Chromatin

Chromatin refers to the complex of DNA and thousands of proteins that make up the chromosomal axes. With regards to eukaryotic DNA, cells have 2 main problems:

  1. DNA packaging: 2m of DNA must be able to fit into each 10um cell
  2. DNA accessibility: DNA must always be accessible for DNA binding factors, in the right region and at the right time

The answer to these problems is chromatin which enables a large amount of DNA to become highly condensed, while also making DNA accessible to important proteins (such as transcription factors) by the highly flexible structure of some regions of the chromatin. Thus, chromatin is a combination of nuclear DNA and proteins allowing continuous accessibility of genes in the cell nucleus.

    The packaging problem



    Classical model of chromatin structure



    The 10nm fiber

    The nucleosomal 10nm fiber is often referred to as 'beads on a string' owing to its appearance under the electron microscopy. It is also known as being the primary level of chromatin organization. The nucleosomes (i.e. the beads) are made up approximately 147 base pairs of DNA wrapped around a core histone octamer. The histone octamer is made up of two copies of each of the histones H2A, H2B, H3 and H4. The N-terminal tails of H2B and H3 pass through the two DNA strands wrapped around them, and can undergo covalent modifications. The nucleosomes are linked together by linker DNA of variable lengths forming the string. The structure of the core nucleosome is well conserved (highlighting its importance), other than the linker region of DNA that can be variable in length.

    Compaction in the form of the 10nm nucleosomal fiber could be very restricting upon DNA accessibility, thus nucleosome structure is susceptible to modification. These modifications can include:

    • ATP-dependent chromatin remodelling factors which result in nucleosome sliding, disruption of histone-DNA interaction and can generate DNA torsion.
    • Histone variants that can replace each other. This increases the diversity of histone function and affects chromatin structure resulting in the recruitment of other chromatin proteins subjective to variant.
    • Histone post translational modifications (PTMs) that include phosphorylation, ubiquitination, methylation and acetlyation (all covalent modifications). These can affect histone-DNA interactions, histone-histone interactions and can also recrut other chromatin proteins.

     

    The above factors have been proven as the key to regulate the dynamics of the nucleosome and the correct spatial and temporal accessibility of the DNA.

      The Histone octamer



      The 30nm fiber

      The 30nm fiber is known as the secondary structural level of chromatin. The histone H1 is thought to be involved in the promotion and formation of the 30nm fiber. This can be shown in nucleosomes lacking H1 which do not readily form the 30nm fiber. Histone H1 is also known as the linker histone, due to its association with the linker DNA between nucleosomes. However, unlike the 10nm fiber the exact structure of the 30nm fiber remains still to be resolved because the structure is too compact for us to visualise the spatial arrangement of the nucleosomes. It is also hard to structurally characterise as the native chromatin is very heterogeneous, being made up of different DNA sequences and different histone variants and modifications. There are currently two different models for the 30nm fiber:

      1. The solenoid model describes consecutive nucleosomes folding together in a simple one start helix
      2. The zig-zag model refers to two rows of nucleosomes with the linker DNA criss-crossing between the two. This produces a double helix/two start helical structure.

      Currently results from electron microscopy and analysis of crystal structures favour the Zig-Zag model.

      Solenoid Vs. Zig-Zag



      Higher order chromatin structure

      Higher order chromatin is polymorphic in its structure, and it is still unclear as to whether there is a definite hierarchical set of structures above the 30nm fiber. The mitotic chromosome is an obvious example of higher order structure. Light and electron microscopy, plus newer immunogold labelling techniques have uncovered banding patterns of chromatin, with untranscribed gene deserts more tightly compacted compared to gene rich areas. There is little sound evidence for a conserved higher order structure, but below are some examples.

      Mitotic metaphase chromosome, chromosome scaffolds and chromatin loops

      A consistent example of higher order chromatin structure is the mitotic metaphase chromosome. However, little is known about its organization. In the metaphase chromosome DNA is compacted 10,000-20,000 fold. For any given species the arm dimension of the metaphase chromosome remains constant, independent of the DNA sequence associated with it.  

      The core structures of higher order chromatin are chromosome scaffolds.  The chromosome scaffold is made up of two primary components:

      1. The SC1 (topoisomerase II) changes the topology of DNA by generating transient double strand breaks (DSBs).
      2. The SC2 (condensin complex: SMC2-SMC4) makes up the SMC (structural chromosome maintenance) family of ATPases. There are two different types of condensin, condensin I and II. Condensin I is localized at the chromosome shortly after nuclear envelope break down (end of prophase). Condensin II is localized at the chromosomes during interphase and early prophase.

       

      Attached to the scaffolds are chromatin loops. These loops are connected to the chromosome scaffolds via SARs (scaffold associated regions). SARs are AT (Adenine/ Thymine) rich regions of the chromosome scaffold that unfold more readily (possibly facilitating the access of factors required for DNA processes). AT-queue regions are formed by the arrangement of the SARs along the chromosome scaffold, with relatively tight folding in some areas and more unfolded in others.

         

        Evidence for the chromosome scaffold can also be seen in lampbrush chromosomes (LBC's). LBC's are generally confined to meiosis in oocytes. They are large with a linear chromosome axis with large loops emerging from them. Each loop is rich in actively expressed genes (transcriptional units) suggesting LBC's are an adaptation to maximize transcriptional output in oocytes. However, the majority of the DNA (mostly non-expressed genes) is still found condensed at the chromosome axis.

          Condensin



          Epigenetics

          Epigenetics is the study of inherited changes caused by mechanisms other than changes in DNA sequence. Human disorders such as Prader-Willi syndrome are known to have been caused by epigenetic changes. Chromatin component changes such as in histone variants, chromatin re-modelling factors and histone modifications can produce these effects. Sometimes chromatin components can be sensitive to environmental and metabolic circumstances that alter gene expression. This altered gene expression is heritable in cells, and if such occur in germ cells they can be passed onto the offspring.

          Useful links

          http://www.youtube.com/watch?v=eYrQ0EhVCYA

          http://www.youtube.com/watch?v=nbMjLk3r2zk

          http://www.youtube.com/watch?v=fecfROFrp_c

          References

          Li and Reinberg (2011) Chromatin higher order structures and gene regulation. Current opinion genetic development; 21(2): 175-186

           

          Woodcock and Goosh (2010) Chromatin higher order structure and dynamics. Cold spring harbour prespectives

           

          Tremethick (2007) Higher order structures of chromatin: the elusive 30nm fiber. Cell 128

           

          Becker (2009) The world of the cell; Seventh edition;chapter 18: pages 534-544

           

           

          Advertisement

          Fastbleep © 2019.