Life Hacks


      

LOCATION OF GENE



Gene

clip_image002

For a non-technical introduction to the topic, see Introduction to genetics.

This stylistic diagram shows a gene in relation to the double helix structure of DNA and to a chromosome (right). Introns are regions often found in eukaryote genes that are removed in the splicing process (after the DNA is transcribed into RNA): only the exons encode the protein. This diagram labels a region of only 40 or so bases as a gene. In reality most genes are hundreds of times larger.

A gene is the basic unit of heredity in a living organism. The field of genetics predates modern molecular biology, but it is now known that all living things depend on DNA to pass on their traits to offspring. Loosely speaking, a gene is a segment of genomic information that, taken as a whole, specifies a trait. The colloquial usage of the term gene often refers to the scientific concept of an allele.

The notion of a gene has evolved with the science of genetics, which began when Gregor Mendel noticed that biological variations were only inherited from parent organisms as specific, discrete traits. For example, if one parent has blue eyes and the other has brown eyes, there is a 3/4 chance that the child will have brown eyes. The biological entity responsible for defining eye color was termed a “gene”, but the biological basis for inheritance remained unknown until the discovery of the genetic code in mid 1950s, when genes were determined to be encoded by DNA. All organisms have many genes corresponding to many different biological traits, some of which are immediately visible, such as eye color or number of limbs, and some of which are not, such as blood type or increased risk for certain diseases, or the thousands of basic biochemical processes which comprise life.

In cells, a gene is a portion of an organism’s DNA which contains both “coding” sequences that determine what the gene does, and “non-coding” sequences that determine when the gene is active (expressed.) When a gene is active, the coding and non-coding sequences are copied in a process called transcription, producing an RNA copy of the gene’s information. This piece of RNA can then direct the synthesis of proteins via the genetic code. In other cases, the RNA is used directly, for example as part of the ribosome. The RNA may undergo special post-transcriptional processing steps required to convert it into a mature, functional form. These molecules resulting from gene expression, whether RNA or protein, are known as gene products, and are responsible for the development and functioning of all living things.

More technically, a gene is a locatable region of genomic sequence, corresponding to a unit of inheritance, and is associated with regulatory regions, transcribed regions and/or other functional sequence regions.[1][2] The physical development and phenotype of organisms can be thought of as a product of genes interacting with each other and with the environment.[3] A concise definition of a gene, taking into account complex patterns of regulation and transcription, genic conservation and non-coding RNA genes, has been proposed by Gerstein et al:[4] “A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products

Structure and mapping of the human β-defensin HBD-2 gene and its expression at a site of inflammation

Abstract

We cloned a second human β-defensin gene, HBD-2, and determined its gene structure and expression in inflamed tissue sections. The entire gene spanned about 2 kb with two small exons and one intron. Radiation hybrid studies confirmed the location on chromosome 8p, were consistent with the order HNP-1, HBD-1 and HBD-2, and located HBD-2 as the most centromeric of the genes. By three-color fluorescence in situ hybridization on both free chromatin fiber mapping and interphase mapping, HBD-1, HBD-2 and HNP-1 were mapped to chromosome 8p23. HBD-1 was within 40–100 kb of HNP-1, while HBD-2 was about 500–600 kb from HBD-1, with the most likely order HNP-1, HBD-1, HBD-2. The expression of HBD-2 was locally regulated by inflammation. HBD-2 mRNA was markedly increased in the epidermis surrounding inflamed regions, but not detectable in adjacent non-inflamed areas, a distribution that was confirmed at the peptide level by immunostaining with HBD-2 antibody. The HBD-2 gene is the first member of the human defensin family that is locally inducible by inflammation.

Author Keywords: Host defense; Epithelia; Chromosome 8p23; Antimicrobial peptides

How do geneticists indicate the location of a gene?

Geneticists use maps to describe the location of a particular gene on a chromosome. One type of map uses the cytogenetic location to describe a gene’s position. The cytogenetic location is based on a distinctive pattern of bands created when chromosomes are stained with certain chemicals. Another type of map uses the molecular location, a precise description of a gene’s position on a chromosome. The molecular location is based on the sequence of DNA building blocks (base pairs) that make up the chromosome.

Cytogenetic location

Geneticists use a standardized way of describing a gene’s cytogenetic location. In most cases, the location describes the position of a particular band on a stained chromosome:

17q12

It can also be written as a range of bands, if less is known about the exact location:

17q12-q21

The combination of numbers and letters provide a gene’s “address” on a chromosome. This address is made up of several parts:

Sometimes, the abbreviations “cen” or “ter” are also used to describe a gene’s cytogenetic location. “Cen” indicates that the gene is very close to the centromere. For example, 16pcen refers to the short arm of chromosome 16 near the centromere. “Ter” stands for terminus, which indicates that the gene is very close to the end of the p or q arm. For example, 14qter refers to the tip of the long arm of chromosome 14. (“Tel” is also sometimes used to describe a gene’s location. “Tel” stands for telomeres, which are at the ends of each chromosome. The abbreviations “tel” and “ter” refer to the same location.)

 

The CFTR gene is located on the long arm of chromosome 7 at position 7q31.2.

Molecular location

The Human Genome Project, an international research effort completed in 2003, determined the sequence of base pairs for each human chromosome. This sequence information allows researchers to provide a more specific address than the cytogenetic location for many genes. A gene’s molecular address pinpoints the location of that gene in terms of base pairs. For example, the molecular location of the APOE gene on chromosome 19 begins with base pair 50,100,901 and ends with base pair 50,104,488. This range describes the gene’s precise position on chromosome 19 and indicates the size of the gene (3,588 base pairs). Knowing a gene’s molecular location also allows researchers to determine exactly how far the gene is from other genes on the same chromosome.

Different groups of researchers often present slightly different values for a gene’s molecular location. Researchers interpret the sequence of the human genome using a variety of methods, which can result in small differences in a gene’s molecular address. For example, the National Center for Biotechnology Information (NCBI) identifies the molecular location of the APOE gene as base pair 50,100,901 to base pair 50,104,488 on chromosome 19. The Ensembl database identifies the location of this gene as base pair 50,100,879 to base pair 50,104,489 on chromosome 19. Neither of these addresses is incorrect; they represent different interpretations of the same data. For consistency, Genetics Home Reference presents data from NCBI for the molecular location of genes.

20 strains of Pseudomonas aeruginosa were isolated from burn patients of Xijing Hospital in Xi’an. These 20 strains which showed resistance to multiple antibiotics were selected to be

studied regarding the location of multi-resistant gene. According to the sensitivity tests before and after plasmid removal, we found that in 70% of the bacteria resistance to multiple antibiotics was mediated by the plasmid. In 30% the bacteria remained resistant to antibiotics after plasmids were removed. Two explanations were postulated. (1) plasmids were not removed completely; (2) resistance gene was encoded by the chromosomes.

PMID: 8697243

Location of gene for beta subunit of human T-cell receptor at band 7q35, a region prone to rearrangements in T cells

The T-cell receptor is formed by two chains, alpha and beta, for which specific clones were recently obtained. In this report the gene for the beta chain of the human T-cell receptor was located on the long arm of chromosome 7, band q35, by means of in situ hybridization. This chromosome region in T cells is unusually prone to develop breaks in vivo, perhaps reflecting instability generated by somatic rearrangement of T-cell receptor genes during normal differentiation in this cell lineage.


Researchers find gene location that gives rise to neuroblastoma, an aggressive childhood cancer

Medicine & Health / Cancer

Using advanced gene-hunting technology, an international team of researchers has for the first time identified a chromosome region that is the source of genetic events that give rise to neuroblastoma, an often fatal childhood cancer.

The investigators found that the presence of common DNA variations in a region of chromosome 6 raises the risk that a child will develop a particularly aggressive form of neuroblastoma, a cancer of the peripheral nervous system that usually appears as a solid tumor in the chest or abdomen. Neuroblastoma accounts for 7 percent of all childhood cancers, but due to its aggressive nature, causes 15 percent of all childhood cancer deaths.
Neuroblastoma is the most common solid cancer of early childhood and has long been known to include subtypes that behave very differently. Some cases strike infants but spontaneously disappear with minimal treatment, while other cases in older children may be relentlessly aggressive from the start.
The researchers repeated the analysis in blood samples from additional groups of patients and control subjects from the U.S. and the U.K., and confirmed their finding that variants in the 6p22 region were implicated in neuroblastoma. There are two genes in the 6p22 region, but their functions are largely unknown.
The researchers found that patients with these at-risk SNPs on chromosome 6 were more likely to develop aggressive neuroblastoma. The initial changes on chromosome 6 in all their body cells eventually led to the genetic abnormalities seen in tumor cells in high-risk forms of the disease.
Because their finding reveals only the first step in a series of molecular events, it would be premature to do prenatal genetic testing for the SNPs on chromosome 6. His research team will continue to perform genetic analyses, in search of other gene changes that interact with those SNPs. One data source will be 5,000 tissue samples in Maris’s lab—the world’s largest collection of neuroblastoma samples,

“This discovery lays the foundation for learning how these initial changes influence biological pathways that lead to neuroblastoma. Understanding those pathways may guide us to new and tter therapies that precisely target this cancer.

Leave a Reply