Chapter 01 Introduction to Genetics - Tagged.pdf

Welcome to Genetics! Dra Veronica Veses – Lead Professor Dr Joan Climent and Dra Antonella Locascio – Practicals and Seminars Course Contents UNIT I: Genetic information, expression and gene regulation Chapter 1. Introduction to Genetics Chapter 2. DNA replication and DNA repa...

Welcome to Genetics! Dra Veronica Veses – Lead Professor Dr Joan Climent and Dra Antonella Locascio – Practicals and Seminars Course Contents UNIT I: Genetic information, expression and gene regulation Chapter 1. Introduction to Genetics Chapter 2. DNA replication and DNA repair systems Chapter 3. Transcription and translation Chapter 4. Regulation of gene expression 2 Course Contents UNIT II: Inheritance and genetic disorders Chapter 5. Patterns of Inheritance Chapter 6. Genetic Variability in Humans Chapter 7. Genetic Diseases Chapter 8. Genetic factors in common diseases Chapter 9. Cancer genetics. Virus and cancer 3 Course Contents UNIT III: Diagnostic in Genetics Chapter 10. Genetic Diagnosis Chapter 11. Prenatal diagnosis 4 Course Contents UNIT IV: Personalized Medicine and Pharmacogenomics Chapter 12. Introduction to Precision Medicine Chapter 13. Gene Therapy Chapter 14. Ethical and legal issues in Genetics 5 Text books Hartwell. Genetics: From Genes to Genomes; 4th Edition 2010 Lehninger. Principles of Biochemistry; 6th Edition 2008 Cann. Principles of Molecular Virology; 5th Edition 2011 Emery´s. Elements of Medical Genetics. 14th Edition 2015 Thompson and Thompson. Genetics in Medicine. 7th Edition 2008 6 Evaluation Criteria Final Exam (50%) Theoretical-Practical Continuous Evaluation (50%) Weekly quizzes (30%) Practical Reports (10 %) Seminar activities (10 %) Students must score a minimum of a 5 in the final exam for the continuous evaluation score to be applied. To pass the course, students should achieve a minimum of 5 by adding the scores of each of the assessments. 7 Activities Four practical sessions: – P1 Culture of human cell lines. – P2 DNA extraction. – P3 Polymerase chain reaction. – P4 Study of mutations and karyotypes. Eight seminar sessions: – S1: How to write a report – S2,3,4,5: Medical Dictionary of Rare Genetic Disorders I – S6: Invited guest – S7: Genetic Engineering – S8: CRISPR-CAS Final Exam: June Resit Exam: July 8  Contact Dra Veronica Veses: – Office 307 (third floor) – Office hours: Monday and Thursday 10:00 to 13:00 – [email protected] Dr Joan Climent: [email protected] Dr Antonella Locascio: [email protected] 9  https://www.sciencenews.org/topic/genetics The past: Plague may have caused die-offs of ancient Siberians A genetic variant that boosts Crohn’s disease risk may have helped people survive bubonic plague 10 https://www.sciencenews.org/topic/genetics Gene therapies for sickle cell disease come with hope and challenges 11  https://www.sciencenews.org/topic/genetics The future: What FamilyTreeDNA sharing genetic data with police means for you 12 13 FUTURE OF MEDICAL GENETICS 14 In USA The National Human Genome Research Institute (NHGRI) offers a three-year residency program in medical genetics that trains physicians to diagnose, manage and counsel patients with genetic disorders. Participants gain broad experience in clinical and molecular genetics, metabolic diseases and cytogenetics. 15 In Europe Spain is the only country in which Genetics is not offered as a recognized official specialization route. Health Ministry in Spain has a draft as to include a “Genetic Diagnosis” MIR specialty but not a Medical Genetics one. 16 INTRODUCTION TO GENETICS  Basic Concepts in Genetics: – Genetics; Gene; DNA; Chromosome Organization of genetic material – Prokaryotes – Eukaryotes Genetics Historical Landmarks Medical Genetics: – Definition and historical landmarks Human Genome 18 Genetics Genetics is defined by the World Health Organization as the study of heredity. Heredity is the transmission of genetic characters from parents to offspring. A person's appearance -- height, hair color, skin color, and eye color -- is determined by genes. Genomics is defined as the study of genes and their functions, and related techniques. 19 Definition of a Gene Genetic information is stored in the highly stable macromolecule Deoxyribonucleic Acid (DNA). Gene: a portion of deoxyribonucleic acid (DNA) coding for the primary structure of a polypeptide or for a functional RNA. 20 DNA building blocks: deoxyribonucleotides 21 Purine or Pyrimidine Nitrogenous Bases 22 Deoxyribonucleotides 23 DNA is a double helix made from two strands 24 The two strands are complementary to each other and run in antiparallel directions 25 DNA can adopt three basic forms Comparing the three distinct forms of DNA A Form B Form Z Form Direction of helical turn Right Right Left Diameter (Angstrom) 26 Å 20 Å 18 Å Bases per helical turn 11 10.5 12 Distance between consecutive bases 2.6 Å 3.4 Å 3.7 Å Angle of the bases with respect to 20º 6º 7º the central axis of the DNA strand 26 DNA packaging In the nucleus of each eukaryotic cell, the DNA molecule is packaged into thread-like structures, the chromosomes. Each chromosome is made up of DNA tightly coiled many times around proteins called histones that support its structure. The complex of DNA and protein is called chromatin 27 Chromosomes Each chromosome has a constriction point called the centromere, which divides the chromosome into two sections, or “arms.” The short arm of the chromosome is labeled the “p arm.” The long arm of the chromosome is labeled the “q arm.” The location of the centromere on each chromosome gives the chromosome its characteristic shape, and can be used to help describe the location of specific genes 28 Summary: DNA>Chromatin>Chromosome 29 Chromosome classification According to the situation of the centromere: – Metacentric: Central – Submetacentric: slightly off center – Subtelocentric or acrocentric: near one end of the chromosome (the arms are unequal) – Telocentric: at one end of chromosome 30 Karyotype Ordination of chromosomes from by size, shape, and banding pattern, according to the Paris classification 31  Ideograms Ideograms are a schematic representation of chromosomes. They show the relative size of the chromosomes and their banding patterns. A banding pattern appears when a tightly coiled chromosome is stained with specific chemical solutions and then viewed under a microscope. Some parts of the chromosome are stained (G-bands) while others refuse to adopt the dye (R-bands). The resulting alternating stained parts form a characteristic banding pattern which can be used to identify a chromosome. 32 GENES AND GENOMES 33 Genome It is the collection of genes in a living organism. Number of genes vary from species to species: – Bacteria contain a few thousand genes – Human cell contains between 20.000 and 30.000 genes 34 Size and number of chromosomes also varies from species to species Bacteria – a single circular chromosome Humans –23 sets of chromosomes (22 autosomes, 1 pair of sex chromosomes) – Gametes-single set and haploid (n) – Somatic cells – two sets and diploid(2n) 35 Eukaryotes vs Prokaryotes Genomes Prokaryotic and eukaryotic cells both contain double-stranded DNA, but their genomes are organized differently Eukaryotic chromosomes contain an enormous amount of DNA, which requires an elaborate system of DNA packing to fit all of the cell’s DNA into the nucleus 36 Prokaryotic genome The bacterial chromosome, has less associated protein, compared to eukaryotes The chromosome is typically a covalently closed circular structure Not membrane bound, but tends to aggregate as a distinct structure within the cell, known as the nucleoid Prokaryotes may contain one or more extra circular DNA molecules, called plasmids 37 Eukaryotic Genomes  Complex organisation  Contain coding and non- coding DNA  Contain repeated sequences  There is genetic information stored in the nucleus and in the mitochondria / chloroplast 38 Eukaryotic genes can be discontinuous: 39 Some Bacterial Genomes Also Contain Introns It was thought until 1993 that introns are exclusive feature of eukaryotic genes About 25% of sequenced bacterial genomes show presence of introns Introns in bacterial chromosome do not interrupt protein-coding sequences They interrupt mainly tRNA sequences 40 DNA, Chromosomes, Genes, and Complexity Neither the total length of DNA, nor the number of chromosomes correlates strongly with the perceived complexity of the organisms – Amphibians have much more DNA than humans – Plants have more genes than humans – Dogs and coyotes have 78 chromosomes in the diploid cell The correlation between complexity and genome size is poor because most of eukaryotic DNA is non-coding 41 Non coding regions DNA contains genes… But also contains other sequences that have purely regulatory function. These regions may correspond to the areas immediately before or after a gene, and function as initiation sites for replication or participate in the regulation of transcription. 42 Flow of genetic information Chapter 2 Chapter 3 Chapter 4 43 44 Landmarks 1866: Mendel Laws 1869: DNA is discovered by Friedrich Miescher 1953: Watson and Crick describe the DNA structure 1956: Number of human chromosomes is determined 1990: Beginning of Human Genome Project 2022: The completion of the human genome (Telomere-to-Telomere (T2T) Consortium) 45 MEDICAL GENETICS 46 Definition Is the branch of Genetics that studies the implication of the genetic content of an individual in his own health, with particular emphasis in the genetic basis of (some) human diseases. Incorrect transfer of genetic information to offspring is going to cause congenital genetic diseases Mutations in the genetic content of somatic (adult ) cells can lead to cancer 47 Applications of medical genetics include: Clinical diagnosis Gene identification Cancer genomics Disease treatment Prenatal diagnosis 48 THE HUMAN GENOME The Human Genome Sequencing programs and initiatives Human Genome Organization 50 Nuclear and Mitochondrial Genome The human genome is distributed between the nucleus (mainly) and the mitochondria 51 Mitochondrial Genome Double stranded circular molecule 17,000 base pairs long 97 % of the genome is coding. 37 coding genes – 2 encode ribosomal RNA – 22 encode transfer RNA – 13 encode proteins Sequence is deposited in – http://mitomap.org Some mutations will lead to mitochondrial inheritance diseases (Chapter 7) 52 Nuclear Genome 46 (2 sets of 23) lineal chromosomes in each cell 3300 million base pairs long 50 % of the genome corresponds to genes encoding proteins, introns and regulatory sequences 50 % of the genome correspond to repeated sequences. The human genome has a much greater portion of repeat sequences than the mustard seed (11%), the worm (7%), and the fly (3%). 53 Human Genome Project (HGP) Started in the 90´with the objective to sequence the nuclear human DNA International scientific research project, funded by the NIH (National Institute of Health, USA), with 20 participant Universities (United States, United Kingdom, Japan, France, Germany, and China) It was first published in 2001 and totally completed in April 2003 54 Celera Genomics In parallel, the company Celera Genomics decided to sequence the Human Genome using a cheaper and faster technology (although less accurate). They published 5 complete genomes, including the company´s president one, Craig Venter). By competing (and cooperating) the governmentally financed human genome project (HGP) and the private biotechnology company Celera have completed a reference DNA sequence of the human genome. Both parties made their information simultaneously available in February 2001, by publishing it on the Internet and in the scientific journals Nature and Science 55 Beyond the HGP: What’s Next? HapMap ENCODE 56 HapMap: An NIH program to chart genetic variation within the human genome It is multi-country effort to identify and catalog genetic similarities and differences in human beings. Using the information in the HapMap, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. The Project is a collaboration among scientists and funding agencies from Japan, the United Kingdom, Canada, China, Nigeria, and the United States 57 ENCODE: Encyclopedia of DNA Elements It is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. 58 The 1000 Genomes Project Consortium The goal of the 1000 Genomes Project is to find most genetic variants that have frequencies of at least 1% in the populations studied Draft results published in Nature in 2010 http://www.1000genomes.org/ 59 100.000 genomes In late 2012, Prime Minister David Cameron announced the 100,000 Genomes Project. Genomics England, was set up sequence 100,000 whole genomes from UK patients. Its four main aims were: – to create an ethical and transparent programme based on consent; – to bring benefit to patients and set up a genomic medicine service for the NHS; – to enable new scientific discovery and medical insights – to kick start the development of a UK genomics industry. The project focused on patients with a rare disease and their families and patients with cancer. 60 Updated information of the Human Genome http://www.ensembl.org/Homo_sapiens/Info/Index The genetic information is annotated, displaying all available data 61 HUMAN GENOME ORGANIZATION 62 Nuclear DNA Repeated (50%) – In tandem – interspersed Not repeated (50%) – Coding (1,5 %; 20,769 genes) – Introns – Non-coding RNAs (25,173 genes) 63 Tandem repeats Three categories, according to the length of the region that contains the repetition, not by the length of the repeated sequence itself: – Satellite DNA – Minisatellites – Microsatellites 64 Satellite DNA Repetions (5-171 bp) cover regions of hundreds of Kb Include several families: a, b, d, satellite 1, 2 and 3 Mainly located in centromeric and pericentromeric regions Play a role in mitotic segregation of chromosomes 65 Minisatellites Mini satellites consists of repetitive, generally GC rich, variant repeats that range in length from 10 to over 65 bp, covering regions up to 20 kb. They are also called Variable Number of Tandem Repeats (VNTRs) because the number of repeats in a given mini satellite varies greatly among individuals. Due to their high level of polymorphism, minisatellites have been extensively used for DNA fingerprinting 66 DNA Fingerprinting DNA fingerprinting is a method for identifying individuals based on their minisatellite DNA. It was developed in the mid-80s and is widely used in forensics, paternity analysis, and for research purposes. Due to the variation in the number of repeats at each locus, different individuals can be readily distinguished based on banding patterns. Chapter 11 67 Microsatellites Repetitions of di-, tri-, and tetra-nucleotides, covering regions of less than 150 bp It is the second most common human genetic variation. Therefore also widely used for DNA fingerprinting Usually have no effect on human disease 68 Diseases related to trinucleotide repeats Characterized by the expansion of repeats of three nucleotides: – from a few to a hundred repetitions – The expansion results in the formation of a defective protein and subsequent disease (many neurodegenerative) – The number of expansions can be increased over generations 69 Example: Huntington´s disease It is a fatal genetic disorder that causes the progressive breakdown of nerve cells in the brain. It deteriorates a person’s physical and mental abilities during their prime working years and has no cure Due to excessive repetitions of the triplet CAG (normal is 9-35; patients have 37-100 repeats) 70 Tandem repeats: summary Class Size of repeat Repeat block Chromosomal location Satellite 5-171 bp > 100 kb centromeric Minisatellite 9-64 bp 0,1-20 kb telomeric Microsatellite 1-13 bp < 150 bp dispersed 71 Nuclear DNA Repeated (50%) – In tandem – interspersed Not repeated (50%) – Coding (1,5 %; 20,769 genes) – Introns – Non-coding RNAs (25,173 genes) 72 Interspersed DNA DNA transposons: can excise themselves from the genome, move as DNA and insert themselves into new genomic sites. Retrotransposons: most frequent in eukaryotic DNA. They duplicate through RNA intermediates that are reverse transcribed and may integrate back to the genome – LTR-retrotransposons – non LTR-retrotransposons Processed pseudogenes 73  DNA transposons vs Retrotransposons “cut-and-paste” “copy-and-paste” Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-8 74 Retrotransposons Retrotransposons can be subdivided into two groups distinguished by the presence or absence of long terminal repeats (LTRs): – non-LTR retrotransposons LINE SINE – LTR retrotransposons - Human LTR elements are endogenous retroviruses (HERVs). Not active currently 75 Non LTR retrotransposons LINES (long interspersed nuclear elements) 6 – 8 kb segments that encode the proteins that enable the transposition. They account for 21% of the genome SINES (short interspersed nuclear elements) 100 – 400 bp sections containing remnants of tRNA transcription machinery. They account for 13% of the genome. They are not autonomous, needing LINE Endonuclease and Reverse Transcriptase for activity 76 Pseudogenes Pseudogenes are defective copies of genes. They contain most of the gene’s sequence, but have stop codons or frameshifts in the middle, or they lack promoters, or are truncated or are just fragments of genes. 77 Types of Pseudogenes Non-processed (duplicated) pseudogenes are the result of tandem gene duplication or transposable element movement. When a functional gene get duplicated, one copy isn’t necessary for life. Sometimes the copy will evolve a new function. Other times one copy will become inactivated by random mutation and become a pseudogene. Processed pseudogenes come from mRNA that has been reverse-transcribed and then randomly inserted into the genome. Processed pseudogenes lack introns because the mRNA was spliced. They also often have poly A tails and they lack promoters and other control regions. 78 Repeated DNA: summary 79 References David L. Nelson, 2012. Lehninger Principles of Biochemistry. 6th Edition. W.H. Freeman. Robert L. Nussbaum MD FACP FACMG, 2007. Thompson & Thompson Genetics in Medicine. 7th Edition. Saunders. Bruce Alberts, 2012. Molecular Biology of the Cell, 5th Edition. Garland Science. 80 References II http://mitomap.org http://www.genome.gov/12011238 http://hapmap.ncbi.nlm.nih.gov/ https://www.encodeproject.org/ http://www.1000genomes.org/ http://www.ensembl.org/Homo_sapiens/Info/Index Harvey Lodish, 2016. Molecular Cell Biology. 8th Edition. W. H. Freeman. Tucker, Marra and Friedman. 2009. Massively parallel sequencing: the next big thing in genetic medicine. Am J Hum Genet 85: 142-54 81