Human Genome Organization Flashcards

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1
Q

size of haploid human genome sequence

A

3 x 10^9 bp

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2
Q

Human genomic DNA is distributed on __________ chromosomes

A

46

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3
Q

The chromosomes are found in __________ pairs:

1) 22 \_\_\_\_\_\_\_\_\_\_ 
2) 1 \_\_\_\_\_\_\_\_\_\_
A

23
autosomes (1-22)
pair of sex chromosomes (XX or XY)

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4
Q

Each chromosome is believed to consist of a __________

A

single, continuous DNA double helix

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5
Q

Human Genome

A
  • is a record of human evolutionary history
  • Reflects results of different selection pressures that have occurred over evolutionary time and shaped our genome (and shaped us)
  • Genes and genomic features that have been adaptive have been retained
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6
Q

Genotype + environment = __________

A

phenotype

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7
Q

Random genomic variation

A
  • is the fuel of evolution
  • Random variation in a highly ordered structure = almost always deleterious consequences
  • Genetic disease is the price we pay as a species to continue to have a genome that can evolve, i.e., that can adapt to new and changing environments
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8
Q

The human genome is __________ and continues to evolve

  • ~30 new mutations occur in each individual
  • Shuffling of regions at each meiosis due to __________
  • Can produce __________ DNA changes as well as __________ DNA changes
A

dynamic
recombination
somatic
germ-line

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9
Q

Organization of the genome

A
  • Gene-rich regions/chromosomes
  • Gene-poor regions/chromosomes
  • Stable regions: majority of genome
  • Unstable, dynamic regions; many are disease-associated
  • GC-rich regions (38% of genome), AT-rich regions (54% of genome)
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10
Q

__________ (i.e. non-random distribution) of GC-rich and AT-rich regions is basis for chromosomal banding patterns (cytogenetics, karyotype analysis)

A

Clustering

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11
Q

Clustering (i.e. non-random distribution) of GC-rich and AT-rich regions is basis for __________ (cytogenetics, karyotype analysis)

A

chromosomal banding patterns

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12
Q

Euchromatic regions

A

more relaxed

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13
Q

heterochromatic regions

A

more condensed; more repeat-rich

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14
Q

Genome sequencing effort focused on __________ region

A

euchromatic

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15
Q

__________ regions essentially unsequenced

A

Heterochromatic

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16
Q

Genome composition

A

1) 1.5% is translated (protein coding)
2) 20-25% is represented by genes (exons, introns, flanking sequences involved in regulating gene expression)
3) 50% “single copy” sequences
4) 40-50% classes of “repetitive DNA” - Sequences that are repeated hundreds to millions of times

17
Q

Tandem repeats

A

i.e. “satellite DNAs”

18
Q

examples of tandem repeats

A
  • Some are in different parts of genome, e.g. used as the basis for cytogenetic banding
  • Some (a particular pentanucleotide sequence) are found as part of human-specific heterochromatic regions on the long arms of Chr 1, 9, 16 and Y (hotspots for human-specific evolutionary changes)
  • “α-satellite” repeats (171 bp repeat unit) found near centromeric region of all human chromosomes; may be important to chromosome segregation in mitosis and meiosis.
19
Q

Dispersed repetitive elements

A
  • Alu family
  • L1 family
  • Alu’s and L1’s can be of significant medical relevance
20
Q

In dispersed repetitive elements, __________ may cause insertional inactivation of genes

A

Retrotransposition

21
Q

In dispersed repetitive elements, __________ may facilitate aberrant recombination events between different copies of dispersed repeats leading to diseases

A

repeats

22
Q

Alu family

A

e. g. of SINEs: Short Interspersed repetitive Elements
- ~300 bp related members
- 500,000 copies in genome

23
Q

L1 family

A

e. g. of LINES: Long Interspersed repetitive Elements
- ~6 kb related members
- 100,000 copies in genome

24
Q

Insertion-deletion polymorphisms

A

Minisatellites

Microsatellites

25
Q

Minisatellites

A
  • tandemly repeated 10-100 bp blocks of DNA

- VNTR (variable number of tandem repeats)

26
Q

Microsatellites

A
  • di-, tri-, tetra-nucleotide repeats
  • ->5 x 104 per genome
  • STRPs (Short Tandem Repeat Polymorphisms)
27
Q

Single Nucleotide Polymorphisms (SNPs)

A
  • frequency of 1 in ~1000 bp

- PCR-detectable markers, easy to score, widely distributed

28
Q

Copy number variations (CNVs)

A
  • variation in segments of genome from 200 bp – 2 Mb
  • can range from one additional copy to many
  • array comparative genomic hybridization (array CGH)
  • loci may cover 12% of genome
29
Q

Gene family is

A

composed of genes with high sequence similarity that may carry out similar but distinct functions

30
Q

__________ arise through gene duplication, a major mechanism underlying evolutionary change

A

Gene families

31
Q

Some CNV regions are involved in rapid & recent evolutionary change. Such regions are often

A
  • enriched for human specific gene duplications
  • enriched for genome sequence gaps
  • enriched for recurrent human diseases
32
Q

Role of genome architecture

A

Link between evolutionarily adaptive copy number increases and increase in human disease

33
Q

Limitations of genome sequencing and genotyping platforms

A

Nextgen DNA sequencing and Genome-wide association studies (GWAS)

34
Q

Nextgen DNA sequencing

A

– No mammalian genome has been completely sequenced & assembled
– Nextgen sequencing relies on short read sequences
—Complex, highly duplicated regions are typically unexamined
—Such regions are implicated in numerous diseases, e.g. 1q21

35
Q

Genome-wide association studies (GWAS)

A

– “Missing heritability” for complex diseases: Many large-scale studies implicate loci (e.g. SNPs) that account for only a small fraction of the expected genetic contribution
– Many regions of the genomes are unexamined by available “genome-wide” screening technologies: is this where the “missing heritability” lies?