Genome Organization

Question 1

What are the components of chromatin?

Answer 1

DNA + histones + non-histone proteins (acidic)

Question 2

How many base pairs are in the haploid human genome sequence?

Answer 2

3e9 base pairs

Question 3

What were some of the findings from the first human genome sequence?

Answer 3

• Human genome is not static
• There is no “one” human genome; there are many.
• Genome is not organized in a random manner

Question 4

Give three examples of how the human genome is not static.

Answer 4

1. ~30 new mutations occur in each individual
2. Shuffling of regions occur at each meiosis due to recombination
3. Somatic DNA changes can be produced as well as germ-line changes

Question 5

What is single nucleotide polymorphism?

Answer 5

A comparative difference in a single base pair

Question 6

If there is an average of 1 SNP for every 1000 base pairs between any two randomly chosen human genomes, approximately how many differences are there?

Answer 6

3 million

even though 99.9% identical

Question 7

Which chromosome is classified as “gene-rich”?

Answer 7

Chromosome 19

Question 8

Which chromosomes are classified as “gene-poor”?

Answer 8

Chromosomes 13, 18, 21

Question 9

What are the differences between euchromatic and heterochromatic regions of the genome?

Answer 9

Euchromatic regions are more relaxed and the focus of genome sequencing effort; still many unsequenced gaps in the regions; make up most of the genome

Heterochromatic regions are more condense with more repeats; the regions are essentially unsequenced; tend to be near centromeres and make up less of the genome

Question 10

What is the general genome composition?

Answer 10

1.5% is translated
20-25% is represented by genes
50% “single copy” sequences
40-50% classes of “repetitive DNA” related hundred of millions of times

Question 11

Acknowledging that GC-rich and AT-rich regions are not random, what percent of the genome is GC- and AT-rich?

Answer 11

38% GC-rich

54% AT-rich

Question 12

What are the two classes of repetitive DNAs?

Answer 12

1. Tandem repeats (“satellite DNAs”)

2. Dispersed repetitive elements

Question 13

What are two of the locations of certain tandem repetitive DNA?

Answer 13

A particular pentanucleotide sequence is found as part of a heterochromatic region on the long arms of Chromosome 1, 9, 16, and Y, which are hotspots

“alpha-satellite” repeats are a 171 bp repeat found near centromeric region of all chromosomes; may be important to segregation during mitosis/meiosis

Question 14

Give an example of a short interspersed repetitive element.

Answer 14

Alu family
~ 300 base pair related members
500,000 copies in the genome

Question 15

Give an example of a long interspersed repetitive element.

Answer 15

L1 family
~6 kilobase pair related members
100,000 copies in the genome

Question 16

What are dispersed repeats in the genome and how can they be medically relevant?

Answer 16

They are retrotransposition elements that can effectively copy their own sequences into other locations in the DNA
=> retrotransposition of a copy into the middle of another gene may inactivate that gene
=> NAHR leading to disease

Question 17

What is NAHR (non-allelic homologous recombination?

Answer 17

When repeats facilitate aberrant recombination events between different copies of dispersed repeats leading to disease

Question 18

What are the types of DNA variation that occur between genomes?

Answer 18

Insertion-deletion polymorphisms
SNPs (single nucleotide polymorphisms)
CNVs (copy number variations)

Other:
Chromosomal variation, larger scale variation, rearrangements, translocations
Silent variants

Question 19

What are the two types of insertion-deletion polymorphisms?

Answer 19

Minisatellites:
tandemly repeated 10-100 bp blocks of DNA = highly variable number
VNTR (variable number of tandem repeats) = can be used for genetic fingerprinting

Microsatellites:
di-, tri-, and tetra- nucleotide repeats
more than 5e4 per genome
aka STRPs (short tandem repeat polymorphisms)

Question 20

Why can SNPs be used for genetic fingerprinting?

Answer 20

SNPs can be detected by PCR markers
They are easy to score
They are widely distributed

Question 21

What is copy number variation?

Answer 21

Variance in the number of copies of a particular gene in an individual
In segments from 200 bp to 2 million bp

Question 22

What is a gene family and how did they arise?

Answer 22

Gene families are genes that have high sequence similarity, over 85%, that may carry out similar but distinct functions

They arise through gene duplication; when a gene duplicates it frees up one copy to vary while the other copy continues to carry out a critical function

Question 23

What is structural variation of the human genome?

Answer 23

All changes in the genome are NOT due to single base pair substitutions
=> CNV (copy number variations) is the primary type of structural variation

Question 24

What are the characteristics and implications of CNV (copy number variations)?

Answer 24

• CNV loci are the primary type of structural variation and may cover 12% of the genome
• CNV is implicated in increasingly larger number of diseases
• CNV regions are involved in rapid/recent evolutionary change

Question 25

CNV regions involved in recent evolutionary change are often enriched for what?

Answer 25

• human specific gene duplications
• genome sequence gaps
• recurrent human diseases

Question 26

What are the limitations of NextGen DNA sequencing?

Answer 26

• No mammalian genome has been completely sequenced/assembled
• NextGen relies on short read sequences => complex regions go unexamined, these can be regions implicated in many diseases (i.e. 1q21)

Question 27

What are the limitations of GWAS (genome-wide association studies)?

Answer 27

• Many large scale studies implicate loci that account for only a fraction of the expected genetic contribution = ‘missing heritability’
• Many regions of the genomes are unexamined by available ‘genome-wide’ screen technologies

Question 28

What makes up the histone octamer?

Answer 28

Two copies each of four core histones:

H2A, H2B, H3 & H4.

Question 29

Human cells have hundreds to thousands of mitochondria. What are the features of the mitochondrial genome?

Answer 29

• Reside in cytoplasm => inheritance is exclusively maternal (allows tracing of maternal lineages over human evolutionary history)
• 16 kb genome; few dozen genes; uses slightly different triplet code; vast majority of proteins that function in mitochondria are encoded by nuclear genes
• Several genetic diseases caused by mutations in mitochondrial genes.

Question 30

What is the estimated number of human genes, and what are the different types of genes?

Answer 30

25,000-30,000 genes

▪ protein-encoding genes
▪ RNA-encoding genes
▪ “pseudogenes” = non-functional but homologous copies of existing genes.