Regulome
Encyclopedia
Regulome refers to the whole set of regulation components in a cell
. Those components can be gene
s, mRNAs, protein
s, and metabolite
s. The description includes the interplay of regulatory effects between these components, and their dependence on variables such as subcellular localization
, tissue
, developmental stage, and pathological state.
s, proteins that regulate the expression of genes. Other proteins that bind to transcription factors to form transcriptional complexes might modify the activity of transcription factors, for example blocking their capacity to bind to a promoter.
Signaling pathways are groups of proteins that produce an effect in a chain that transmit a signal from one part of the cell to another part, for example, linking the presence of substance at the exterior of the cell to the activation of the expression of a gene.
s, proteomics
analysis) allow the measurement of thousands of biological components such as mRNAs, proteins, or metabolites. Chromatin immunoprecipitation
of transcription factors can be used to map transcription factor binding sites in the genome.
Such techniques allow researchers to study the effects of particular substances and/or situations on a cellular sample at a genomic level (for example, by addition of a drug, or by placing cells in a situation of stress). The information obtained allows parts of the regulome to be inferred.
is the modelization of biological processes using mathematics
and computer simulation
. The production of data from techniques of genomic analysis is not always amenable to interpretation mainly due to the complexity of the data and the large amount of data points. Modelization can handle the data and allow to test a hypothesis (for example, gene A is regulated by protein B) that can be verified experimentally.
for therapy, the control of stem cell
differentiation, and the prognosis of disease
.
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....
. Those components can be gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s, mRNAs, protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s, and metabolite
Metabolite
Metabolites are the intermediates and products of metabolism. The term metabolite is usually restricted to small molecules. A primary metabolite is directly involved in normal growth, development, and reproduction. Alcohol is an example of a primary metabolite produced in large-scale by industrial...
s. The description includes the interplay of regulatory effects between these components, and their dependence on variables such as subcellular localization
Subcellular localization
The cells of eukaryotic organisms are elaborately subdivided into functionally distinct membrane bound compartments. Some major constituents of eukaryotic cells are: extracellular space, cytoplasm, nucleus, mitochondria, Golgi apparatus, endoplasmic reticulum , peroxisome, vacuoles, cytoskeleton,...
, tissue
Biological tissue
Tissue is a cellular organizational level intermediate between cells and a complete organism. A tissue is an ensemble of cells, not necessarily identical, but from the same origin, that together carry out a specific function. These are called tissues because of their identical functioning...
, developmental stage, and pathological state.
Components
One of the major players in cellular regulation are transcription factorTranscription factor
In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow of genetic information from DNA to mRNA...
s, proteins that regulate the expression of genes. Other proteins that bind to transcription factors to form transcriptional complexes might modify the activity of transcription factors, for example blocking their capacity to bind to a promoter.
Signaling pathways are groups of proteins that produce an effect in a chain that transmit a signal from one part of the cell to another part, for example, linking the presence of substance at the exterior of the cell to the activation of the expression of a gene.
Measuring
High-throughput technologies for the analysis of biological samples (for example, DNA microarrayDNA microarray
A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome...
s, proteomics
Proteomics
Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
analysis) allow the measurement of thousands of biological components such as mRNAs, proteins, or metabolites. Chromatin immunoprecipitation
Chromatin immunoprecipitation
Chromatin Immunoprecipitation is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. It aims to determine whether specific proteins are associated with specific genomic regions, such as transcription factors on promoters or...
of transcription factors can be used to map transcription factor binding sites in the genome.
Such techniques allow researchers to study the effects of particular substances and/or situations on a cellular sample at a genomic level (for example, by addition of a drug, or by placing cells in a situation of stress). The information obtained allows parts of the regulome to be inferred.
Modeling
One of the objectives of systems biologySystems biology
Systems biology is a term used to describe a number of trends in bioscience research, and a movement which draws on those trends. Proponents describe systems biology as a biology-based inter-disciplinary study field that focuses on complex interactions in biological systems, claiming that it uses...
is the modelization of biological processes using mathematics
Mathematics
Mathematics is the study of quantity, space, structure, and change. Mathematicians seek out patterns and formulate new conjectures. Mathematicians resolve the truth or falsity of conjectures by mathematical proofs, which are arguments sufficient to convince other mathematicians of their validity...
and computer simulation
Computer simulation
A computer simulation, a computer model, or a computational model is a computer program, or network of computers, that attempts to simulate an abstract model of a particular system...
. The production of data from techniques of genomic analysis is not always amenable to interpretation mainly due to the complexity of the data and the large amount of data points. Modelization can handle the data and allow to test a hypothesis (for example, gene A is regulated by protein B) that can be verified experimentally.
Applications
The complete knowledge of the regulome will allow researchers to model cell behaviour entirely. This will facilitate the design of drugsDrug design
Drug design, also sometimes referred to as rational drug design or structure-based drug design, is the inventive process of finding new medications based on the knowledge of the biological target...
for therapy, the control of stem cell
Stem cell
This article is about the cell type. For the medical therapy, see Stem Cell TreatmentsStem cells are biological cells found in all multicellular organisms, that can divide and differentiate into diverse specialized cell types and can self-renew to produce more stem cells...
differentiation, and the prognosis of disease
Disease
A disease is an abnormal condition affecting the body of an organism. It is often construed to be a medical condition associated with specific symptoms and signs. It may be caused by external factors, such as infectious disease, or it may be caused by internal dysfunctions, such as autoimmune...
.
See also
- GenomeGenomeIn modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
- ProteomeProteomeThe proteome is the entire set of proteins expressed by a genome, cell, tissue or organism. More specifically, it is the set of expressed proteins in a given type of cells or an organism at a given time under defined conditions. The term is a portmanteau of proteins and genome.The term has been...
- CytomeCytomeCytomes are the cellular systems, subsystems, and functional components of thebody. The cytome is the collection of the complex and dynamic cellular processes underlying physiological processes. It describes the structural and functional heterogeneity of the cellular diversity of an organism...
- BioinformaticsBioinformaticsBioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
- Systems biologySystems biologySystems biology is a term used to describe a number of trends in bioscience research, and a movement which draws on those trends. Proponents describe systems biology as a biology-based inter-disciplinary study field that focuses on complex interactions in biological systems, claiming that it uses...
- DNA microarrayDNA microarrayA DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome...
- Mass spectrometryMass spectrometryMass spectrometry is an analytical technique that measures the mass-to-charge ratio of charged particles.It is used for determining masses of particles, for determining the elemental composition of a sample or molecule, and for elucidating the chemical structures of molecules, such as peptides and...
- 2-D electrophoresis
- Protein engineeringProtein engineeringProtein engineering is the process of developing useful or valuable proteins. It is a young discipline, with much research taking place into the understanding of protein folding and recognition for protein design principles....
- Swiss-Prot
- List of omics topics in biology