Effects of histone acetylation on the equilibrium accessibility of nucleosomal DNA target sites 1 1Edited by R. Ebright

Intrinsically disordered proteins (IDP) are a broad class of proteins with relatively flat energy landscapes showing a high level of functional promiscuity, which are frequently regulated through posttranslational covalent modifications. Histone tails, which are the terminal segments of the histone proteins, are prominent IDPs that are implicated in a variety of signaling processes, which control chromatin organization and dynamics. Although a large body of work has been done on elucidating the roles of posttranslational modifications in functional regulation of IDPs, molecular mechanisms behind the observed behaviors are not fully understood. Using extensive atomistic molecular dynamics simulations, we found in this work that H4 tail mono-acetylation at LYS-16, which is a key covalent modification, induces a significant reorganization of the tail's conformational landscape, inducing partial ordering and enhancing the propensity for alpha-helical segments. Furthermore, our calculations of the potentials of mean force between the H4 tail and a DNA fragment indicate that contrary to the expectations based on simple electrostatic reasoning, the Lys-16 monoacetylated H4 tail binds to DNA stronger than the unacetylated protein. Based on these results, we propose a molecular mechanism for the way Lys-16 acetylation might lead to experimentally observed disruption of compact chromatin fibers.histone tails | atomistic simulations | polyelectrolytes

supporting

confidence: 67%

Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation

Potoyan

Papoian

2012

“…The RNA polymerase II motor also is expected to be capable of generating forces that overcome obstacles during translocation and is thus a source of peeling force for nucleosomal invasion. The destabilization of chromatin structure and subsequent increase in polymerase access achieved by covalent modifications such as acetylation has been documented (23,24). Chromatinremodeling machines like SWI͞SNF, whose motor subunits are members of the helicase family of proteins, are known to modify the structure of nucleosomes by perturbing DNA-protein interactions and by inducing topological changes in nucleosomal DNA that are conducive to transcriptional activation (25,26).…”

Section: Resultsmentioning

confidence: 99%

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA

Brower-Toland

Smith

Yeh

et al. 2002

452

465

The dynamic structure of individual nucleosomes was examined by stretching nucleosomal arrays with a feedback-enhanced optical trap. Forced disassembly of each nucleosome occurred in three stages. Analysis of the data using a simple worm-like chain model yields 76 bp of DNA released from the histone core at low stretching force. Subsequently, 80 bp are released at higher forces in two stages: full extension of DNA with histones bound, followed by detachment of histones. When arrays were relaxed before the dissociated state was reached, nucleosomes were able to reassemble and to repeat the disassembly process. The kinetic parameters for nucleosome disassembly also have been determined.

“…5 and 6). Generally, DNA is more accessible to restriction enzymes in unfolded (open) chromatin (39,40). EcoRI digestion of nuclei, combined with psoralen as a probe for chromatin structure, indicates that rDNA becomes less accessible to EcoRI during early repair times (up to 1 h) and more accessible at later repair times (2-4 h) (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…5B). Because nucleosomes are an impediment to restriction enzyme accessibility (39,40), only the active rDNA (s-band) is released (Fig. 5B, lanes 3-8).…”

Section: Release Of Active Ribosomal Genes By Ecori Digestion Of Nucleimentioning

confidence: 99%

Transcription-coupled repair in RNA polymerase I-transcribed genes of yeast

Conconi

Bespalov

Smerdon

2002

Nucleotide excision repair (NER) of UV-induced cyclobutane pyrimidine dimers (CPDs) was measured in the individual strands of transcriptionally active and inactive ribosomal genes of yeast. Ribosomal genes (rDNA) are present in multiple copies, but only a fraction of them is actively transcribed. Restriction enzyme digestion was used to specifically release the transcriptionally active fraction from yeast nuclei, and selective psoralen crosslinking was used to distinguish between active and inactive rDNA chromatin. Removal of CPDs was followed in both rDNA populations, and the data clearly show that strand-specific repair occurs in transcriptionally active rDNA while being absent in the inactive rDNA fraction. Thus, transcription-coupled repair occurs in RNA polymerase I-transcribed genes in yeast. Moreover, the nontranscribed strand of active rDNA is repaired faster than either strand of inactive rDNA, implying that NER has preferred access to the active, non-nucleosomal rDNA chromatin. Finally, restriction enzyme accessibility to active rDNA varies during NER, suggesting that there is a change in ribosomal gene chromatin structure during or soon after CPD removal. N ucleotide excision repair (NER) removes different types of lesions from DNA, including bulky adducts caused by chemicals, interstrand or intrastrand crosslinks, and the UV photoproducts cis-syn cyclobutane pyrimidine dimer (CPD) and pyrimidine (6-4) pyrimidone (1). If DNA lesions are not removed, mutations can occur after translesion replication (2). It is now well established that many transcriptionally active genes are repaired faster than inactive DNA (3, 4). Furthermore, preferential removal of CPDs from active genes is caused mainly by an increased rate of repair of the transcribed strand (TS). This transcription-coupled repair (TCR) was first discovered in mammalian cells (5), then in Escherichia coli (6) and yeast (7). Elongation by RNA polymerase II (pol II) is required for TCR (8, 9), and it is thought that only pol II-transcribed genes are subject to TCR (10).RNA polymerase I (pol I) transcribes ribosomal genes (rDNA) at a very high rate. The rDNA is localized in the nucleolus, which is a dense chromatin region composed of rDNA, pol I, rRNA, assembling ribosomes, and proteins involved in cell-cycle regulation (11,12). It is known that mammalian cells repair rDNA damaged by UV radiation (13) and chemicals (14-16). However, in rodent and human cells, CPDs are less efficiently repaired in rDNA than in either total genomic DNA or pol II-transcribed genes (16)(17)(18)(19)(20). Moreover, DNA repair does not exhibit strand bias in the rDNA of these cells (17,19). To the contrary, CPDs are rapidly removed from both strands of total rDNA in yeast (21,22). In addition, a strand bias during repair of total rDNA was observed in rad7 and rad16 mutants, even though strand-specific repair was not observed in total rDNA of wild-type cells (21).Ribosomal genes are present in multiple copies organized in long tandem repeats (11), and in most cells only a f...