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Intelligent Design, the best explanation of Origins » Molecular biology of the cell » Nucleosomes function and design

Nucleosomes function and design

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1 Nucleosomes function and design on Sat Jun 20, 2015 8:38 am

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Origin of histones and nucleosomes in Eukaryotic Cells, how is best explained, by evolution, or design?

Evolution is proposed as a mechanism to create an increase of complexity of organisms. Supposedly there was a transition from simpler, prokaryotic Cells to Eukaryotic Cells. The common explanation is the endosymbiotic theory, but the following case, this has no importance.  While eukaryotes wrap their DNA around proteins called histones to help package the DNA into smaller spaces, most prokaryotes do not have histone proteins.

So how could that transition and the setup of nucleosomes and the make of histones have occurred?  

DNA in chromatin is organized in arrays of nucleosomes. Two copies of each histone protein, H2A, H2B, H3 and H4, are assembled into an octamer.  The nucleosome, in its role as the principal packaging element of DNA within the nucleus, is the primary determinant of DNA accessibility.

Dr. Stephen C. Meyer in his 1996 essay The Origin of Life and the Death of Materialism, wrote that "the information storage density of DNA, thanks in part to nucleosome spooling, is several trillion times that of our most advanced computer chips  So not only is there real information stored in DNA, but it is stored at a density on a molecular level, we can’t even approach with our best computers.

Bruce Alberts writes in his landmark book: " The molecular biology of the Cell"
The amino acid sequence of histone H4 from a pea differs from that of a cow at only 2 of the 102 positions. This strong evolutionary conservation suggests that the functions of histones involve nearly all of their amino acids so that a change in any position is deleterious to the cell.

This rises immediately the pertinent question, which Alberts, a rusted believer in evolution, avoids to ask: How could histones have evolved, if their specificity is essential, and less than the existent - about 100 amino acids - would not do the job, but, as the author admits "  the functions of histones involve nearly all of their amino acids " ? Is that not an implicit admittance of irreducible complexity? 

The interface between DNA and histone is extensive: 142 hydrogen bonds are formed between DNA and the histone core in each nucleosome. Nearly half of these bonds form between the amino acid backbone of the histones and the phosphodiester backbone of the DNA.  More than one-fifth of the amino acids in each of the core histones are either lysine or arginine (two amino acids with basic side chains), and their positive charges can effectively neutralize the negatively charged DNA backbone. These numerous interactions explain in part why DNA of virtually any sequence can be bound on a histone octamer core. The sequence preference of nucleosomes must be weak enough to allow other factors to dominate, inasmuch as nucleosomes can occupy any one of a number of positions relative to the DNA sequence in most chromosomal regions.

What would happen if the net charge of histones would not neutralize the charge of the DNA backbone? DNA would bind in such a strong manner, that other factors would be unable to unwind the DNA, it could not be read, and effectively, the Cell would die. How could and would evolution find in a vast sequence space the right amino acids, providing the forces that permit the unwinding? Trial and error? Each time, it would try a sequence which is non-functional, the Cell would die. That makes the proposal of evolution as extremely unlikely. The histones had to be fully operational right from the beginning, what demonstrates that design is a far better and more case-adequate explanation rather than nonguided selective forces of evolution. 

There is more:

Nucleosomes must dynamically change so that DNA binding complexes can access their binding sites. These dynamic changes, which include nucleosome unwrapping, rewrapping, sliding, assembly, and disassembly, involve the formation and/or disruption of interactions within the interfaces between the DNA, H3/H4, and H2A/H2B components of the nucleosome. Histone protein tails are critical for controlling gene expression: they are dynamically modified by post-translational modifications (PTMs) many of the modifications have been correlated with regulatory cellular processes and chromatin structure.

A book cannot be found amongst thousands, or millions of books, in a library, unless there is an organization through a library management program which is necessary for the fast retrieval and return of books. The fast retrieval of information where to find a book in a library depends on the organized labeling of each library section, shelf, and eventually even the individual books, and is ordered in theme and genre sections, and every shelf has a tag which can be recognized and informs what books are there, and what themes. The books need first to be separated by genre and put together in categories. Then they have to be cataloged, one by one, before put together to the right shelf.

Histone protein tails are critical for controlling gene expression since they are like a computer which stores a library management program, containing, for example, the instruction: " its time to unwrap the DNA section of this histone, and express the DNA blueprint ". If the Cell cannot perform that critical information extraction at the right place, and the right time, the Cell is non-functional. Its a failure in its entirety. A factory cannot be built, unless the engineers know where and how to find the blueprints to build it. Reader proteins scan the histone tail, and signal to transcription factors and the transcription machinery: Come here, begin your job !! There is a large number of Histone tail  reader proteins which can read, "understand", and pass information on, but if just ONE of them is missing, like "histone acetyltransferase" (HAT), there would be no eukaryotic life !!  

Histone acetylation and deacetylation are essential parts of gene regulation, and crucial for life.  
Histone acetylation and deacetylation are the processes by which the lysine residues within the N-terminal tail protruding from the histone core of the nucleosome are acetylated and deacetylated as part of gene regulation.  Acetyl is a moiety ( a part of a molecule), and the introduction of an acetyl group into a molecule is called acetylation.  Acetylation removes the positive charge on the histones, thereby decreasing the interaction of the N termini of histones with the negatively charged phosphate groups of DNA. As a consequence, the condensed chromatin is transformed into a more relaxed structure that is associated with greater levels of gene transcription.

The make of histones is an engineering marvel.

Nucleosome assembly
Nucleosome assembly following DNA replication, DNA repair, and gene transcription is critical for the maintenance of genome stability and epigenetic information. Nucleosomes are assembled via replication-coupled or replication-independent pathways with the aid of histone chaperone proteins.

The sequence of correct histone octamer assembly is a multistep process, requiring several sequential folds and steps in a highly organized and precise manner, and must have been fully functional right from the beginning. The right process and sequence had to be programmed. The presence of histone chaperone proteins, which are specific, and could not have been co-opted from other systems, are essential. Histone chaperones promote chromatin assembly, disassembly and histone exchange to facilitate DNA replication, repair, and transcription. It's not feasible that they arose in a stepwise fashion, no function would be granted unless they were fully developed to exercise its specific function.


Nucleosomes function and design

The DNA in the chromatin is very tightly associated with proteins called histones, which package and order the DNA into structural units called nucleosomes. Each type of histone is subject to enzymatic modification by methylation, acetylation, ADP-ribosylation, phosphorylation, glycosylation, sumoylation, or ubiquitination. Such modifications affect the net electric charge, shape, and other properties of histones, as well as the structural and functional properties of the chromatin, and they play a role in the regulation of transcription. Eukaryotes generally have several variant forms of certain histones, most notably histones H2A and H3.  The variant forms, along with their modifications, have specialized roles in DNA metabolism. This compaction involves several levels of highly organized folding. Subjection of chromosomes to treatments that partially unfold them reveals a structure in which the DNA is bound tightly to beads of protein, often regularly spaced. The beads in this “beads-on-a-string” arrangement are complexes of histones and DNA. The bead plus the connecting DNA that leads to the next bead form the nucleosome, the fundamental unit of organization on which the higher-order packing of chromatin is built. 

The continuous DNA fiber of each chromosome is packaged into many hundreds of thousands of nucleosomes linked in series. The nucleosome core particle is disk-shaped, with DNA coiled in a left-handed superhelix around an
octamer of core histones. The amino-terminal approximately 30 amino acid residues of the core histones (referred to as N-terminal tails) are important for interactions both inside and outside the nucleosome. They project outward from the cylindrical faces of the nucleosomal core as well as between the adjacent winds of the DNA on the nucleosome surface. Although these N-terminal tails are not ordered either in crystals of nucleosome core particles
or in solution, they are among the most highly conserved regions of these very highly conserved proteins. This is because they serve as signaling platforms and mediate packing interactions between nucleosomes. Modifications
of the N-terminal tails regulate DNA accessibility within the chromatin fiber to the transcription, replication, and repair machinery.14

A nucleosome is a basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores. This structure is often compared to thread wrapped around a spool. Nucleosomes form the fundamental repeating units of eukaryotic chromatin, which is used to pack the large eukaryotic genomes into the nucleus while still ensuring appropriate access to it (in mammalian cells approximately 2 m of linear DNA have to be packed into a nucleus of roughly 10 µm diameter). Nucleosomes are folded through a series of successively higher order structures to eventually form a chromosome; this both compacts DNA and creates an added layer of regulatory control, which ensures correct gene expression. Nucleosomes are thought to carry epigenetically inherited information in the form of covalent modifications of their core histones.

DNA in chromatin is organized in arrays of nucleosomes. Two copies of each histone protein, H2A, H2B, H3 and H4, are assembled into an octamer that has 145–147 base pairs (bp) of DNA wrapped around it to form a nucleosome core. The repeating nucleosome cores further assemble into higher-order structures which are stabilized by the linker histone H1 and these compact linear DNA overall by a factor of 30–40. The nucleosome (nucleosome core, linker DNA and H1) thereby shapes the DNA molecule both at the atomic level through DNA bending, and on the much larger scale of genes by forming higher-order helices. The nucleosome, in its role as the principal packaging element of DNA within the nucleus, is the primary determinant of DNA accessibility. The physical properties of nucleosomes depend on solution conditions such as ionic strength, divalent-ion concentration, and on the histone-modification state. The characteristics of an individual nucleosome, however, depend on the actual DNA sequence incorporated, and this can have functional significance for specific gene promoters .
 12

Nucleosomes. 
Regularly spaced nucleosomes consist of histone complexes bound to DNA. (a) Schematic illustration and (b) electron micrograph.

The nucleosomal subunit organization of chromatin provides a multitude of functions. Nucleosomes elicit an initial ~7-fold linear compaction of genomic DNA. They provide a critical mechanism for stable repression of genes and other DNA-dependent activities by restricting binding of trans-acting factors to cognate DNA sequences. Conversely, they are engineered to be nearly meta-stable and disassembled (and reassembled) in a facile manner to allow rapid access to the underlying DNA during processes such as transcription, replication and DNA repair. 25

Nucleosomes protect the genome from DNA damaging agents and provide a lattice onto which a myriad of epigenetic signals are deposited. Moreover, vast strings of nucleosomes provide a framework for assembly of the chromatin fiber and higher-order chromatin structures.


Composition and Biophysical Properties of Nucleosomes
The canonical nucleosome is a protein octamer consisting of two copies of each of the four core/canonical histone proteins (H3, H4, H2A, and H2B), around which 147 bp of DNA are wrapped. The octamer can be subdivided into four histone dimer pairs: two H3/H4 dimers form the central H3/H4 tetramer, which is capped on each end by an H2A/H2B dimer. These dimer pairs interact to form an interlocked right-handed helical staircase, forming a surface upon which the DNA climbs. Here, positively charged amino acids facing outward from the histone staircase contact the negatively charged phosphate backbone of the DNA. Each histone dimer pair contacts the DNA backbone along about three consecutive turns each involving 10–11 bp (totaling ~31 bp), with the four dimer pairs providing a total of 12 histone–DNA contact sites. Two additional histone–DNA contacts are provided by extensions from histone H3, which form the initial (weaker) contacts at the two entry/exit sites to the nucleosome—reaching 14 total histone–DNA contacts. Although each contact in isolation is relatively weak (~1 kcal/mol, requiring ~1 pN of force to disrupt), all 14 added together confer considerable positional stability (~12–14 kcal). These histone–DNA contacts provide the energetic and biophysical obstacle that Remodelers must overcome, as Remodelers must disrupt these contacts to perform their roles. As ATP hydrolysis provides ~7.3 kcal/mol of free energy, Remodelers must either break only a few histone–DNA contacts at a time (providing a partially unwrapped intermediate), or alternatively utilize more than one ATP hydrolysis to yield a repositioned (or ejected) nucleosome product. Beyond the four core/canonical histones, all eukaryotes also contain histone variant proteins that can be incorporated into nucleosomes to specialize in chromatin regions. 

Variant nucleosomes can specialize a nucleosome by affecting its biophysical properties/stability, and by presenting unique epitopes that may affect protein associations, including Remodeler targeting or activity. Furthermore, higher eukaryotes also employ a “linker” histone (most commonly an H1 or H5 subtype), which joins the nucleosome, to form the chromatosome, which may also provide a steric or thermodynamic barrier to Remodeler action. In general, linker histones help stabilize and assemble higher-order forms of chromatin and can affect Remodeler function.

The Nucleosome Core
Nucleosomes constitute the basic repeating subunit of chromatin. Each nucleosome can be considered as composed of a nucleosome ‘core’, linker DNA, and in most instances, a linker histone.

Dr. Stephen C. Meyer in his 1996 essay The Origin of Life and the Death of Materialism, wrote that
"the information storage density of DNA, thanks in part to nucleosome spooling, is several trillion times that of our most advanced computer chips  So not only is there real information stored in DNA, but it is stored at a density on a molecular level, we can’t even approach with our best computers. 16

There are about 30 million nucleosomes in each human cell. So many are needed because the DNA strand wraps around each one only 1.65 times, in a twist containing 147 of its units, and the DNA molecule in a single chromosome can be up to 225 million units in length. 17

DNA has a striking property to pack itself in the appropriate solution conditions with the help of ions and other molecules. Usually, DNA condensation is defined as "the collapse of extended DNA chains into compact, orderly particles containing only one or a few molecules" 18

The basic level of DNA compaction is the nucleosome, where the double helix is wrapped around the histone octamer containing two copies of each histone H2A, H2B, H3 and H4. Linker histone H1 binds the DNA between nucleosomes and facilitates packaging of the 10 nm "beads on the string" nucleosomal chain into a more condensed 30 nm fiber. Most of the time, between cell divisions, chromatin is optimized to allow easy access of transcription factors to active genes, which are characterized by a less compact structure called euchromatin, and to alleviate protein access in more tightly packed regions called heterochromatin. During the cell division, chromatin compaction increases even more to form chromosomes, which can cope with large mechanical forces dragging them into each of the two daughter cells.

The structure of the nucleosome core particle reveals how DNA is packaged
The high-resolution structure of a nucleosome core particle, solved in 1997, revealed a disc-shaped histone core around which the DNA was tightly wrapped 1.7 turns in a left-handed coil


SECONDARY STRUCTURE OF THE HISTONES WITHIN THE CORE PARTICLE. 
A, A ribbon diagram shows that each histone protein in the octameric core of the nucleosome has a characteristic Z-shaped α-helical structure (the histone-fold). The flexible N-terminal portions of the histones, which have a critical role in regulating chromatin structure, did not occupy a unique location in the crystal and do not appear in this structure. 
B, The histone octamer surrounded by one of the two turns of DNA.









a, Nucleosome core particle: ribbon traces for the 146-bp DNA phosphodiester backbones (brown and turquoise) and eight histone protein main chains (blue: H3; green: H4; yellow: H2A; red: H2B. The views are down the DNA superhelix axis for the left particle and perpendicular to it for the right particle. For both particles, the pseudo-twofold axis is aligned vertically with the DNA centre at the top. 
b, DNA phosphate B-factors versus base pair. The sequence of the DNA used is shown with corresponding B-factors (A˚ 2 ) plotted for the 59phosphate group of each base. The contacts of the DNA phosphodiester chains with the histones are indicated: squares for main-chain hydrogen bonds; circles for side-chain hydrogen bonds, and triangles for hydrophobic bonds. The bases coloured blue, green, red, and yellow indicate close proximity to an arginine side chain inserted into the minor groove. The DNA phosphate groups have high mobility or are disordered when not contacted by the histones. 
c, Core histone sequences. The histone fold regions for H3, H4, H2A and H2B are aligned on the basis of their structures and labelled on the left (top). The a-helix (a1, a2, a3) and loop (L1, L2) secondary structural elements are labelled; a-helices are underlined. L designates an arginine side chain that is inserted into the DNA minor groove at the indicated SHL. The overlying lines indicate b-strand hydrogen bonds between L1 and L2 loops. The side chains indicate the positions of buried arginine–aspartate pairs for H3–H4 and the lack of a homologous pair for H2A– H2B. The histone-fold extensions and tail (italics) regions are shown with the core histone name representing the histone fold (bottom). Grey-shaded sequences were not included in the atomic model. Sites of in vivo acetylation are indicated with a letter ‘a’. Trypsin cleavage sites that produce a ‘tailless’ core particle are denoted by T. The site of ubiquitination is marked U. SHL labels above the sequence indicate contacts with DNA at those points. The H4 sequence at amino acids 16–25 and underlined in orange makes a clear interparticle contact with a H2A–H2B dimer. Some interaction sites are highlighted: (1) H3–H4 a2-a2 (blue-green); (2) H2A–H2B a2-a2 (orange); (3) H3 4-helix bundle (blue); (4) H4–H2B 4-helix bundle (brown). 
d, Nucleosome core particle: 73-bp half. The view is down the superhelix axis with the pseudodyad axis aligned vertically. The central base pair through which the dyad passes is above the SHL0 label, 0 (SHL, superhelix axis location). Each SHL label represents one further DNA double helix turn from SHL0. The complete histone proteins primarily associated with the 73-bp superhelix half are shown (interparticle tail regions are not shown). The two copies of each histone pair are distinguished as unprimed and primed copies, where the histone fold of the unprimed copy is primarily associated with the 73-bp DNA half and the primed copy with the 72-bp half. The 4-helix bundles are labelled as H39H3 and H2B H4; histone-fold extensions of H3 and H2B are labelled as aN9, aN and aC, respectively; the interface between the H2A docking domain and the H4 C terminus as b; and Nand C-terminal tail regions as N or C. 

All four of the histones that make up the core of the nucleosome are relatively small proteins (102-135 amino acids), and they share a structural motif, known as the histone fold, formed from three cr helices connected by two loops


The overall structural organization of the core histones. 
(A) Each of the core histones contains an N-terminal tail, which is subject to several forms of covalent modification, and a histone fold region, as indicated. 
(B) The structure of the histone fold, which is formed by all four of the core histones. 
(C) Histones 2A and 2B form a dimer through an interaction known as the “handshake.” Histones H3 and H4 form a dimer through the same type of interaction. 
(D) The final histone octamer on DNA. Note that all eight N-terminal tails of the histones protrude from the disc-shaped, core structure. Their conformations are highly flexible, and they serve as binding sites for sets of other proteins. 11

Nucleosome assembly
In assembling a nucleosome, the histone folds first bind to each other to form H3-H4 and H2A-H2B dimers, and the H3-H4 dimers combine to form tetramers. An H3-H4 tetramer then further combines with two HZA-H2B dimers to form the compact octamer core, around which the DNA is wound (In assembling a nucleosome, the histone folds first bind to each other to form H3-H4 and H2A-H2B dimers, and the H3-H4 dimers combine to form tetramers. An H3-H4 tetramer then further combines with two HZA-H2B dimers to form the compact octamer core, around which the DNA is wound.


Schematic representation of the assembly of the core histones into the nucleosome
The nucleosome assembles when DNA wraps around the histone octamer, two H2A-H2B dimers bound to an H3-H4 tetramer.

This probably explains some striking, but unusual, cases of very precise positioning of nucleosomes along a stretch of DNA. However, the sequence preference of nucleosomes must be weak enough to allow other factors to dominate, inasmuch as nucleosomes can occupy any one of a number of positions relative to the DNA sequence in most chromosomal regions.

As a reflection of their fundamental role in DNA function through controlling chromatin structure, the histones are among the most highly conserved eukaryotic proteins. For example, the amino acid sequence of histone H4 from a pea differs from that of a cow at only 2 of the 102 positions. This strong evolutionary conservation suggests that the functions of histones involve nearly all of their amino acids so that a change in any position is deleterious to the cell. But in addition to this remarkable conservation, eukaryotic organisms also produce smaller amounts of specialized variant core histones that differ in amino acid sequence from the main ones. These variants, combined with the surprisingly large number of covalent modifications that can be added to the histones in nucleosomes, give rise to a variety of chromatin structures in cells.

The interface between DNA and histone is extensive: 142 hydrogen bonds are formed between DNA and the histone core in each nucleosome. Nearly half of these bonds form between the amino acid backbone of the histones and the phosphodiester backbone of the DNA.  More than one-fifth of the amino acids in each of the core histones are either lysine or arginine (two amino acids with basic side chains), and their positive charges can effectively neutralize the negatively charged DNA backbone. These numerous interactions explain in part why DNA of virtually any sequence can be bound on a histone octamer core. The sequence preference of nucleosomes must be weak enough to allow other factors to dominate, inasmuch as nucleosomes can occupy any one of a number of positions relative to the DNA sequence in most chromosomal regions.

 The path of the DNA around the histone core is not smooth; rather, several kinks are seen in the DNA, as expected from the non-uniform surface of the core. The bending requires a substantial compression of the minor groove of the DNA helix. Certain dinucleotides in the minor groove are especially easy to compress, and some nucleotide sequences bind the nucleosome more tightly than others. 


The bending of DNA in a nucleosome.
The DNA helix makes 1.7 tight turns around the histone octamer. This diagram illustrates how the minor groove is compressed on the inside of the turn. Owing to structural features of the DNA molecule, the indicated dinucleotides
are preferentially accommodated in such a narrow minor groove, which helps to explain why certain DNA sequences will bind more tightly than others to the nucleosome core.


If the composition of the histones would not be as it is, with the predominance of lysines and arginine amino acids, but other ones, they would not be able to neutralize the negatively charged DNA backbone, and DNA would eventually bind  

Histone chaperone proteins
Nucleosome assembly following DNA replication, DNA repair, and gene transcription is critical for the maintenance of genome stability and epigenetic information. Nucleosomes are assembled via replication-coupled or replication-independent pathways with the aid of histone chaperone proteins. How these different nucleosome assembly pathways are regulated remains relatively unclear. Recent studies have provided insight into the mechanisms and the roles of histone chaperones regulating nucleosome assembly.19

Following DNA replication during S phase, nucleosomes are assembled, using both parental histones and newly synthesized histones, in a process called replication-coupled nucleosome assembly. Nucleosome assembly during gene transcription and histone exchange occur throughout the cell cycle in a replication-independent manner

Histone chaperone proteins have prominent roles in facilitating these processes as well as in replacing old histones with new canonical histones or histone variants during the process of histone exchange. Histone chaperones promote chromatin assembly, disassembly and histone exchange to facilitate DNA replication, repair and transcription. Beyond that, histone chaperones play important roles in regulating the intricate steps involved in folding of histones together with DNA to form correctly assembled nucleosomes.  20

Stepwise assembly and disassembly of nucleosomes mediated by histone chaperones  
DNA is wrapped around two H3–H4 dimers and two H2A–H2B dimers to form the nucleosome core particle. There is a stepwise assembly, along with the different possible intermediates including the tetrasome. Histone chaperones mediate each step of the assembly/disassembly process. 


Histone H2A is depicted in yellow, H2B in red, H3 in blue, and H4 in green.





Histones and DNA fail to self-assemble into nucleosomes under physiological conditions because of the strong tendency for histones to associate non-specifically with DNA and form aggregates. Thus there is a need for histone chaperones to guide the process and each step along the assembly pathway is carefully controlled and regulated by these histone chaperones.

It is evident that a stepwise evolutionary fashion of development of histone chaperones to guide the process would result in a disaster. They had to be there fully working and programmed to do their job right from the start.

Many specialized chaperones for the histones that form the nucleosome core particle (core histones) and those that interact with the nucleosome core and the linker DNA (linker histones) participate at each step in the processes of nucleosome assembly, disassembly and histone exchange during different genomic processes

Location and function of linker histones
The linker histones, H1 and its variant forms, have been implicated in the formation of higher orders of chromatin structure and gene repression.21 Outstanding amongst the many functions proposed for the linker histone are its ability to stabilize the nucleosomal particle structure and its participation in the condensation of the 'beads-on-a-string' fiber into higher order structures. This correlation between the presence of linker histones on chromatin and a compacted structure, which limits the access of components of the transcriptional machinery, has led to the suggestion that linker histones may function as generalized repressors of transcription

there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure ( so its irreducible ) H1 links nucleosomes into higher order structures. 22

The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes.

A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterized by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome.

highly preserved means, it did not evolve, and " is essential " means, its irreducible.

H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher-order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy-terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber 23  see below:

Conserved Protein Domain Family H15



Histone acetyltransferase  (HATs)

are enzymes that acetylate conserved lysine amino acids on histone proteins by transferring an acetyl group from acetyl CoA to form ε-N-acetyllysine. DNA is wrapped around histones, and, by transferring an acetyl group to the histones, genes can be turned on and off. In general, histone acetylation increases gene expression. In general, histone acetylation is linked to transcriptional activation and associated with euchromatin. When it was first discovered, it was thought that acetylation of lysine neutralizes the positive charge normally present, thus reducing affinity between histone and (negatively charged) DNA, which renders DNA more accessible to transcription factors. Research has emerged, since, to show that lysine acetylation and other posttranslational modifications of histones generate binding sites for specific protein-protein interaction domains, such as the acetyllysine-binding bromodomain.[citation needed] Histone acetyltransferases can also acetylate non-histone proteins, such as nuclear receptors and other transcription factors to facilitate gene expression.24

Histone deacetylase ( HDAC )
are a class of enzymes that remove acetyl groups (O=C-CH3) from an ε-N-acetyl lysine amino acid on a histone, allowing the histones to wrap the DNA more tightly. This is important because DNA is wrapped around histones, and DNA expression is regulated by acetylation and de-acetylation. Its action is opposite to that of histone acetyltransferase. HDAC proteins are now also called lysine deacetylases (KDAC), to describe their function rather than their target, which also includes non-histone proteins.

The interface between DNA and histone is extensive: 142 hydrogen bonds are formed between DNA and the histone core in each nucleosome. Nearly half of these bonds form between the amino acid backbone of the histones and the phosphodiester backbone of the DNA. Numerous hydrophobic interactions and salt linkages also hold DNA and protein together in the nucleosome. For example, more than one-fifth of the amino acids in each of the core histones are either lysine or arginine (two amino acids with basic side chains), and their positive charges can effectively neutralize the negatively charged DNA backbone. These numerous interactions explain in part why DNA of virtually any sequence can be bound on a histone octamer core. The path of the DNA around the histone core is not smooth; rather, several kinks are seen in the DNA, as expected from the non-uniform surface of the core. The bending requires a substantial compression of the minor groove of the DNA helix. Certain dinucleotides in the minor groove are especially easy to compress, and some nucleotide sequences bind the nucleosome more tightly than others. This probably explains some striking, but unusual, cases of very precise positioning of nucleosomes along a stretch of DNA. For most of the DNA sequences found in chromosomes, however, the sequence preference of nucleosomes must be small enough to allow other factors to dominate, inasmuch as nucleosomes can occupy any one of a number of positions relative to the DNA sequence in most chromosomal regions. In addition to its histone fold, each of the core histones has an N-terminal amino acid "tail", which extends out from the DNA-histone core. These histone tails are subject to several different types of covalent modifications that in turn control critical aspects of chromatin structure and function. As a reflection of their fundamental role in DNA function through controlling chromatin structure, the histones are among the most highly conserved eukaryotic proteins. For example, the amino acid sequence of histone H4 from a pea and from a cow differ at only 2 of the 102 positions. This strong evolutionary conservation suggests that the functions of histones involve nearly all of their amino acids so that a change in any position is deleterious to the cell. This suggestion has been tested directly in yeast cells, in which it is possible to mutate a given histone gene in Vitro and introduce it into the yeast genome in place of the normal gene. As might be expected, most changes in histone sequences are lethal; the few that are not lethal cause changes in the normal pattern of gene expression, as well as other abnormalities.

If a change in histone sequences are lethal, how could it probably come to be in gradual steps, or trial and error?



Despite the high conservation of the core histones, eucaryotic organisms also produce smaller amounts of specialized variant core histones that differ in amino acid sequence from the main ones. As we shall see, these variants, combined with a surprisingly large variety of covalent modifications that can be added to the histones in nucleosomes, make possible the many different chromatin structures that are required for DNA function in higher eukaryotes.

Nucleosomes have a dynamic structure and are frequently subjected to changes catalyzed by ATP-dependent chromatin-remodeling complexes For many years biologists thought that once formed in a particular position on DNA, a nucleosome remains fixed in place because of the very tight association between its core histones and DNA. If true, this would pose problems for genetic readout mechanisms, which in principle require rapid access to many specific DNA sequences, as well as for the rapid passage of the DNA transcription and replication machinery through chromatin. But kinetic experiments show that the DNA in an isolated nucleosome unwraps from each end at rate of about 4 times per second, remaining exposed for 10 to 50 milliseconds before the partially unwrapped structure recloses. Thus, most of the DNA in an isolated nucleosome is in principle available for binding other proteins. For the chromatin in a cell, a further loosening of DNA-histone contacts is clearly required, because eucaryotic cells contain a large variety of ATP-dependent chromatin remodeling complexes. The subunit in these complexes that hydrolyzes ATP is evolutionarily related to the DNA helicases, and it binds both to the protein core of the nucleosome and to the double-stranded DNA that winds around it. By using the energy of AIP hydrolysis to move this DNA relative to the core, this subunit changes the structure of a nucleosome temporarily, making the DNA less tightly bound to the histone core. Through repeated cycles of ATP hydrolysis, the remodeling complexes can catalyze nucleosome sliding, and by pulling the nucleosome core along the DNA double helix in this way, they make the nucleosomal DNA available to other proteins in the cell. In addition, by cooperating with negatively






11. Molecular biology of the Cell, 6th ed., page 189
12. http://sci-hub.tw/https://www.nature.com/articles/38444
13. Cell biology, 3td ed. elsiever, page 127 
14) http://en.wikipedia.org/wiki/Nucleosome
15) Lehninger, principles of biochemistry, 5th ed. page 963
16) http://www.conservapedia.com/Creation_science
17) http://able2know.org/topic/72452-35
18) https://en.wikipedia.org/wiki/DNA_condensation
19) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4004355/
20) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4004086/
21) http://www.nature.com/nsmb/journal/v5/n12/full/nsb1298_1025.html
22) http://www.ebi.ac.uk/interpro/entry/IPR005818
23) http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cl00073
24) https://en.wikipedia.org/wiki/Histone_acetyltransferase
25. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4598263/



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2 Nucleosomes function and design on Mon Jun 22, 2015 2:39 pm

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Nucleosomes and irreducible complexity

A nucleosome is a basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight  histone protein cores. This structure is often compared to thread wrapped around a spool. The basic level of DNA compaction is the nucleosome, where the double helix is wrapped around the histone octamer containing two copies of each histone H2A, H2B, H3 and H4. Linker histone H1 binds the DNA between nucleosomes and facilitates packaging of the 10 nm "beads on the string" nucleosomal chain into a more condensed 30 nm fiber.

Histones are among the most highly conserved eucaryotic proteins. For example, the amino acid sequence of histone H4 from a pea and from a cow differ at only 2 of the 102 positions. This strong evolutionary conservation suggests that the functions of histones involve nearly all of their amino acids, so that a change in any position is deleterious to the cell. This suggestion has been tested directly in yeast cells, in which it is possible to mutate a given histone gene in uitro andintroduce it into the yeast genome in place of the
normal gene. As might be expected, most changes in histone sequences are lethal; the few that are not lethal cause changes in the normal pattern of gene expression, as well as other abnormalities.

If a change in histone sequences are lethal, how could it probably come to be in gradual steps, or trial and error ? As long as the correct sequence is not reached, no function.....

Nucleosome assembly following DNA replication, DNA repair and gene transcription is critical for the maintenance of genome stability and epigenetic information.

In assembling a nucleosome, the histone folds first bind to each other to form H3-H4 and H2A-H2B dimers, and the H3-H4 dimers combine to form tetramers. An H3-H4 tetramer then further combines with two HZA-H2B dimers to form the compact octamer core, around which the DNA is wound

The  assembly is a sequential  multistep process, requiring several  folds and steps in a highly organized, regulated and precise manner, and must have been programmed and functional right from the beginning.   Histone chaperones play important roles in regulating the intricate steps involved in folding of histones together with DNA to form correctly assembled nucleosomes, furthermore  assembly, disassembly and histone exchange to facilitate DNA replication, repair and transcription. There is a need for histone chaperones to guide the process and each step along the assembly pathway is carefully controlled and regulated by these histone chaperones. It is evident that a stepwise evolutionary fashion of development of histone chaperones to guide the process would result in a disaster. They had to be there fully working and programmed to do their job right from the start.  
Furthermore, to add to the already amazing machine like performance,  (linker histones) have to participate at each step in the processes of nucleosome assembly, disassembly and histone exchange during different genomic processes.   Linker histone H1 is an essential component of chromatin structure ( so its irreducible ).  H1 links nucleosomes into higher order structures.

Nucleosome formation is dependent on the positive charges of the H4 histones and the negative charge on the surface of H2A histone fold domains. Acetylation of the histone tails disrupts this association, leading to weaker binding of the nucleosomal components. Histone acetyltransferases (HATs) and Histone deacetylase ( HDAC ) are also essential enzymes, that  remove through acetylation the  positive charge on the histones, and as a consequence, the condensed chromatin is transformed into a more relaxed structure that is associated with greater levels of gene transcription. This relaxation can be reversed by HDAC activity.

So we can conclude that all these parts, DNA,  Linker histone H1, histones H2A, H2B, H3 and H4,and acetyltransferases (HATs) and Histone deacetylase ( HDAC ) form a  set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function.  The set of these indispensable parts is known as the irreducible core of the system, while Histone chaperones are also essential to build the since they guide the process and each step along the assembly pathway.

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Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach

Eukaryotic DNA is strongly bent inside fundamental packaging units: the nucleosomes. It is known that their positions are strongly influenced by the mechanical properties of the underlying DNA sequence. Here we discuss the possibility that these mechanical properties and the concomitant nucleosome positions are not just a side product of the given DNA sequence, e.g. that of the genes, but that a mechanical evolution of DNA molecules might have taken place. We first demonstrate the possibility of multiplexing classical and mechanical genetic information using a computational nucleosome model. In a second step we give evidence for genome-wide multiplexing in Saccharomyces cerevisiae and Schizosacharomyces pombe. This suggests that the exact positions of nucleosomes play crucial roles in chromatin function.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0156905

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4 Re: Nucleosomes function and design on Sat Oct 06, 2018 6:33 am

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Nucleosomes function and design

http://reasonandscience.catsboard.com/t2051-nucleosomes-function-and-design#3509

A nucleosome is a basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores. This structure is often compared to thread wrapped around a spool. The basic level of DNA compaction is the nucleosome, where the double helix is wrapped around the histone octamer containing two copies of each histone H2A, H2B, H3, and H4Linker histone H1 binds the DNA between nucleosomes and facilitates packaging of the 10 nm "beads on the string" nucleosomal chain into a more condensed 30 nm fiber.

Histones are among the most highly conserved eukaryotic proteins. For example, the amino acid sequence of histone H4 from a pea and from a cow differ at only 2 of the 102 positions. This strong evolutionary conservation suggests that the functions of histones involve nearly all of their amino acids so that a change in any position is deleterious to the cell. This suggestion has been tested directly in yeast cells, in which it is possible to mutate a given histone gene in Vitro and introduce it into the yeast genome in place of the normal gene. As might be expected, most changes in histone sequences are lethal; the few that are not lethal cause changes in the normal pattern of gene expression, as well as other abnormalities.

If a change in histone sequences are lethal, how could it probably come to be in gradual steps, or trial and error? As long as the correct sequence is not reached, no function.....

Nucleosome assembly following DNA replication, DNA repair and gene transcription is critical for the maintenance of genome stability and epigenetic information.

In assembling a nucleosome, the histone folds first bind to each other to form H3-H4 and H2A-H2B dimers, and the H3-H4 dimers combine to form tetramers. An H3-H4 tetramer then further combines with two HZA-H2B dimers to form the compact octamer core, around which the DNA is wound

The assembly is a sequential multistep process, requiring several folds and steps in a highly organized, regulated and precise manner, and must have been programmed and functional right from the beginning.   Histone chaperones play important roles in regulating the intricate steps involved in folding of histones together with DNA to form correctly assembled nucleosomes, furthermore assembly, disassembly, and histone exchange to facilitate DNA replication, repair and transcription. There is a need for histone chaperones to guide the process and each step along the assembly pathway is carefully controlled and regulated by these histone chaperones. It is evident that a stepwise evolutionary fashion of development of histone chaperones to guide the process would result in a disaster. They had to be there fully working and programmed to do their job right from the start.   Furthermore, to add to the already amazing machine like performance,  (linker histones) have to participate at each step in the processes of nucleosome assembly, disassembly and histone exchange during different genomic processes.   Linker histone H1 is an essential component of chromatin structure ( so its irreducible ).  H1 links nucleosomes into higher order structures.

Nucleosome formation is dependent on the positive charges of the H4 histones and the negative charge on the surface of H2A histone fold domains. Acetylation of the histone tails disrupts this association, leading to weaker binding of the nucleosomal components. Histone acetyltransferases (HATs) and Histone deacetylase ( HDAC ) are also essential enzymes, that remove through acetylation the positive charge on the histones, and as a consequence, the condensed chromatin is transformed into a more relaxed structure that is associated with greater levels of gene transcription. This relaxation can be reversed by HDAC activity.

So we can conclude that all these parts, DNA,  Linker histone H1, histones H2A, H2B, H3 and H4,and acetyltransferases (HATs) and Histone deacetylase ( HDAC ) form a  set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function.  The set of these indispensable parts is known as the irreducible core of the system, while Histone chaperones are also essential to build the since they guide the process and each step along the assembly pathway.

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