TOPIC: -HOW CAN WE KNOW LOCATION OF GENES

SUBJECT:-CONCEPTS OF BIOTECHNOLOGY

SUBJECT CODE: - BTC012

SUBMITTED TO: - SUBMITTED BY:-

MR. HARSH KUMAR ROLL NO.R108B039

(LECT. IN BIOTECH.) REG.NO.1040070114

B.TECH. BIOTECH 3RD SEM

CONTENT
• Introduction

• How do geneticist indicate the location of gene

• References
ACKNOWLEDGEMENT

I would like to express my gratitude to all those who gave me the possibility to
complete this term paper. I want to thank the Department of BIOTECHNOLOGY of
LOVELY PROFESSIONAL UNIVERSITY for giving me permission to commence
this Term paper, to do the necessary research work and to use departmental data. I
have furthermore to thank to Mr. Harsh Kumar, Lect.In Concepts of Biotech., which
gave and confirmed this permission and encouraged me to go ahead with my term
paper.

I am deeply indebted to my supervisor Lect. Harsh Kumar whose help, stimulating

suggestions and encouragement helped me in all the time of research for and writing
of this term paper.

• Thank you
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:
• The chromosome on which the gene can be found. The first number or letter used
to describe a gene’s location represents the chromosome. Chromosomes 1 through
22 (the autosomes) are designated by their chromosome number. The sex
chromosomes are designated by X or Y.
• The arm of the chromosome. Each chromosome is divided into two sections
(arms) based on the location of a narrowing (constriction) called the centromere.
By convention, the shorter arm is called p, and the longer arm is called q. The
chromosome arm is the second part of the gene’s address. For example, 5q is the
long arm of chromosome 5, and Xp is the short arm of the X chromosome.
• The position of the gene on the p or q arm. The position of a gene is based on a
distinctive pattern of light and dark bands that appear when the chromosome is
stained in a certain way. The position is usually designated by two digits
(representing a region and a band), which are sometimes followed by a decimal
point and one or more additional digits (representing sub-bands within a light or
dark area). The number indicating the gene position increases with distance from
the centromere. For example: 14q21 represents position 21 on the long arm of
chromosome 14. 14q21 is closer to the centromere than 14q22.
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 Centre 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 Ensemble 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.

Cells become cancerous mainly because they lose control of their growth. To better
understand how this happens, a new study at Ohio State University's Comprehensive
Cancer Center looks at four genes that help regulate cell growth in embryos and that
contribute to cancer in adults. The genes – E2f1, E2f2, and E2f3a and E2f3b – are
generally believed to work together to help control cell proliferation, a belief that
comes from experiments using only cells. Cancer researchers at The Ohio State
University carried out several studies in an animal model to learn if it is also true in
the body during development. The scientists also hoped to learn why many organisms,
including humans, have multiple E2F genes of this type, while other animals have just
one copy.Their study, published in the Aug. 28 issue of the journal Nature, shows that
mice need just one of the four genes to develop from fertilized eggs through
adulthood."We found that if E2f3a is present, the animals can develop normally
through adulthood, even when all the other genes are absent," says study leader
Gustavo Leone, an associate professor of molecular virology, immunology and
medical genetics at Ohio State's Comprehensive Cancer Center. Then came the real
surprise. To learn if the E2f3a gene was doing something truly critical and different
from the other three E2Fs, the scientists swapped it with one of the others – they
replaced it first with E2f3 gene, then with the E2f1. Neither change made any
difference; these "swapped" mice developed quite normally. "If the E2F3a gene was
doing something unique, replacing it with one of the others should prevent
development," Leone says. "But the animals still developed just fine. "We conclude
from this that it is the gene's location in the genome, plus the timing and level of its
activity, that makes it so important during development," he says. But if just one of
the genes is sufficient for development, why are the others needed? "Organisms above
insects have multiple E2Fs, and these findings don't tell us what the others are doing,"
Leone says. "We surmise that the other genes are required for adult survival under the
stressful conditions in the wild. We are investigating that now."
Chromosomal location of human metallothionein
genes: implications for Menkes' disease
CJ Schmidt, DH Hamer, and OW McBride
Human metallothioneins are encoded by a complex multigene family. The
chromosomal location of these genes has been determined by gel transfer
hybridization analysis of the DNA from human-rodent cell hybrids. Chromosome 16
contains a cluster of metallothionein sequences, including two functional
metallothionein I genes and a functional metallothionein II gene. The remaining
sequences, including a processed pseudogene, are dispersed to at least four other
autosomes. The absence of metallothionein sequences from the X chromosome
indicates that Menkes' disease, an X-linked disorder of copper metabolism, affects
metallothionein expression by a trans-acting mechanism.

Mutants of Escherichia coli K-12 unable to synthesize the iron-sequestering

compound, enterochelin, from 2,3-dihydroxybenzoate have been isolated and divided
into three classes on the basis of tests for enzymatic complementation. The genes
affected (designated entD, entE, and entF) have been mapped by cotransduction and
are located at about minute 14 on the E. coli genome. They were found to be closely
linked to other genes (entA, entB, and entC) concerned with enterochelin biosynthesis
and a gene (fep) concerned with the uptake of the iron-enterochelin complex. No
detectable diffusible intermediate in the formation of enterochelin from 2,3-
dihydroxybenzoate was formed by cell extracts of mutants carrying mutations in the
entD, entE, or entF genes.
Karnal bunt (Tilletia indica Mitra) infestation of wheat (Triticum aestivum L.) kernels
reduces grain quality. Deployment of genetic resistance would be preferable to
chemical applications for control of the disease. Inoculation studies were carried out in
a wheat mapping population with the aim of locating genes for resistance.
Recombinant inbred (RI) lines from a cross between resistant synthetic wheat
(Triticum turgidum ‘Altar 84’ & T. tauschii) and the susceptible common wheat
cultivar ‘Opata 85’ were inoculated with Karnal bunt sporidial suspension and
evaluated for symptom development in the field for three seasons and in the
greenhouse. Based on restriction fragment length polymorphism (RFLP) analyses,
regions on chromosome arms 3BS and SAL carrying marker alleles from the Altar
durum parent were consistently associated with reduced kernel disease. Main marker
effects accounted for up to 32% of disease variation in the field but only 15% in the
greenhouse, where the level of disease was higher, suggesting an environmental
component of resistance. The tagging of these Karnal bunt partial-resistance genes in
tetraploid and hexaploid backgrounds may facilitate the accumulation of resistance via
marker-assisted transfer to susceptible durum and common wheat cultivars. This
practice should reduce laborious disease screening requirements.
Location, Location, Location Important For Genes, Too
Cells become cancerous mainly because they lose control of their growth. To better
understand how this happens, a new study at Ohio State University’s Comprehensive
Cancer Centre looks at four genes that help regulate cell growth in embryos and that
contribute to cancer in adults. The genes – E2f1, E2f2, and E2f3a and E2f3b – are
generally believed to work together to help control cell proliferation, a belief that
comes from experiments using only cells. Cancer researchers at The Ohio State
University carried out several studies in an animal model to learn if it is also true in
the body during development.
The scientists also hoped to learn why many organisms, including humans, have
multiple E2F genes of this type, while other animals have just one copy.Their study,
published in the Aug. 28 issue of the journal Nature, shows that mice need just one of
the four genes to develop from fertilized eggs through adulthood.“We found that if
E2f3a is present, the animals can develop normally through adulthood, even when all
the other genes are absent,” says study leader Gustavo Leone, an associate professor
of molecular virology, immunology and medical genetics at Ohio State’s
Comprehensive Cancer Center.Then came the real surprise. To learn if the E2f3a gene
was doing something truly critical and different from the other three E2Fs, the
scientists swapped it with one of the others – they replaced it first with E2f3 gene,
then with the E2f1. Neither change made any difference; these “swapped” mice
developed quite normally.
“If the E2F3a gene was doing something unique, replacing it with one of the others
should prevent development,” Leone says. “But the animals still developed just fine.
“We conclude from this that it is the gene’s location in the genome, plus the timing
and level of its activity, that makes it so important during development,” he says.
But if just one of the genes is sufficient for development, why are the others needed?
“Organisms above insects have multiple E2Fs, and these findings don’t tell us what
the others are doing,” Leone says. “We surmise that the other genes are required for
adult survival under the stressful conditions in the wild. We are investigating that
now.”

The tetrasomics of the homoeologous groups 2, 5 and 7 of ‘Chinese Spring’ wheat

were, together with the euploid standard, screened at the seedling stage for sensitivity
to exogenously applied gibberellic acid (GA3). Whilst the seedling length of lines
tetrasomic for group 2 chromosomes were taller and those for chromosomes 5A, 5D
and 7D shorter in both treatments (with and without GA3) compared to the euploid
control, the remaining tetrasomics — 5B, 7A and 7B — were significantly shorter
than the euploids in the GA variant only. These results suggest the presence of
additional genetic factors for GA insensitivity on chromosomes of the groups 5 and 7
of hexaploid wheat. This corresponds with the localization of GA insensitive dwarfing
genes on the homoeologous chromosomes 5R and 7R in diploid rye.
Chromosomal location of the genes encoding complement
components C5 and factor H in the mouse
P D'Eustachio, T Kristensen, RA Wetsel, R Riblet, BA Taylor and
BF Tack
Complementary DNA probes corresponding to the factor H and C5 polypeptides have
been used to determine the chromosomal localizations of these two complement
components. Both probes revealed complex and polymorphic arrays of DNA
fragments in Southern blot analysis of mouse genomic DNA. Following the
distribution of these bands in panels of somatic cell hybrids carrying various
combinations of mouse chromosomes on a constant rat or Chinese hamster
background allowed the localization of the C5-associated fragments to proximal
chromosome 2 and the localization of the factor H-associated fragments to
chromosome 1 or chromosome 3. Following the inheritance of DNA restriction
fragment-length polymorphisms revealed by the probes in recombinant inbred mouse
strains allowed the factor H-associated fragments to be mapped to Sas-1 on
chromosome 1, and the C5-associated fragments to be mapped to Hc. Analysis of
three-point crosses, in turn, placed the latter locus 19 cM distal to Sd on chromosome
2. We have designated the two loci Cfh and C5, respectively. This genetic analysis
raises the possibility that C5 and factor H are both encoded by complex loci composed
of distinct structural and regulatory genes.

ABSTRACT

In Escherichia coli, the following genes are involved in motility and chemotaxis. The
H gene is the structural gene for flagellin. Mutation in the mot gene results in
paralysis of the flagella, and mutation in the fla genes leads to an absence of flagella.
The cheA, cheB, and cheC genes are required for chemotaxis. The chromosomal
location of these genes has now been determined. The majority are clustered in a
small region around uvrC, between his and aroD, in the order his-cheC-H-uvrC-mot-
cheA-cheB-aroD. The Fla genes are located in the same region, and also between trp
and gal. The results indicate that many of the genes are homologous to those which
have been studied in Salmonella typhimurium.

Autonomic location of genes from the conserved

mammalian X in the platypus (Ornithorhynchus
anatinus): implications for mammalian sex
chromosome evolution.

Mammalian sex chromosomes evolved from an ancient autosomal pair. Mapping of

human X- and Y-borne genes in distantly related mammals and non-mammalian
vertebrates has proved valuable to help deduce the evolution of this unique part of the
genome. The platypus, a monotreme mammal distantly related to eutherians and
marsupials, has an extraordinary sex chromosome system comprising five X and five
Y chromosomes that form a translocation chain at male meiosis. The largest X
chromosome (X1), which lies at one end of the chain, has considerable homology to
the human X. Using comparative mapping and the emerging chicken database, we
demonstrate that part of the therian X chromosome, previously thought to be
conserved across all mammals, was lost from the platypus X1 to an autosome. This
region included genes flanking the XIST locus, and also genes with Y-linked
homologues that are important to male reproduction in therians. Since these genes lie
on the X in marsupials and eutherians, and also on the homologous region of chicken
chromosome 4, this represents a loss from the monotreme X rather than an additional
evolutionary stratum of the human X.

Chromosomal location of additional genes for resistance to

Corynebacterium (Clavibacter) michiganense ssp.
nebraskense
Goss's wilt (Leaf Freckles and Wilt) is a vascular and foliar disease incited by the
bacterial pathogen Corynebacterium (Clavibacter) michiganense ssp. nebraskense.
We previously reported use of crosses between M14 (resistant) translocation stocks
and inbred A632 (susceptible) to locate a gene for resistance on the long arm of
chromosome 7 (MGCNL 59:57, 1985). Similar field tests conducted in 1985 indicate
that genes for resistance are also located on the short arm of chromosome 4 and the
long arm of chromosome 8 (Table 1). These findings are consistent with a quantitative
mode of inheritance for resistance to this disease.Environment appears to influence
expression of this disease. The genetic stocks involving translocation T4-9e
demonstrated a significant difference in 1985 but did not in 1984. T8-9(6673) was not
in 1984 tests. The effect of environment was also demonstrated in greenhouse tests.
Genetic stocks involving translocations T4-9e, T7-9a and T8-9(6673), all of which
demonstrated differences in the field, were greenhouse tested in fall 1985. Only stocks
involving translocation T4-9e demonstrated a significant difference.Preliminary
results from greenhouse studies conducted with A632 (susceptible) translocation
stocks crossed with Mo20W (resistant) are supportive of a quantitative mode of
inheritance for susceptibility to this disease. These stocks will be field tested before
chromosomal locations of genes effecting susceptibility are reported. Of interest is the
potential location of a gene on the short arm of chromosome 4 that causes a
susceptible reaction. Many sweet corn and popcorn cultivars have demonstrated
susceptibility to this disease. The sugary-1 locus and the gametophyte factor locus,
Ga, are both found on the short arm of chromosome 4. It may be worthwhile to
evaluate for a possible relationship between selection for sugary-1 in sweet corn or
selection for gametophyte factor in popcorn and the level of susceptibility to Goss's
wilt.

Divergent location of ribosomal genes in chromosomes

of fish thorny-headed worms, Pomphorhynchus laevis
and Pomphorhynchus tereticollis (Acanthocephala).

We studied distribution of ribosomal DNA (rDNA) sequences along with

chromosomal location of the nucleolar organizer regions (NORs) in males of two fish
parasites, Pomphorhynchus laevis and Pomphorhynchus tereticollis (Acanthocephala).
Fluorescence in situ hybridization with 18S rDNA probe identified two clusters of
rDNA in each species, but revealed a remarkable difference in their location on
chromosomes. In P. laevis, the rDNA-FISH signals were found in long arms of the
first chromosome pair and in short arms of the second pair. Whereas in P. tereticollis,
rDNA clusters were located in long arms of both the first and second chromosome
pairs. The divergent location of rDNA clusters in the chromosome No. 2 supports
current classification of P. tereticollis, previously considered a synonym of P. laevis,
as a separate species. A possible scenario of the second chromosome rearrangement
during karyotype evolution of the two species involves two successive pericentric
inversions. In both species, one or two prominent nucleoli were apparent within
interphase nuclei stained with either silver nitrate or a fluorescent dye YOYO-1.
However, a single large nucleolus was observed in early stages of mitosis and meiosis
I regardless the number of rDNA clusters. Nevertheless, two bivalents with silver-
stained NORs in diakinesis and two silver-stained sites in early prophase II nuclei
indicated that all NORs are active. This means that each Pomphorhynchus NOR
generates a nucleolus, but the resulting nucleoli have a strong tendency to associate in
a large body.