Information

1.2: Chromosomes and chromatin - Biology


Learning Objectives

  • Understand that chromosomes contain genes, which are DNA sequences that encode products and describe how the positions of individual genes on a given chromosome are related to their positions on the homolog of that chromosome.
  • Discuss how DNA is packaged in the chromosomes in terms of histones, nucleosomes, and chromatin (heterochromatin and euchromatin).
  • Explain the meaning of ploidy (haploid, diploid) and how it relates to the number of homologues of each chromosome.
  • Compare prokaryotic and eukaryotic chromosomes.
  • Interpret a karyotype.

What is a chromosome?

Chromosomes are units of DNA stored within cells. In prokaryotes, these units are most often circular, whereas in eukaryotes the units are typically linear.

Genes are sequences within chromosomes that contain information in the sequence of nucleotide bases that encodes a product (RNA or a protein).

Features and Compaction of Circular Chromosomes

The bacterial chromosome is typically one molecule of double-stranded, helical DNA. In most bacteria, the two ends of the double-stranded DNA covalently bond together to form both a physical and genetic circle. The chromosome is generally around 1000 µm long and frequently contains as many as 3,500 genes. E. coli, a bacterium that is 2-3 µm in length, has a chromosome approximately 1400 µm long.

To enable a macromolecule this large to fit within the bacterium, proteins bind to the DNA, segregating the DNA molecule into around 50 chromosomal domains and making it more compact. Prokaryotes primarily compact chromosomes by supercoiling, the process of twisting a piece of DNA that causes it to "fold up" on itself. Think of an old-fashioned phone cord or piece of string that you keep twisting. Supercoiling is not random, but is controlled by enzymes (topoisomerases) that can add or remove "twists" in the double helix to loosen or tighten the chromosome compaction.

Features of Linear Chromosomes

Linear chromosomes contain structural features such as centromeres and telomeres. In most cases, each chromosome contains one centromere. These sequences are bound by proteins that will link the centromere to microtubules that facilitate chromosome movement during cell division. Under the microscope, centromeres of metaphase chromosomes can sometimes appear as constrictions in the body of the chromosome. If a centromere is located near the middle of a chromosome, it is metacentric, whereas a telocentric centromere is at, or near, the very end of the chromosome. Some organisms also do not have a single centromere but are holocentric. Telomeres are repetitive sequences near the ends of linear chromosomes, and are important in maintaining the length of the chromosomes during replication, and protecting the ends of the chromosomes from alterations.

Homologous chromosomes are typically pairs of similar, but non-identical, chromosomes in which one member of the pair comes from the male parent, and the other comes from the female parent. Homologs contain the same gene loci in the same order. Non-homologous chromosomes contain different gene loci, and are usually distinguishable based on cytological features such as length, centromere position, and banding patterns produced by staining.

What does it mean to be diploid?

Most eukaryotic organisms are diploid, meaning they have two sets of chromosomes.

Remember this means that each cell has:

  • two homologs of each chromosome
  • two copies of each gene

The number of non-homologous chromosomes varies by organism.

Levels of compaction in eukaryotes

If stretched to its full length, the DNA molecule of the largest human chromosome would be 85mm. Yet during mitosis and meiosis, this DNA molecule is compacted into a chromosome approximately 5µm long (17,000 times smaller!). Although this compaction makes it easier to transport DNA within a dividing cell, it also makes DNA less accessible for other cellular functions such as DNA synthesis and transcription. Thus, chromosomes vary in how tightly DNA is packaged, depending on the stage of the cell cycle and also on the level of gene activity required in any particular region of the chromosome.

There are several different levels of structural organization in eukaryotic chromosomes, with each successive level contributing to the further compaction of DNA. The compaction of DNA requires proteins and the combination of proteins and DNA is chromatin. For more loosely compacted DNA, only the first few levels of organization may apply. Each level involves a specific set of proteins that associate with the DNA to compact it. First, proteins called the core histones act as spool around which DNA is coiled twice to form a structure called the nucleosome, which is composed of eight polypeptides, two copies of histone proteins H2A, H2B, H3, and H4. Nucleosomes are formed at regular intervals along the DNA strand, giving the molecule the appearance of “beads on a string”.

At the next level of organization, histone H1 helps to compact the DNA strand and its nucleosomes into a 30nm fiber. Subsequent levels of organization involve the addition of scaffold proteins that wind the 30nm fiber into coils, which are in turn wound around other scaffold proteins.

Chromatin Packaging Varies Within a Chromosome: Euchromatin & Heterochromatin

Classically, there are two major types of chromatin, but these are more the ends of a continuous and varied spectrum. Euchromatin is more loosely packed, and tends to contain genes that are being transcribed (or actively being utilized by the cell). For example, there might be widely-spaced nucleosomes within a euchromatin region, leaving more of the DNA accessible for proteins that interact with that region. In contrast, heterochromatin usually contains densely-packed nucleosomes, is often rich in repetitive sequences, and tends not to contain genes that are actively being transcribed. Within these regions, nucleosomes might be close together, restricting protein access to DNA. Both the centromeres and telomeres are usually heterochromatin, whereas other regions of chromosomes can be switched from heterochromatin to euchromatin or vice versa, often by proteins that modify histones and nucleosomes.

Keeping chromosomes organized in nuclei

During interphase, the decondensed chromosomes often have specific locations within the nucleus and relative to one another, which has been studied using a technique called FISH, fluorescent in situ hybridization. In FISH, fluorescently-tagged probes (pieces of single-stranded DNA) recognize complementary sequences specific to each chromosome and allow visualization of specific chromosome locations within a nucleus full of DNA.

Breaking down terms to understand FISH:

F = fluorescent because a small molecule that is excited by a certain wavelength of light is attached to the probe

IS = in situ is a Latin term that means in the orginal place because the experiment examines something within a cell

H = hybridization because the probe and the cellular DNA are complementary and therefore bind each other (or hybridize)

Exercise (PageIndex{1})

How to DNA probes recognize sequences of DNA in cells in this experiment?

Answer

The rules of base pairing A-T and G-C and anti-parallel orientation! The probes are complementary to sequences of DNA specific to each chromosome.

Karyotypes

Chromosomes stain with some types of dyes, which is how they got their name (chromosome means “colored body”). Certain dyes stain some regions along a chromosome more intensely than others, giving some chromosomes a banded appearance when stained. A karyotype is a representation of a complete set of chromosomes. Karyotypes are usually determined by isolating mitotic chromosomes to view them as a karyogram. Chemicals that arrest the cells in metaphase are used and then the chromosomes are released from nuclei, usually onto a slide. Chromosomes at this stage are at the most compact state. The images of these chromosomes can be captured digitally and arranged into pairs to examine the complete set of chromosomes in the cell.

For additional information about karyotyping: https://www.nature.com/scitable/topicpage/karyotyping-for-chromosomal-abnormalities-298/

References

Bolzer A, Kreth G, Solovei I, Koehler D, Saracoglu K, Fauth C, et al. (2005) Three-Dimensional Maps of All Chromosomes in Human Male Fibroblast Nuclei and Prometaphase Rosettes. PLoS Biol 3(5): e157. https://doi.org/10.1371/journal.pbio.0030157

Duan J, Jiang W, Cheng Z, Heikkila JJ, Glick BR (2013) The Complete Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. UW4. PLoS ONE 8(3): e58640. https://doi.org/10.1371/journal.pone.0058640

Qing L, Xia Y, Zheng Y, Zeng X (2012) A De Novo Case of Floating Chromosomal Polymorphisms by Translocation in Quasipaa boulengeri (Anura, Dicroglossidae). PLoS ONE 7(10): e46163. https://doi.org/10.1371/journal.pone.0046163


Mitosis: Chromosome DNA packed in stacked layers

A new study based on electron microscopy techniques at low temperatures demonstrates that, during mitosis, chromosome DNA is packed in stacked layers of chromatin. The research, published in EMBO Journal, confirms a surprising structure proposed by UAB researchers over a decade ago, but criticized due to the limitations of the technique used.

In the cell nuclei the DNA is bound to histone proteins and forms long chains of nucleosomes that are called chromatin fibers. In the Chromatin Laboratory at the Department of Biochemistry and Molecular Biology of the UAB, directed by Professor Joan-Ramon Daban, it was discovered in 2005 that the chromatin of mitotic chromosomes forms multilaminar plates. This was a surprising result, which has been criticized because it was not expected that linear fibers of chromatin could give rise to planar structures, and because it is based on conventional electron microscopy and atomic force microscopy techniques that require adsorbing the sample, respectively, on flat surfaces of carbon and mica. In addition, in the case of electron microscopy, the sample has to be fixed with chemical crosslinkers, treated with contrasting agents, and dehydrated.

A new study based on electron microscopy under cryogenic conditions, and synchrotron X-ray scattering, published in EMBO Journal, has shown that in mitotic chromosomes the DNA is densely packed forming stacked sheets of chromatin, which are stabilized by interactions between nucleosomes.

The advantage of the cryo-electron microscopy techniques, used in this new study, is that the sample (uncrosslinked and untreated with contrasting agents) is suspended in an aqueous solution that is kept frozen at -180 ° C, even during imaging. Since the structures to be studied are large and complex, in this work cryo-electron tomography was used because this technique allows capturing many images with different tilt angles and, in the end, a three-dimensional reconstruction of the analyzed structures is obtained.

The three-dimensional reconstructions showed that the chromatin emanating from human chromosomes maintained under physiological ionic conditions is planar and forms multilaminar plates. The thickness measurements obtained (single layer 7.5 nm two layers in contact 13 nm) suggest that the plates are formed by mononucleosome layers, which are interdigitated between them. The complementary X-ray scattering experiments showed a dominant peak at 6 nm, which can be correlated with the distance between layers and between nucleosomes associated through their lateral faces.

There are multilaminar plates that have the dimensions corresponding to the diameter of a human chromosome (600 nm). This suggests that the chromosomes are formed by stacked layers of chromatin that are oriented perpendicular to the axis of the chromosome. This structure is very compact and probably has the function of protecting the integrity of genomic DNA during cell division.


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Karyotype:

Complete set of chromosomes in a species or in an individual organism.

  • Karyotypes describe the chromosome number in an organism and how these chromosomes look like under a light microscope.
  • Length of a chromosome, the position of the centromere, its banding pattern, differences between the sex chromosomes and autosomes and any other physical characteristics are considered.

Idiogramis a diagrammatic representation of a karyotype of a species.

Genome: is the complete set of chromosomes/genes in an organism.

Autosomes: Chromosomes other than sex chromosomes (X & Y)are autosomes.

Homologous chromosomes are chromosomes having the same number, type, and arrangement of genes. But one is paternal and one is maternal.


Euchromatin and Heterochromatin

Chromatin within a cell may be compacted to varying degrees depending on a cell's stage in the cell cycle.

In the nucleus, chromatin exists as euchromatin or heterochromatin. During interphase of the cycle, the cell is not dividing but undergoing a period of growth.

Most of the chromatin is in a less compact form known as euchromatin. More of the DNA is exposed in euchromatin allowing replication and DNA transcription to take place.

During transcription, the DNA double helix unwinds and opens to allow the genes coding for proteins to be copied. DNA replication and transcription are needed for the cell to synthesize DNA, proteins, and organelles in preparation for cell division (mitosis or meiosis).

A small percentage of chromatin exists as heterochromatin during interphase. This chromatin is tightly packed, not allowing gene transcription. Heterochromatin stains more darkly with dyes than does euchromatin.


Biologists' discovery may force revision of biology textbooks: Novel chromatin particle halfway between DNA and a nucleosome

Basic biology textbooks may need a bit of revising now that biologists at UC San Diego have discovered a never-before-noticed component of our basic genetic material.

According to the textbooks, chromatin, the natural state of DNA in the cell, is made up of nucleosomes. And nucleosomes are the basic repeating unit of chromatin.

When viewed by a high powered microscope, nucleosomes look like beads on a string. But in the Aug. 19 issue of the journal Molecular Cell, UC San Diego biologists report their discovery of a novel chromatin particle halfway between DNA and a nucleosome. While it looks like a nucleosome, they say, it is in fact a distinct particle of its own.

"This novel particle was found as a precursor to a nucleosome," said James Kadonaga, a professor of biology at UC San Diego who headed the research team and calls the particle a "pre-nucleosome." "These findings suggest that it is necessary to reconsider what chromatin is. The pre-nucleosome is likely to be an important player in how our genetic material is duplicated and used."

The biologists say that while the pre-nucleosome may look something like a nucleosome under the microscope, biochemical tests have shown that it is in reality halfway between DNA and a nucleosome.

These pre-nucleosomes, the researchers say, are converted into nucleosomes by a motor protein that uses the energy molecule ATP.

"The discovery of pre-nucleosomes suggests that much of chromatin, which has been generally presumed to consist only of nucleosomes, may be a mixture of nucleosomes and pre-nucleosomes," said Kadonaga. "So, this discovery may be the beginning of a revolution in our understanding of what chromatin is."

"The packaging of DNA with histone proteins to form chromatin helps stabilize chromosomes and plays an important role in regulating gene activities and DNA replication," said Anthony Carter, who oversees chromatin grants at the National Institute of General Medical Sciences of the National Institutes of Health, which funded the research. "The discovery of a novel intermediate DNA-histone complex offers intriguing insights into the nature of chromatin and may help us better understand how it impacts these key cellular processes."


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Watch the video: Aufbau u0026 Zustand des Chromatins (January 2022).