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Encyclopedia > Chromatin

Chromatin is the complex of DNA and protein found inside the nuclei of eukaryotic cells. The nucleic acids are in the form of double-stranded DNA (a double helix). The major proteins involved in chromatin are histone proteins, although many other chromosomal proteins have prominent roles too. The functions of chromatin are to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis, and to serve as a mechanism to control expression. Changes in chromatin structure are affected mainly by methylation (DNA and proteins) and acetylation (proteins). Chromatin structure is also relevant to DNA replication and DNA repair. The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... The eukaryotic cell nucleus. ... Kingdoms Animalia - Animals Fungi Plantae - Plants Protista A eukaryote (IPA: ) is an organism with a complex cell or cells, in which the genetic material is organized into a membrane-bound nucleus or nuclei. ... Drawing of the structure of cork as it appeared under the microscope to Robert Hooke from Micrographia which is the origin of the word cell. Cells in culture, stained for keratin (red) and DNA (green). ... This article or section does not cite its references or sources. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Schematic representation of the assembly of the core histones into the nucleosome. ... Mitosis divides genetic information during cell division. ... Not to be confused with miosis. ... Gene expression, or simply expression, is the process by which a genes DNA sequence is converted into the structures and functions of a cell. ... Methylation is a term used in the chemical sciences to denote the attachment or substitution of a methyl group on various substrates. ... Acetylation describes a reaction, usually with acetic acid, that introduces an acetyl functional group into an organic compound. ... This article or section is in need of attention from an expert on the subject. ... DNA damage resulting in multiple broken chromosomes DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. ...


Chromatin is easily visualised by staining, hence its name, which literally means coloured material.

Fig. 1: The major structures in DNA compaction; DNA, the nucleosome, the 10nm "beads-on-a-string" fibre, the 30nm fibre and the metaphase chromosome.
Fig. 1: The major structures in DNA compaction; DNA, the nucleosome, the 10nm "beads-on-a-string" fibre, the 30nm fibre and the metaphase chromosome.

Simplistically, there are three levels of chromatin organization (Fig. 1): Image File history File links Download high-resolution version (1312x432, 203 KB) By Richard Wheeler (Zephyris) 2005; The major chromatin structures. ... Image File history File links Download high-resolution version (1312x432, 203 KB) By Richard Wheeler (Zephyris) 2005; The major chromatin structures. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ... A nucleosome is a unit made of DNA and histones. ... An image of a newt lung cell stained with flourescent dyes during metaphase. ... Figure 1: A representation of a condensed eukaryotic chromosome, as seen during cell division. ...

  1. DNA wrapping around nucleosomes - The "beads on a string" structure.
  2. A 30 nm condensed chromatin fiber consisting of nucleosome arrays in their most compact form.
  3. Higher level DNA packaging into the metaphase chromosome.

These structures are not found in all eukaryotic cells; there are examples of more extreme packaging, for example sperm cells and avian red blood cells. A nucleosome is a unit made of DNA and histones. ... NM may stand for: Neurofiber Mitosis, a nerve disease, sometimes confused with Neurofibromatosis nm (Unix), a computer program Nautical mile (nm) New Mexico (NM) Newton metre (N m or N·m), a unit of moment Nanometre (nm, 10-9 m), a thousand-millionth of a metre Never mind or not... Figure 1: A representation of a condensed eukaryotic chromosome, as seen during cell division. ... A spermatozoon or spermatozoan ( spermatozoa), from the ancient Greek σπέρμα (seed) and ζῷον (living being) and more commonly known as a sperm cell, is the haploid cell that is the male gamete. ... The word Avian can refer to different things: .. Most commonly it is used referring to the class of animals named birds. Avians are a fantasy race in several fantasy settings. ... Human red blood cells Red blood cells are the most common type of blood cell and are the vertebrate bodys principal means of delivering oxygen to body tissues via the blood. ...



The different levels of chromatin compaction are clearly visible in cells. In non-dividing cells there are two types of chromatin: euchromatin and heterochromatin. These correspond to uncompacted actively transcribed DNA and compacted untranscribed DNA. Euchromatin is a type of chromatin that is rich in gene concentration (contrast this to heterochromatin). ... Heterochromatin is (usually but not always) tightly packed form of DNA. Its major characteristic is that it is not transcribed. ...


The structure of chromatin varies considerably as the cell progresses through the cell cycle. The changes in structure are required to allow the DNA to be used and managed, whilst minimising the risk of damage. Drawing of the structure of cork as it appeared under the microscope to Robert Hooke from Micrographia which is the origin of the word cell. Cells in culture, stained for keratin (red) and DNA (green). ... The cell cycle, or cell-division cycle (CDC), is the series of events in a eukaryotic cell between one cell division and the next. ...

Contents

Interphase Chromatin

The structure of chromatin during interphase (the period of normal cell function between division) is optimised to allow easy access of transcription and DNA repair factors to the DNA while compacting the DNA into the nucleus. The structure varies depending on the access required to the DNA, for example expressed genes require regular access by RNA polymerase and so have a looser structure - euchromatin. This article or section does not cite its references or sources. ... Transcription is the process through which a DNA sequence is enzymatically copied by an RNA polymerase to produce a complementary RNA. Or, in other words, the transfer of genetic information from DNA into RNA. In the case of protein-encoding DNA, transcription is the beginning of the process that ultimately... DNA damage resulting in multiple broken chromosomes DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. ... In cell biology, the nucleus is an organelle, found in most eukaryotic cells, which contains most of the cells genetic material. ... This stylistic schematic diagram shows a gene in relation to the double helix structure of DNA and to a chromosome (right). ... RNAP from pictured during elongation. ...


DNA structure

The structures of A-, B- and Z-DNA.
Main articles: Mechanical properties of DNA and Z-DNA

The vast majority of DNA within the cell is the normal DNA structure. However in nature DNA can form three structures, A-, B- and Z-DNA. A and B-DNA are very similar, forming right handed helices, while Z-DNA is a more unusual left handed helix with a zig-zag phosphate backbone. Z-DNA is thought to play a specific role in chromatin structure and transcription because of the properties of the junction between B- and Z-DNA. Image File history File links Download high-resolution version (2486x1620, 2113 KB) By Richard Wheeler (Zephyris) 2007. ... Image File history File links Download high-resolution version (2486x1620, 2113 KB) By Richard Wheeler (Zephyris) 2007. ... The mechanical properties of DNA are closly related to its molecular structure and the relative weakness of the hydrogen bonds and electronic interactions that hold strands of DNA together compared to the strength of the bonds within each strand. ... The Z-DNA structure. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ... The Z-DNA structure. ... Transcription is the process through which a DNA sequence is enzymatically copied by an RNA polymerase to produce a complementary RNA. Or, in other words, the transfer of genetic information from DNA into RNA. In the case of protein-encoding DNA, transcription is the beginning of the process that ultimately...


At the junction of B- and Z-DNA one pair of bases is flipped out from normal bonding. These play a dual role of a site of recognition by many proteins and as a sink for torsional stress from RNA polymerase or nucleosome binding. RNAP from pictured during elongation. ... A nucleosome is a unit made of DNA and histones. ...


The Nucleosome and "Beads-on-a-String"

Main articles: Nucleosome, Chromatosome and Histone
A cartoon representation of the nucleosome structure. From PDB 1KX5.
A cartoon representation of the nucleosome structure. From PDB 1KX5.

The basic repeat element of chromatin is the nucleosome, linked by sections of linker DNA. The nucleosome consists of 1.65 turns of DNA (about 146 base pairs), which are wrapped around the histone octamer complex. There are four different types of core histone proteins which form the octamer, which is made up of two copies each of H2A, H2B, H3 and H4. The small diameter (~10nm) around which the DNA bends is far smaller than can be reached by DNA in solution. A nucleosome is a unit made of DNA and histones. ... A chromatosome is a nucleosome with one bound linker histone H1. ... Schematic representation of the assembly of the core histones into the nucleosome. ... Image File history File links Download high-resolution version (1024x1024, 1067 KB) By Richard Wheeler (Zephyris) 2005; Nucleosome structure. ... Image File history File links Download high-resolution version (1024x1024, 1067 KB) By Richard Wheeler (Zephyris) 2005; Nucleosome structure. ... The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. ... A nucleosome is a unit made of DNA and histones. ...


In addition to the core histones there is the linker histone, H1, which contacts the exit/entry of the DNA strand on the nucleosome. The nucleosome, together with histone H1, is known as a chromatosome. Chromatosomes, connected by about 20 to 60 base pairs of linker DNA, form an approximately 10nm "beads-on-a-string" fibre. (Fig. 1-2). A chromatosome is a nucleosome with one bound linker histone H1. ... A chromatosome is a nucleosome with one bound linker histone H1. ...


The nucleosomes bind DNA non-specifically, as required by their function in general DNA packaging. There is, however, some preference in the sequences the nucleosomes will bind. This is largely through the properties of DNA, adenosine (A) and thymine (T) bases are more favorably compressed into the inner minor grooves. This means nucleosomes bind preferentially at one position every 10 base pairs - where the DNA is rotated to maximise the number of A and T bases which will lie in the inner minor groove. See mechanical properties of DNA. The chemical structure of adenosine Adenosine is a nucleoside comprised of adenine attached to a ribose (ribofuranose) moiety via a β-N9-glycosidic bond. ... For the similarly-spelled vitamin compound, see Thiamine Thymine, also known as 5-methyluracil, is a pyrimidine nucleobase. ... The mechanical properties of DNA are closly related to its molecular structure and the relative weakness of the hydrogen bonds and electronic interactions that hold strands of DNA together compared to the strength of the bonds within each strand. ...


30nm chromatin fibre

Two proposed structures of the 30nm chromatin filament. Left: 1 start helix "solenoid" structure. Right: 2 start loose helix structure. Note: the nucleosomes are omitted in this diagram - only the DNA is shown.
Two proposed structures of the 30nm chromatin filament.
Left: 1 start helix "solenoid" structure.
Right: 2 start loose helix structure.
Note: the nucleosomes are omitted in this diagram - only the DNA is shown.

The "beads-on-a-string" structure in turn coils into a 30nm diameter helical structure known as the 30nm fibre or filament. The precise structure of the chromatin fibre in the cell is not known in detail, and there is still some debate over the exact structure. There are, however, three well established models. Image File history File links Download high-resolution version (1024x768, 357 KB) By Richard Wheeler (Zephyris) 2005; Cartoon representation of the alternative 30nm chromatin fibre structures. ... Image File history File links Download high-resolution version (1024x768, 357 KB) By Richard Wheeler (Zephyris) 2005; Cartoon representation of the alternative 30nm chromatin fibre structures. ...


This level of chromatin structure is thought to be the form of euchromatin, which contains actively transcribed genes. EM studies have demonstrated the 30nm fibre is highly dynamic such that it unfold into a 10nm fiber ("beads-on-a-string") structure when transversed by an RNA polymerase engaged in transcription.


The three models are based on the accepted facts that the nucleosomes lie perpendicular to the axis of the fibre, the linker histones lie on the inside of the structure and that it readily unwinds into the 10nm "beads-on-a-string" fibre.


A stable 30nm fibre relies on the regular positioning of nucleosomes along the DNA. The mechanical properties of DNA mean linker DNA is relatively resistant to bending and rotation. This makes the length of linker DNA critical to the stability of the fibre, nucleosomes must separated by lengths which allow them to rotate and then fold into the required orientation without significant stress to the DNA. The mechanical properties of DNA are closly related to its molecular structure and the relative weakness of the hydrogen bonds and electronic interactions that hold strands of DNA together compared to the strength of the bonds within each strand. ...


Spatial Organization of Chromatin in the Cell Nucleus

The layout of the genome within the nucleus is not random - specific regions of the genome are always found in certain areas, and un-transcribed regions clump together into the nucleolus. Specific regions of the chromatin are thought to be bound to the nuclear membrane, while other regions are bound together by protein complexes. The layout of this is not, however, well characterised. In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... The nucleolus is contained within the cell nucleus. ... The nuclear envelope refers to the double membrane of the nucleus that encloses genetic material in eukaryotic cells. ...


One well characterised aspect of genome layout within nucleus (in mammals) is the compaction of one of the two X chromosomes in females into the barr body. This serves the role of permanently deactivating these genes, which prevents females getting a 'double dose' of these genes relative to males. Subclasses Allotheria* Order Multituberculata (extinct) Order Volaticotheria (extinct) Order Palaeoryctoides (extinct) Order Triconodonta (extinct) Prototheria Order Monotremata Theria Infraclass Marsupialia Infraclass Eutheria The mammals are the class of vertebrate animals characterized by the production of milk in females for the nourishment of young, from mammary glands present on most species... The hand mirror and comb of the Roman Goddess Venus is often used to represent the female sex. ... In those species in which sex is determined by the presence of the Y or W chromosome rather than the diploidy of the X or Z, a Barr body is the inactive X chromosome in a female cell, or the inactive Z in a male (Lyon, 2003), rendered inactive in... The shield and spear of the Roman God Mars are often used to represent the male sex In heterogamous species, male is the sex of an organism, or of a part of an organism, which typically produces smaller, mobile gametes (spermatozoa) that are able to fertilise female gametes (ova). ...


Metaphase Chromatin

Karyogram of human male using Giemsa staining, showing the classic metaphase chromatin structure.
Karyogram of human male using Giemsa staining, showing the classic metaphase chromatin structure.

The metaphase structure of chromatin is vastly different to during interphase. The structure of the chromatin is optimised for physical strength and manageability, forming the classic chromosome structure seen, for example, in karyotypes. Image File history File links NHGRI_human_male_karyotype. ... Image File history File links NHGRI_human_male_karyotype. ... A complex of stains specific for the phosphate groups of DNA. Used in Giemsa banding (or G-banding) to stain chromosomes and often used to create a karyotype. ... An image of a newt lung cell stained with flourescent dyes during metaphase. ... An image of a newt lung cell stained with flourescent dyes during metaphase. ... Figure 1: A representation of a condensed eukaryotic chromosome, as seen during cell division. ... Karyogram of human male using Giemsa staining. ...


The structure of the condensed chromosome is thought to be loops of 30nm fibre to a central scaffold of proteins. It is, however, not well characterised, and little solid evidence exists.


The physical strength of chromatin is vital for this stage of division to prevent shear damage to the DNA as the daughter chromosomes are separated. To maximise strength the composition of the chromatin changes as you approach the centromere, primarily through alternative histone H1 anologues.


Non-Histone Chromosomal Proteins

The proteins that are found associated with isolated chromatin fall into several functional categories:

Enzymes associated with chromatin are those involved in DNA replication and repair, in transcription, and in post-translational modification of histones. Examples are various types of nucleases and proteases. Scaffold proteins encompass chromatin proteins such as insulators, domain boundary factors and cellular memory modules (CMMs). In molecular biology, a transcription factor is a protein that binds DNA at a specific promoter or enhancer region or site, where it regulates transcription. ... A scaffold protein is a protein whose function is to promote other protein-protein interactions. ...


Chromatin: Alternative Definitions

  1. Simple & Concise Definition: Chromatin is DNA plus the proteins (and RNA) that package DNA within the cell nucleus.
  2. A Biochemists’ Operational Definition: Chromatin is the DNA/protein/RNA complex extracted from eukaryotic lysed interphase nuclei. Just which of the multitudinous substances present in a nucleus will constitute a part of the extracted material will depend in part on the technique each researcher uses. Furthermore, the composition and properties of chromatin vary from one cell type to the another, during development of a specific cell type, and at different stages in the cell cycle.
  3. The DNA plus Histone – Equals – Chromatin - Definition: The DNA double helix in the cell nucleus is packaged by special proteins termed histones. The formed protein/DNA complex is called chromatin. The structural entity of chromatin is the nucleosome.

History

In 1882 Walther Flemming used the term Chromatin for the first time. Flemming assumed that within the nucleus there was some kind of a nuclear-scaffold. Further there were nucleoli, the nuclear plasm and the nuclear membranes. He wrote (transl. from German): “The scaffold owes its capability of refraction, the way how it behaves, and in particular its colorability to a substance which, with regard to its latter attribute, I have termed Chromatin. It is possible that this substance is really identical with the Nuclein-bodies. .... I’ll retain the name Chromatin as long as Chemistry has decided about it, and I empirically refer to it as that substance in the cell's nucleus which takes up the dye upon staining the nucleus ("Kerntinktionen"). Illustrations of cells with chromosomes and mitosis, from the book Zell-substanz, Kern und Zelltheilung, 1882 Walther Flemming (born April 21, 1843 in Sachsenberg, Germany; died August 4, 1905 in Kiel) was a founder of the study of cytogenetics. ...


Nobel Prizes Related to Chromatin

Albrecht Kossel (University of Heidelberg) was awarded the Nobel Prize in Physiology or Medicine 1910 "in recognition of the contributions to our knowledge of cell chemistry made through his work on proteins, including the nucleic substances". Ludwig Karl Martin Leonhard Albrecht Kossel (September 16, 1853 - July 5, German medical doctor. ...


Thomas Hunt Morgan (California Institute of Technology) was awarded the Nobel Prize in Physiology or Medicine 1933 "for his discoveries concerning the role played by the chromosome in heredity". Thomas Hunt Morgan (September 25, 1866 – December 4, 1945) was an American geneticist and embryologist. ...


Francis Crick, James Watson and Maurice Wilkins (MRC Laboratory of Molecular Biology, Harvard University, London University) were awarded the Nobel Prize in Physiology or Medicine 1962 "for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material". Francis Harry Compton Crick OM (8 June 1916 – 28 July 2004) was an English physicist, molecular biologist and neuroscientist, most noted for being one of the co-discoverers of the structure of the DNA molecule in 1953. ... There is more than one person with the name James Watson: James Watson, participant in the Battle of the Little Bighorn James Watson, author of the novel Talking in Whispers James Watson, U.S. Senator from New York (1797-1801) James Watson, painter of 77 portraits held by the U... To meet Wikipedias quality standards, this article or section may require cleanup. ...


Aaron Klug (MRC Laboratory of Molecular Biology) was awarded the Nobel Prize in Chemistry 1982 "for his development of crystallographic electron microscopy and his structural elucidation of biologically important nucleic acid-protein complexes". Sir Aaron Klug, OM, FRS (born 11 August 1926 in Zelvas, Lithuania) is a Lithuanian-born British chemist and biophysicist, and winner of the 1982 Nobel Prize in Chemistry for his development of crystallographic electron microscopy and his structural elucidation of biologically important nucleic acid-protein complexes. ...


Roger Kornberg (Stanford University) was awarded the Nobel Prize in Chemistry in 2006 "for his studies of the molecular basis of eukaryotic transcription". In 1974 published the discovery that the nucleosome consists of a tetramer of histones H3 and H4 and two dimers of histones H2A and H2B. Roger D. Kornberg Roger David Kornberg (born April 24, 1947) is an American scientist and professor of structural biology at Stanford University School of Medicine. ...


See also

Bookmarking is a biological phenomenon believed to function as an epigenetic mechanism for transmitting cellular memory of the pattern of gene expression in a cell through mitosis to its daughter cells. ... Figure 1: A representation of a condensed eukaryotic chromosome, as seen during cell division. ... A chromatid forms one part of a chromosome after it has coalesced for the process of mitosis or meiosis. ... This article or section does not cite its references or sources. ... A nucleosome is a unit made of DNA and histones. ...

References

  • Corces, V. G. 1995. Chromatin insulators. Keeping enhancers under control. Nature 376:462-463.
  • Cremer, T. 1985. Von der Zellenlehre zur Chromosomentheorie: Naturwissenschaftliche Erkenntnis und Theorienwechsel in der frühen Zell- und Vererbungsforschung, Veröffentlichungen aus der Forschungsstelle für Theoretische Pathologie der Heidelberger Akademie der Wissenschaften. Springer-Vlg., Berlin, Heidelberg.
  • Elgin, S. C. R. (ed.). 1995. Chromatin Structure and Gene Expression, vol. 9. IRL Press, Oxford, New York, Tokyo.
  • Gerasimova, T. I., and V. G. Corces. 1996. Boundary and insulator elements in chromosomes. Current Op. Genet. and Dev. 6:185-192.
  • Gerasimova, T. I., and V. G. Corces. 1998. Polycomb and Trithorax group proteins mediate the function of a chromatin insulator. Cell 92:511-521.
  • Gerasimova, T. I., and V. G. Corces. 2001. CHROMATIN INSULATORS AND BOUNDARIES: Effects on Transcription and Nuclear Organization. Annu Rev Genet 35:193-208.
  • Gerasimova, T. I., K. Byrd, and V. G. Corces. 2000. A chromatin insulator determines the nuclear localization of DNA [In Process Citation]. Mol Cell 6:1025-35.
  • Ha, S. C., K. Lowenhaupt, A. Rich, Y. G. Kim, and K. K. Kim. 2005. Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature 437:1183-6.
  • Pollard, T., and W. Earnshaw. 2002. Cell Biology. Saunders.
  • Saumweber, H. 1987. Arrangement of Chromosomes in Interphase Cell Nuclei, p. 223-234. In W. Hennig (ed.), Structure and Function of Eucaryotic Chromosomes, vol. 14. Springer-Verlag, Berlin, Heidelberg.
  • Sinden, R. R. 2005. Molecular biology: DNA twists and flips. Nature 437:1097-8.
  • Van Holde KE. 1989. Chromatin. New York: Springer-Verlag. ISBN 0-387-96694-3.
  • Van Holde, K., J. Zlatanova, G. Arents, and E. Moudrianakis. 1995. Elements of chromatin structure: histones, nucleosomes, and fibres, p. 1-26. In S. C. R. Elgin (ed.), Chromatin structure and gene expression. IRL Press at Oxford University Press, Oxford.

1989 (MCMLXXXIX) was a common year starting on Sunday of the Gregorian calendar. ... NY redirects here. ... Springer Science+Business Media or Springer (IPA: ) is a worldwide publishing company based in Germany which focuses on academic journals and books in the fields of science, technology and medicine. ...

External links

  • Recent chromatin publications and news

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