Genes

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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.

Theoretical genes[edit]

Def.

  1. 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"[1] or
  2. 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" [1]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.

Gene clusters[edit]

Main sources: Genes/Clusters and Gene clusters

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[edit]

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."[2]

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."[2]

Gene regulations[edit]

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.

Gene similarities[edit]

There are genes on other chromosomes that are similar to each gene being considered. For example, GeneID: 338, Apolipoprotein B, is on chromosome 2.

Eukaryote genes[edit]

This diagram of a eukaryote cell shows that the DNA is located in the nucleus. Credit: Sponk.

Def. "[a]ny of the single-celled or multicellular organisms whose cells contain at least one distinct nucleus"[3] is called a eukaryote.

Those specific genes that cause cells to contain at least one distinct nucleus are eukaryote genes.

Human genes[edit]

Main sources: Genes/Human and Human 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."[4]

Gene ID: 1602 is the human gene DACH1 dachshund homolog 1 also known as DACH.[5] 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)."[6] This is Gene ID: 5743.

The Drosophila hsp70 has a TATA box containing promoter.[7] This suggests that GeneID: 3308 HSPA4 heat shock 70kDa protein 4 [Homo sapiens], also known as hsp70,[8] has a TATA box in its core promoter.

Genotypes[edit]

Main sources: Genes/Genotypes and Genotypes

"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."[9]

"[O]nly about 1.5% of the human genome consists of protein-coding exons".[9]

Pseudogenes[edit]

Main sources: Genes/Pseudogenes and Pseudogenes

"An abundant form of noncoding DNA in humans are pseudogenes, which are copies of genes that have been disabled by mutation.[10] 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.[11]"[9]

About 2700 formerly active genes are now pseudogenes.

Deaminations[edit]

"[T]he CpG deficiency is due to an increased vulnerability of methylcytosines to spontaneously deaminate to thymine in genomes with CpG cytosine methylation.[12]"[13]

Methylations[edit]

"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."[13]

"In mammals, 70% to 80% of CpG cytosines are methylated.[14]"[13]

"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."[13]

"Unmethylated CpG sites can be detected by Toll-Like Receptor 9[15] (TLR 9) on plasmacytoid dendritic cells and B cells in humans. This is used to detect intracellular viral, fungal, and bacterial pathogen DNA."[13]

"Methylation is central to imprinting, along with histone modifications.[16] Most of the methylation occurs a short distance from the CpG islands (at "CpG island shores") rather than in the islands themselves.[17]"[18]

"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.[19]"[13]

Mutations[edit]

Main sources: Genes/Mutations and Mutations

"Alu elements are a common source of mutation in humans, but such mutations are often confined to non-coding regions where they have little discernible impact on the bearer.[20]"[21]

"[T]he mutagenic effect of Alu[22] and retrotransposons in general[23] has played a major role in the recent evolution of the human genome."[21]

"The first report of Alu-mediated recombination causing a prevalent inherited predisposition to cancer was a 1995 report about hereditary nonpolyposis colorectal cancer.[24]"[21]

"The human diseases caused by Alu insertions include":[25]

"[T]he following diseases have been associated with single-nucleotide DNA variations in Alu elements impacting transcription levels:[26]

"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[27]"[21]

"The opsin gene duplication which resulted in the re-gaining of trichromacy in Old World primates (including humans) is flanked by an Alu element,[28] implicating the role of Alu in the evolution of three colour vision."[21]

Hypotheses[edit]

Main source: Hypotheses
  1. Each gene may be expressed by one of more isoforms usually subject to cell type.

See also[edit]

References[edit]

  1. 1.0 1.1 "gene, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. 6 August 2015. Retrieved 2015-08-24. 
  2. 2.0 2.1 Tamar Juven-Gershon and James T. Kadonaga (15 March 2010). "Regulation of gene expression via the core promoter and the basal transcriptional machinery". Developmental Biology 339 (2): 225-9. doi:10.1016/j.ydbio.2009.08.009. http://www.sciencedirect.com/science/article/pii/S0012160609011166. Retrieved 2016-01-16. 
  3. "eukaryote, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. October 16, 2012. Retrieved 2012-10-27. 
  4. Marcelo A. Nobrega, Ivan Ovcharenko, Veena Afzal, and Edward M. Rubin (October 2003). "Scanning human gene deserts for long-range enhancers". Science 302 (5644): 413. doi:10.1126/science.1088328. PMID 14563999. http://www.sciencemag.org/content/302/5644/413.short. Retrieved 2012-12-26. 
  5. HGNC (December 20, 2012). "DACH1 dachshund homolog 1 (Drosophila) [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2012-12-26. 
  6. Tetsuya Kosaka, Atsuro Miyata, Hayato Ihara, Shuntaro Hara, Tamiko Sugimoto, Osamu Takeda, Ei-ichi Takahashi, Tadashi Tanabe (May 1994). "Characterization of the human gene (PTGS2) encoding prostaglandin‐endoperoxide synthase 2". European Journal of Biochemistry 221 (3): 889-97. doi:10.1111/j.1432-1033.1994.tb18804.x. http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1994.tb18804.x/full. Retrieved 2012-12-26. 
  7. Thomas W. Burke and James T. Kadonaga (November 15, 1997). "The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila". Genes & Development 11 (22): 3020–31. doi:10.1101/gad.11.22.3020. PMID 9367984. PMC 316699. http://genesdev.cshlp.org/content/11/22/3020.long. 
  8. HGNC (February 3, 2013). "HSPA4 heat shock 70kDa protein 4 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-07. 
  9. 9.0 9.1 9.2 "DNA, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. December 4, 2012. Retrieved 2012-12-13. 
  10. Harrison P, Hegyi H, Balasubramanian S, Luscombe N, Bertone P, Echols N, Johnson T, Gerstein M (2002). "Molecular Fossils in the Human Genome: Identification and Analysis of the Pseudogenes in Chromosomes 21 and 22". Genome Res 12 (2): 272–80. doi:10.1101/gr.207102. PMID 11827946. PMC 155275. //www.ncbi.nlm.nih.gov/pmc/articles/PMC155275/. 
  11. Harrison P, Gerstein M (2002). "Studying genomes through the aeons: protein families, pseudogenes and proteome evolution". J Mol Biol 318 (5): 1155–74. doi:10.1016/S0022-2836(02)00109-2. PMID 12083509. 
  12. Scarano E, Iaccarino M, Grippo P, Parisi E (1967). "The heterogeneity of thymine methyl group origin in DNA pyrimidine isostichs of developing sea urchin embryos". Proc. Natl. Acad. Sci. USA 57 (5): 1394–400. doi:10.1073/pnas.57.5.1394. PMID 5231746. PMC 224485. //www.ncbi.nlm.nih.gov/pmc/articles/PMC224485/. 
  13. 13.0 13.1 13.2 13.3 13.4 13.5 "CpG site, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. January 30, 2013. Retrieved 2013-02-07. 
  14. Jabbari K, Bernardi G (May 2004). "Cytosine methylation and CpG, TpG (CpA) and TpA frequencies". Gene 333: 143–9. doi:10.1016/j.gene.2004.02.043. PMID 15177689. http://linkinghub.elsevier.com/retrieve/pii/S0378111904000836. 
  15. Ramirez-Ortiz ZG, Specht CA, Wang JP, Lee CK, Bartholomeu DC, Gazzinelli RT, Levitz SM (2008). "Toll-like receptor 9-dependent immune activation by unmethylated CpG motifs in Aspergillus fumigatus DNA". Infect Immun. 76 (5): 2123–9. doi:10.1128/IAI.00047-08. PMID 18332208. PMC 2346696. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2346696/. 
  16. Feil R, Berger F (2007). "Convergent evolution of genomic imprinting in plants and mammals". Trends Genet 23 (4): 192–9. doi:10.1016/j.tig.2007.02.004. PMID 17316885. 
  17. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, Ji H, Potash JB, Sabunciyan S, Feinberg AP (2009). "The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores". Nature Genetics 41 (2): 178-86. PMID 19151715. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2729128/. 
  18. "CpG island, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. October 2, 2012. Retrieved 2013-02-07. 
  19. Jones PA, Laird PW (February 1999). "Cancer epigenetics comes of age". Nat. Genet. 21 (2): 163–7. doi:10.1038/5947. PMID 9988266. 
  20. International Human Genome Sequencing Consortium (2001). "Initial sequencing and analysis of the human genome". Nature 409 (6822): 860–921. doi:10.1038/35057062. PMID 11237011. http://www.nature.com/nature/journal/v409/n6822/abs/409860a0.html. 
  21. 21.0 21.1 21.2 21.3 21.4 21.5 "Alu element, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. February 6, 2013. Retrieved 2013-02-07. 
  22. Shen S, Lin L, Cai JJ, Jiang P, Kenkel EJ, Stroik MR, Sato S, Davidson BL, Xing Y (2011). "Widespread establishment and regulatory impact of Alu exons in human genes". PNAS 108 (7): 2837–42. doi:10.1073/pnas.1012834108. http://www.pnas.org/content/108/7/2837. 
  23. Cordaux R, Batzer MA (2009). "The impact of retrotransposons on human genome evolution". Nature Reviews Genetics 10: 691–703. doi:10.1038/nrg2640. PMID 19763152. PMC 2884099. http://rcordaux.voila.net/pdfs/42.pdf. 
  24. Nyström-Lahti M, Kristo P, Nicolaides NC, et al. (November 1995). "Founding mutations and Alu-mediated recombination in hereditary colon cancer". Nat. Med. 1 (11): 1203–6. doi:10.1038/nm1195-1203. PMID 7584997. 
  25. Batzer MA, Deininger PL (May 2002). "Alu repeats and human genomic diversity". Nat. Rev. Genet. 3 (5): 370–9. doi:10.1038/nrg798. PMID 11988762. http://batzerlab.lsu.edu/Publications/Batzer%20and%20Deininger%202002%20Nature%20Reviews%20Genetics.pdf. 
  26. "SNPedia: SNP in the promoter region of the myeloperoxidase MPO gene". 
  27. Puthucheary Z, Skipworth J, Rawal J, Loosemore M, Van Someren K, Montgomery H (2011). "The ACE Gene and Human Performance: 12 Years On". Sports Medicine 41: 433–448. doi:10.2165/11588720-000000000-00000. PMID 21615186. 
  28. Dulai KS, Von Dornum M, Mollon JD, Hunt DM (1999). "The Evolution of Trichromatic Color Vision by Opsin Gene Duplication in New World and Old World Primates". Genome Research 9 (7): 629–638. doi:10.1101/gr.9.7.629. PMID 10413401. http://genome.cshlp.org/content/9/7/629.full. 

External links[edit]

{{Gene project}}