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Chromatin
Chromatin
is a complex of macromolecules found in cells, consisting of DNA, protein, and RNA.[1] The primary functions of chromatin are 1) to package DNA
DNA
into a more compact, denser shape, 2) to reinforce the DNA macromolecule to allow mitosis, 3) to prevent DNA
DNA
damage, and 4) to control gene expression and DNA
DNA
replication. The primary protein components of chromatin are histones that compact the DNA. Chromatin is only found in eukaryotic cells (cells with defined nuclei). Prokaryotic
Prokaryotic
cells have a different organization of their DNA
DNA
(the prokaryotic chromosome equivalent is called genophore and is localized within the nucleoid region). Chromatin's structure is currently poorly understood despite being subjected to intense investigation. Its structure depends on several factors. The overall structure depends on the stage of the cell cycle. During interphase, the chromatin is structurally loose to allow access to RNA
RNA
and DNA
DNA
polymerases that transcribe and replicate the DNA. The local structure of chromatin during interphase depends on the genes present on the DNA. That DNA
DNA
which codes genes that are actively transcribed ("turned on") is more loosely packaged and associated with RNA
RNA
polymerases (referred to as euchromatin) while that DNA
DNA
which codes inactive genes ("turned off") is more condensed and associated with structural proteins (heterochromatin).[2][3] Epigenetic
Epigenetic
chemical modification of the structural proteins in chromatin also alters the local chromatin structure, in particular chemical modifications of histone proteins by methylation and acetylation. As the cell prepares to divide, i.e. enters mitosis or meiosis, the chromatin packages more tightly to facilitate segregation of the chromosomes during anaphase. During this stage of the cell cycle this makes the individual chromosomes in many cells visible by optical microscope. In general terms, there are three levels of chromatin organization:

DNA
DNA
wraps around histone proteins forming nucleosomes; the "beads on a string" structure (euchromatin). Multiple histones wrap into a 30 nm fibre consisting of nucleosome arrays in their most compact form (heterochromatin). (Definitively established to exist in vitro, the 30-nanometer fibre was not seen in recent X-ray studies of human mitotic chromosomes.[4]) Higher-level DNA
DNA
packaging of the 30 nm fibre into the metaphase chromosome (during mitosis and meiosis).

There are, however, many cells that do not follow this organisation. For example, spermatozoa and avian red blood cells have more tightly packed chromatin than most eukaryotic cells, and trypanosomatid protozoa do not condense their chromatin into visible chromosomes for mitosis.

Contents

1 Dynamic chromatin structure and hierarchy

1.1 DNA
DNA
structure 1.2 Nucleosomes and beads-on-a-string 1.3 30 nanometer chromatin fibre 1.4 Spatial organization of chromatin in the cell nucleus 1.5 Cell-cycle dependent structural organization

2 Chromatin
Chromatin
and bursts of transcription

2.1 Alternative chromatin organizations

3 Chromatin
Chromatin
and DNA
DNA
repair 4 Methods to investigate chromatin 5 Chromatin: alternative definitions 6 Nobel Prizes 7 See also 8 References 9 Other references 10 External links

Dynamic chromatin structure and hierarchy[edit] Chromatin
Chromatin
undergoes various structural changes during a cell cycle. Histone
Histone
proteins are the basic packer and arranger of chromatin and can be modified by various post-translational modifications to alter chromatin packing ( Histone
Histone
modification). Most of the modifications occur on the histone tail. The consequences in terms of chromatin accessibility and compaction depend both on the amino-acid that is modified and the type of modification. For example, Histone acetylation results in loosening and increased accessibility of chromatin for replication and transcription. Lysine tri-methylation can either be correlated with transcriptional activity (tri-methylation of histone H3 Lysine 4) or transcriptional repression and chromatin compaction (tri-methylation of histone H3 Lysine 9 or 27). Several studies suggested that different modifications could occur simultaneously. For example, it was proposed that a bivalent structure (with tri-methylation of both Lysine 4 and 27 on histone H3) was involved in mammalian early development.[5] Polycomb-group proteins
Polycomb-group proteins
play a role in regulating genes through modulation of chromatin structure.[6] For additional information, see Histone
Histone
modifications in chromatin regulation and RNA
RNA
polymerase control by chromatin structure. DNA
DNA
structure[edit]

The structures of A-, B-, and Z-DNA.

Main articles: Mechanical properties of DNA
DNA
and Z-DNA In nature, DNA
DNA
can form three structures, A-, B-, and Z-DNA. A- and B- DNA
DNA
are very similar, forming right-handed helices, whereas Z- DNA
DNA
is a left-handed helix with a zig-zag phosphate backbone. Z- DNA
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. 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
RNA
polymerase or nucleosome binding. Nucleosomes and beads-on-a-string[edit]

Main articles: Nucleosome, Chromatosome and Histone

A cartoon representation of the nucleosome structure. From PDB: 1KX5​.

The basic repeat element of chromatin is the nucleosome, interconnected by sections of linker DNA, a far shorter arrangement than pure DNA
DNA
in solution. In addition to the core histones, there is the linker histone, H1, which contacts the exit/entry of the DNA
DNA
strand on the nucleosome. The nucleosome core particle, together with histone H1, is known as a chromatosome. Nucleosomes, with about 20 to 60 base pairs of linker DNA, can form, under non-physiological conditions, an approximately 10 nm "beads-on-a-string" fibre. (Fig. 1-2). . The nucleosomes bind DNA
DNA
non-specifically, as required by their function in general DNA
DNA
packaging. There are, however, large DNA sequence preferences that govern nucleosome positioning. This is due primarily to the varying physical properties of different DNA sequences: For instance, adenine and thymine are more favorably compressed into the inner minor grooves. This means nucleosomes can bind preferentially at one position approximately every 10 base pairs (the helical repeat of DNA)- where the DNA
DNA
is rotated to maximise the number of A and T bases that will lie in the inner minor groove. (See mechanical properties of DNA.) 30 nanometer chromatin fibre[edit]

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

With addition of H1, the beads-on-a-string structure in turn coils into a 30 nm diameter helical structure known as the 30 nm 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 this.[7] This level of chromatin structure is thought to be the form of heterochromatin, which contains mostly transcriptionally silent genes. EM studies have demonstrated that the 30 nm fibre is highly dynamic such that it unfolds into a 10 nm fiber ("beads-on-a-string") structure when transversed by an RNA
RNA
polymerase engaged in transcription.

Four proposed structures of the 30 nm chromatin filament for DNA repeat length per nucleosomes ranging from 177 to 207 bp. Linker DNA
DNA
in yellow and nucleosomal DNA
DNA
in pink.

The existing models commonly accept that the nucleosomes lie perpendicular to the axis of the fibre, with linker histones arranged internally. A stable 30 nm fibre relies on the regular positioning of nucleosomes along DNA. Linker DNA
DNA
is relatively resistant to bending and rotation. This makes the length of linker DNA critical to the stability of the fibre, requiring nucleosomes to be separated by lengths that permit rotation and folding into the required orientation without excessive stress to the DNA. In this view, different lengths of the linker DNA
DNA
should produce different folding topologies of the chromatin fiber. Recent theoretical work, based on electron-microscopy images[8] of reconstituted fibers supports this view.[9] Spatial organization of chromatin in the cell nucleus[edit] The spatial arrangement of the chromatin within the nucleus is not random - specific regions of the chromatin can be found in certain territories. Territories are, for example, the lamina-associated domains (LADs), and the topological association domains (TADs), which are bound together by protein complexes.[10] Currently, polymer models such as the Strings & Binders Switch (SBS) model[11] and the Dynamic Loop (DL) model[12] are used to describe the folding of chromatin within the nucleus. Cell-cycle dependent structural organization[edit]

Interphase: The structure of chromatin during interphase of mitosis is optimized to allow simple access of transcription and DNA
DNA
repair factors to the DNA
DNA
while compacting the DNA
DNA
into the nucleus. The structure varies depending on the access required to the DNA. Genes that require regular access by RNA
RNA
polymerase require the looser structure provided by euchromatin.

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

Metaphase: The metaphase structure of chromatin differs vastly to that of interphase. It is optimised for physical strength[citation needed] and manageability, forming the classic chromosome structure seen in karyotypes. The structure of the condensed chromatin is thought to be loops of 30 nm fibre to a central scaffold of proteins. It is, however, not well-characterised.The physical strength of chromatin is vital for this stage of division to prevent shear damage to the DNA
DNA
as the daughter chromosomes are separated. To maximise strength the composition of the chromatin changes as it approaches the centromere, primarily through alternative histone H1 analogues.It should also be noted that, during mitosis, while most of the chromatin is tightly compacted, there are small regions that are not as tightly compacted. These regions often correspond to promoter regions of genes that were active in that cell type prior to entry into chromatosis. The lack of compaction of these regions is called bookmarking, which is an epigenetic mechanism believed to be important for transmitting to daughter cells the "memory" of which genes were active prior to entry into mitosis.[13] This bookmarking mechanism is needed to help transmit this memory because transcription ceases during mitosis.

Chromatin
Chromatin
and bursts of transcription[edit] Chromatin
Chromatin
and its interaction with enzymes has been researched, and a conclusion being made is that it is relevant and an important factor in gene expression. Vincent G. Allfrey, a professor at Rockefeller University, stated that RNA
RNA
synthesis is related to histone acetylation.[14] The lysine amino acid attached to the end of the histones is positively charged. The acetylation of these tails would make the chromatin ends neutral, allowing for DNA
DNA
access. When the chromatin decondenses, the DNA
DNA
is open to entry of molecular machinery. Fluctuations between open and closed chromatin may contribute to the discontinuity of transcription, or transcriptional bursting. Other factors are probably involved, such as the association and dissociation of transcription factor complexes with chromatin. The phenomenon, as opposed to simple probabilistic models of transcription, can account for the high variability in gene expression occurring between cells in isogenic populations[15] Alternative chromatin organizations[edit] During metazoan spermiogenesis, the spermatid's chromatin is remodeled into a more spaced-packaged, widened, almost crystal-like structure. This process is associated with the cessation of transcription and involves nuclear protein exchange. The histones are mostly displaced, and replaced by protamines (small, arginine-rich proteins).[16] It is proposed that in yeast, regions devoid of histones become very fragile after transcription; HMO1 an HMGB protein helps in stabilizing nucleosomes-free chromatin.[17][18] Chromatin
Chromatin
and DNA
DNA
repair[edit] The packaging of eukaryotic DNA
DNA
into chromatin presents a barrier to all DNA-based processes that require recruitment of enzymes to their sites of action. To allow the critical cellular process of DNA
DNA
repair, the chromatin must be remodeled. In eukaryotes, ATP dependent chromatin remodeling complexes and histone-modifying enzymes are two predominant factors employed to accomplish this remodeling process.[19] Chromatin
Chromatin
relaxation occurs rapidly at the site of a DNA
DNA
damage.[20] This process is initiated by PARP1
PARP1
protein that starts to appear at DNA
DNA
damage in less than a second, with half maximum accumulation within 1.6 seconds after the damage occurs.[21] Next the chromatin remodeler Alc1 quickly attaches to the product of PARP1, and completes arrival at the DNA
DNA
damage within 10 seconds of the damage.[20] About half of the maximum chromatin relaxation, presumably due to action of Alc1, occurs by 10 seconds.[20] This then allows recruitment of the DNA
DNA
repair enzyme MRE11, to initiate DNA
DNA
repair, within 13 seconds.[21] γH2AX, the phosphorylated form of H2AX is also involved in the early steps leading to chromatin decondensation after DNA
DNA
damage occurrence. The histone variant H2AX constitutes about 10% of the H2A histones in human chromatin.[22] γH2AX (H2AX phosphorylated on serine 139) can be detected as soon as 20 seconds after irradiation of cells (with DNA double-strand break formation), and half maximum accumulation of γH2AX occurs in one minute.[22] The extent of chromatin with phosphorylated γH2AX is about two million base pairs at the site of a DNA
DNA
double-strand break.[22] γH2AX does not, itself, cause chromatin decondensation, but within 30 seconds of irradiation, RNF8
RNF8
protein can be detected in association with γH2AX.[23] RNF8
RNF8
mediates extensive chromatin decondensation, through its subsequent interaction with CHD4,[24] a component of the nucleosome remodeling and deacetylase complex NuRD. After undergoing relaxation subsequent to DNA
DNA
damage, followed by DNA repair, chromatin recovers to a compaction state close to its pre-damage level after about 20 min.[20] Methods to investigate chromatin[edit]

ChIP-seq ( Chromatin
Chromatin
immunoprecipitation sequencing), aimed against different histone modifications, can be used to identify chromatin states throughout the genome. Different modifications have been linked to various states of chromatin. DNase-seq ( DNase I
DNase I
hypersensitive sites Sequencing) uses the sensitivity of accessible regions in the genome to the DNase I
DNase I
enzyme to map open or accessible regions in the genome. FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements sequencing) uses the chemical properties of protein-bound DNA
DNA
in a two-phase separation method to extract nucleosome depleted regions from the genome.[25] ATAC-seq (Assay for Transposable Accessible Chromatin
Chromatin
sequencing) uses the Tn5 transposase to integrate (synthetic) transposons into accessible regions of the genome consequentially highlighting the localisation of nucleosomes and transcription factors across the genome. DNA
DNA
footprinting is a method aimed at identifying protein-bound DNA. It uses labeling and fragmentation coupled to gel electrophoresis to identify areas of the genome that have been bound by proteins.[26] MNase-seq (Micrococcal Nuclease sequencing) uses the micrococcal nuclease enzyme to identify nucleosome positioning throughout the genome.[27][28] Chromosome
Chromosome
conformation capture determines the spatial organization of chromatin in the nucleus, by inferring genomic locations that physically interact. MACC profiling ( Micrococcal nuclease
Micrococcal nuclease
ACCessibility profiling) uses titration series of chromatin digests with micrococcal nuclease to identify chromatin accessibility as well as to map nucleosomes and non-histone DNA-binding proteins in both open and closed regions of the genome.[29]

Chromatin: alternative definitions[edit] The term, introduced by Walther Flemming, has multiple meanings:

Simple and concise definition: Chromatin
Chromatin
is a macromolecular complex of a DNA
DNA
macromolecule and protein macromolecules (and RNA). The proteins package and arrange the DNA
DNA
and control its functions within the cell nucleus. A biochemists’ operational definition: Chromatin
Chromatin
is the DNA/protein/ RNA
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 partly depends 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. The DNA
DNA
+ histone = chromatin definition: The DNA
DNA
double helix in the cell nucleus is packaged by special proteins termed histones. The formed protein/ DNA
DNA
complex is called chromatin. The basic structural unit of chromatin is the nucleosome.

Nobel Prizes[edit] The following scientists were recognized for their contributions to chromatin research with Nobel Prizes:

Year Who Award

1910 Albrecht Kossel
Albrecht Kossel
(University of Heidelberg) Nobel Prize
Nobel Prize
in Physiology or Medicine for his discovery of the five nuclear bases: adenine, cytosine, guanine, thymine, and uracil.

1933 Thomas Hunt Morgan
Thomas Hunt Morgan
(California Institute of Technology) Nobel Prize
Nobel Prize
in Physiology or Medicine for his discoveries of the role played by the gene and chromosome in heredity, based on his studies of the white-eyed mutation in the fruit fly Drosophila.[30]

1962 Francis Crick, James Watson and Maurice Wilkins
Maurice Wilkins
(MRC Laboratory of Molecular Biology, Harvard University and London University respectively) Nobel Prize
Nobel Prize
in Physiology or Medicine for their discoveries of the double helix structure of DNA
DNA
and its significance for information transfer in living material.

1982 Aaron Klug
Aaron Klug
(MRC Laboratory of Molecular Biology) Nobel Prize
Nobel Prize
in Chemistry "for his development of crystallographic electron microscopy and his structural elucidation of biologically important nucleic acid-protein complexes"

1993 Richard J. Roberts
Richard J. Roberts
and Phillip A. Sharp Nobel Prize
Nobel Prize
in Physiology "for their independent discoveries of split genes," in which DNA
DNA
sections called exons express proteins, and are interrupted by DNA
DNA
sections called introns, which do not express proteins.

2006 Roger Kornberg
Roger Kornberg
(Stanford University) Nobel Prize
Nobel Prize
in Chemistry for his discovery of the mechanism by which DNA
DNA
is transcribed into messenger RNA.

See also[edit]

Active chromatin sequence Chromatid Epigenetics Histone-Modifying Enzymes Position-effect variegation Salt-and-pepper chromatin Transcriptional bursting

References[edit]

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insulators. Keeping enhancers under control". Nature. 376 (6540): 462–463. doi:10.1038/376462a0. PMID 7637775.  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
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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
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External links[edit]

Chromatin, Histones & Cathepsin; PMAP The Proteolysis Map-animation [ Recent chromatin publications and news] Protocol for in vitro Chromatin
Chromatin
Assembly ENCODE threads Explorer Chromatin
Chromatin
patterns at transcription factor binding sites. Nature (journal)

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Cytogenetics: chromosomes

Basic concepts

Karyotype Ploidy Genetic material/Genome Chromatin

Euchromatin Heterochromatin

Chromosome Chromatid Nucleosome Nuclear organization

Types

Autosome/Sex chromosome (or allosome or heterosome) Macrochromosome/Microchromosome Circular chromosome/Linear chromosome Extra chromosome
Extra chromosome
(or accessory chromosome) Supernumerary chromosome A chromosome/B chromosome Lampbrush chromosome Polytene chromosome Dinoflagellate chromosomes Homologous chromosome Isochromosome Satellite chromosome Centromere
Centromere
position

Metacentric Submetacentric Telocentric Acrocentric Holocentric

Centromere
Centromere
number

Acentric Monocentric Dicentric Polycentric

Processes and evolution

Mitosis Meiosis Structural alterations

Chromosomal inversion Chromosomal translocation

Numerical alterations

Aneuploidy Euploidy Polyploidy Paleopolyploidy

Polyploidization

Structures

Telomere: Telomere-binding protein (TINF2) Protamine

Histone

H1 H2A H2B H3 H4

Centromere

A B C1 C2 E F H I J K M N O P Q T

See also

Extrachromosomal DNA

Plasmid

List of organisms by chromosome count List of chromosome lengths for various organisms List of sequenced genomes International System for Human Cytogenetic Nomenclature

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Structures of the cell nucleus / nuclear protein

Envelope (membrane)/ nuclear lamina

Pore complex: Nucleoporin

NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214

AAAS

Nucleolus

Cajal (coiled) body

SMN GEMIN2 GEMIN4 GEMIN5 GEMIN6 GEMIN7 DDX20 COIL

Perinucleolar compartment

PTBP1 CUGBP1

TCOF ATXN7

Other

Chromatin Dot (PML body) Paraspeckle

SMC protein:

Cohesin

SMC1A SMC1B SMC3

Condensin

NCAPD2 NCAPD3 NCAPG NCAPG2 NCAPH NCAPH2 SMC2 SMC4

DNA
DNA
repair

SMC5 SMC6

Transition nuclear protein:

TNP1 TNP2

Nuclear matrix (Nucleoskeleton) Nucleoplasm
Nucleoplasm
(Nucleosol)

LITAF

see also transcription factors and intracellular receptors

see also nucleus diseases

Authority control

GND: 40101

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