BIMS 320 Dr. Dobsen TAMU Final Exam ch 16

What is genomics?

- DEF: The study of whole genomes or genomes in their entirety

- Genome:

1. the haploid set of chromosomes in a gamete. Or

2. The complete set of genes or genetic material present in a cell of an organism.

What are genomics areas of inquiry?

- Encompasses many areas of inquiry:

i. structural genomics

ii. functional genomics

comparative genomics

What is bioinformatics and what is it used for?

- What is Bioinformatics:

i. Use of computer hardware and mathematical software applications

ii. Organize, share and analyze data related to:

1. Gene structure

2. Sequence and expression

3. Protein structure and function

What is bioinformatics applications?

- Applications of bioinformatics:

1. Comparing D N A sequences

2. Identify genes in genomic D N A sequence

3. Finding gene-regulatory regions (promoters and enhancers)

4. Identify telomeric sequences

5. Predicting amino acid sequences

6. Deducing evolutionary relationships between genes

What is bioinformatics algorithms?

--> Algorithm-based software programs:

- Create D N A-sequence alignment:

1. Similar sequences of bases are lined up for comparison.

2. Alignment identifies overlapping sequences.

Allows scientists to reconstruct their order in the chromosome

What is the insert size for a BAC?

insert size capacity of 100-200 kb and are the preferred artificial chromosome for use as a cloning vector

What is the main difference between genomic and cDNA libraries?

- Libraries derived from the genomic D N A of an organism are called genomic libraries

- Those derived by m R N A are called complementary DNA (cDNA) libraries

True/False: Both subunits of insulin are needed to unite and make active insulin?

True

--> i. Synthetic human insulin was originally produced in bacteria

- Insulin regulates glucose metabolism

ii. The two insulin subunits were produced as fusion polypeptides, purified, and cleaved to release the insulin polypeptides

iii. The two subunits spontaneously unite to form active insulin.

True/False: Transgenic coho salmon express the growth hormone gene only in spring and summer?

true

True/False: Next-generation sequencing uses in vivo cloning and amplification?

False; uses In vitro

True/False: Next-generation sequencing uses cyclic flowcell sequencing?

True!

What was the benefit of whole-genome sequencing?

???? All DNA fragments in a genomic sample are sequenced without the need to insert DNA fragments into vectors and cloning them in host cells

How do restriction enzymes help with WGS and assembly?

- One strategy (shown here) involves using restriction enzymes to digest genomic D N A into contigs.

- Contigs sequenced and aligned using bioinformatics to identify overlapping fragments based on sequence identity.

Know ex of restriction enzymes that help with WGS and assembly discussed in class and how many contigs each one can give (Slide 14)

--> Eco R I digestion produces two fragments:

- Contigs 1 and 2-4

--> Bam H I produces three fragments

- Contigs 1-2,3, and 4

Contig def

DEF: continuous fragments:

- Overlapping fragments adjoining segments that collectively form one continuous D N A molecule within chromosome

Process of alignment of contigs to make a scaffold

- Alignment of the three contigs allows a portion of chromosome 2 to be assembled.

- Alignment of all contigs for a particular chromosome would result in assembly of a completely sequenced chromosome.

- ***In paired-end sequencing, a sequence is generated from both ends of D N A fragments of known size

- If the paired-end sequences flank a repetitive element, they can be used in assembling scaffold, a set of contigs physically linked by paired-end sequences that contain the repetitive element

- This approach cannot be used in cases when repetitive elements are longer than the largest available clones

What was the main problem of repetitive DNA

- >50% of mammalian genomes are comprised of repetitive DNA elements

- LINES (long interspersed elements: ~6-7 kb)

1. 500,000 in human genome (17%)

- SINES (short interspersed elements: ~300-bp)

1. ~1.6M in human genome (13%)

- Endogenous retroviruses

1. XXXX in human genome (8%)

- Satellite repeats

- Telomeres

How does paired end sequencing remove the main problem of repetitive DNA

- In paired-end sequencing, a sequence is generated from both ends of D N A fragments of known size

- If the paired-end sequences flank a repetitive element, they can be used in assembling scaffold, a set of contigs physically linked by paired-end sequences that contain the repetitive element

- This approach cannot be used in cases when repetitive elements are longer than the largest available clones

Know the paired end sequencing correlation of insert size and sequence coverage?

????????

What is the process of a de novo assembly? (ie., making libraries, sequencing, contigs, alignment, etc.)

- assembling a genome from scratch by overlapping DNA sequences into entire chromosomes

- (Look at review for picture)

True/False: PacBio SMRT sequencing uses a nanopore and electrical signature for each nucleotide

??????

What is used for resequencing home genomes?

Reference based genome assembly

What are SNPS, INDELs, and CNVs?

- Genetic variation ranges from single nucleotide polymorphism (SNP) differences to larger-scale structural variations, such as insertions and deletions (indels) and inversions

- A specific type of indel, called a copy-number variant (CNV), is a repeated section of genome where each repeat is greater than 1 k b long

- Many CNVs are small, but some are hundreds of k b in length and span multiple genes, resulting in alterations in gene dosage

How are SNPS, INDELs, and CNVs a part of WGS?

???????

What is a homologous gene and ortholog?

- Homologous genes:

i. Genes that are evolutionarily related

ii. Similarity searches are able to identify homologous genes.

- Orthologs:

i. Genes from different species thought to have descended from common ancestor

What is the most important part of building a genome sequence?

- Locating and identifying structural & functional elements in the genome:

i. protein-coding genes

ii. promoters, enhancers

iii. repetitive elements

iv. previously unknown regulatory elements

- This is the most important part of building a genome sequence.

What is the percent of the genome that codes for proteins? (how many genes does that make***)

- 2%

- 20000 protein coding genes

Alternative splicing lead to ______ number of genes than the number of predicted genes?

less

T/F: WES fails to identify gene regulatory regions that influence gene expression?

True

Transcriptome analysis can study expression of genes by the genome ________(a)________ and _________(b)________.

(a) qualitatively

(b) quantitatively

What are the two transcriptomic methods discussed in class?

- Qualitatively: identifies which genes are expressed and which are not

- Quantitatively: measures varying levels of expression of different genes

Proteomics uses ____________(a)______________ for separating hundreds of thousands of ________(b)_________ with high resolution.***

(a) Two dimensional gel electrophoresis (2DGE)

(b) proteins

Mass spectrometry uses what ratio of different ions in sample?***

Mass to charge (m/z)