Faculty Opinions recommendation of Domain-wide regulation of gene expression in the human genome.

2007 ◽  
Author(s):  
Wendy Bickmore
Keyword(s):  
Gene Expression ◽  
Human Genome ◽  
Regulation Of Gene Expression

scholarly journals Domain-wide regulation of gene expression in the human genome

2007 ◽  
Vol 17 (9) ◽  
pp. 1286-1295 ◽  
Author(s):  
H. J. Gierman ◽  
M. H.G. Indemans ◽  
J. Koster ◽  
S. Goetze ◽  
J. Seppen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Genome ◽  
Regulation Of Gene Expression

scholarly journals  ALUminating the Path of Atherosclerosis Progression: Chaos Theory Suggests a Role for Alu Repeats in the Development of Atherosclerotic Vascular Disease

2018 ◽  
Author(s):  
Miguel Hueso ◽  
Josep M Cruzado ◽  
Joan Torras ◽  
Estanis Navarro
Keyword(s):  
Gene Expression ◽  
Human Genome ◽  
Chaos Theory ◽  
Molecular Mechanisms ◽  
Regulation Of Gene Expression ◽  
Structural Constraints ◽  
Linear Dynamical Systems ◽  
Alu Elements ◽  
Non Linear ◽  
The Impact

Atherosclerosis (ATH) and Coronary Artery Disease (CAD) are chronic inflammatory diseases with an important genetic background which derive from the cumulative effect of multiple common risk alleles, most of them located in genomic non-coding regions. These complex diseases behave as non-linear dynamical systems that show a high dependence on their initial conditions, so that long-term predictions of disease progression are unreliable. One likely possibility is that the non-linear nature of ATH could be dependent on non-linear correlations in the structure of the human genome. In this review we show how Chaos theory analysis highlighted genomic regions that shared specific structural constraints that could have a role in ATH progression. These regions were shown to be enriched in repetitive sequences of the Alu family, genomic parasites which colonized the human genome, which show a particular secondary structure and have been involved in the regulation of gene expression. We also review the impact of Alu elements on the mechanisms that regulate gene expression, especially highlighting the molecular mechanisms by which the Alu elements could alter the inflammatory homeostasis. We devise especial attention to their relationship with the lncRNA ANRIL, the strongest risk factor for ATH, their role as miRNA sponges, and their ability to interfere with the regulatory circuitry of the NF-kB response. We aim to characterize ATH as a non-linear dynamic system in which small initial alterations in the expression of a number of repetitive elements are somehow amplified to reach phenotypic significance.

The 4D Living Genome

2021 ◽  
Author(s):  
Julianna Arlene Sherman Goelzer
Keyword(s):  
Gene Expression ◽  
Human Genome ◽  
Genomic Sequence ◽  
Critical Role ◽  
Regulation Of Gene Expression ◽  
Correlation Spectroscopy ◽  
Microscopy Technique ◽  
Temporal Aspects ◽  
Key Factor ◽  
Dynamics Simulations

Over the last few decades great advances have been made in our understanding of gene expression and the human genome. In 2003 the human genome was sequenced for the first time, allowing us to discover its true importance in human health. While sequencing the human genome was a great advance, it ultimately created more questions than it answered. It is known that the genomic sequence is extremely important in genome regulation, however recent studies have shown that the 4D (spatiotemporal) organization and dynamics of the living genome plays an equally critical role in regulation of gene expression. A key factor in the spatiotemporal genome is the temporal and spatial coordination of transcription factors required for gene expression. We focus on addressing both the spatial and temporal aspects of the genome through a cutting-edge microscopy technique known as 3D Orbital Tracking Fluorescence Correlation Spectroscopy (3DOT-FCCS) in conjunction with Molecular Dynamics simulations. The synergistic use of these techniques will provide a clearer picture of the rules that govern the human genome.

scholarly journals Isochores and the Regulation of Gene Expression in the Human Genome

2011 ◽  
Vol 3 ◽  
pp. 1080-1089 ◽  
Author(s):  
Stilianos Arhondakis ◽  
Fabio Auletta ◽  
Giorgio Bernardi
Keyword(s):  
Gene Expression ◽  
Human Genome ◽  
Regulation Of Gene Expression

Long antisense non-coding RNAs and the epigenetic regulation of gene expression

2013 ◽  
Vol 4 (4) ◽  
pp. 411-415 ◽  
Author(s):  
Nadia Vadaie ◽  
Kevin V. Morris
Keyword(s):  
Gene Expression ◽  
Human Genome ◽  
Protein Complexes ◽  
Regulation Of Gene Expression ◽  
Biological Significance ◽  
Genome Project ◽  
Positive Role ◽  
Protein Coding ◽  
Encode Project ◽  
Non Coding Rnas

AbstractShortly after the completion of the human genome project in 2003, the Encode project was launched. The project was set out to identify the functional elements in the human genome, and unexpectedly it was found that >80% of the genome is transcribed. The Encode project identified those transcribed regions of the genome to be encoded by non-coding RNAs (ncRNAs). With only 2% of the genome carrying gene-encoding proteins, the conundrum was then, what is the function, if any, of these non-coding regions of the genome? These ncRNAs included both short and long RNAs. The focus of this review will be on antisense long non-coding RNAs (lncRNAs), as these transcripts have been observed to play a role in gene expression of protein-coding genes. Some lncRNAs have been found to regulate protein-coding gene transcription at the epigenetic level, whereby they suppress transcription through the recruitment of protein complexes to target loci in the genome. Conversely, there are lncRNAs that have a positive role in gene expression with less known about mechanism, and some lncRNAs have been shown to be involved in post-transcriptional processes. Additionally, lncRNAs have been observed to regulate their own expression in a positive feedback loop by functioning as a decoy. The biological significance of lncRNAs is only just now becoming evident, with many lncRNAs found to play a significant role in several human diseases.

Linking transcription, RNA polymerase II elongation and alternative splicing

2020 ◽  
Vol 477 (16) ◽  
pp. 3091-3104 ◽  
Author(s):  
Luciana E. Giono ◽  
Alberto R. Kornblihtt
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Polymerase Ii ◽  
Environmental Changes ◽  
Transcription Elongation ◽  
Single Gene ◽  
Regulation Of Gene Expression ◽  
Regulation Of Transcription ◽  
Stepping Stones ◽  
Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

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