Download PPT: Genetics: From Mendel to Genome and Epigenome

Genetics: From Mendel to Genome
and Epigenome
Xiwen Cai
North Dakota State University, Fargo, USA
http://images.search.yahoo.com/search/images?_adv_prop=image&fr=moz35&sz=all&va=fargo+winter
Outline
 Mendel and his discoveries
 Discovery of chromosomes, genes, and DNA
 Molecular genetics and genomics
 Epigenetics
- Excellent in high school and studied
philosophy afterward
- Monastery-pastoral duties in Czech
Republic 1843-1849
- Monastery-teaching appointment in
Czech Republic 1849-1851
- Studied physics and botany at
University of Vienna 1851-1853
- Returned to the monastery-teaching
physics and natural science 16 years
1854-1870
- Hybridization experiments with
garden pea 1856-1868
- Presented his work to the Brunn
Society of Natural Science 1865 and
published 1866, but was neglected
- Abbot of the monastery 1868-1884
Gregor Johann Mendel (1822-1884)
2010 Pearson Education, Inc.
Mendel’s Hybridization Experiments
2010 Pearson Education, Inc.
Mendel’s Postulates/Principles of Inheritance
(1865-1866)
• A unit character (trait) is controlled by a pair
of unit factors (genes/alleles), i.e. unit factors
exist in pairs.
• Dominance and recessiveness
• Segregation
• Independent assortment
Discovery of DNA - 1869
Johann Friedrich Miescher, a Swiss
chemist, extracted an acid
substance containing DNA that he
called nuclein from the nuclei of
white blood cells.
Johann Friedrich Miescher
(1844 – 1895)
http://www.genomenewsnetwork.org/resources/timeline/
Discovery of Chromatin/Chromosomes - 1882
Walther Flemming
(1843 -1905)
Walther Flemming, a German
anatomist and a founder of
cytogenetics, found a structure he
called chromatin in the nucleus and
observed chromatin was correlated
to threadlike structures in the
nucleus – chromosomes (meaning
“colored body”), which were
named later on by German
anatomist Wilhelm von WaldeyerHartz (1841–1923).
http://en.wikipedia.org/wiki/Walther_Flemming
Individuality and Continuity of Chromosome - 1888
• Chromosomes remained organized and
individual structures through the
process of cell division.
• Sperm and egg contribute the same
number of chromosomes.
• Boveri's early studies set the stage for
his hypothesis that chromosomes
Theodor Boveri
transmit hereditary characteristics after
(1862-1915; German Biologist)
the rediscovery of Mendel's laws.
http://www.genomenewsnetwork.org/resources/timeline/
Rediscovery of Mendel’s Work
Three botanists, Hugo de Vries, Erich von
Tschermak, and Carl Correns, independently
rediscovered Mendel and his work in other
plant species in 1900.
Chromosome Theory of Inheritance
Walter Sutton
(1877-1916)
Theodor Boveri
(1862-1915)
In 1902, the German scientist Theodor Boveri and the
American Walter Sutton, working independently,
suggested that chromosomes could carry the material
of heredity. Both recognized that Mendel’s postulates of
segregation and independent assortment had an
excellent fit with facts about chromosomes.
http://www.genomenewsnetwork.org/resources/timeline/
Discovery of Linkage - 1904
• William Bateson, a English
geneticist, co-discovered genetic
linkage with Reginald Punnett
who created Punnett Square, a
tool widely used in genetic
analysis.
William Bateson
(1861-1926)
• Bateson first suggested using the
word "genetics" (from the Greek
gennō, γεννώ; "to give birth") to
describe the study of inheritance
and variation.
http://www.genomenewsnetwork.org/resources/timeline/
Morgan’s Work on Linkage - 1910
• Morgan, an American geneticist, confirmed the
hypothesis of Boveri and Sutton that genes are
located on chromosomes.
• Expanded the idea of genetic linkage and
hypothesized the phenomenon of crossing over.
• He proposed that the amount of crossing over
between linked genes differs and that crossover
frequency might indicate the distance between
genes on the chromosome.
Thomas Hunt Morgan
(1866-1945)
• The later English geneticist J. B. S. Haldane
suggested that the unit of measurement for
linkage be called “morgan”. Morgan's student
Alfred Sturtevant developed the first genetic
map in 1913.
• Won Nobel prize in Physiology or Medicine in
1933.
http://en.wikipedia.org/wiki/Thomas_Hunt_Morgan
One-Gene:One-Enzyme Hypothesis - 1941
George W. Beadle
(1903-1989; US Geneticist)
Edward L. Tatum
(1909-1975; US Biochemist)
• Proposed One-Gene:One-Enzyme hypothesis
based on their work on pink bread mold.
• Provided significant insights into gene function at
the molecular level.
• Won Nobel prize in Physiology or Medicine in 1958.
http://www.genomenewsnetwork.org/resources/timeline/
DNA as the Genetic Material - 1944
Oswald T. Avery
(1877-1955; US
Immunochemist )
Colin MacLeod
(1909-1972; US
Immunochemist)
Maclyn McCarty
(1911- ; US
Immunochemist)
• Identified DNA, not proteins, as the "transforming
principle" responsible for heredity in bacteria.
• Marked the beginning of the molecular genetics era.
http://www.genomenewsnetwork.org/resources/timeline/
The Watson-Crick DNA Model - 1953
James D. Watson
(1928-)
Francis H. C. Crick
(1916-2004)
http://www.nature.com
• Won Nobel prize in Physiology or Medicine in 1962
http://www.genomenewsnetwork.org/resources/timeline/
Isolation of DNA polymerase - 1956
• Isolated first DNA
polymerizing enzyme – DNA
polymerase I in 1956.
Arthur Kornberg
(1918-2007; US Biochemist)
• Won Nobel prize with Severo
Ochoa for "for their discovery
of the mechanisms in the
biological synthesis of RNA
and DNA“ in Physiology or
Medicine in 1959.
http://en.wikipedia.org/wiki/Arthur_Kornberg/
Discovery of mRNA - 1960
Francois Jacob
(1920-2013; French Biologist)
Jacques Monod
(1910-1976; French Biologist)
• By working with Sydney Brenner and Francis Crick,
Jacob and Monod discovered mRNA.
http://www.genomenewsnetwork.org/resources/timeline/
Cracking the Genetic Code - 1961
• Won Nobel prize with Har
Gobind Khorana and Robert W.
Holley for "breaking the
genetic code" and describing
how it operates in protein
synthesis in Physiology or
Medicine in 1968.
Marshall Nirenberg
(1927-2010; US Biochemist)
http://www.genomenewsnetwork.org/resources/timeline/
1st Recombinant DNA Molecules - 1972
Paul Berg
(1926-; US Biochemist)
• Paul Berg won the Nobel
Prize in Chemistry with
Walter Gilbert and Frederick
Sanger, for "his fundamental
studies of the biochemistry
of nucleic acids, with
particular regard to
recombinant DNA in 1980.”
http://www.genomenewsnetwork.org/resources/timeline/
DNA Sequencing - 1977
Walter Gilbert
(1932-; US Physicist and Biochemist)
Frederick Sanger
(1918-; UK Biochemist)
• Gilbert and Sanger shared the Nobel Prize
in Chemistry in 1980
http://www.nobelprize.org
Polymerase Chain Reaction (PCR) - 1983
• Kary Mullis conceives and helps
develop polymerase chain
reaction (PCR).
• Won the Nobel Prize in Chemistry
"for his invention of PCR method"
in 1993.
Kary Mullis
(1944-; US Biochemist)
http://www.nobelprize.org
Automated DNA Sequencer- 1986
• In conjunction with a team that included
Lloyd Smith and Michael and Tim
Hunkapiller, Leroy Hood (1938-) conceived
the automated sequencer in 1985 and
Applied Biosystems brought it to market in
June 1986.
http://www.genomenewsnetwork.org/resources/timeline/
Human Genome Sequencing - 1986-1990-2000
• 1986-1990: Launching the effort to sequence the human
genome. In the US, the government-funded Human
Genome Project was launched in 1990.
• 1988: The US DOE and NIH set a budget for the human
genome project. Meanwhile, sequencing efforts were
beginning in Japan, France, Italy, the United Kingdom,
and Canada.
• 1990: Human Genome Project – 1) Improve genetic map;
2) Develop physical map; 3) Sequence the entire
genome; 4) Take 15 years and $3 billion.
• 2000: The human genome, sequenced and assembled.
Celera Genomics and international Human Genome
Project speeded the sequencing efforts and completed
the project 5 years earlier than targeted.
http://www.genomenewsnetwork.org/resources/timeline/
Expressed Sequence Tags (ESTs) - 1991
• Venter was Involved in human
genome sequencing and founded
Celera Genomics, the Institute for
Genomic Research (TIGR), and the
J. Craig Venter Institute (JCVI).
• Described a fast new approach for
gene discovery using ESTs.
J. Craig Venter
(1946-; US Biologist)
http://www.genomenewsnetwork.org/resources/timeline/
Whole Genome Sequencing - 1991
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Viruses (2kb-2Mb) – mid-1990s
Bacteria (Haemophilus influenzae Rd., 1.8 Mb) – 1995
Yeast (12.1 Mb) – 1996
Archaea (Methanococcus jannaschii, 1.66Mb) – 1996
A translucent worm (Caenorhabditis elegans, 100Mb) – 1998
Fruit fly (165 Mb) – 1999-2000
Human (3.2 Gb) – 2000
Arabidopsis thaliana (119 Mb) – 2000
Mouse (3 Gb) – 2002
Rice (420 Mb) – 2002
Rat (2.75 Mb) – 2004
• Poplar (550 Mb) – 2006
• Many more ……
Mendel-Chromosome-Gene-Genome
Mendel’s Hybridization Experiments
Mendelian Genetics
1st and 2nd Principles of Inheritance
Discovery of chromosomes and their behavior
Chromosome theory of inheritance
Linkage
Discovery of DNA
How a gene works and what a gene is
DNA structure, replication, and gene expression
Recombinant DNA and genetic engineering
DNA and whole genome sequencing
Gene discovery/cloning and functional analysis
Transmission
Genetics
Cytogenetics
Molecular Genetics
Genomics
The Beginning of Epigenetics



Conrad Hal Waddington (1905–1975) coined the term
“epigenetics” in the 1940s to describe how environmental
influences on developmental events can affect the phenotype of
the adult.
The Greek prefix “epi” means “on top of” or “over”, so the term
“Epigenetics” literally describes regulation at a level above, or in
addition to, those of genetic mechanisms.
Robin Holliday and John Pugh proposed that changes in gene
expression during development depends on the methylation of
specific bases in DNA, and that altering methylation patterns
affects the resulting phenotype in the 1970s.
Epigenetics


“Epigenetics” refers to covalent modification of DNA, protein,
or RNA, resulting in changes to the function and/or regulation
of these molecules, without altering their primary sequences. In
some cases, epigenetic modifications are stable and passed on
to future generations, but in other instances they are dynamic
and change in response to environmental stimuli.
Mechanisms of epigenetics: 1) DNA methylation; 2) Histone
modification; 3) Chromatin remodeling; and 4) Regulation by
small and non-coding RNAs.
http://www.zymoresearch.com/learning-center/epigenetics/what-is-epigenetics
http://upload.wikimedia.org/wikipedia/commons/d/dd/Epigenetic_mechanisms.jp
Methylation
Methylation: 1) Occurs after DNA replication and during cell differentiation; 2)
Involves addition of a methyl group (-CH3) to cytosine by methyltransferases; 3) Takes
place almost exclusively on cytosine bases adjacent a guanine base, a combination
called CpG dinucleotide. Many CpG cluster in and near promoter sequences of genes,
called CpG islands.
2010 Pearson Education, Inc.
Histone Modification and Chromatin Configuration

Histone modification: Addition of acetyl, methyl, and phosphate groups to the
histone tails (N-terminal amino acids). These modifications alter the structure of
chromatin, making genes accessible or inaccessible for transcription. Specific
combinations of histone modifications (called histone code) control the
transcriptional status of a chromatin region.
2010 Pearson Education, Inc.
Epigenetic Modifications and Gene Expression
Epigenetic modifications to the genome alter the spacing of nucleosomes and
the availability of genes for transcription.
2010 Pearson Education, Inc.
MicroRNAs (miRNAs)

Single-stranded RNA molecules approximately 20-30 nucleotides
in length that regulate gene expression by participating in the
degradation of mRNA.

Form RNA-Induced Silencing Complexes (RISC) with a protein
complex. RISCs act posttranscriptional repressors of gene
expression by binding to and destroying target mRNA molecules
complementary to the RISC miRNA.

miRNA can also associate with a different protein complex to form
RNA-Induced Transcriptional Silencing (RITS) complexes. RITSs
convert euchromatin into facultative heterochromatin, which
silences the genes within the chromatin region.
Detection of Methylation
Bisulfite-induced conversion of unmethylated cytosines to uracil. Nucleotides in blue
are unmethylated cytosines converted to uracils by bisulfite, while red nucleotides are
5-methylcytosines resistant to conversion.
http://upload.wikimedia.org/wikipedia/en/c/c9/Wiki_Bisulfite_sequencing_Figure_1_small.png
Detection of Methylation
Methylation-specific PCR is a sensitive method to discriminately amplify and detect a methylated
region of interest using methylated-specific primers on bisulfite-converted genomic DNA. Such primers
will anneal only to sequences that are methylated, and thus containing 5-methylcytosines that are
resistant to conversion by bisulfite. In alternative fashion, unmethylated-specific primers can be used.
http://upload.wikimedia.org/wikipedia/en/c/c9/Wiki_Bisulfite_sequencing_Figure_1_small.png
Detection of Methylation
Non-methylation-specific PCR: Following bisulfite conversion, the genomic DNA
is amplified with PCR that does not discriminate between methylated and nonmethylated sequences. The numerous methods available are then used to make the
discrimination based on the changes within the amplicon as a result of bisulfite
http://upload.wikimedia.org/wikipedia/en/c/c9/Wiki_Bisulfite_sequencing_Figure_1_small.png
conversion.
Thoughts on Epigenetics
• DNA sequence vs. epi-DNA sequence
• Genome vs. epigenome
• Genetic code vs. epigenetic code
• Genotype vs. epigenotype
• Epigenetics vs. human/animal/plant
health, therapy, and improvement