255-H2262 ◽  
Author(s):  
Sara Danzi ◽  
Kaie Ojamaa ◽  
Irwin Klein
Keyword(s):  
Myosin Heavy Chain ◽  
Heavy Chain ◽  
Time Course ◽  
Molecular Mechanisms ◽  
Chain Gene ◽  
Regulation Of Transcription ◽  
Mhc Genes ◽  
Coordinated Regulation ◽  
Relationship Of

We developed an RT-PCR assay to study both the time course and the mechanism for the triiodothyronine (T3)-induced transcription of the α- and β-myosin heavy chain (MHC) genes in vivo on the basis of the quantity of specific heterogeneous nuclear RNA (hnRNA). The temporal relationship of changes in transcriptional activity to the amount of α-MHC mRNA and the coordinated regulation of transcription of more than one gene in response to T3 are demonstrated here for the first time. Quantitation of α-MHC hnRNA demonstrated that T3 induced α-MHC transcription in hypothyroid rats within 30 min of a single injection of T3 (0.5 μg/100 g body wt). Maximal transcription rates (135% ± 15.8 of euthyroid values) occurred 6 h after injection and subsequently declined in parallel with serum T3 levels. The transcription of β-MHC was reduced to 86% of peak hypothyroid levels 6 h after a single T3injection and reached a nadir of 59% of hypothyroid levels at 36 h. Analysis of the time course of T3-mediated induction of α-MHC hnRNA and repression of β-MHC hnRNA indicates that separate molecular mechanisms are involved in the coordinated regulation of these genes.

scholarly journals Transcriptional Regulation and Implications for Controlling Hox Gene Expression

2022 ◽  
Vol 10 (1) ◽  
pp. 4
Author(s):  
Zainab Afzal ◽  
Robb Krumlauf
Keyword(s):  
Transcriptional Regulation ◽  
Molecular Mechanisms ◽  
Hox Genes ◽  
Regional Identity ◽  
Regulatory Mechanisms ◽  
Regulation Of Transcription ◽  
Axial Patterning ◽  
Hox Gene ◽  
Molecular Framework ◽  
Combinatorial Code

Hox genes play key roles in axial patterning and regulating the regional identity of cells and tissues in a wide variety of animals from invertebrates to vertebrates. Nested domains of Hox expression generate a combinatorial code that provides a molecular framework for specifying the properties of tissues along the A–P axis. Hence, it is important to understand the regulatory mechanisms that coordinately control the precise patterns of the transcription of clustered Hox genes required for their roles in development. New insights are emerging about the dynamics and molecular mechanisms governing transcriptional regulation, and there is interest in understanding how these may play a role in contributing to the regulation of the expression of the clustered Hox genes. In this review, we summarize some of the recent findings, ideas and emerging mechanisms underlying the regulation of transcription in general and consider how they may be relevant to understanding the transcriptional regulation of Hox genes.

High resolution mapping of nucleic acid containing complexes in vitro and in situ

1996 ◽  
Vol 54 ◽  
pp. 48-49
Author(s):  
D. P. Bazett-Jones ◽  
M. J. Hendzel
Keyword(s):  
Nucleic Acid ◽  
High Resolution ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Heavy Atom ◽  
Regulation Of Transcription ◽  
High Exposure ◽  
Resolution Mapping ◽  
Tata Sequence

Structural analysis of combinations of nucleosomes and transcription factors on promoter and enhancer elements is necessary in order to understand the molecular mechanisms responsible for the regulation of transcription initiation. Such complexes are often not amenable to study by high resolution crystallographic techniques. We have been applying electron spectroscopic imaging (ESI) to specific problems in molecular biology related to transcription regulation. There are several advantages that this technique offers in studies of nucleoprotein complexes. First, an intermediate level of spatial resolution can be achieved because heavy atom contrast agents are not necessary. Second, mass and stoichiometric relationships of protein and nucleic acid can be estimated by phosphorus detection, an element in much higher proportions in nucleic acid than protein. Third, wrapping or bending of the DNA by the protein constituents can be observed by phosphorus mapping of the complexes. Even when ESI is used with high exposure of electrons to the specimen, important macromolecular information may be provided. For example, an image of the TATA binding protein (TBP) bound to DNA is shown in the Figure (top panel). It can be seen that the protein distorts the DNA away from itself and much of its mass sits off the DNA helix axis. Moreover, phosphorus and mass estimates demonstrate whether one or two TBP molecules interact with this particular promoter TATA sequence.

scholarly journals Embryo-induced transcriptome changes in bovine endometrium reveal species-specific and common molecular markers of uterine receptivity

Reproduction ◽  
2006 ◽  
Vol 132 (2) ◽  
pp. 319-331 ◽  
Author(s):  
Stefan Bauersachs ◽  
Susanne E Ulbrich ◽  
Karin Gross ◽  
Susanne E M Schmidt ◽  
Heinrich H D Meyer ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Molecular Mechanisms ◽  
Cdna Array ◽  
Early Embryo ◽  
Cdna Libraries ◽  
Control Group ◽  
Regulation Of Transcription ◽  
Uterine Receptivity ◽  
Subtracted Cdna Libraries ◽  
Species Specific

The endometrium plays a central role among the reproductive tissues in the context of early embryo–maternal communication and pregnancy. This study investigated transcriptome profiles of endometrium samples from day 18 pregnant vs non-pregnant heifers to get insight into the molecular mechanisms involved in conditioning the endometrium for embryo attachment and implantation. Using a combination of subtracted cDNA libraries and cDNA array hybridisation, 109 mRNAs with at least twofold higher abundance in endometrium of pregnant animals and 70 mRNAs with higher levels in the control group were identified. Among the mRNAs with higher abundance in pregnant animals, at least 41 are already described as induced by interferons. In addition, transcript levels of many new candidate genes involved in the regulation of transcription, cell adhesion, modulation of the maternal immune system and endometrial remodelling were found to be increased. The different expression level was confirmed with real-time PCR for nine genes. Localisation of mRNA expression in the endometrium was shown byin situhybridisation forAGRN,LGALS3BP,LGALS9,USP18,PARP12andBST2. A comparison with similar studies in humans, mice, and revealed species-specific and common molecular markers of uterine receptivity.

The impact of Traditional Chinese Medicine on mitophagy in disease models

2021 ◽  
Vol 27 ◽  
Author(s):  
Li-Ping Yu ◽  
Ting-Ting Shi ◽  
Yan-Qin Li ◽  
Jian-Kang Mu ◽  
Ya-Qin Yang ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Molecular Mechanisms ◽  
Human Diseases ◽  
Regulatory Mechanisms ◽  
Disease Models ◽  
Relationship Of ◽  
The Impact ◽  
The Relationship

: Mitophagy plays an important role in maintaining mitochondrial quality and cell homeostasis through the degradation of damaged, aged, and dysfunctional mitochondria and misfolded proteins. Many human diseases, particularly neurodegenerative diseases, are related to disorders of mitochondrial phagocytosis. Exploring the regulatory mechanisms of mitophagy is of great significance for revealing the molecular mechanisms underlying the related diseases. Herein, we summarize the major mechanisms of mitophagy, the relationship of mitophagy with human diseases, and the role of traditional Chinese medicine (TCM) in mitophagy. These discussions enhance our knowledge of mitophagy and its potential therapeutic targets using TCM.

scholarly journals A DNA fragment containing the upstream activator sequence determines nucleosome positioning of the transcriptionally repressed PHO5 gene of Saccharomyces cerevisiae.

1986 ◽  
Vol 6 (7) ◽  
pp. 2298-2304 ◽  
Author(s):  
L W Bergman
Keyword(s):  
Transcriptional Regulation ◽  
Nucleosome Positioning ◽  
Vector System ◽  
Growth Media ◽  
Flanking Sequences ◽  
Dna Fragment ◽  
Acid Phosphatase Gene ◽  
Nucleosomal Structure ◽  
Relationship Of ◽  
Pho5 Gene

The functional relationship of nucleosome positioning and gene expression is not known. Using high-copy plasmids, containing the yeast phosphate-repressible acid phosphatase gene (PHO5) and the TRP1/ARS1 vector system, I have determined the nucleosomal structure of the 5' region of the PHO5 gene and demonstrated that the nucleosomal positioning of this region is independent of orientation or position in the various plasmid constructions utilized. However, deletion of a 278-base pair BamHI-ClaI fragment from the 5'-flanking sequences of the PHO5 gene causes the nucleosome positioning to become dependent on orientation or position in the plasmids tested. Use of PHO5-CYC1-lACZ fusions have demonstrated that this DNA fragment contains the sequences responsible for the transcriptional regulation of the PHO5 gene in response to the level of phosphate in the growth media. The nucleosome positioning in the 5' region of PHO5 may be determined by an interaction with the sequences or machinery responsible for transcriptional regulation of the gene.

scholarly journals The ETS-Domain Transcription Factor Elk-1 Regulates COX-2 Gene Expression and Inhibits Glucose-Stimulated Insulin Secretion in the Pancreaticβ-Cell Line INS-1

2013 ◽  
Vol 2013 ◽  
pp. 1-8
Author(s):  
Xiong-Fei Zhang ◽  
Yi Zhu ◽  
Wen-Biao Liang ◽  
Jing-Jing Zhang
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcriptional Regulation ◽  
Insulin Secretion ◽  
Cell Line ◽  
Molecular Mechanisms ◽  
Cell Function ◽  
Cell Dysfunction ◽  
Cox 2 ◽  
Glucose Stimulated Insulin Secretion

Cyclooxygenase-2 (COX-2) expression is associated with many aspects of physiological and pathological conditions, including pancreaticβ-cell dysfunction. Prostaglandin E2 (PGE2) production, as a consequence of COX-2 gene induction, has been reported to impairβ-cell function. The molecular mechanisms involved in the regulation of COX-2 gene expression are not fully understood. We previously demonstrated that transcription factor Elk-1 significantly upregulated COX-2 gene promoter activity. In this report, we used pancreaticβ-cell line (INS-1) to explore the relationships between Elk-1 and COX-2. We first investigated the effects of Elk-1 on COX-2 transcriptional regulation and expression in INS-1 cells. We thus undertook to study the binding of Elk-1 to its putative binding sites in the COX-2 promoter. We also analysed glucose-stimulated insulin secretion (GSIS) in INS-1 cells that overexpressed Elk-1. Our results demonstrate that Elk-1 efficiently upregulates COX-2 expression at least partly through directly binding to the −82/−69 region of COX-2 promoter. Overexpression of Elk-1 inhibits GSIS in INS-1 cells. These findings will be helpful for better understanding the transcriptional regulation of COX-2 in pancreaticβ-cell. Moreover, Elk-1, the transcriptional regulator of COX-2 expression, will be a potential target for the prevention ofβ-cell dysfunction mediated by PGE2.

Molecular mechanisms of transcriptional regulation by the nuclear zinc-finger protein Zfat in T cells

2016 ◽  
Vol 1859 (11) ◽  
pp. 1398-1410 ◽  
Author(s):  
Shuhei Ishikura ◽  
Toshiyuki Tsunoda ◽  
Kazuhiko Nakabayashi ◽  
Keiko Doi ◽  
Midori Koyanagi ◽  
...  
Keyword(s):  
T Cells ◽  
Transcriptional Regulation ◽  
Zinc Finger ◽  
Molecular Mechanisms ◽  
Zinc Finger Protein ◽  
Finger Protein

Cooperation in the financial services sector

2019 ◽  
pp. 417-428
Author(s):  
John Child ◽  
David Faulkner ◽  
Stephen Tallman ◽  
Linda Hsieh
Keyword(s):  
Strategic Alliances ◽  
Financial Services ◽  
Business Models ◽  
Modern Technology ◽  
Services Sector ◽  
Financial Services Sector ◽  
Software Companies ◽  
New Business ◽  
Cooperative Relationship ◽  
Relationship Of

Chapter 19 examines alliances in the financial services sector, focusing on banks as the major players. It describes how banks have traditionally formed strategic alliances with other banks and established deep networks. As such they have made themselves into the sector’s banking blocks. However, since the financial crisis of 2008 the terrain has changed and banks are facing the need to digitize and adopt modern technology to a greater degree than previously. The chapter considers the impact of digitization leading to cooperation between banks and software companies and the development of new business models based on the efficiencies digitization offers. It also looks at the cooperative relationship of banks with the new area characterized as Fintech and the emergence of new financial tools like cryptocurrencies and blockchain.

scholarly journals Transcriptional regulation in model organisms: recent progress and clinical implications

Open Biology ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 190183 ◽  
Author(s):  
Jiaqi Tang ◽  
Zhenhua Xu ◽  
Lianfang Huang ◽  
Hui Luo ◽  
Xiao Zhu
Keyword(s):  
Transcriptional Regulation ◽  
Molecular Mechanisms ◽  
The Body ◽  
Model Organisms ◽  
Clinical Implications ◽  
Regulation Mechanism ◽  
Biological Behaviour ◽  
E Coli ◽  
Different Types

In this review, we will summarize model organisms used by scientists in the laboratory, including Escherichia coli , yeast, Arabidopsis thaliana , nematodes, Drosophila , zebrafish, mice and other animals. We focus on the progress in research exploring different types of E. coli in the human body, and the specific molecular mechanisms by which they play a role in humans. First, we discuss the specific transcriptional regulation mechanism of E. coli in cell development, maturation, ageing and longevity, as well as tumorigenesis and development. Then, we discuss how the synthesis of some important substances in cells is regulated and how this affects biological behaviour. Understanding and applying these mechanisms, presumably, can greatly improve the quality of people's lives as well as increase their lifespan. For example, some E. coli can activate certain cells by secreting insulin-like growth factor-1, thus activating the inflammatory response of the body, while other E. coli can inactivate the immune response of the body by secreting toxic factors.

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