Genetics: From Genes to Genomes PowerPoint to accompany Genetics: From Genes to Genomes Fourth Edition Leland H. Hartwell, Leroy Hood, Michael L. Goldberg, Ann E. Reynolds, and Lee M. Silver Prepared by Mary A. Bedell University of Georgia Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display

12 The Eukaryotic Chromosome CHAPTER OUTLINE PART IV How Genes Travel on Chromosomes CHAPTER The Eukaryotic Chromosome CHAPTER OUTLINE 12.1 Chromosomal DNA and Proteins 12.2 Chromosome Structure and Compaction 12.3 Chromosomal Packaging and Function 12.4 Replication and Segregation of Chromosomes Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Chromosomal DNA and proteins Chromosomes have a versatile, modular structure for packaging DNA that supports flexibility of form and function Chromatin is the generic term for any complex of DNA and protein found in a nucleus of a cell Chromosomes are the separate pieces of chromatin that behave as a unit during cell division Chromatin is ~ 1/3 DNA, 1/3 histones, 1/3 nonhistone proteins DNA interaction with histones and nonhistone proteins produces sufficient level of compaction to fit into a cell nucleus Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Histone proteins Histones – small, positively-charged, and highly conserved Bind to and neutralize negatively charged DNA Make up half of all chromatin protein by weight Five types - H1, H2A, H2B, H3, and H4 Core histones (H2A, H2B, H3, and H4) make up the nucleosome Posttranslational modifications of histones H3 and H4 Methylation and acetylation of histone tails Affect chromatin structure and gene expression in specific chromosomal regions Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Nonhistone proteins Hundreds of other proteins that make up chromatin and are not histones 200 – 200,000 molecules of each kind of nonhistone protein Large variety of functions Structural role – chromosome scaffold (see Figure 12.2) Chromosome replication – e.g. DNA polymerases Chromosome segregation – e.g. kinetochore proteins (see Figure 12.3) Active in transcription – largest group Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Different levels of chromosome compaction Table 12.1 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

The nucleosome is the fundamental unit of chromosomal packaging DNA wraps twice around nucleosome core octamer (Figure 12.5) and forms 100 Å fiber Results in 7-fold compaction of DNA Spacing and structure of nucleosomes affect genetic function Determines whether DNA between nucleosomes is accessible for proteins that initiate transcription, replication and further compaction Arrangement along chromatin is highly defined and transmitted from parent to daughter cells during DNA replication Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Nucleosomes look like "beads on a string" in the electron microscope Diameter of DNA helix (string) is 20 Å Diameter of nucleosome core (bead) is 100 Å Fig. 12.4 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

The nucleosome core is an octamer of two each of histones H2A, H2B, H3, and H4 160 bp of DNA wraps twice around a nucleosome core 40 bp of linker DNA connects adjacent nucleosomes Histone H1 associates with linker DNA as it enters and leaves the nucleosome core Fig. 12.5 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

X-ray crystallography of a nucleosome DNA bends sharply at several places as it wraps around the core histone octamer Base sequence dictates preferred nucleosome positions along the DNA Fig. 12.6 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Models of higher-order packaging 100 Å fiber is compacted into 300 Å fiber by supercoiling Results in an additional 6-fold compaction of DNA Fig. 12.7a Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

The radial loop-scaffold model for higher levels of compaction Several nonhistone proteins (NHPs) bind to chromatin every 60-100 kb and tether the 300 Å fiber into structural loops Other NHPs gather several loops together into daisylike rosettes Fig. 12.7b Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

The radial loop-scaffold model for higher levels of compaction (cont) Condensins may further condense chromosomes into a compact bundle for mitosis Fig. 12.7c Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

The karyotype of a human female examined by high-resolution G-banding Metaphase chromosomes stained with Giemsa have alternating bands of light and dark staining Each band is contains many DNA loops and ranges from 1 to 10 Mb in length Banding patterns on each chromosome are highly reproducible Fig. 12.9 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Locations of genes in relation to chromosomal bands Short arm = p arm Long arm = q arm Within each arm, light and dark bands are numbered consecutively Fig. 12.10 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Comparison of chromosomes from humans and great apes Banding patterns in some chromosomes (i.e. Chr 1) are nearly identical The metacentric Chr 2 in humans was formed by fusion of two acrocentric chromosomes in great apes Chromosome 1 Acrocentric chromosomes of great apes Fig. 12.11 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Chromosomal packaging and function Heterochromatin – highly condensed, usually inactive transcriptionally Darkly stained regions of chromosomes Constitutive – condensed in all cells [e.g. most of the Y chromosome and all pericentromeric regions (see Fig 12.12)] Facultative – condensed in only some cells and relaxed in other cells (e.g. position effect variegation, X chromosome in female mammals) Euchromatin – relaxed, usually active transcriptionally Lightly stained regions of chromosomes Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Position-effect variegation (PEV) in Drosophila White+ (w+) gene is normally located in euchromatin Chromosomal inversion can result in w+ gene being located adjacent to heterochromatin w+ gene is expressed in all cells (red pigment) w+ gene is silenced in some cells (no pigment) but is expressed in other cells (red pigment) Fig. 12.13a Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

PEV in Drosophila (cont) Gene silencing can be caused by spreading of heterochromatin into nearby genes Spreading can occur over > 1000 kb of chromatin Heterochromatin spreads further in some cells than in others Fig. 12.13b Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Identification of molecules involved in heterochromatin formation Genetic screens in Drosophila were used to identify mutations that enhance or suppress the extent of PEV Mutation in enhancer of PEV results in more cells having gene inactivation Encodes protein that localizes to heterochromatin Mutation in suppressor of PEV results in fewer cells having gene inactivation Encodes protein that adds methyl group to lysines on histone H3, signal for chromatin condensation Barriers – specific sites on DNA that block the spread of heterochromatin Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

X-chromosome inactivation in female mammals occurs through heterochromatin formation Example of facultative heterochromatin Dosage compensation in mammals so that X-linked genes in XX and XY individuals are expressed at same level Random inactivation of all except one X chromosome in XX Barr bodies – darkly stained heterochromatin masses observed in somatic cells at interphase XX person has one Barr body XXX person has two Barr bodies XXY person has one Barr body Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

X chromosome mosaicism In very early embryo, both X chromosomes are active In humans, random X-inactivation occurs ~ 2 weeks after fertilization Some cells have maternal X inactivated, other cells have paternal X inactivated All cell descendants have the same inactive X Adult females are mosaic at X-linked genes In females heterozygous for X-linked mutation: Some cells have wild-type allele inactivated Some cells have mutant allele inactivated Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

X-inactivation is initiated by expression of the Xist gene Xist, X inactivation specific transcript One of the few genes expressed on the inactive X but is not expressed on the active X Xist RNA is a large, non-coding, cis-acting regulatory RNA Binds to the X-chromosome that it was expressed from Initiates histone modifications (methylation, deacetylation) that result in heterochromatin formation Deletion of the Xist gene abolishes X inactivation Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Transcription is controlled by chromatin structure and nucleosome position Spacing and structure of nucleosomes affect transcription Three major mechanisms can regulate chromatin patterns Histone modifications – addition of methyl or acetyl groups Remodeling complexes can alter nucleosome patterns Change accessibility of promoter sequences Assays for DNase hypersensitive sites (Figure 12.14) Remove or reposition promoter-blocking nucleosomes Histone variants can cause different nucleosomal structures, e.g. CENP-A at centromeres Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Assay for chromosomal regions that lack nucleosomes DNase hypersensitive sites - promoters of transcribed genes are more susceptible to nuclease digestion than promoters of non-transcribed genes Fig. 12.14 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Origins of replication in eukaryotes Rate of DNA synthesis in human cells ~ 50 nt/sec Most mammalian cells have ~ 10,000 origins It would take 800 hours to replicate the human genome if there was only one origin of replication! Many origins are active at the same time (see Fig. 12.15) Accessible regions of DNA that are devoid of nucleosomes Replication unit (replicon) – DNA running both ways from one origin to the endpoints Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Origins of replication in yeast are "autonomously replicating sequences" (ARSs) ARSs permit replication of plasmids in yeast cells AT-rich consensus sequence found in all ARS elements, flanked by sequences that promote replication initiation ARS1 (below) is the first ARS to be characterized Fig. 12.16 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Telomeres are "caps" that protect the ends of eukaryotic chromosomes Telomeres consist of specific repetitive sequences and don't contain genes Species-specific sequences e.g. TTAGGG in humans, TTGGGG in Tetrahymena 250-1500 repeats with variable number between different cell types Prevent chromosome fusions and maintain integrity of chromosomal ends Fig. 12.17 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Replication at the ends of chromosomes After removal of the last RNA primer, DNA polymerase cannot replicate some of the sequences at the 5' end DNA synthesis occurs only in 5'-to-3' direction Without a special mechanism, DNA would be lost from every new DNA strand at each cell cycle Fig. 12.18 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Telomerase is a ribonucleoprotein that extends telomeres Telomerase RNA is complementary to telomere repeat sequences Serves as template for addition of new DNA repeat sequences to telomere Additional rounds of telomere elongation occur after telomeres translocate to newly-synthesized end Fig. 12.19 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Telomerase activity and cell proliferation In yeast that has deletion of telomerase, telomeres shorten by 3 bp per generation Eventually the chromosomes break and the cells die In humans, the levels of telomerase and cellular life-span varies between different types of cells Most somatic cells have low expression of telomerase Telomeres shorten slightly at each cell division Senescence after < 50 generations in culture Germ cells, stem cells, and tumor cells have high expression of telomerase At each generation, telomere length is maintained Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Chromosome duplication includes reproduction of chromatin structure Chromatin fiber unwinds before DNA synthesis occurs Synthesis of histones and their transport into nucleus must be tightly coordinated with DNA synthesis Newly-synthesized DNA must associate with either preexisting histones or with newly-synthesized histones After DNA replication, nucleosomal DNA must produce the same level of compaction as before replication In differentiating cells, a slightly different chromatin condensation pattern can appear after replication Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Segregation of condensed chromosomes depends on centromeres During anaphase of mitosis and meiosis II, sister chromatids must segregate to different daughter cells During anaphase of meiosis I, sister chromatids do not separate and homologous chromosomes segregate to different daughter cells Centromeres have two functions: Hold sister chromatids together (through action of cohesin) Attachment sites for chromosome segregation machinery (through formation of kinetochore) Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Characteristics of centromeres Appear as constrictions in chromosomes Can be in middle of chromosome (metacentric) or near one end of the chromosome (acrocentric) Consist of satellite DNAs, which are repetitive, noncoding sequences Tandem repeats of 5 – 300 bp long, can extend over megabases of DNA Have different chromatin structure and higher-order packaging than other chromosomal regions Predominant human satellite DNA is a-satellite 171 bp repeat, present in > 1 Mb block of tandem repeats Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Action of cohesin during mitosis Cohesin is a protein complex that holds sister chromatids during metaphase At anaphase, cohesin is enzymatically cleaved and sister chromatids are released from each other Fig. 12.20a Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Action of cohesin during meiosis I At anaphase I, cohesin along chromosome arms is enzymatically cleaved but cohesin at centromeres is not cleaved Shugoshin protects centromeric cohesin from degradation Fig. 12.20b Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Action of cohesin during meiosis II After entry into metaphase II, shugoshin is removed and centromeric cohesin is degraded Fig. 12.20c Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Structure of centromeres in higher organisms Centromeres hold sister chromatids together and contain information for construction of a kinetochore Cohesin binds sister chromatids together at the centromere Fig. 12.21 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Structure and DNA sequence organization of yeast centromeres Fig. 12.22 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12

Histone variants at centromeres Specialized chromatin in central core of centromere marks this region for attachment of kinetochore proteins Central core of each centromere: Composed of unique chromatin that does not recombine and is not transcribed Surrounded by regions of heterochromatin interspersed with euchromatin Histone variant CENP-A is present in central core of all eukaryotes examined Differs from histone H3 in N-terminal region Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 12