DNA and Chromatin Organization PDF

WE MAKE DOCTORS DNA and Chromatin Organization Ana Gabriela Colima Fausto, PhD Learning objectives Outline the basic components of the DNA Describe the different levels of organization of chromatin Contrast the difference between heterochromatin and euchromatin Explain and demonst...

WE MAKE DOCTORS DNA and Chromatin Organization Ana Gabriela Colima Fausto, PhD Learning objectives Outline the basic components of the DNA Describe the different levels of organization of chromatin Contrast the difference between heterochromatin and euchromatin Explain and demonstrate the influence of chromatin condensation on gene expression Relate clinical conditions associated with an improper packaging of the chromatin: Hutchinson-Gilford progeria syndrome DNA DNA in each cell contains all instructions necessary to direct the growth and development of cells into an organism and to maintain cellular function throughout the individual's lifespan. Within DNA are nucleotide bases that are arranged in specific sequences to form genes. DNA BUILDING BLOCKS Nitrogenous bases Pyrimidines (Thymine and Cytosine) Purines (Adenine and Guanine) Phosphate group Pentose (Deoxyribose) Nucleoside (Nitrogenous base+ pentose) Nucleotide (Nitrogenous base + pentose + phosphate group)  DNA exists as a double helix, with about 10 nucleotide pairs per helical turn. DNA The spatial relationship between the two strands creates furrows in DNA— the major and minor grooves. A sugar phosphate backbone with attached bases and is connected to a complementary strand by hydrogen bonding. The pairing of the nucleotide bases occurs such that adenine (A) binds with thymine (T) and guanine (G) with cytosine (C).  DNA BUILDING BLOCKS Deoxyribonucleotid are joined by covalent phosphodiester bonds (form between the 3′- OH groups of the deoxyribose sugar on one nucleotide with the 5′ phosphate groups on the adjacent nucleotide) DNA BUILDING BLOCKS The phosphate group linking the sugars has a negative charge.  DNA BUILDING BLOCKS There is a free phosphate group at the 5′-end and a free hydroxyl group at the 3′-end of a nucleic acid strand. 5′ to 3′ direction: sense and antisense The two complementary strands of DNA double helix are therefore in antiparallel directions. The 5′ end of one strand is base paired with the 3′ end of the other strand. EUKARYOTIC DNA DNA REPEAT SEQUENCES They make up at least 50% of the human genome. These sequences do not appear to have direct functions but are important for chromosome structure and dynamics. These sequences are also associated with the centromeres and telomeres of chromosomes. Satellites, LINES and SINES Satellites Highly repetitive sequences repeated many times in tandem. Not transcribed. Centromeres and telomeres of chromosomes. Polymorphic (a common genetic variation in nucleotide sequence) Alpha satellite (171 bp sequence that extends several million bp) Minisatellite (20 to 70 bp sequence with a length of a few thousand base pairs) Microsatellite (2, 3, or 4 bp sequence and a total length of a few hundred)  Microsatellites Short tandem repeats (STRs) , microsatellites of 2 to 6 bp in length. FBI Combined DNA Index System (CODIS). Y chromosome STR and mitochondrial DNA data are utilized in missing person–related searches. Trinucleotide repeats are microsatellite sequences that are normally present in certain genes and can undergo expansion. LINES and SINES Sequences that are found interspersed with unique sequences. They are transcribed into RNA and can be grouped according to their size. LINES (long, interspersed elements) 7,000 bp (20 to 50,000 copies) SINES (short, interspersed elements) 90 to 500 bp (about 100,000 copies)  DNA packaging Four levels of packaging of DNA take place in order that DNA in individual chromosomes fits into the nuecleus. Nucleosomes are the fundamental organization upon which the higher-order packing of chromatin is built.  Nucleosome Each nucleosome core consists of a complex of eight histone proteins (two molecules each of histone H2A, H2B, H3, and H4) with double- stranded DNA wound around it. The 146 base pairs (bp) of DNA are associated with the nucleosome particle, and a 50- to 70-bp span of linker DNA bound by a linker histone H1 separates each nucleosome.  Nucleosomes Nucleosomes are in turn successively packed into higher- order structures by coiling and looping The histone tails aid in the formation of the higher order structures such as the 30-nm chromatin arrangement. Modification of chromatin Enzymatic modification of the amino-terminal tails (e.g., by acetylation, methylation, or phosphorylation) modifies the histones' net electric charge and shape. These modifications are physiologically reversible and are thought to prepare the chromatin for DNA replication and transcription. Heterochromatin and Euchromatin  Heterochromatin and Euchromatin Heterochromatin: Densely packed, genetically inactive. Transcription is inhibited in heterochromatin. DNA inaccessible. Euchromatin: Less densely compact, transcriptionally active. Sequence available to the RNA polymerases and transcription factors that influence the rate at which the gene is transcribed. Electron micrograph of neurons and glial cells AMBOSS GmbH.Chromatin condensation. https://amboss.com/. Accessed January 8th, 2025. The second level: the solenoid The nucleosomes in turn form a helical solenoid; each turn of the solenoid includes about six nucleosomes. The H1 histone aggregate causing 6 nucleosomes to coil together. Is also known as the 30nm fiber Each solenoid stack on top of each other forming the chromatin fiber.  The third level: the chromatin loops Chromatin fibers forms loops which attach to nonhistone proteins Nonhistone proteins forms a scaffold Scaffold Attachment Regions Cohesins 300 nm diameter  The fourth level: the cromosome The highest level of packaging. Looped domains coil and fold, further compacting chromatin Such packaging occurs during mitosis and meiosis  The fourth level: the cromosome Highly organized structures, consisting of DNA and proteins, which contains most of the genetic information of an individual. Somatic cells have 46 chromosomes (diploid) while gametic cells have only 23 (haploid).  DNA packaging and gene expression In addition to their role in packaging DNA, nucleosomes also regulate gene expression, or activity, by determining whether the DNA sequences can be accessed by transcription factors In Nucleosomes there are genes under active transcription When DNA is compacted into the solenoid structure it is not transcriptionally active  Why all these levels of organization? 1) To package DNA into a more compact, denser shape 2) To reinforce the DNA macromolecule to allow mitosis 3) To prevent DNA damage 4) To control gene expression and DNA replication BIBLIOGRAPHY Chapter 6 Chandar, Nalini and Viselli, Susan. Lippincott's Illustrated Reviews: Cell and Molecular Biology, 2nd Edition Lippincott Williams & Wilkins, a Wolters Kluwer Health Publication, 2019. AMBOSS