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

Molecular genetics and genomics

Epigenetics

Discovery of chromosomes, genes, and DNA

2010 Pearson Education, Inc.

Gregor Johann Mendel (1822-1884)

- Monastery-pastoral duties in Czech Republic 1843-1849

- Excellent in high school and studied philosophy afterward

- 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

- Abbot of the monastery 1868-1884

- Presented his work to the Brunn Society of Natural Science 1865 and published 1866, but was neglected

Mendel’s Hybridization Experiments


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.

• Segregation

• Dominance and recessiveness

• Independent assortment

Discovery of DNA - 1869

Johann Friedrich Miescher, a Swisschemist, 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, 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 Waldeyer-Hartz (1841–1923). Walther Flemming

(1843 -1905)

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.

Theodor Boveri (1862-1915; German Biologist)

• Sperm and egg contribute the same number of chromosomes.

• Boveri's early studies set the stage for his hypothesis that chromosomes transmit hereditary characteristics after the rediscovery of Mendel's laws.


Rediscovery of Mendel’s WorkThree 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.


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.

• Bateson first suggested using the word "genetics" (from the Greek gennō, γεννώ; "to give birth") to describe the study of inheritance and variation.William Bateson

(1861-1926)

Morgan’s Work on Linkage - 1910

• Won Nobel prize in Physiology or Medicine in 1933.

Thomas Hunt Morgan (1866-1945)

• Morgan, an American geneticist, confirmed the hypothesis of Boveri and Sutton that genes are located on chromosomes.

http://en.wikipedia.org/wiki/Thomas_Hunt_Morgan

• 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.

• 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.

One-Gene:One-Enzyme Hypothesis - 1941

• Won Nobel prize in Physiology or Medicine in 1958.

George W. Beadle(1903-1989; US Geneticist)

Edward L. Tatum(1909-1975; US Biochemist)


• Provided significant insights into gene function at the molecular level.

• Proposed One-Gene:One-Enzyme hypothesis based on their work on pink bread mold.

DNA as the Genetic Material - 1944

• Identified DNA, not proteins, as the "transforming principle" responsible for heredity in bacteria.


Oswald T. Avery(1877-1955; US

Immunochemist )

Colin MacLeod (1909-1972; US

Immunochemist)

Maclyn McCarty (1911- ; US

Immunochemist)

• Marked the beginning of the molecular genetics era.

The Watson-Crick DNA Model - 1953


James D. Watson (1928-)

Francis H. C. Crick(1916-2004)

• Won Nobel prize in Physiology or Medicine in 1962

http://www.nature.com

http://www.google.com/url?sa=i&rct=j&q=watson+crick+dna+model&source=images&cd=&cad=rja&docid=46GzxzfiQ8YlQM&tbnid=ECUY1YOoQzXJbM:&ved=0CAUQjRw&url=http://www.nature.com/scitable/topicpage/discovery-of-dna-structure-and-function-watson-397&ei=KoKWUc2HKcGhrgHb6oDwBA&bvm=bv.46751780,d.aWc&psig=AFQjCNG67--vhe1Cfw9WUnfI1dwbj0hhIQ&ust=1368904541910621

Isolation of DNA polymerase - 1956

http://en.wikipedia.org/wiki/Arthur_Kornberg/

• 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.Arthur Kornberg

(1918-2007; US Biochemist)

• Isolated first DNA polymerizing enzyme – DNA polymerase I in 1956.

Discovery of mRNA - 1960

• By working with Sydney Brenner and Francis Crick, Jacob and Monod discovered mRNA.


Francois Jacob (1920-2013; French Biologist)

Jacques Monod (1910-1976; French Biologist)

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)

1st Recombinant DNA Molecules - 1972

• 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.”


Paul Berg (1926-; US Biochemist)

DNA Sequencing - 1977

• Gilbert and Sanger shared the Nobel Prize in Chemistry in 1980

Walter Gilbert (1932-; US Physicist and Biochemist)

Frederick Sanger (1918-; UK Biochemist)

http://www.nobelprize.org

Polymerase Chain Reaction (PCR) - 1983

• Kary Mullis conceives and helps develop polymerase chain reaction (PCR).

Kary Mullis (1944-; US Biochemist)

• Won the Nobel Prize in Chemistry "for his invention of PCR method" in 1993.

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.


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.

Expressed Sequence Tags (ESTs) - 1991

• Described a fast new approach for gene discovery using ESTs.


J. Craig Venter (1946-; US Biologist)

• Venter was Involved in human genome sequencing and founded Celera Genomics, the Institute for Genomic Research (TIGR), and the J. Craig Venter Institute (JCVI).

Whole Genome Sequencing - 1991• Viruses (2kb-2Mb) – mid-1990s

• Bacteria (Haemophilus influenzae Rd., 1.8 Mb) – 1995

• Yeast (12.1 Mb) – 1996

• A translucent worm (Caenorhabditis elegans, 100Mb) – 1998

• Archaea (Methanococcus jannaschii, 1.66Mb) – 1996

• Fruit fly (165 Mb) – 1999-2000 • Human (3.2 Gb) – 2000

• Mouse (3 Gb) – 2002 • Rice (420 Mb) – 2002

• Arabidopsis thaliana (119 Mb) – 2000

• Rat (2.75 Mb) – 2004

• Poplar (550 Mb) – 2006

• Many more ……

Mendel-Chromosome-Gene-GenomeMendel’s Hybridization Experiments

1st and 2nd Principles of Inheritance

Discovery of chromosomes and their behaviorChromosome theory of inheritance

Linkage

Mendelian Genetics

Cytogenetics

Discovery of DNAHow a gene works and what a gene isDNA structure, replication, and gene

expressionRecombinant DNA and genetic engineering

Transmission Genetics

Molecular Genetics

DNA and whole genome sequencingGene discovery/cloning and functional analysis

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.

http://www.zymoresearch.com/learning-center/epigenetics/what-is-epigenetics

Mechanisms of epigenetics: 1) DNA methylation; 2) Histone modification; 3) Chromatin remodeling; and 4) Regulation by small and non-coding RNAs.

http://upload.wikimedia.org/wikipedia/commons/d/dd/Epigenetic_mechanisms.jpg

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.

Methylation


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.

Histone Modification and Chromatin Configuration


Epigenetic modifications to the genome alter the spacing of nucleosomes and the availability of genes for transcription.

Epigenetic Modifications and Gene Expression


Single-stranded RNA molecules approximately 20-30 nucleotides in length that regulate gene expression by participating in the degradation of mRNA.

MicroRNAs (miRNAs)

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.

http://upload.wikimedia.org/wikipedia/en/c/c9/Wiki_Bisulfite_sequencing_Figure_1_small.png

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.

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.



Non-methylation-specific PCR: Following bisulfite conversion, the genomic DNA is amplified with PCR that does not discriminate between methylated and non-methylated sequences. The numerous methods available are then used to make the discrimination based on the changes within the amplicon as a result of bisulfite conversion.


• Genetic code vs. epigenetic code

Thoughts on Epigenetics

• DNA sequence vs. epi-DNA sequence

• Genome vs. epigenome

• Genotype vs. epigenotype

• Epigenetics vs. human/animal/plant health, therapy, and improvement

genetics: from mendel to genome and epigenome

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