OMICS -

JT5 DIVERSIFICATION

Omics is a field of biology that aims to understand the structure, function, and
interactions of biological molecules, such as DNA, RNA, proteins, and
metabolites, at a system-wide level. Omics technologies have revolutionized
biological research by enabling the high-throughput and comprehensive
analysis of multiple biological molecules simultaneously.

Omics is a highly diverse field, with several sub-disciplines, each focusing on a

specific type of biological molecule or system. Some of the major omics sub-
disciplines include:

Genomics: This involves the study of the structure, function, and evolution of
genomes, which are the complete set of DNA in an organism.

Transcriptomics: This involves the study of the structure, function, and

regulation of all the RNA molecules in a cell or organism, including messenger
RNA (mRNA), non-coding RNA (ncRNA), and small RNA (sRNA).

Proteomics: This involves the study of the structure, function, and interactions
of all the proteins in a cell or organism, including their post-translational
modifications (PTMs).

Metabolomics: This involves the study of the structure, function, and

interactions of all the small-molecule metabolites in a cell or organism, which
are involved in various metabolic pathways.

Lipidomics: This involves the study of the structure, function, and interactions
of all the lipids in a cell or organism, including their role in cellular signaling and
membrane structure.

Glycomics: This involves the study of the structure, function, and interactions of
all the carbohydrates in a cell or organism, including their role in cellular
signaling and protein modification.

Pharmacogenomics: This involves the study of the relationship between an

individual's genetic makeup and their response to drugs, with the aim of
developing personalized medicine.
 WHAT IS GENOME

A genome is "all the DNA contained in an organism or a cell, which

includes both the chromosomes within the nucleus and the DNA in
mitochondria...
all our genes together."
WHAT IS GENOMICS

•Genomics is "the study of functions and interactions of all the genes in

the genome, including their interactions with
environmental factors
Term genome used by German botanist Hans Winker in 1920 as ‘Collection of genes in
haploid set of chromosomes’
Now it encompasses all DNA in a cell
In 1986 mouse geneticist Thomas Roderick used Genomics for “mapping, sequencing
and characterizing genomes
 APPLICATION GENOMICS
OF

Understanding genetic variation: Genomics is used to study genetic variation within

populations, which is important for understanding the genetic basis of complex traits
and diseases.

Identification of disease-causing mutations: Genomics can help identify mutations in

genes that cause or contribute to diseases, leading to the development of targeted
therapies.

Personalized medicine: Genomics can help predict an individual's risk of developing

certain diseases, and guide personalized treatment plans based on their genetic
makeup.

Evolutionary biology: Genomics is used to study the evolutionary history of

organisms, including their divergence and adaptation to different environments.

Biotechnology: Genomics is used in biotechnology to engineer microorganisms for

the production of biofuels, pharmaceuticals, and other useful products.
APPLICATION OF PROTEOMICS

Biomarker discovery: Proteomics can identify proteins that are differentially

expressed in disease states, leading to the discovery of new biomarkers for early
disease diagnosis and treatment monitoring.

Drug discovery: Proteomics is used to identify proteins that are potential drug
targets, leading to the development of new drugs and therapies.

Protein function and interactions: Proteomics can help identify the functions and
interactions of proteins, providing insight into complex biological processes.

Systems biology: Proteomics is used in systems biology to model and simulate

complex biological systems, leading to a better understanding of biological
processes.

Agriculture and food science: Proteomics is used in agriculture and food science to
improve crop yield and quality, and to detect contaminants and pathogens in food.
 WHAT IS (-value Paradox

The C-value paradox is the amount, in picograms, of DNA contained within a

haploid nucleus (e.g. a gamete) or one-half the amount in a diploid somatic
cell of a eukaryotic organism.

The c-value paradox refers to the observation that genome does not
necessarily correlate with an organism's complexity or gene content. In other
words, some organisms with smaller genomes may have more genes and
higher complexity than organisms with larger genomes.

The c-value paradox is often cited as evidence that genome size is not a
reliable indicator of an organism's biological complexity. Instead, it is believed
that the functional complexity of an organism is more closely related to the
number and organization of its genes, as well as the regulatory mechanisms
that control gene expression.

For example, E.Coli have high gene density approx 2500 gene /mm of e.coli
DNA whereas eukaryotic genome has low gene density approx 50 gene/mm
of DNA in human

gene density-nogegenane
~

G-value--no. of genes found in haploid genome

High throughput technology: gives high input and output.

Includes data science with biology.
Accuracy and speed and with no background
Features of high throughput
1) automation: handling of instruments and material
2) specificity: less background and good output
3) sensitivity: good reading of enormous data
4) multiplexing: multiple analysis and experiment
5) parallelism: parallel analysis, replication
6) miniaturisation: smaller sample size still accurate reading
 WHAT IS GENOME DIVERSITY
Genome diversity refers to the variation in DNA sequences and structural variations among
individuals of the same species or between different species. Every organism has its unique
genome, which is composed of genetic material in the form of DNA. This genetic material
determines the physical and functional characteristics of the organism.

Genome diversity arises from a variety of mechanisms, including mutations, recombination, and
horizontal gene transfer. Mutations are the primary source of genetic diversity, which can occur
spontaneously or as a result of exposure to various environmental factors, such as radiation or
chemical agents. Recombination during sexual reproduction also contributes to genome diversity
by shuffling genetic material between parents.

PROKARYOTIC/BACTERIAL GENOME DIVERSITY

Bacterial genomes are the complete set of genetic material, including both chromosomal DNA
and any plasmids, present in a bacterial cell. Bacterial genomes are much smaller and simpler
than eukaryotic genomes, with typical sizes ranging from a few hundred thousand to a few
million base pairs.

Bacterial genomes encode all the genetic information necessary for the bacteria to grow, divide,
and perform all the functions required for survival. The bacterial genome includes genes that
code for proteins, as well as regulatory elements, non-coding RNA molecules, and other
functional elements.

Bacterial genomes are organized into circular chromosomes, which are typically compact and
densely packed with genes
high density with approx 2500 gene per mm of E.coli DNA
Plasmids often carry genes that provide additional functions, such as antibiotic resistance or the
ability to infect specific hosts.
 FACTORS AFFECTING GENOME
DIVERSITY
Horizontal gene transfer: Bacteria can acquire new genetic material through
horizontal gene transfer, which can introduce novel functions and traits into
the bacterial genome. This can occur through processes such as conjugation,
transformation, and transduction.

Gene duplication and divergence: Gene duplication followed by divergence is

a common mechanism of genome evolution in bacteria, which can lead to the
evolution of new gene functions or the optimization of existing functions.

Mobile genetic elements: Bacteria can carry mobile genetic elements such as
plasmids, transposons, and integrons, which can carry multiple genes and
facilitate their transfer between bacteria. These elements can also be
responsible for the spread of antibiotic resistance genes and virulence factors.

Genome rearrangement: Bacterial genomes can undergo rearrangements such

as inversions, translocations, and deletions, which can lead to changes in gene
order and regulatory elements.

Adaptation to different environments: Bacteria have adapted to a wide range

of environments, from soil and water to host organisms. This has led to the
evolution of specialized metabolic pathways and stress response systems.

Mutation rates: Bacteria have high mutation rates compared to eukaryotic

organisms, which can contribute to the rapid evolution of bacterial genomes.
 PROKARYOTIC PACKAGING

Prokaryotic genomes are packaged differently than eukaryotic genomes.

Prokaryotic cells lack a nucleus, so their DNA is not packaged into a complex
chromatin structure as in eukaryotic cells.

the DNA is located in a single circular chromosome, which is typically found in

the nucleoid region of the cell.

The nucleoid region is not enclosed by a membrane, so the DNA is exposed to

the cytoplasm.

Genome can be negatively supercoiled I.e DNA is twisted in opp direction of

double helix (E. coli is negatively supercoiled 40-50 supercoil loop of DNA
radiate from Center coat protein .)

One mechanism for genome packaging in prokaryotes involves the use of

DNA-binding proteins. The most abundant of these proteins is called HU,
which can bend and wrap DNA around itself, condensing the chromosome and
organizing it into loops. HU protein forms tetramer around which approx. 60 bp
of DNA becomes bound .Other proteinsn , such as Fis and IHF, can also help
to organize the DNA by binding to specific DNA sequences and promoting
looping.

In addition to protein-mediated genome packaging, prokaryotes also use

supercoiling to compact their DNA. Supercoiling is a twisting of the DNA double
helix that can occur when the DNA is under tension or when it is subject to the
action of enzymes called topoisomerases. By supercoiling their DNA,
prokaryotes can fit more genetic material into a smaller space.
 YEAST GENOME DIVERSITY

1.Yeast genomes refer to the complete set of genetic material (DNA) of yeast species.
Yeasts are single-celled fungi that are widely used in biotechnology, food science, and
medical research due to their ease of cultivation and genetic tractability.
2.The genomes of yeast species have been extensively studied, with the first complete
genome sequence of a eukaryotic organism, Saccharomyces cerevisiae,

3.Yeast genomes vary in size, from approximately 12 Mb in S. cerevisiae to over 50 Mb in

some Candida species. They also vary in gene content, with some species possessing over
10,000 genes while others have less than 6,000 genes. Yeast genomes typically contain both
coding and non-coding DNA, including regulatory elements such as promoters and
enhancers.
GENOME
FACTORS AFFECTING YEAST RIVERSITY
Polyploidy: Some yeast species, such as Saccharomyces cerevisiae, are diploid, while
others, such as Candida albicans, are tetraploid or higher ploidy. Polyploidization can lead
to changes in gene expression and can facilitate the evolution of new traits.

Horizontal gene transfer: Yeast genomes can acquire genetic material from other yeast
species, as well as from other fungi and bacteria, through processes such as transduction,
transformation, and hybridization.

Gene duplication and divergence: Gene duplication followed by divergence is a common

mechanism of genome evolution in yeast, which can lead to the evolution of new gene
functions or the optimization of existing functions.

Mobile genetic elements: Yeast genomes can carry mobile genetic elements such as
transposons, retrotransposons, and extrachromosomal circular DNA elements, which can
facilitate the spread of genes and contribute to genome plasticity.

Genome rearrangement: Yeast genomes can undergo rearrangements such as translocations,

inversions, and duplications, which can lead to changes in gene order and regulatory
elements.

Sexual reproduction: Yeast can undergo sexual reproduction, which allows for the exchange
of genetic material and can lead to the formation of new hybrid strains.
 CAENORHABDJIIS GENOME DIVERSITY
The Caenorhabditis genome refers to the complete set of genetic material (DNA) of the
nematode Caenorhabditis elegans

The genome of C. elegans was the first multicellular animal genome to be fully sequenced, and
it has since been used as a reference genome for comparative studies with other nematode
species.

The genome of C. elegans is relatively small, at approximately 100 million base pairs, and
contains around 20,000 protein-coding genes. It also contains a significant amount of non-
coding DNA, including regulatory elements such as promoters, enhancers, and non-coding RNA
genes.

The annotation of the C. elegans genome has revealed many insights into the molecular
mechanisms underlying various biological processes, such as development, aging, and behavior.

The C. elegans genome has also been used as a platform for genetic and functional analysis,
with techniques such as RNA interference (RNAi) and CRISPR/Cas9 gene editing enabling the
manipulation of specific genes and pathways.

ARABIDOPSIS GENE DIVERSITY

The genome of Arabidopsis thaliana was the first plant genome to be fully sequenced, and it
has since been used as a reference genome for comparative studies with other plant species.
The genome is relatively small, at approximately 125 million base pairs, and contains around
27,000 protein-coding genes.
The Arabidopsis genome is arranged into five chromosomes, which range in size from
approximately 20 to 30 million base pairs. The genome contains a significant amount of non-
coding DNA, including regulatory elements such as promoters, enhancers, and non-coding
RNA genes.

The annotation of the Arabidopsis genome has revealed many insights into the molecular
mechanisms underlying various biological processes, such as development, photosynthesi

The Arabidopsis genome has also been used as a platform for genetic and functional analysis,
with techniques such as gene editing and transformation enabling the manipulation of
specific genes and pathways.
 EUKARYOTIC GENOMEDIVERSITY
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 ORGANELLE GENOME

Organelles are specialized structures within eukaryotic cells that have their own
genomes. The two most well-known organelles with genomes are mitochondria
and chloroplasts.

MITOCHONDRIA: Mitochondria are organelles responsible for producing

energy in the form of ATP. They have their own genome, which is a circular
DNA molecule that is typically about 16,000 base pairs in length.
The mitochondrial genome contains genes that encode proteins involved in
oxidative phosphorylation, the process by which cells produce ATP from food
molecules
In addition to protein-coding genes, the mitochondrial genome also contains
genes for transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs) that are
necessary for protein synthesis within the mitochondria. These tRNAs and
rRNAs are similar in structure and function to those found in the cytoplasm of
the cell, but they are specific to mitochondrial protein synthesis.
The mitochondrial genome is inherited maternally in most organisms, meaning
that it is passed down from the mother to her offspring. This is because the egg
cell contributes most of the cytoplasm to the developing embryo, including the
mitochondria, while the sperm cell contributes very little.
The study of mitochondrial genomes has provided insights into various aspects
of human biology and evolution.

CHLOROPLAST: The chloroplast genome is the DNA molecule found within

the chloroplasts of plant cells and algae. The chloroplast genome is a circular
DNA molecule that is typically much larger than the mitochondrial genome,
ranging from 100,000 to 200,000 base pairs in length. It contains genes that
encode proteins involved in photosynthesis, including the light-harvesting
complexes, photosystem I and II, and the cytochrome b6f complex. The
chloroplast genome also contains genes for tRNAs and rRNAs, which are
necessary for protein synthesis within the chloroplasts.
Like the mitochondrial genome, the chloroplast genome is inherited maternally
in most organisms
 SIGNSFJCANCE OF REPEAT

REPETITIVE DNA:
Repetitive DNA sequences are DNA elements that occur in multiple copies throughout
the genome. They can be classified into two main types: tandem repeats and interspersed
repeats.
Britten and Kohne in 1968 identified repetitive DNA classes.
1) TANDEM REPEAT: Tandem repeats are repetitive DNA sequences that occur in a
head-to-tail fashion, where the copies are adjacent to each other. They can be further
classified into microsatellites, minisatellites, and satellite DNA. Microsatellites consist
of short repeats of 1-6 nucleotides, while minisatellites consist of longer repeats of
10-100 nucleotides. Satellite DNA consists of large blocks of repetitive sequences, often
located near the centromeres or telomeres of chromosomes.
2) Interspersed repeats are repetitive DNA sequences that occur at multiple locations
throughout the genome, and they can be further classified into two main types:
transposable elements and satellite DNA. Transposable elements are DNA sequences
that can move around within the genome, while satellite DNA consists of large blocks of
repetitive sequences, often located near the centromeres or telomeres of chromosomes.

TYPES OF INTERDESPERSED REPEATS :

1) Retrotransposons: Retrotransposons are a type of mobile genetic element that move
within the genome via an RNA intermediate. They are also known as retroelements
because they use a "copy and paste" mechanism that involves reverse transcription of
their RNA intermediates back into DNA, which is then integrated back into the genome
at a new location. There are two types of retrotransposons:
• Long terminal repeat (LTR) retrotransposons: These retrotransposons contain LTR
sequences at their ends, which facilitate their integration into the host genome. LTR
retrotransposons can also have additional genes, such as gag, pol, and env, which are
involved in their replication and assembly.
• Non-LTR retrotransposons: These retrotransposons lack LTR sequences and instead
use a poly-A tail and a primer binding site for reverse transcription. Non-LTR
retrotransposons can be further divided into two classes:
a) LINEs (long interspersed elements) LINEs are autonomous and encode the
necessary proteins for their transposition, LINE refers A-T rich euchromatic beads. In
everyone’s genome 60-100 copies of LINE-1 are capable of transposing. Uses RNA
intermediate do not have inverted terminal repeats.
b) SINE( short interspersed nuclear element) while SINEs are non-autonomous and rely
on LINE proteins for their transposition. Use LINE protein for life cycle.
2. DNA transposons: DNA transposons are a type of mobile genetic element
that move within the genome via a "cut and paste" mechanism that involves
excision of the transposon from one location and reinsertion into another
location.
DNA transposons typically encode a transposase enzyme that mediates their
transposition. There are several families of DNA transposons, including the hAT,
P, and mariner families. Replicate without RNA intermediary.
The significance of repetitive DNA in the genome is multifaceted. Here are some
of the main roles of repetitive DNA:
1. Structural role: Repetitive DNA sequences can contribute to the structural
organization of chromosomes and play a role in chromosome stability.
2. Regulatory role: Repetitive DNA sequences can play a role in gene regulation
by acting as binding sites for transcription factors or other regulatory proteins.
3. Evolutionary role: Repetitive DNA sequences can contribute to genome
evolution by providing a substrate for recombination and gene conversion, and
by allowing for the rapid evolution of new genes and gene families through gene
duplication.
4. Disease association: Some repetitive DNA sequences are associated with
genetic diseases. For example, the expansion of trinucleotide repeats in certain
genes is associated with disea

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 ORIGIN OF GENOME

The origin of the genome can be traced back to the early history of life on Earth,
around 3.5 to 4 billion years ago. The first organisms were likely simple prokaryotic
cells, which lacked a distinct nucleus and membrane-bound organelles. These cells
had a relatively small genome consisting of a single circular chromosome that
contained the genetic information necessary for their survival and reproduction.

Over time, these simple cells evolved into more complex organisms, including
eukaryotic cells that possess a distinct nucleus and membrane-bound organelles.
The genomes of eukaryotes are typically larger and more complex than those of
prokaryotes, and may include multiple linear chromosomes.

The origin of the genome is thought to have involved a combination of horizontal

gene transfer, gene duplication and divergence, and other evolutionary processes.
Horizontal gene transfer refers to the exchange of genetic material between different
organisms, which can result in the acquisition of new genes and traits. Gene
duplication can occur when a segment of DNA is replicated and retained in the
genome, allowing for the evolution of new functions through the accumulation of
mutations.

ACQUISITION OF
NEW GENE

The acquisition of new genes and gene families can occur through several mechanisms,
including horizontal gene transfer, gene duplication and divergence, de novo gene
evolution, and gene fusion or fission.

1.Horizontal gene transfer (HGT) is the process by which genes are transferred between
different organisms, often through mechanisms such as transduction, conjugation, or
transformation. HGT can allow organisms to rapidly acquire new traits and functions that
are advantageous in specific environments, and has played a major role in the evolution of
bacteria and archaea.
 2.Gene duplication and divergence occurs when a segment of DNA is replicated,
resulting in multiple copies of a gene or gene family in the genome. Over time, these
copies can accumulate mutations that alter their function, leading to the evolution of
new traits and functions.

3.De novo gene evolution involves the formation of entirely new genes from non-
coding DNA sequences or from the fusion of existing genes. This process can occur
through the acquisition of new regulatory elements or the evolution of novel protein-
coding sequences.
4.Gene fusion or fission occurs when two or more genes merge or split to form a
new gene or gene family. This can occur through mechanisms such as gene
rearrangements or trans-splicing, and can result in the evolution of new
functions and protein domains.