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Biology LibreTexts

4: Genomes and Chromosomes

  • Page ID
    309
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    Chapter 4 has two parts: genomes and chromosomes. Initial studies on genome structure used the kinetics of hybridization of nucleic acids to determine the bulk features of genomes, e.g. how big is a particular genome, how much is single-copy and how much is repeated, and how much of that genome is transcribed into nuclear or mRNA in a particular tissue. More detailed whole-genome mapping and sequencing projects are now revolutionizing biology. Some of the information on whole-genome sequences of bacteria, the yeast Saccharomyces cerevisiae, worms, flies and mammals (humans and mice) will be reviewed. All this genomic DNA is packaged into chromosomes, and Chapter 4 will also review some of their cytological features, and discuss their packaging into nucleosomes and higher order structure. Transitions between types of chromatin structure are fundamental to issues of gene regulation in eukaryotes; this will be explored in more biochemical detail in Part Four of the text.

    • 4.1: Reassociation kinetics measure sequence complexity
      The components of complex genomes differ not only in repetition frequency (highly repetitive, moderately repetitive, single copy) but also in sequence complexity. Complexity (denoted by N) is the number of base pairs of unique or nonrepeating DNA in a given segment of DNA, or component of the genome. This is different from the length (L) of the sequence if some of the DNA is repeated.
    • 4.2: Analysis of Renaturation curves with Multiple Components
      this section, the analysis in Section 4.1 is applied quantitatively in an example of renaturation of genomic DNA. If an unknown DNA has a single kinetic component, meaning that the fraction renatured increases from 0.1 to 0.9 as the value of C0t increases 100-fold, then one can calculate its complexity easily.
    • 4.3: RNA Abundance
      The availability of cloned DNA probes for many genes has greatly facilitated the analysis of amounts of RNAs in different cells or under different conditions. For instance, it is very common to label a DNA probe that will hybridize to mRNA; the DNA comes from either a cDNA clone or a genomic clone containing an exon. The labeled probe is then hybridized to total or polyA-containing RNA (the latter is called polyA+ RNA, and is roughly equivalent to mRNA) from a cell.
    • 4.4: Genome Analysis by Large Scale Sequencing
      Whole genomes can be sequenced both by random shot-gun sequencing and by a directed approach using mapped clones.
    • 4.5: Sizes of genomes - The C‑value paradox
      The C-value paradox is basically this: how can we account for the amount of DNA in terms of known function? The C-value is the amount of DNA in the haploid genome of an organism. It varies over a very wide range, with a general increase in C-value with complexity of organism from prokaryotes to invertebrates, vertebrates, plants.
    • 4.6: Large Scale Genome Organization
    • 4.7: Comparative Genome Analysis
    • 4.E: Genomes and Chromosomes (Exercises)
    • 4.S: Genomes and Chromosomes (Summary)