Chromosome in Genetic Inheritance and Cellular Processes

Chromosome Structure and Function DNA is packaged into chromosomes ▪ ▪ ▪ ▪ ▪ DNA is packaged into linear or circular units called chromosomes o Eukaryotes = linear chromosomes o Most bacteria & archaea = circular chromosomes In eukaryotes, DNA is wrapped round packing proteins (histones) and compacted in a space-efficient way Some cells have small extra pieces of DNA (plasmids) The genome is the collection of all chromosomes in a cell A gene is a region that controls a discrete hereditary characteristic, usually a specific product like a protein Genome size varies widely across organisms ▪ ▪ ▪ ▪ Genomes vary widely in the size of genome, number of genes and gene spacing o E. coli is 98% genic Single-celled organisms generally have fewer genes that multicellular organisms Larger genome size and increased genome complexity do not always correlate Genomes often have transposable elements – pieces of DNA that copy themselves within a genome and lead to increases in genome size Cell cycle: duplication & segregation of chromosomes ▪ ▪ Chromosomes must be copied and transferred to the next generation of cells faithfully Cells must copy DNA and separate the chromosomes before they can divide The eukaryotic cell cycle has four stages ▪ ▪ ▪ ▪ G1 (gap phase 1) – cells grow to a minimum size required for the next stage S (synthesis phase) – DNA is copied, duplicating the chromosomes. The two copies (sister chromatids) remain associated with one another G2 (gap phase 2) – the cell prepares for mitosis M (mitotic phase) – sister chromatids are separated and a full set of chromosomes is moved to each pole of the cell (chromosome segregation) Chromosomes are segregated during M phase ▪ ▪ ▪ ▪ On entry to M phase, the nuclear membrane breaks down Chromosomes condense, but sister chromatids are still associated Centromeres of the sister chromatids bind to microtubules from each pole The associations between sister chromatids are removed and the sister chromatids move apart to opposite poles of the cell Chromosomes have a distinctive appearance at mitosis ▪ Condensed chromosomes have characteristic lengths and banding patters ▪ A karyotype is a display of the chromosomes from an individua, derived from microscopy images prior to separation of sister chromatids How many chromosomes are in a cell? ▪ ▪ ▪ Ploidy refers to how many sets of identical chromosomes an organism has o Humans are diploid – two copies of chromosomes 1-22 and either 2 X chromosomes or one X and one Y o Human egg and sperm cells are haploid, and only have one copy of chromosomes 1-22 plus an X or Y o A small number of human cells are polyploid, and have multiple sets of each chromosome Eukaryotic cells can contain DNA outside of the nuclear chromosomes: o Mitochondria, which provide cells with ATP, have their own chromosome o Chloroplasts, which derive energy from sunlight in plants, have their own chromosome o Mitochondria and chloroplasts are thought to have derive from ancestral freeliving bacteria that were absorbed and maintained by other single-celled organisms Bacterial cells often have additional DNA within their cells: o Plasmid = small circular DNA molecule. Often encode a few proteins that confer a selective advantage, such as antibiotic resistance DNA is packaged by nucleosomes in chromatin ▪ ▪ ▪ ▪ ▪ ▪ ▪ ▪ ▪ ▪ ▪ Chromosomes are made up of chromatin; a DNA-protein complex that condenses DNA In eukaryotes, the basic binding proteins are called histones There are four core histones – they arose early in eukaryotic evolution and, as they are crucial for survival, are very highly conserved Histones are rich in lysine and arginine which have positive charges and stabilize the DNA-histone interaction DNA wraps 1.67 times around a histone octamer to form a nucleosome – this is the basic repeating unit of chromatin The histone octamer has two each of the four core histones H2A, H2B, H3, and H4 The H3-H4 heterotetrametric associates with DNA The two H2A-H2B dimers then associate to form the octamer About 146bp of DNA wraps around the octamer to form the nucleosome The DNA is wound around the histone octamer in a left-handed direction – when the octamer is removed, this leaves negatively supercoiled DNA Negative supercoiling makes strand separation easier, which is required for replication and transcription Histone variants may have distinct functions ▪ Other histone variants can be incorporated into nucleosomes, and are found at special chromatin locations ▪ For example, H2A.X is phosphorylated at sites of DNA double-strand breaks and recruits repair machinery Histone tails can be chemically modified ▪ ▪ ▪ ▪ ▪ ▪ ▪ Each core histone has an N-terminal “tail” that extends outwards between the DNA coils Tails are up to 25 amino acids, and have and undefined structure Tails interact with other nucleosomes to compact DNA further Histone tails can also be chemically modified – these modifications are important chromatin structure and function Histone side chains are subject to modifications that act as signals during regulation – mainly acetylation, methylation, phosphorylation and ubiquitination Modifications are thought to recruit specific proteins to the chromatin – modifications of unstructured histone tails are common Histone modifications are reversible – specialized enzymes add and remove the chemical groups Histone modification enzymes add/remove histone marks ▪ ▪ Histone acetyltransferases (HATs) add acetyl groups to lysine side chains. Histone deacetylases (HDACs) remove the acetyl groups Histone methyltransferases (HMTs) add methyl groups to lysine and arginine side chains. Histone demethylases remove the methyl groups Histone modifications are associated with gene regulation ▪ ▪ ▪ ▪ ▪ ▪ ▪ Acetylation is associated with active transcription – euchromatin has more acetylation than heterochromatin Acetylation removes the positive charge from lysine side chains, which affects interactions with negatively-charged DNA Histone acetylation also generates binding sites for bromodomain proteins, which bind specifically to certain acetyl-lysine’s Bromodomains then recruit other proteins like nucleosome remodeling complexes Up to three methyl groups can be added to a lysine, and up to two can be added to arginine Methylation is associated with transcription activation or repression, depending on the residue that is methylated, so the position as well as the modification are significant for regulation o Methylation of lysine 9 in the H3 tail is associated with silent chromatin o Methylation of H3 lysine 4 is associated with active chromatin Chromodomains bind to specific methylated lysine’s, and are often associated with transcriptional silencing Nucleosome remodeling complexes control access to DNA ▪ Chromatin packing presents a barrier to proteins that need to access DNA, and hence inhibits processes like transcription ▪ ▪ ▪ ▪ Nucleosome locations can be changed to allow proteins to access the DNA ATP-dependent nucleosome remodeling complexes increase accessibility of DNA by: o Sliding the histone octamer along the DNA, or o Removing the histone octamer and transferring it elsewhere, or o Introducing transient loops into the DNA wrapped around a histone core Several classes of nucleosome remodeling complexes exist, with different subunit compositions, such as: o SWI/SNF: disrupts nucleosome positioning o ACF (ISWI family): positions nucleosomes during chromatin assembly Nucleosome remodeling complexes have subunits such as: o ATPase domain (in all complexes), in two parts – Dexx and HELICc o Bromodomain (binds acetylated lysine’s) o Chromodomain (binds methylated lysine’s) o SANT-SLIDE (binds histone tails) Nucleosome remodeling complexes can be recruited by transcription factors or histone modifications ▪ ▪ ▪ Nucleosome remodeling is require to be precise, to allow exposure to specific regions of DNA Cells recruit remodeling complexes via proteins that bind in a sequence specific manner Transcriptional regulators and histone modifications can recruit nucleosome remodeling complexes DNA can be methylated ▪ ▪ ▪ Methylation occurs in bacteria and many eukaryotes Methyl groups can be added to cytosine residues to make 5-methyl cytosine by DNA methyltransferases Eukaryotic methylation is usually at CpG or CpXpG sites (p means phosphodiester bond, X means any base) DNA methylation can lead to base changes ▪ ▪ ▪ DNA methylation is risky – DNA can be altered permanently Methylated cytosines are less chemically stable, so more likely to undergo deamination, which changes the base to thymine This recognized as damage to the DNA and is repaired to restore the original cytosine DNA methylation plays roles in gene regulation ▪ ▪ ▪ ▪ Methylation in eukaryotes is used to silence transcription Up to 60% of human CpGs are methylated, and methylation state can be inherited Some DNA binding complexes bind specifically to methylated DNA, such as histone modification enzymes and nucleosome remodeling complexes Similarly, some histone binding proteins can recruit DNA methyltransferases Centromeres direct chromosome segregation ▪ ▪ ▪ ▪ ▪ ▪ ▪ ▪ ▪ In eukaryotes, centromeres direct chromosome segregation Centromeres are found in all eukaryotic chromosomes and are necessary for correct chromosome segregation during cell division Most species have a single centromere per chromosome The centromere is in a heterochromatic region, and is inherited After DNA replication, but before chromosomes separate, two sister chromatids are present. The centromere appears as a constriction Centromeres bind specific proteins to form a structure called a kinetochore In mitosis, kinetochores attach to microtubules from opposite spindle poles This attachment lets the spindle pull the sister chromatids apart This mechanism of chromosome segregation is highly conserved, but centromere sequences in different species are distinct Centromere structure varies across species ▪ ▪ ▪ ▪ ▪ Centromeres vary in size and sequence in different organisms Some organisms have no defined centromere, and spindles attach along the length of the chromosome Human centromeres are made of tandem repeats that are arranged in higher order repeats Centromeres all have defined region where the nucleosomes have a histone H3 variant The CENP-A marked region is the domain where kinetochores assemble and accurate CENP-A deposition is crucial for correct centromere function Telomeres are defined by repetitive sequences ▪ ▪ ▪ ▪ ▪ Telomeres stabilize the ends of chromosomes and help solve the problem or replicating chromosome ends Telomere DNA consists of simple tandem repeats with one C-rich strand and one G-rich strand The G-rich strand in all eukaryotes is the strand that extends 5’-3’ towards the chromosome end and terminates in a small single-stranded region Human telomeres consist of repeats TTAGGG; other organisms have different repeats The total length of the repetitive region ranges from 50-30,000bp, depending on species Telomeres protect the ends of linear chromosomes ▪ ▪ ▪ ▪ The G-rich strand in all eukaryotes is the strand that extends 5’-3’ towards the chromosome end, and it terminates in a small single-stranded region In organisms with long telomeres, the overhang may be processed into a t-loop, formed by base-pairing of the overhang with the double-stranded region Telomere repeats are binding sites for proteins that mark them as natural ends and distinguish them from DNA breaks DNA polymerase cannot copy the ends of a DNA molecule – telomerases maintain the ends of the chromosomes Chromatin packing has several layers ▪ ▪ ▪ The first level is the 10nm fiber, which arises from nucleosome association with DNA, and has a “beads on a string” appearance The 10nm fiber is folded further into the 30nm fiber Formation of the 30nm fiber involves the linker histone H1 Chromatin compaction may reflect transcriptional activity ▪ ▪ ▪ ▪ ▪ In interphase, there is a range of compaction along a chromosome Chromatin in relatively decondensed regions stains lightly – euchromatin More compact regions stain more darkly – heterochromatin Heterochromatin is associated with less transcriptional activity Telomeres, centromeres, and regions of highly repetitive DNA are typically located in heterochromatin Chromosomes are packaged hierarchically ▪ ▪ ▪ ▪ DNA is first packaged into nucleosomes Nucleosome-bound DNA is then assembled into topologically associated domains (TADs) The chromosomes then occupy distinct chromosome territories in the nucleus The nuclear location of a chromosome is correlated with its transcriptional activity Chromosomes occupy specific territories in the eukaryotic nucleus ▪ ▪ Each chromosome occupies a characteristic space – a chromosome territory – as shown by chromosome fluorescence in-situ hybridization (FISH) staining The mechanism for establishing chromosome territories is not yet understood Nuclear location correlates with gene activity ▪ ▪ ▪ Heterochromatic regions are often associated with the nuclear periphery Human chromosomes 18 and 19 are of similar size – gene-rich 19 is found near the center of the nucleus, gene-poor 18 is at the periphery In female mammals, the inactive X chromosome is always at the nuclear periphery