A gene is a distinct sequence of nucleotides forming part of a chromosome, the order of which determines the order of monomers in a polypeptide or nucleic acid molecule which a cell (or virus) may synthesize.
- a "theoretical unit of heredity of living organisms ; a gene may take several values and in principle predetermines a precise trait of an organism's form (phenotype), such as hair color" or
- a "segment of DNA or RNA from a cell's or an organism's genome, that may take several forms and thus parameterizes a phenomenon, in general the structure of a protein; locus" is called a gene.
Here's a theoretical definition:
Def. a specific nucleotide sequence within a gene locus with its own transcription start site(s), introns, exons, and UTRs, that transcribes a specific RNA product is called an isoform, or gene isoform.
GeneID: 348 APOE apolipoprotein E description contains this: "This gene maps to chromosome 19 in a cluster with the related apolipoprotein C1 and C2 genes."
Gene expressions is a suite of genes, and their isoforms, that appear to be biochemically involved in the appearance of a trait.
Although it is harder to regulate the transcription of genes with multiple transcription start sites, "variations in the expression of a constitutive gene would be minimized by the use of multiple start sites."
Earlier "studies led to the design of a super core promoter (SCP) that contains a TATA, Inr, MTE, and DPE in a single promoter (Juven-Gershon et al., 2006b). The SCP is the strongest core promoter observed in vitro and in cultured cells and yields high levels of transcription in conjunction with transcriptional enhancers. These findings indicate that gene expression levels can be modulated via the core promoter."
Each gene, or its isoforms, is likely to have upregulation and downregulation transcription factors. As each gene is investigated, these enhancers and inhibitors are noted as discovered.
For example, submitting "gene regulation" APOE human to the NCBI gene database returns 28 genes and 21 mouse analogs. The first on the list is GeneID: 2099 ESR1 estrogen receptor 1. "This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. [...] Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis." from the page url=http://www.ncbi.nlm.nih.gov/gene/2099. The database also maintains the DNA sequence upstream, downstream, and through the entire gene locus so that analysis of "Alternative promoter usage and alternative splicing result in dozens of transcript variants, but the full-length nature of many of these variants has not been determined. [provided by RefSeq, Mar 2014]" can be attempted. The site lists gene interactions and six variants for three isoforms (1, 2, and 3) and ten experimental transcriptions.
There are genes on other chromosomes that are similar to each gene being considered. For example, GeneID: 338, Apolipoprotein B, is on chromosome 2.
Def. "[a]ny of the single-celled or multicellular organisms whose cells contain at least one distinct nucleus" is called a eukaryote.
Those specific genes that cause cells to contain at least one distinct nucleus are eukaryote genes.
"Nine elements were tested, representing a sampling of elements present in the two gene deserts and DACH introns, spread over a 1530-kb region surrounding the human DACH's TATA box."
Gene ID: 1602 is the human gene DACH1 dachshund homolog 1 also known as DACH. DACH1 has three isoforms: a, b, and c.
"[T]he human ... prostaglandin-endoperoxide-synthase-2 [gene contains] a canonical TATA box (nucleotide residues at positions -31 to -25 for the human gene)." This is Gene ID: 5743.
The Drosophila hsp70 has a TATA box containing promoter. This suggests that GeneID: 3308 HSPA4 heat shock 70kDa protein 4 [Homo sapiens], also known as hsp70, has a TATA box in its core promoter.
"The genetic information in a genome is held within genes, and the complete set of this information in an organism is called its genotype. A gene is a unit of heredity and is a region of DNA that influences a particular characteristic in an organism. Genes contain an open reading frame that can be transcribed, as well as regulatory sequences such as promoters and enhancers, which control the transcription of the open reading frame."
"An abundant form of noncoding DNA in humans are pseudogenes, which are copies of genes that have been disabled by mutation. These sequences are usually just molecular fossils, although they can occasionally serve as raw genetic material for the creation of new genes through the process of gene duplication and divergence."
About 2700 formerly active genes are now pseudogenes.
"Cytosines in CpG dinucleotides can be methylated to form 5-methylcytosine. In mammals, methylating the cytosine within a gene can turn the gene off, a mechanism that is part of a larger field of science studying gene regulation that is called epigenetics. Enzymes that add a methyl group are called DNA methyltransferases."
"CpG dinucleotides have long been observed to occur with a much lower frequency in the sequence of vertebrate genomes than would be expected due to random chance. For example, in the human genome, which has a 42% GC content, a pair of nucleotides consisting of cytosine followed by guanine would be expected to occur 0.21 * 0.21 = 4.41% of the time. The frequency of CpG dinucleotides in human genomes is 1% — less than one-quarter of the expected frequency."
"Unmethylated CpG sites can be detected by Toll-Like Receptor 9 (TLR 9) on plasmacytoid dendritic cells and B cells in humans. This is used to detect intracellular viral, fungal, and bacterial pathogen DNA."
"Methylation is central to imprinting, along with histone modifications. Most of the methylation occurs a short distance from the CpG islands (at "CpG island shores") rather than in the islands themselves."
"Methylation of CpG sites within the promoters of genes can lead to their silencing, a feature found in a number of human cancers (for example the silencing of tumor suppressor genes). In contrast, the hypomethylation of CpG sites has been associated with the over-expression of oncogenes within cancer cells."
"The human diseases caused by Alu insertions include":
- Breast cancer
- Ewing's sarcoma
- Familial hypercholesterolemia
- Diabetes mellitus type II.
"[T]he following diseases have been associated with single-nucleotide DNA variations in Alu elements impacting transcription levels:
"The ACE gene, encoding angiotensin-converting enzyme, has 2 common variants, one with an Alu insertion (ACE-I) and one with the Alu deleted (ACE-D). This variation has been linked to changes in sporting ability: the presence of the Alu element is associated with better performance in endurance-oriented events (e.g. triathlons), whereas its absence is associated with strength- and power-oriented performance"
"The opsin gene duplication which resulted in the re-gaining of trichromacy in Old World primates (including humans) is flanked by an Alu element, implicating the role of Alu in the evolution of three colour vision."
- Each gene may be expressed by one of more isoforms usually subject to cell type.
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- "SNPedia: SNP in the promoter region of the myeloperoxidase MPO gene".
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