Unit 15 - Functional Genomics and Bioinformatics

What are the three basic components that computer analysis of genetic sequences usually relies on?

-A computer -A computer program -Some type of data

What do approaches to bioinformatics include?

-Analyzing sequences for characteristics of genes, such as open reading frames -Comparison of sequences to known genes -Annotation to indicate distribution and other characteristics of a gene

What are examples of applications of DNA microarrays?

-Cell-specific gene expression -Tumor profiling -Elucidation of metabolic pathways

Besides the examples listed in Table 24.3, list five types of short sequences that a geneticist might want to locate within a DNA sequence.

-Centromeric sequences -Origins of replication -Telomeric sequences -Repetitive sequences -Enhancers

What are some examples in which RNA sequencing is used?

-Comparison of different cell types -Healthy vs diseased cells -Transcripts in cells from different stages of development -Changes in response to different environmental agents such as hormones or toxic chemicals

List different types of short sequence elements that a geneticist might want to locate within a DNA sequence.

-Promoter -Response elements -Start codon -Stop codons -Splice site -Polyadenylation signal -Highly repetitive sequences -Transposable elements

Discuss the objectives of a genome database.

-To organize the genetic information of a single species -To identify all of the known genes and indicate their map locations within the genome -To have a concise description of a sequence, the name of the organism from which the sequence was obtained, and the function of the encoded protein, if it is known

If there is a 100% match between the sequence used for searching and a sequence in the database the E value would be ____________ .

0

Describe the steps to RNA sequencing.

1. Isolate RNA 2. Break RNA into fragments 3. Attach short oligonucleotide linkers to the ends of mRNA 4. Make cDNA via reverse transcriptase PCR, using RNA as templates. The primers are complementary to the linkers. 5. Sequence cDNA using next-generation sequencing. 6. Using computer technology, align the cDNA sequences along the genomic sequence.

Describe the steps to making a DNA microarray.

1. Obtain the sequence of the genome. 2. Make primers that flank any given gene. 3. Use PCR to synthesize the DNA 4. Spot sequences individually onto a slide.

What are the steps of a microarray experiment?

1. RNA is isolated from cells and used to make labeled cDNA. 2. Labeled cDNA is layered onto a DNA microarray. 3. Microarray is washed with a buffer to remove unbound cDNAs. 4. Microarray is placed in laser scanner. 5. Fluorescence intensity of spots is quantified and used to estimate cDNA amount.

When comparing (i.e., aligning) two or more genetic sequences, it is sometimes necessary to put in gaps. Explain why.

A gap is necessary when two homologous sequences are not the same length.

If the files in the database include additional information such as the name of the organism from which the sequence was obtained the database is said to be ____________ .

Annotated

You are carrying out an RNA-Seq experiment. You encounter a problem with attaching the oligonucleotide linkers to the RNA fragments. At what step will RNA-Seq be halted?

At the cDNA synthesis step

What does BLAST stand for?

Basic Local Alignment Search Tool

The collection, storage, and analysis of DNA, RNA, and protein sequences is called _____________.

Bioinformatics

The goal of _____________ is to analyze biological information using a mathematical/computational approach.

Bioinformatics

What field of study of genetics applies statistics and mathematical tools to genetic sequences in order to better understand the genetic information?

Bioinformatics

BLAST is a ______.

Computer program that can locate homologous sequences within a large database

A ____________ is a site that is identical or similar across multiple species.

Conserved site

A ____________ microarray is a slide with many DNA sequences spotted on it.

DNA

What types of information are stored within a database?

DNA, RNA, or protein sequences

A first step in the computer analysis of genetic data is the generation of a ____________.

Data file

What best describes a collection of information in a form suitable for storage and manipulation?

Data file

A ____________ is a collection of computer files stored in one place.

Database

Discuss two changes (mutations) that could happen during the evolution of homologous genes that would explain the occurrence of gaps in a multiple-sequence alignment.

During evolution, the sequences can incur deletions and/or additions that make the sequences shorter or longer than in the original ancestral gene.

When comparing sequences with the BLAST program, the _____________ represents the number of times that the match or a better one would be expected to occur purely by random chance in a search of the entire database.

E-value

In ______________, the chromosomal coding sequences may be interrupted by introns (analyze for regulatory elements, motifs, start/stop codons, etc.).

Eukaryotes

The goal of _______________ is to elucidate the roles of genetic sequences in a given species. In most cases, it aims to understand gene function.

Functional genomics

An example of a nucleotide database is _____________.

Genbank

The most common use for DNA microarrays is the study of ________________.

Gene expression patterns

A ____________ consists of two or more copies of homologous genes within the genome of a single organism.

Gene family

DNA microarrays can be used to look for insertions or deletions if labeled ____________ DNA is used.

Genomic

The study of the structure, function, and inheritance of the genome (entire set of genetic material) of an organism is ____________.

Genomics

In a microarray, what do the colors stand for?

Green - expression exclusively in normal cell Red - expression exclusively in abnormal cell Yellow - equal expression Black - no expression Different shades correlate with expression in one cell more than the other

A sequence element or motif is a specialized sequence that ______.

Has a particular meaning or function

The BLAST program starts with a protein or DNA sequence and then locates ____________ sequences within a database.

Homologous

What are genes that are derived from the same ancestral gene called?

Homologous

Orthologs are ______.

Homologous genes in different species

Paralogs are ______.

Homologous genes within the same species

cDNA from two cell types can be differentially labeled and ____________ to the microarray.

Hybridized

The program BLAST would be best used for what purpose?

Identify related sequences to a given DNA sequence in a database.

The amount of similarity between two DNA sequences is related to the ______.

Length of time that has passed since the two species diverged from a common ancestor

In BLAST, the better the match the _________ the E value.

Lower

What technique would be most useful and efficient in comparing the different gene-expression patterns between different developmental stages of mouse embryogenesis?

Microarray analysis

What is a region of a nucleotide sequence that does not contain any stop codons called?

Open reading frame

What is the term for two genes from two different species that are similar in sequence and serve the same function in each species?

Orthologs

An example of a protein motif database is _____________.

PIR

The human genome contains three genes for enolase (α, β, γ), whereas yeast contains just one gene for enolase. The three human enolase genes are _____ of each other, whereas the human and yeast enolase genes are _____ of each other.

Paralogs; orthologs

In __________, long ORFs are contained within the chromosomal gene sequences.

Prokaryotes

The study of the functions and interactions of proteins is termed ______________.

Proteomics

The transcriptome is the set of all ______ produced in one cell or a population of cells.

RNA molecules

What is a method for sequencing cDNA using next-generation sequencing?

RNA sequencing

The multiple sequence alignment approach was originally proposed by _______________ and ______________ in 1970.

Saul Needleman and Christian Wunsch

RNA-Seq is a method used to ______.

Sequence complementary DNAs derived from RNAs

A specialized sequence with a particular meaning or function is called a __________.

Sequence element or motif

Two DNA sequences are likely to be ______ if a short length of time has passed since the two species diverged from a common ancestor.

Similar

What is the difference between similarity and homology?

Similarity means that two genetic sequences are similar to each other. Homology means that two genetic sequences have evolved from a common ancestral sequence. Homologous sequences are similar to each other, but not all short similar sequences are due to homology.

Each spot on a microarray contains ___________ DNA from ___________ gene(s).

Single-stranded; specific

A DNA microarray contains __________ on a ____________ silica glass or plastic slide.

Tens of thousands of different DNA sequences; small

What did Saul Needleman and Christian Wunsch demonstrate?

They demonstrated that whale myoglobin and human b-hemoglobin have similar sequences.

What can gene chips be used for?

To establish levels of genetic variation

The set of all RNA molecules that are transcribed in one cell or a population of cells is called the ______________.

Transcriptome

What is each hemoglobin protein composed of?

Two a-chains and two b-chains

When mRNA is used to direct the synthesis of DNA, the resulting DNA is called __________.

cDNA

To compare gene expression between two cells ____________ is isolated from each cell type.

mRNA

What are disadvantages of using RNA sequencing over a microarray?

•Data storage challenging (large data set) *** •Analysis more complex e.g. bioinformatics - computer Infrastructure and trained Personnel •Cost

What are disadvantages of using a microarray over RNA sequencing?

•Depends on prior sequence knowledge •Hybridization biases •Can't detect structural or isoform variations •Less quantitative

What are advantages of using RNA sequencing over a microarray?

•More comprehensive •Not dependent on prior sequence knowledge •Can detect structural variants - e.g. gene fusions and alternative splicing

What are advantages of using a microarray over RNA sequencing?

•Robust, reliable •High-throughput •Easily automated •Straightforward data analysis *** •Low(er) cost

In humans, 9 paralogous genes are functionally expressed. The 9 paralogous genes fall into what two categories?

•a-chains •b-chains