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BMS-II > Human Genome And Karyotype > Flashcards

Human Genome And Karyotype Flashcards

1
Q

What is another term for genome size?

A

C-value.

Humans: 3.2X10^9 BP of DNA in each somatic cell

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2
Q

How many genes do we have?

A

22,000

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3
Q

When is DNA packed into chromosomes? What is it referred to during other times?

A

During mitosis.

Chromatin (DNA+histones)

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4
Q

What is DNA wrapped twice around 8 core histone proteins?

A

Nucleosome

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5
Q

When does chromatin condense into chromosomes?

A

During prophase of mitotic cell division (after replication)

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6
Q

After DNA is replicated, what do they form into?

A

Sister chromatids (attached at centromere)

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7
Q

How does increased genome complexity arise?

A
  1. Duplication of existing sequences followed by divergence and selection
  2. Incorporation of DNA from other species (lateral transfer)
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8
Q

What was/is the ENCODE project responsible for?

A

Encyclopedia of DNA elements

Mapped genome in 80 diff cell types:

  • > transcripes ans protein encoding exons
  • > chromatin (histone) modification and DNA methylation
  • > DNAse hypersensitivity (binding of regulatory factors exposes DNA to cleavage while DNA in nucleosomes is protected)

->Binding of 100 known TF, RNA Pol II/III and other proteins

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9
Q

What are some conclusions from the ENCODE project?

A

Chromatin has 7 functional states

60-75% is transcribed into RNA

Non-coding transcripts (regulatory role) are nearly as abundant as protein-encoding genes.

At least 80% of genome is likely to be functional

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10
Q 
How many SNPs are in the genome?
Insertions/Deletions?
Block substitutions?
Inversions?
Copy Number variations?
A

3,000,000

800,000 indels

50,000 block

100 inversion

50-100 small and large (alpha amylase varies from 3-14 tandem copies)

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11
Q

What do repetitive sequences consist of?

A
  1. Tandem repeats (genes or blocks of genes)
  2. Short repeats (each present in many copies)
  3. Retrotransposons - repeats which are products of reverse transcriptions

**Repeats are difficult to sequence

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12
Q

Why are repeats substrates/’hot spots’ for recombination?

A

Similiar/identical in nucleotide sequence.

Recombination between them may cause inversion, duplication, or deletions.

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13
Q

What are examples of recombination?

A

Red-green color blindness
Rh-factor
Velocardiofacial syndrome
Hemophilia A (x-linked)

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14
Q

What is red-green color blindness caused by?

A

Recombination between duplicated genes with almost identical sequences on x-chromosomes.

Misalignment in chromosomes leads to only one gene being expressed in color blind pts.

Misalignment followed by meiosis (trait gets missed)

X with only single receptor gene -> inability to distinguish red/green

X with 1 red + 2 green receptors (still be phenotypically normal)

Red (long receptor)
Green (medium)

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15
Q

Where does recombination occur in a microdeletion or segemental aneuploidy syndrome? What are some examples?

A

Occurs between large repeats resulting in deletion of a block of DNA that contains multiple genes

DiGeorge(Velocardiofacial Syndrome)
->del 22q11; failure of pharyngeal pouches to develop (parathyroid, thymus, cardiac defects)

Prader-Willi and Angelman syndrome
->del 15q11-13

Dx with FISH probe for deleted region

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16
Q

Why are DNA satellites called that?

A

Old technique when DNA was fractionated by density , reoeats would form a small satellite seen next to DNA peak b/c they differ from it in base composition

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17
Q

Where do satellite sequences occur most frequently?

A

Mostly at centromeres and telomeres

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18
Q

What are micro-satellites used most frequently for?

A

Identigy specific chromosomes in genetic counseling

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19
Q

What are retroransposons?

A

I.e. Transcription by RNA Pol II,

MRNA gets converted to dscDNA via reverse transcription & that gets integrated into a new genomic site

Estimated for up to 25% of increased complexity of human genome.

The inserted rtRNA into DNA can disrupt a gene at the integration site.

20
Q

What kind of retrotransposons exist?

A

LINE - long interspersed nuclear elements; mRNAs encoding reverse transcriptase

SINE - short interspersed nuclear elements; copies of short cellular RNA

–>Alu sequences (1/kb,, contain a restriction site more Alu1, unique to human DNA

Pseudogenes - copies of cellular mRNAs, not transcribed because they lack promoter sequences.

21
Q

When should we consider a diagnosis of chromosome abnormality?

A
  1. Problems with physical or mental development
  2. Infertility, spontaneous abortion, still birth
  3. Pregnancy in woman 35 and older
  4. Cancer
22
Q

What are some karyotyping techniques used?

A
  1. G banding: Giemsa staining creates pattern of dark and light bands unique to each chromosome
  2. FISH: detects changes too small to see in g banding
  3. Comparitive genomic hybridization (CGH)L detects deletions or duplications even if their location is not known

Only can see changes that a technique is able to pick up on

23
Q

How do we do G-banding technique? Why is colchicine important for this technique?

A

Incubate cells in colchicine (binds tubulin and prevent spindle function arresting cell in metaphase)

Chromosomes condense steadily during prolonged metaphase. Over time number of cells in mitosis increases, but number of visual bands decrease

Stain with Giemsa dye

Std Karyotype: 500-800 bands per haploid set of chromosomes

24
Q

How do we identify chromosomes based on their G bands?

A

Size (1largest-22smallest)
Centromere position
Dividing pattern

25
Q

what is p arm? Q arm?

A 
P= petite
Q= queue (long arm)
26
Q

What are metacentric chromosomes? Sub-metacentric? Acrocentric?

A 
Meta = centromere occur in middle (Chr3)
Sub-meta = Off center centromere (Chr 18)
Acrocentric = centromere located very close to telomere, still some DNA on the other side

Telocentric - not present in humans, always some DNA btwn centromere and telomere

27
Q

What is g-banding resolution good for?

A

Detect structural change regardless of nature or location, but:

  • Detects only relatively large changes on chromosome
  • Lower resolution limit is one band
  • 500-800 bands for metaphase G banding
  • 1band is about 4-7MB; 45 or so genes

Smaller changes -> need FISH or CGH

28
Q

What is a requirement of FISH?

A

Need to know what sequence you are looking for!

Chromatin/chromosomes are fixed to slode and probe binds to DNA of complenetary site

29
Q

What is difference between interphase FISH and metaphase FISH?

A

Interphase: happens on chromatin, faster b/c we can do it on clinical samples. LOWER RESOLUTION (DNA isnt condensed)

Metaphase: chromosomes, requires a culture to amplify cell number and then incubate in colchicine

30
Q

What is general sequence of FISH?

A

Usually have at least 2 probes.

One is used for locating chromosome (internal control) other is used for detecting the critical region.

FISH wont rule out minor changes like a SNP

31
Q

What is a disadvantage of FISH detection?

A

Only detects presence/absence/position of DNA to which the probe binds

Cannot detect single nucleotide changes

32
Q

What is comparative genome hybridization?

A

Array of oligonucleotides immobilized at different positions on a glass slide (microarray) complementary to sequences spaced across genome.

33
Q

What are some strengths of CGH? Limitations?

A

Can detect very small changes anywhere in genome, we do not need to know where to look

Detects only increase/decrease in copy number –>deletions/duplications

CANNOT DETECT REARRANGEMENTS W/O GAIN or LOSS (inversions or translocations)

34
Q

Are diploid conceptions with two maternal or two paternal chromosome sets viable?

A

NO

35
Q

What is euploidy?

Aneupolidy?

A

Euploidy: normal number of chromosomesl 22 pairs of autosomes and one pair of sex chromosomes. (46, XX or 46,XY)

Aneuploidy: extra or missing chromosomes
Missing-> monosomy (2N-1)
Trisomy-> extra (2N+1)

Most are lethal

36
Q

What are the aneuploidys that aren’t lethal?

A

Exception:
Monosomy X
Trisomy 13,18,21
Triploidy (3N) = 2 sperm fertilizing 1 egg = 3 complete sets of chromosomes = lethal)

37
Q

Give karyotypes for Male w/ DS
F w/ trisomy 13
Kleinfeelter syndrome (male)
Female with Turner syndrome

A

47, XY, +21

47, XX, +13

47, XXY

45, X

38
Q

What are the abnormalities of chromosome structure?

A

Translocation: genetic material moved from one chromosome to another
->Reciprocal = two chromosomes exchange segments

->Non-reciprocal = movement of DNA from one chromosome to another

Inversion: segment is inverted in respect to rest of chromosome

39
Q

How do we identify and name abnormal chromosome identity?

A

Chromosome centromere stays constant.

40
Q

Where do the most common translocations happen?

A

Acrocentric chromosomes

Short (p) arms of these chromosomes contain only genes for ribosomal RNA (rDNA gene copy number is very large)

41
Q

What are robertsonian translocations?

A

45, XX, -14, -21, +rob(14q;21q)

Carrier usually has a normal phenotype.

Don’t lose DNA b/c q arms maintained.
P arms have the mRNA copy numbers.

Maintain 1 normal copy of 14/21

42
Q

What are the lethal gametes produced by Robertsonian translocation?

A

Trisomy 14 [rob(14;21)+14]

Trisomy 21 [rob(14;21)+21]

43
Q

What is the karyotype of isochromosome 21?

A

45, XX, t(21;21)(q10,q10)

This is viable since it is diploid for 21q. ->gametes recieve either i21q or no chromosome 21)

Fertilization leads to -Trisomy 21 (only viable in Down Syndrome)
-Monosomy 21 (lethal)

44
Q

How would we label a pericentric conversion? How can we tell a pericentric inversion from a paracentric?

A

46, XY, inv(6)(p23;q21)

May be phenotypically normal

Pericentric INVOLVES THE CENTROMERE

Paracentric inversion -> breakpoints occur in the same arm

45
Q

How would we karotype a duplication?

Deletion?

A

46, XX, dup8(q13->qter) ; ter=terminus

46, XY, del19(q13.1,q13.3)

BMS-II (9 decks)

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