Chapter 21 Lecture

Concepts Of Genetics Tenth Edition

Genomics, Bioinformatics, and Proteomics

Chapter Contents

21.1 Whole-Genome Shotgun Sequencing Is a Widely Used Method for Sequencing and Assembling Entire Genomes

21.2 DNA Sequence Analysis Relies on Bioinformatics Applications and Genomic Databases

21.3 Functional Genomics Attempts to Identify Potential Functions of Genes and Other Elements in a Genome

21.4 The Human Genome Project Reveals Many Important Aspects of Genome Organization in Humans

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Chapter Contents

21.5 The "Omics" Revolution Has Created a New Era of Biological Research

21.6 Comparative Genomics Analyzes and Compares Genomes from Different Organisms

21.7 Metagenomics Applies Genomics Techniques to Environmental Samples

21.8 Transcriptome Analysis Reveals Profiles of Expressed Genes in Cells and Tissues

21.9 Proteomics Identifies and Analyzes the Protein Composition of Cells

21.10 Systems Biology Is an Integrated Approach to Studying Interactions of All Components of an Organism's Cells

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21.1 Whole-Genome Shotgun Sequencing Is a Widely Used Method for

Sequencing and Assembling Entire Genomes

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Section 21.1

• Genome: complete set of DNA in a single cell of an organism

• Genomics, the study of genomes, allows the sequencing of entire genomes. It encompasses structural genomics, functional genomics, comparative genomics, Metagenomics

• Structural genomics focuses on sequencing

genomes and analyzing nucleotide sequences to identify genes and other important sequences such as gene-regulatory elements

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Section 21.1

• Approaches to genome sequencing include the clone-by-clone method and whole-genome shotgun method (shotgun cloning)

• The shotgun method is the favored method and was used to generate the first genome sequence

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Section 21.1

• The entire chromosome is cut into short, overlapping fragments using restriction enzymes

• The overlapping fragments are adjoining segments that collectively form one continuous DNA molecule within a chromosome and are called continuous fragments or "contigs"

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Section 21.1

• Algorithm-based software programs were developed for creating a DNA-sequence alignment where similar sequence of bases are lined up for comparison

• Alignment identifies overlapping sequences, allowing scientists to reconstruct their order in a chromosome

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Section 21.1

• The first computer-automated DNA sequencing instruments utilized dideoxynucleotides labeled with fluorescent dyes

• A single reaction tube is used, and sequencing reaction mixtures are separated on an ultra-thin diameter polyacrylamide tube gel called a capillary gel

• DNA fragments moving through the gel are scanned with a laser beam that stimulates the fluorescent dye on each DNA fragment to emit different wavelengths

• The emitted light is collected by a detector that amplifies and then feeds this information to a computer to process and convert into the DNA sequence

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Section 21.1

• The clone-by-clone approach generates contigs that are aligned first by fingerprinting the clones (e.g., use of restriction maps), and a minimal number of overlapping clones are then sequenced

• This approach is the organized sequencing of contigs from a restriction map instead of random sequencing and assembly

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Section 21.1

• The decision to designate a sequence as "final" is dictated by the amount of error genome scientists are willing to accept as a cutoff. This is called compiling

• Once compiled, a genome is analyzed to identify gene sequences, regulatory elements, and other features that reveal important information

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21.2 DNA Sequence Analysis Relies on Bioinformatics and Genomic

Databases

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Section 21.2

• Bioinformatics uses computer-based approaches to organize, share, and analyze data related to – gene structure – gene sequence and expression – protein structure and function

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Section 21.2

• GenBank is one of the most important genomic databases

• It is maintained by the National Center for Biotechnology Information (NCBI)

• Each sequence deposited in GenBank receives an accession number

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Section 21.2

• Annotation is the process of identifying – genes – their regulatory sequences – their functions

• BLAST is a software application used to compare a

segment of genomic DNA to sequences throughout the major databases to identify portions that align with or are the same as existing sequences

• Identification of open reading frames requires translation of all six reading frames

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BLAST results

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characteristics of a protein-coding gene

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Annotation of a DNA sequence containing part of the human b-globin gene

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Annotation of the sequence reveals several identifiable indicators that the sequence contains a protein-coding gene: it includes a promoter sequence, an initiation sequence, and three exons 22

two unshaded between exons represent introns that would be spliced out during mRNA processing

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Section 21.2

• Open reading frames (ORFs) are stretches of nucleotides that when translated to protein by computer analysis generate a series of amino acids prior to a stop codon and are suggestive of a protein-encoding gene

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21.3 Functional Genomics Attempts to Identify Potential Functions of Genes and

Other Elements in a Genome

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Section 21.3

• Functional genomics is the study of gene functions based on the resulting RNAs or possible proteins they encode as well as regulatory elements

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Section 21.3

• BLAST searches can be used to screen databases to compare a sequence to known sequence

• Similarity searches are able to identify homologous genes that are evolutionary-related in other organisms

• Figure 21.9 compares portions of the human leptin gene (LEP) with its homolog in mice (ob/Lep)

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Section 21.3

• Homologous genes from different species thought to have descended from a common ancestor are called orthologs

• Homologous genes in the same species are called paralogs

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Section 21.3

• A gene sequence is used to predict a polypeptide sequence

• The polypeptide can be analyzed for specific protein domains and motifs – Protein domains: ion channels, membrane-spanning regions,

secretion, and export signals – Motifs: helix-turn-helix, leucine zipper, or zinc finger motifs

• There are different genomic techniques being used that

are designed to map protein-DNA interactions and are useful for identifying genes that are regulated by DNA-binding transcription factors – Chromatin immunoprecipitation (ChIP) – ChIP-on-chip

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21.4 The Human Genome Project Reveals Many Important Aspects of Genome

Organization in Humans

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Section 21.4

• The Human Genome Project (HGP) was a coordinated effort to sequence and identify all the genes of the human genome

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Section 21.4

• HGP revealed that less than 2% of the genome codes for proteins and that there are only about 20,000 protein coding genes, although the exact number of human genes is still not certain

• Many genes code for multiple protein through alternative splicing, which produces an incredible diversity of proteins beyond the number of human genes

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Section 21.4

• Functional categories have been assigned for human genes on the basis of – functions determined previously – comparison to known genes and predicted protein sequences

from other species – predictions based on annotation and analysis of protein

functional domains and motifs

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Section 21.4

• The human genomic sequence is 99.9% the same with most genetic differences resulting from – single-nucleotide polymorphisms (SNPs)

• Single base changes in the genome • Many associated with disease conditions

– copy number variations(CNVs) • Segments of DNA that are duplicated or deleted

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Section 21.4

• It is possible to access databases and other sites on the Internet that display maps for all human chromosomes

• HGP's most valuable contribution will be the identification of disease genes and the development of new treatment strategies – Extensive maps have been developed for genes implicated in

human disease conditions

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