Chromatin Fiber Folding: Requirement for the Histone H4 N-terminal Tail

Dorigo, Benedetta; Schalch, Thomas; Bystricky, Kerstin; Richmond, Timothy J.

doi:10.1016/s0022-2836(03)00025-1

Cited by 495 publications

(564 citation statements)

References 70 publications

Supporting

Mentioning

507

Contrasting

Unclassified

Order By: Relevance

“…Such duplex interpenetration has previously been observed in DNA crossovers 19 and, indeed, has been proposed as a mechanism promoting chromatin fibre compaction 18. Divalent cations facilitate right‐handed crossover formation 28, and also, in contrast to monovalent cations, promote the formation of more compact chromatin fibres 29, 30. We suggest that these close approaches of linker DNA could perhaps contribute to a relative metastability of the more compact fibres.…”

Section: Physical Attributes Of the Proposed Structuresupporting

confidence: 71%

A metastable structure for the compact 30‐nm chromatin fibre

McGeehan

Travers

2016

FEBS Letters

View full text Add to dashboard Cite

The structure of compact 30‐nm chromatin fibres is still debated. We present here a novel unified model that reconciles all experimental observations into a single framework. We propose that compact fibres are formed by the interdigitation of the two nucleosome stacks in a 2‐start crossed‐linker structure to form a single stack. This process requires that the dyad orientation of successive nucleosomes relative to the helical axis alternates. The model predicts that, as observed experimentally, the fibre‐packing density should increase in a stepwise manner with increasing linker length. This model structure can also incorporate linker DNA of varying lengths.

show abstract

Section: Physical Attributes Of the Proposed Structuresupporting

confidence: 71%

A metastable structure for the compact 30‐nm chromatin fibre

McGeehan

Travers

2016

FEBS Letters

View full text Add to dashboard Cite

show abstract

“…It has been known for some time that in vitro nucleosomes have a high preference for certain DNA sequences (11)(12)(13)(14) and tend to avoid other sequences (15)(16)(17)(18)(19)(20)(21)(22). For instance, Kaplan et al (23) concluded from genome-scale nucleosome mapping that intrinsic nucleosome sequence preferences have a dominant role in determining nucleosome organization in vivo.…”

mentioning

confidence: 99%

Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy

Heijden

Vugt

Logie

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Nucleosome positioning dictates eukaryotic DNA compaction and access. To predict nucleosome positions in a statistical mechanics model, we exploited the knowledge that nucleosomes favor DNA sequences with specific periodically occurring dinucleotides. Our model is the first to capture both dyad position within a few base pairs, and free binding energy within 2 kBT, for all the known nucleosome positioning sequences. By applying Percus’s equation to the derived energy landscape, we isolate sequence effects on genome-wide nucleosome occupancy from other factors that may influence nucleosome positioning. For both in vitro and in vivo systems, three parameters suffice to predict nucleosome occupancy with correlation coefficients of respectively 0.74 and 0.66. As predicted, we find the largest deviations in vivo around transcription start sites. This relatively simple algorithm can be used to guide future studies on the influence of DNA sequence on chromatin organization.

show abstract

“…In this regard, previous studies have shown that proper chromatin folding required the presence of the H4 Nterminal tail, and in particular residues 14-19 (Dorigo et al, 2003) and that K16 is intimately involved in regulating DNA topology (Chiani et al, 2006). Moreover, extensive studies of yeast silencing have shown a requirement for hypoacetylated K16 in heterochromatin formation and spreading of the Sir proteins (Braunstein et al, 1996;Grunstein, 1997).…”

Section: Histone H4 Lysine 16 Acetylationmentioning

confidence: 99%

NAD+-dependent deacetylation of H4 lysine 16 by class III HDACs

2007

View full text Add to dashboard Cite

Histone deacetylases (HDACs) catalyse the removal of acetyl groups from the N-terminal tails of histones. All known HDACs can be categorized into one of four classes (I-IV). The class III HDAC or silencing information regulator 2 (Sir2) family exhibits characteristics consistent with a distinctive role in regulation of chromatin structure. Accumulating data suggest that these deacetylases acquired new roles as genomic complexity increased, including deacetylation of non-histone proteins and functional diversification in mammals. However, the intrinsic regulation of chromatin structure in species as diverse as yeast and humans, underscores the pressure to conserve core functions of class III HDACs, which are also known as Sirtuins. One of the key factors that might have contributed to this preservation is the intimate relationship between some members of this group of proteins (SirT1, SirT2 and SirT3) and deacetylation of a specific residue in histone H4, lysine 16 (H4K16). Evidence accumulated over the years has uncovered a unique role for H4K16 in chromatin structure throughout eukaryotes. Here, we review the recent findings about the functional relationship between H4K16 and the Sir2 class of deacetylases and how that relationship might impact aging and diseases including cancer and diabetes.

show abstract

Chromatin Fiber Folding: Requirement for the Histone H4 N-terminal Tail

Cited by 495 publications

References 70 publications

A metastable structure for the compact 30‐nm chromatin fibre

A metastable structure for the compact 30‐nm chromatin fibre

Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy

NAD+-dependent deacetylation of H4 lysine 16 by class III HDACs

Contact Info

Product

Resources

About