Download Chromosome Structure 1 - Dr. Kordula

Chromosome Structure I Tomasz Kordula, Ph.D. Resource: Lodish et al., Molecular Cell Biology, Chapter 10. Learning Objectives: 1. To know the physical characteristics and structural landmarks of human chromosomes. 2. To understand the nucleosome structure and higher­order structures of chromatin. 3. To define the gene and genomic organization of simple genes and gene families. 4. To understand relationship between exons and protein domains. 5. To know the mechanisms underlying repetitive gene formation. I. Human Chromosome Numbers, Sizes and Constituents A. Somatic, diploid cells in Go or G1 contain 46 chromosomes (2 each of numbers 1­22 + 2 sex chromosomes). Females have 2 X’s and males have an X and a Y. Simplistically, we can regard each chromosome in a pair, for instance each of the two number sevens, as if one came from Mom and the other came from Dad. Each of these contains one long, linear DNA molecule. The DNAs range in size between 48 and 280 Mbp (million basepairs). When the cell passes through S phase, each DNA is replicated and the daughter sister chromatids become attached to each other in G2 and early M phases. The structural compaction that occurs gives rise to highly ordered complexes that look something like the following figure. Taken from Lodish et al. “Molecular Cell Biology, © 2004 by W.H. Freeman and Co.
Note that the joining site is called the centromere, the site of microtubule attachment during movement of the sister chromatids to opposite poles in mitosis and meiosis. Centromeric DNA is composed of AT­rich, short (171bp) satellite repeats The ends are identified as telomeres, which protect the DNA’s from shortening during replication. B. Nucleosomes and Higher­Order structures­ The fundamental organizing unit of chromatin is the nucleosome, composed of an octamer of histones 2(H2A, H2B, H3, H4) around which 157 basepairs, or about two wraps of DNA, are wound. The linker DNA between nucleosomes is 40 to 50 basepairs long and is bound by one H1 histone. During interphase, chromatin is much more loosely dispersed than the metaphase chromosome shown above. The looser structure approximates the 30 nm fiber (nucleosomes stacked on nucleosomes) and looped 30 nm fibers that are tethered to nuclear scaffolding. These folded structures are shown in the cartoon below. Taken from Lodish et al. “Molecular Cell Biology, © 2004 by W.H. Freeman and Co. The looser chromatin exists in two levels of compactness. Heterochromatin, the more compacted form contains mostly inactive genes found, for example, at the centromere, the telomers and other places. Euchromatin, the looser form, is composed of active genes that must interact with transcription factors and RNA polymerase etc. during transcription. The two EMs below show chromatin in the (a) extended beads­on­a­string form and in the (b) 30 nm compact form.
Taken from Lodish et al. “Molecular Cell Biology, © 2004 by W.H. Freeman and Co. C. Histone Modification and Gene Expression­ The N­terminal tails of the histones tend to be accessible on the surface of the nucleosome. It is now known that Lys residues in these tails are often reversibly acetylated. The acetylated versions are less positively charged, resulting in less affinity for DNA and looser structures that enhance genetic activity. Alternatively, histone tails may be methylated, phosphorylated, or ubiquitinated. Such adducts will influence the affinity of the nucleosome for non­histone proteins involved in packaging and gene expression. Transcriptional activity typically involves shuffling and sliding of nucleosomes to make way for the transcription apparatus. However, recently it has been shown that expression can also rely on remodeling of nucleosomes by replacing standard histones with variant forms. D. Gene­ Defined as the entire DNA sequence required for the synthesis of some useful RNA (rRNA, tRNA, mRNA, or other RNA). This would include promoters, enhancers, UTR’s etc. These expressible sequences represent only about 25% of the total human genome, and the protein­encoding, reading frames (without introns) are a mere 1.4% of the genome. The rest is spacer DNA between genes, and half of this spacer DNA is derived from ancient mobile genetic elements, some of which is still “jumping” from place to place in the genome. Furthermore, most pre­mRNA genes contain introns that are usually much longer that the exons they interrupt. As we know, the introns are removed from the pre­mRNA transcript and the exons are spliced together. In some cases different mature mRNAs are created by alternative splicing modes that recognize different splice junctions, different cap sites, or different polyA sites. The end result is that there are many more proteins than there are genes that encode them. Exons tend to encode protein domains, and introns are at the junctions between domains.
Taken from Lodish et al. “Molecular Cell Biology, © 2004 by W.H. Freeman and Co. There is a controversy as to whether introns emerged early or late in evolutionary time. The “early­theory” proponents feel introns are ancient fossils and have been eliminated over time in lower forms like bacteria. Proponents of the “late theory” believe introns emerged belatedly to help establish the multiple­domain structure of protein genes during evolution. Introns may also serve the purpose of interrupting unequal cross­overs between exonic sequences. E. Gene Families­ Many of our protein­coding genes are solitary genes. The remainder are duplicated genes or gene families consisting of multiple copies having slightly different sequences. The evolutionary development of such clusters probably result from unequal cross­overs, followed by separate mutations in each version over time. Some of the well­known gene families include: The globins, receptor proteins, protein kinases, HSP 70 family, and many transcription factors. Perhaps the best characterized gene family is the β globin gene cluster:
Taken from Lodish et al. “Molecular Cell Biology, © 2004 by W.H. Freeman and Co. The initial event likely occurred in germline cells and perpetuated itself in subsequent generations. Eventually the β globin gene cluster looked like the following diagram: Taken from Lodish et al. “Molecular Cell Biology, © 2004 by W.H. Freeman and Co. Each of the above green genes encodes a β­type subunit protein, but the Gγ and Aγ subunits have “drifted” such that they have higher affinity for oxygen, and hence are expressed during fetal development only. Interestingly, the arrangement of the β genes is consistent with their temporal order of expression. The epsilon gene expresses in the early embryo, the Gγ and Aγ forms in the later embryo, and the delta and beta forms expesss after birth. Another gene cluster superfamily is the immunoglobulin group whose members are key to recognizing foreign entities and cell­cell recognition. F. Repetitive genes in Clusters (Histones) or inTandem Arrays (rRNAs) ­ Distinguished from the more spread­out variant gene families, repetitive genes are identical or nearly identical in sequence and lie close to each other. For example, the rRNAs are aligned in a head­to­toe fashion, and are coordinately expressed simultaneously. Repetitive histone genes are also coordinately expressed in a burst of activity in S phase. Such multiple arrays may have developed by unequal crossing over as shown below:
Taken from Lodish et al. “Molecular Cell Biology, © 2004 by W.H. Freeman and Co. The image below is an EM of tandem rRNA genes in the process of transcription: Taken from Voet and Voet “Biochemistry” 2nd ed., © 1995 by John Wiley and Sons, Inc