TOPICS & REFERENCES

 The human genome and the chromosomal basis of heredity

 Organization of the human genome.

 Mitochondrial inheritance.
 The Human Karyotype.
 Structure of human chromosomes.
Human genetic diversity:
 Mutation and Polymorphism.
 Single Nucleotide Polymorphisms;
 Insertion-Deletion Polymorphisms;
 Copy Number Variants
 Inversion Polymorphisms
 Human Genome
• The publicly funded Human
Genome Project began in 1990
under the direction of James
Watson, the co-discoverer of the
double-helix structure of DNA.
Eventually the public project was
led by Dr. Francis Collins, who
had previously led a research team
involved in identifying the CFTR
gene as the cause of cystic fibrosis.
In the United States, the Collins-
led HGP was coordinated by the
Department of Energy and the
National Center of Human
Genome Research, a division of
the National Institutes of Health
Project
. It established a 15-year plan
with a proposed budget of $3
billion to identify all human
genes, originally thought to
number between 80,000 and
100,000, to sequence and map
them all, and to sequence the
approximately 3 billion base
pairs thought to be comprised
by the 24 chromosomes (22
autosomes, plus X and Y) in
humans
 Organization of the Human Genome
• The human genome contains 3.1 billion nucleotides, but protein-coding sequences make up only about 1.5
percent of the genome.
• Regulatory elements that influence or determine patterns of gene expression during development or in tissues
were believed to account for only approximately 5% of additional sequence, although more recent analyses of
chromatin characteristics suggest that a much higher proportion of the genome may provide signals that are
relevant to genome functions.
• Only approximately half of the total linear length of the genome consists of so-called single- copy or unique
DNA, that is, DNA whose linear order of specific nucleotides is represented only once (or at most a few times)
around the entire genome.
• This concept may appear surprising to some, given that
there are only four different nucleotides in DNA.
But, consider even a tiny stretch
of the genome that is only 10 bases long; with
four types of bases, there are over a million possible
sequences.
• The rest of the genome consists of several classes of
repetitive DNA and includes DNA whose nucleotide
sequence is repeated, either perfectly or with some
variation, hundreds to millions of times in the genome.
• Whereas most (but not all) of the estimated 20,000
protein-coding genes in the genome are represented
in single-copy DNA,
 Molecular organization and gene products of mitochondrial DNA
• In most eukaryotes, mtDNA exists as a doublestranded, closed circle
• In size, mtDNA is much smaller than cpDNA and varies greatly among organisms, as demonstrated in In a variety of
animals, including humans, mtDNA consists of about 16,000 to 18,000 bp (16 to 18 kb).
• There are several other noteworthy aspects of mtDNA. With only rare exceptions, and unlike cpDNA, introns are
absent from mitochondrial genes, and gene repetitions are seldom present. Nor is there usually much in the way of
intergenic spacer DNA. This is particularly true in species whose mtDNA is fairly small in size, such as humans.
• Human mtDNA encodes two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and 13 polypeptides essential to the
oxidative respiration functions of the organelle. For instance, mitochondrial-encoded gene products are present in all
of the protein complexes of the electron transport chain found in the inner membrane of mitochondria. In most cases,
these polypeptides are part of multichain proteins, many of which also contain subunits that are encoded in the
nucleus, synthesized in the cytoplasm, and then transported into the organelle. Thus, the protein-synthesizing
apparatus and the molecular components for cellular respiration are jointly derived from nuclear and mitochondrial
genes.
Mutations in mitochondrial DNA
 The Human Karyotype
 The condensed chromosomes of a dividing human
cell are most readily analyzed at metaphase or
prometaphase. At these stages, the chromosomes
are visible under the microscope as a so-called
chromosome spread; each chromosome consists
of its sister chromatids, although in most
chromosome preparations, the two chromatids are
held together so tightly that they are rarely visible as
separate entities.
 There are 24 different types of human chromosome,
each of which can be distinguished cytologically by a
combination of overall length, location of the
centromere, and sequence content, the latter
reflected by various staining methods. The
centromere is apparent as a primary constriction,
a narrowing or pinching-in of the sister chromatids
due to formation of the kinetochore. This is a
recognizable cytogenetic landmark, dividing the
chromosome into two arms, a short arm designated
p (for petit) and a long arm designated q
Structure of human chromosomes.
Nucleosomes
 The Concept of Mutation
• Mutation - ranging from the change of a single nucleotide to alterations of an
entire chromosome. To recognize a change means that there has to be a “gold
standard”
• Mutations are sometimes classified by the size of the altered DNA sequence and,
at other times, by the functional effect of the mutation on gene expression.
Although classification by size is somewhat arbitrary, it can be helpful
conceptually to distinguish among mutations at three different levels:
• Mutations that leave chromosomes intact but change the number of
chromosomes in a cell (chromosome mutations)
• Mutations that change only a portion of a chromosome and might involve a
change in the copy number of a subchromosomal segment or a structural
rearrangement involving parts of one or more chromosomes (regional or
subchromosomal mutations)
• Alterations of the sequence of DNA, involving the substitution, deletion, or
insertion of DNA, ranging from a single nucleotide up to an arbitrarily set limit of
approximately 100 kb (gene or DNA mutations)
 The Concept of Genetic Polymorphism
 The DNA sequence of a given region of the genome is remarkably similar among chromosomes carried
by many different individuals from around the world.
 In fact, any randomly chosen segment of human DNA approximately 1000 bp in length contains, on
average, only one base pair that is different between the two homologous chromosomes inherited from
that individual’s parents (assuming the parents are unrelated).
 However, across all human populations, many tens of millions of single nucleotide differences and over a
million more complex variants have been identified and catalogued.
 Because of limited sampling, these figures are likely to underestimate the true extent of genetic diversity
in our species.
 Single Nucleotide Polymorphisms
• The simplest and most common of all polymorphisms are single nucleotide
polymorphisms (SNPs). A locus characterized by a SNP usually has only two alleles,
corresponding to the two different bases occupying that particular location in the genome.
• SNPs are common and are observed on average once every 1000 bp in the genome.
• However, the distribution of SNPs is uneven around the genome; many more SNPs are found
in noncoding parts of the genome, in introns and in sequences that are some distance from
known genes. Nonetheless, there is still a significant number of SNPs that do occur in genes
and other known functional elements in the genome. For the set of protein-coding genes,
over 100,000 exonic SNPs have been documented to date.
The Concept of Genetic Polymorphism
 Insertion-Deletion Polymorphisms
• A second class of polymorphism
is the result of varia- tions
caused by insertion or deletion
(in/dels or simply indels) of
anywhere from a single base
pair up to approximately 1000
bp, although larger indels have
been documented as well.
• Over a million indels have been
described, numbering in the
hundreds of thousands in any
one individual’s genome.
• Approximately half of all indels
are referred to as “simple”
because they have only two
alleles—that is, the presence or
absence of the inserted or
deleted segment
 Microsatellite Polymorphisms
• Other indels, however, are multiallelic due to
variable numbers of the segment of DNA that
is inserted in tandem at a particular location,
thereby constituting what is referred to as a
microsatellite.
• They consist of stretches of DNA composed
of units of two, three, or four nucleotides,
such as TGTGTG, CAACAACAA, or
AAATAAATAAAT, repeated between one and
a few dozen times at a particular site in the
genome
• The different alleles in a microsatellite
polymorphism are the result of differing
numbers of repeated nucleotide units
contained within any one microsatellite and
are therefore sometimes also referred to as
short tandem repeat (STR)
polymorphisms.
 Copy Number Variants
• Another important type of human polymorphism includes copy number variants (CNVs).
• CNVs are conceptually related to indels and microsatellites but consist of variation in the number of
copies of larger segments of the genome, ranging in size from 1000 bp to many hundreds of
kilobase pairs.
• Variants larger than 500 kb are found in 5% to 10% of individuals in the general population, whereas
variants encompassing more than 1 Mb are found in 1% to 2%. The largest CNVs are sometimes
found in regions of the genome characterized by repeated blocks of homologous sequences called
segmental duplications (or segdups).
 Inversion Polymorphisms
• A final group of polymorphisms to be discussed is
inversions, which differ in size from a few base pairs
to large regions of the genome (up to several
megabase pairs) that can be present in either of two
orientations in the genomes of different individuals.
• Most inversions are characterized by regions of
sequence homology at the edges of the inverted
segment, implicating a process of homologous
recombination in the origin of the inversions.
• In their balanced form, inversions, regardless of
orientation, do not involve a gain or loss of DNA, and
the inversion polymorphisms (with two alleles
corresponding to the two orientations) can achieve
substantial frequencies in the general population.
• However, anomalous recombination can result in the
duplication or deletion of DNA located between the
regions of homology, associated with clinical
disorders.