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B312 > L1, Genome Organisation > Flashcards

L1, Genome Organisation Flashcards

1
Q

Human genome vs Mitochondrial Genome: Details

A

Human…

  • 3 millon bps
  • 23 pairs of linear chromosomes

Mit…

  • 16,569 bps
  • Circular DNA
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2
Q

Prokaryotes: Number of protein coding genes examples

A
  • Mycoplasma genitalium (not free-living): 480
  • E.coli (free-living): 4000
  • S. cerveisiae (Brewer’s yeast): 6000
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3
Q

Eukaroytes: Number of protein coding genes, examples

A
  • Often a lot of redundancy in mammals
  • Arabidopsis Thaliana: 15000
  • Fruit flies: 13000
  • Mice: 23000
  • Human: 20000 (approx. 1% of human genome)
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4
Q

C-value paradox

A
  • ‘Lack of correlation between biological complexity and the intuitively expected protein-coding genomic information or DNA content’
  • DNA-complement
  • Proportion of junk DNA found to be higher in salamander than human
  • In salamander, total DNA is around 5x greater than humans
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5
Q

DNA Melt-Reassociation aka Reassociation Kinetics

A
  • Techinque for establishing broad types of DNA
  • Able to separate into highly repeated, moderately repeated and unique fragments
  • Measuring how much ssDNA remains and how much dsDNA has formed at given times
  • More repetition = more rapid reassociation, easier to find a match
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6
Q

Demonstrate the cot curve for DNA melt-reassociation, comment

A
  • See slide 10
  • Fraction reassociated against cot (initial concentration x time for reassociation)
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7
Q

Current Understanding: Broad classes of DNA sequences

A
  • Single copy
  • Gene families
  • Tandem Gene Arrays
  • Intermediate repeats (mostly transposable elements)
  • Simple sequence repeat DNA
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8
Q

Single copy DNA: % of genome and exon content

A
  • Makes up about 25% of genome
  • Only 1% contained in exons
  • Average gene 27kb with 9 exons
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9
Q

Functions of non-coding DNA

A
  • Majority can be transcribed
  • 22,219 non-coding genes
  • Structural RNAs -rRNAs, tRNAs, snRNAs
  • miRNAs - involved in gene regulation
  • lncRNA: Target regulatory proteins, disease markers, possible causative agents in disease (e.g. BACE1)
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10
Q

Human Gene Families: What are they? Give 6 examples with no. members

A

Similar sequences:

  • alpha-globins (4)
  • beta-globins (5)
  • actin (15)
  • keratin type I (19)
  • beta-tubulin (19)
  • alpha-tubulin (10)
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11
Q

What is a pseudogene?

A

Inactive copy within a cluster

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12
Q

TAGs: What are they, proportion of genomes

A
  • Gene clusters created by tandem duplications
  • One gene is duplicated, the copy is next to the original
  • Can encode large numbers of genes at a time
  • 14-17% of the human, mouse and rat coding genomes
    -> faster transcription
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13
Q

TAGs in the human embryo: Why are they particularly useful?

A
  • Human embryo has 5-10 million ribosomes
  • Embryonic cell number doubles within 24 hrs; single RNA gene may not be sufficient for RNA demands but tandem repeats of rRNA encoding genes allow a higher output (needs multiple RNA pols transcribing simultaneously)
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14
Q

Transposable elements in the human genome: Proportion, MEs, LINEs

Class length, acronyms

A
  • IM class length (see: Melt Curve Study)
  • Make up around 30% of the human genome
  • ME: Mobile element
  • LINE: Long interspersed nuclear element
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15
Q

Outline the two key types of transposable element in eukaryotes (with examples)

By transposition route

A

Retrotransposons
Transpose via and RNA intermediate;

  • Viral (retrovirus like e.g. Endogenous retroviruses or LINE-like e.g. LINE1, LINE2)
  • Non-viral (e.g. SINEs, processed pseudogenes)

DNA-DNA transposable elements
Transpose directly from DNA to DNA. Similar to bacterial transposons

  • Non active in human genome
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16
Q

Importance of eukaryotic transposable elements..

A
  • Play an important role in genome evolution (see reading)
  • Source of regulatory elements, sites of recombination
  • Insertions can cause disease
17
Q

Life-cycle of retroviruses:

A
  • Enter host
  • Randomly integrated by integrase
  • Provirus transcribed by host machinery
  • Co-proteins and more integrase thus produced
  • Assembly of full genome of retrovirus progeny
18
Q

Components of viral retrotransposons with functions:

A
  • Gag (Group antigens): Binding to RNA
  • Pol: Reverse transcriptase
  • Env: Envelope protein
  • Int
19
Q

What is HERV?

A
  • Human Endogenous Retrovirus
  • Generally, highly defective genomes
  • See reading
20
Q

LINE-1 (L1) element:

How many copies, length, extra features

A
  • > 500 000 copies in human genome
  • 1-6 kb in length
  • Only 40-50 are active
  • 2 open reading frames (ORF1, ORF2)
  • No long terminal repeats (LTRs)
21
Q

Timing and tissue specificity of L1 transposition

A
  • Mostly repressed by methylation
  • In tumours, demethylation increases transposition
  • Many unique insertions take place in germ cells
  • Also: Early embryos, neural progenitors during childhood -> negative impact on brain function if activity and therefore mobility are high in childhood
22
Q

Characteristics of Non-viral elements (types and features)

A

SINEs; Short interspersed nuclear elements (13% of genome):

  • Genomic copies of small RNAs
  • Most belong to Alu family (7SL RNA) - identifiable feature of human genome
  • Also copies of snRNAs and rRNAs
    Processed pseudogenes:
  • Genomic copies of mRNAs
23
Q

Alu sequences: (stats, comparisons)

A
  • 150-300bp
  • 1 million copies, 10% of human genome
  • Occur approx. every 6kb
  • Transcribed to give RNA
  • Site of recombination (hotspots) can differ (particularly between humans and chimpanzees)
  • Insertions have caused inherited disease
24
Q

What are SVAs?

A

SINE-VNTR-Alu:

  • Non-autonomous hominid specific retrotransposons
  • Don’t exist in old world monkeys
  • Several subtypes
  • Can be transcribed
  • Mobilise by LINE L1 retrotransposase
  • Associated with disease in humans (see examples)
25
Q

STR stats:

A
  • 5% of genome
  • Repeat unit length of 1-6 bp
  • Total array length up to 100bp
  • Length variations can affect gene expression in some hereditary diseases (e.g. HD, autism, schizophrenia)
26
Q

Minisatellite/microsatellite DNA lengths/stats, uses

A
  • Repeat unit length 15-100 bp (mini) and 2-5 bp (micro)
  • Total array length 0.5-30kbp (mini), 60-200b (micro)
  • Array length is variable - VNTRs or STRs
  • Can be used in paternity and forensic analysis and in gene mapping
27
Q

+ Transposable elements make up …. of human DNA

A

Around 30%

28
Q

+ SINEs and LINEs make up … and …. of the human DNA

A
  • 13% (SINEs)
  • 21% (LINEs)
29
Q

+ HERVs are:

A
  • Human endogenous retroviruses
  • About 8% of human genome

B312 (15 decks)

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