Download Introduction to Genetics and Genomics

Introduction to Genetics and
Genomics
51:123
Terry Braun M.S. (EE),
Ph.D. (Genetics)
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Announcements
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Textbook
Survey
Portal
NoMachine
Genetics
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Today
• Basic Mendelian Genetics
– Mendel’s laws
• Rule independent assortment
• Rule of segregation
– mitosis and meiosis
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Mendelian Genetics
• Humans have 22 pairs (diploid) of chromosomes
• Haploid would be 1 of each chromosome
• plus XX or XY
– genes on X/Y have sex-linked consequences
– male pattern baldness is on X (and recessive)
–  why are men twice as likely to get MPB (assuming
only 1 carrier)?
P(X) = ½
P(XX) = ¼ -- more on this later
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Definitions
chromosome – molecule of DNA (linear in eukaryotes)
gene – all portions of a genome that affects the expression of a
molecule (typically protein), but may include RNA and other
molecules (ligands)
allele – a specific variation (or instantiation) of a gene
DNA – deoxyribonucleic acid
RNA – ribonucleic acid
EST – Expressed Sequence Tag (a portion of an mRNA)
nucleotide – subunits of DNA (A,G,T,C), aka bases
gamete – egg or sperm cell
pharmacogenomics: is the study of how an individual's genetic
inheritance affects the body's response to drugs. The term comes
from the words pharmacology and genomics and is thus the
intersection of pharmaceuticals and genetics. It combines traditional
pharmaceutical sciences such as biochemistry with annotated
knowledge of genes, proteins, and single nucleotide polymorphisms.
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Genome Lexicon Overview (3 Bb
haploid)
Adenine
Thymine
Guanine
Cytosine
ATGC
purines AG
pyrimidines
CT
Size
Centromeres
Telomeres
Euchromatin
Heterochromatin
Cytogenetics 6
www.ensembl.org
Some sequence
>sequence
ATGCCGTATGCTAGCCCCTGAAATGAAAT
GATTCCTTTACCTTTCCCGCTGAGGGTAA
aatgcatgcccctgaaa
(FASTA format)
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Nucleus
Graphics used from www.roche.com
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Sizes
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# 0.1 nm (nanometer) diameter of a hydrogen atom
# 0.8 nm Amino Acid
# 2 nm Diameter of a DNA Alpha helix
# 4 nm Globular Protein
# 6 nm microfilaments
# 10 nm thickness cell membranes
# 11 nm Ribosome
# 25 nm Microtubule
# 50 nm Nuclear pore
# 100 nm Large Virus
# 200 nm Centriole
# 200 nm (200 to 500 nm) Lysosomes
# 200 nm (200 to 500 nm) Peroxisomes
# 1 um (micrometer)
# (1 - 10 um) the general sizes for Prokaryotes
# 1 um Diameter of human nerve cell process
# 2 um E.coli - a bacterium
# 3 um Mitochondrion
# 5 um length of chloroplast
# 6 um (3 - 10 micrometers) the Nucleus
# 9 um Human red blood cell
# 10 um
# (10 - 30 um) Most Eukaryotic animal cells
http://www.cbc.umn.edu/~mwd/cell_www/cell_intro.html
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Mendelian Genetics
• Rule of Segregation
– offspring receive ONE allele (genetic material, gene) from the
pair of alleles possessed by BOTH parents (offspring
receives 2 out of 4 possible)
– a gamete receives only one allele from the pair of alleles
possessed by an organism
– fertilization (union of 2 gametes) reestablishes the double
number
– easy to forget that there is very meticulous accounting of
gene number in reproduction
– estimated that 2/3 of fertilized eggs spontaneously abort
– if the gene number goes awry, usually detrimental
consequences for organisms (trisomy – 3 copies of chr 21 ==
Down's syndrome)
– almost never see extra copies of larger chromosomes
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Mendelian Genetics
• Rule of Independent Assortment
– alleles of one gene can segregate
independently of alleles of other genes
– (Linkage Analysis relies on the violation of
Independent Assortment Rule)
– (in general, 1 cM approx. 1 MB, but not
always)
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Dense Packaging
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Nucleotides
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Complementarity between bases
C–G
G–C
T–A
T–A
A–T
G–C
A–T
T–A
G,A = purines
T, C = pyrimidines
(U in RNA)
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Complementarity
http://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide/dnast.htm
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Directionality (5' -> 3'), Reverse
Complement
Seq
Rev
Com
G
A
T
C
T
A
A
C
G
A
T
A
T
A
T
C
A
T
T
C
G
A
G
C
DNA is "directional" -- made 5' to 3' prime
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Wikipedia: Directionality
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Directionality, in molecular biology, refers to the end-to-end chemical
orientation of a single strand of nucleic acid. The chemical convention of
naming carbon atoms in the nucleotide sugar-ring numerically gives rise to
a 3' end and a 5' end. The relative positions of structures along a strand of
nucleic acid, including genes, transcription factors, and polymerases are
usually noted as being either upstream (towards the 5' end) or downstream
(towards the 3' end).
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The importance of having this type of naming convention is easily
demonstrated by the fact that nucleic acids can only be synthesized in vivo
in a 5' to 3' direction, as the polymerase used to construct new strands must
attach a new nucleotide to the 3' hydroxyl (-OH) group via a phosphodiester
bond. Traditionally DNA and RNA sequences are written going from 5' to 3'.
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adenine
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DNA is double stranded
5’
3’
ATGCCCTTTGACG
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TACGGGAAACTGC
3’
5’
• directional
• reverse and reverse complement
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A genomic code for nucleosome positioning.
1: Nature. 2006 Aug 17;442(7104):772-8. Epub 2006 Jul 19.Click here to
read Links
* Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, Moore I, Wang
JP, Widom J.
Department of Computer Science and Applied Mathematics, Weizmann
Institute of Science, Rehovot 76100, Israel. [email protected]
Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA
from interacting with most DNA binding proteins. Nucleosomes have higher affinity for
particular DNA sequences, reflecting the ability of the sequence to bend sharply, as
required by the nucleosome structure. However, it is not known whether these
sequence preferences have a significant influence on nucleosome position in vivo, and
thus regulate the access of other proteins to DNA. Here we isolated nucleosomebound sequences at high resolution from yeast and used these sequences in a
new computational approach to construct and validate experimentally a
nucleosome-DNA interaction model, and to predict the genome-wide
organization of nucleosomes. Our results demonstrate that genomes encode an
intrinsic nucleosome organization and that this intrinsic organization can explain
approximately 50% of the in vivo nucleosome positions. This nucleosome positioning
code may facilitate specific chromosome functions including transcription factor
binding, transcription initiation, and even remodelling of the nucleosomes themselves. 22
Motivation for mitosis/meiosis
• terminology of bioinformatics
– DNA, genes, ESTs, proteins, mRNA,
transcripts, contigs, haplotype, etc.
• omit technical details
– however, provide a biological context for
these terms
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mitosis
• cell duplication (duplicate genetic material)
– DNA synthesis (broad bean)
• S phase (40%), Gap2 (25%), Mitosis (10%), Gap1
(25%)
• DNA duplicates in S phase (engineering marvel)
• Error rate ~ 1/10 billion * VS
1 bit error occurs in 256MB of ram every month **
=> 39 / 10 billion bytes
*Radman, Miroslav and Robert Wagner.
"The High Fidelity of DNA Duplication". Scientific American. pp40-46.
**EE Times, 1998
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mitosis
– mitosis
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prophase
metaphase
anaphase
telophase
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Start of mitosis
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Prophase
prophase
-chromosomes coalesce (shorten,
thicken – analogous to
“packaging”)
-each “chromosome” is now a pair
of sister “chromatids”
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Prophase
-other structural activities (formation
of spindle – microtubules that is
structural mechanism for separating
homologous chromosomes
--centrosome divides [individual
centriole])
--nuclear membrane breaks down
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Metaphase
-microtubules attached to
centromeres
-homologous pairs are lined up
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Anaphase
-physical separation of
chromosomes
-microtubule consumed
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Telophase
-sister chromatids are
separated (end of anaphase)
and pulled to opposite poles of
cell
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Telophase
-nuclear membranes
reform
-cell constricts and
separates
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Telophase
-chromosomes uncoil and
protein synthesis resumes
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2 Cells – complete copy of
genome, assuming no mistakes
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meiosis
• gamete formation (halving of genetic
material, diploid to haploid)
• but also duplicating (cell divides in 2
phases, meiosis I, and meiosis II)
– prophase I
– see Holliday structure for “homologous
recombination”
– origins for "independent assortment" and
"segregation"
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meiosis I
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prophase I
metaphase I
anaphase I
telophase I
meiosis I separates maternal and paternal
chromosome pairs
• meiosis II separates sister ("identical")
chromatids (or chromsome "pairs")
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meiosis II
• metaphase II
• anaphase II
• telophase II
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meiosis I
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prophase I
-chromosomes more
spread out (relative to
mitosis)
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prophase I
-identical pairs matched
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prophase I
-homologous pairs match up
(called a bivalent)
-crossing over can now occur
-note the difference from
meiosis (daughter cells are
unlikely to get identical
genetic material)
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prophase I
-as chromatids shorten, and thicken,
they are called “tetrads”
-“chiasmata” – regions where
crossover occurs
-virtually all tetrads form at least one
“chiasma”
-thought to stabilize the tetrad
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metaphase I
-tetrads line up
-microtubules attach to sister
chromosomes
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maternal centromeres
migrate together (but
independent of other
chromosome pairs)
Metaphase I
nuclear membrane breaks
down
paternal chromosomes
migrate together
tetrad
aster
crossing over
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maternal centromeres
Anaphase I
migrate together (but
independent of other
chromosome pairs)
remember
independent
paternal chromosomes
migrate together
* *
assortment *
**
**
aster
In mitosis, identical chromosomes are pulled apart,
maintaining haploid number. Here, they stay
together, but are shuffled independently.
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Telophase I
If I remove the recombinants….
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meiosis I reductional
reduces number of chromosomes to haploid number
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Total number of unique chromosomes in BOTH cells is 4, each cell now only has 2
anaphase I
–sister chromatids are pulled
to the same pole (in mitosis,
sister chromatids were pulled
apart)
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Telophase I
•cell divides
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metaphase II
–sister pairs line up
(what’s wrong in this figure?)
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Metaphase II
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Anaphase II
What's wrong with this figure?
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Telophase II
each gamete receives 1 allele (rule of segregation)
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meiosis II is equational division
because……
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meiosis II is equational division
reduces genetic material by ½ per cell, but does not reduce haploid number
(each gamete has 1 single complete copy of the genome – but reshuffled)
Again, the total number of distinct chromosomes is 4, but after meiosis, each
gamete has 2 (or ½ of the diploid genome)
When 2 gametes come together, the full complement of the genome is
restored.
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Anaphase II, Telophase II
-sister pairs are pulled apart
- cell constricts and divides
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Significance of mitosis
• two daughter cells (“clones”?)
• identical genetic material to parent cell
(assuming perfect fidelity of copy
mechanism)
• This is process that makes ~10^14 cells
from 1 cell in 9 months
• origins of "independent assortment" and
"segregation"
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meiosis
• significance
– four cells formed
– diploid to haploid in each gamete
– randomness of chromosome separation
• very large number of different chromosomal combinations
• gamete can get either maternal, or paternal chromosome  223 =
>> 8 million combinations
• more combinations of alleles because of recombination
• recombination – new arrangements of alleles due to either crossing
over or by independent segregation of homologous pairs
• 30,000 "genes"  230,023 combinations
• Number is probably larger because of number of regulatory
elements far exceeds the number of genes
– each gamete receives only one chromosome (rule of
segregation)
– anaphase 1 – direction of separation independent of tetrads (rule
of independent assortment)
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mitosis and meiosis
• Worth noting that DNA duplication is
analogous to "digital" copying as opposed
to "analog" copying
• In an analog copy, each copy may be
partially degraded
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End
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