Distinctive sequence patterns in metazoan and yeast nucleosomes: Implications for linker histone binding to AT-rich and methylated DNA

193

223

The authors note that, due to a printer's error, references 41-50 appeared incorrectly. The corrected references follow. The authors note: "Our paper unfortunately missed reference to an earlier suggestion of the T6 structure (43). This work entitled 'A hypothetical dense 3,4-connected carbon net and related B 2 C and CN 2 nets built from 1,4-cyclohexadienoid units' by M. J. Bucknum and R. Hoffmann was published in J Am Chem Soc 116: 11456-11464 (1994), where the electronic structure of a hypothetical 3,4-connected tetragonal allotrope of carbon is discussed. The results in this article are consistent with what we find. The same group had also suggested a metallic carbon structure (44) that was published in J Am Chem Soc 105: 4831-4832 (1983), which we also missed to cite. We thank Prof. Hoffmann for bringing these papers to our attention."The complete references appear below. www.pnas.org/cgi

Section: Discussionsupporting

confidence: 87%

Section: Discussionsupporting

confidence: 69%

Section: Structural Insights Into the Histone H1-nucleosome Complexmentioning

confidence: 99%

See 1 more Smart Citation

Structural insights into the histone H1-nucleosome complex

Zhou

Feng

Kato

et al. 2013

193

223

“…Among the possible explanations are subtle differences in the sequences of the histone octamer between S. pombe and S. cerevisiae, potential differences in histone modifications between these species, or lack of the linker histone H1 in S. pombe. The linker histone H1 is known to seal the nucleosome entry/exit and to be associated with linker DNA (50)(51)(52)(53), and it prefers to bind A/T-rich DNA sequences (54,55). The nonclassical histone H1 gene in S. cerevisiae, Hho1p, plays a similar role in chromosome compaction and chromatin structure (56,57).…”

Section: Discussionmentioning

confidence: 99%

Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning

Moyle-Heyrman¹,

Zaichuk²,

et al. 2013

115

Using a recently developed chemical approach, we have generated a genome-wide map of nucleosomes in vivo in Schizosaccharomyces pombe (S. pombe) at base pair resolution. The shorter linker length previously identified in S. pombe is due to a preponderance of nucleosomes separated by ∼4/5 bp, placing nucleosomes on opposite faces of the DNA. The periodic dinucleotide feature thought to position nucleosomes is equally strong in exons as in introns, demonstrating that nucleosome positioning information can be superimposed on coding information. Unlike the case in Saccharomyces cerevisiae, A/T-rich sequences are enriched in S. pombe nucleosomes, particularly at ±20 bp around the dyad. This difference in nucleosome binding preference gives rise to a major distinction downstream of the transcription start site, where nucleosome phasing is highly predictable by A/T frequency in S. pombe but not in S. cerevisiae, suggesting that the genomes and DNA binding preferences of nucleosomes have coevolved in different species. The poly (dA-dT) tracts affect but do not deplete nucleosomes in S. pombe, and they prefer special rotational positions within the nucleosome, with longer tracts enriched in the 10-to 30-bp region from the dyad. S. pombe does not have a welldefined nucleosome-depleted region immediately upstream of most transcription start sites; instead, the −1 nucleosome is positioned with the expected spacing relative to the +1 nucleosome, and its occupancy is negatively correlated with gene expression. Although there is generally very good agreement between nucleosome maps generated by chemical cleavage and micrococcal nuclease digestion, the chemical map shows consistently higher nucleosome occupancy on DNA with high A/T content.chromatin structure | heterochromatin | gene regulation E ukaryotic DNA is organized into nucleosome arrays that facilitate proper genome compaction and regulation of the genetic information. Genome-wide nucleosome maps from different organisms have provided important insights into how nucleosome positioning regulates chromosome functions (1-6). It is commonly accepted that the DNA sequence itself plays a major role in the exact positions where histone octamers bind DNA to form nucleosomes (7-9). Most remarkably, nucleosomes prefer special dinucleotide motifs at specific rotational angles within the nucleosome core (10, 11) and disfavor poly (dA-dT) tracts (12-15). Although the ability of DNA to interact with the histone core is important, nucleosome occupancy is influenced by additional extrinsic factors, including species-specific DNA binding proteins (16), ATP-dependent remodeling complexes (17,18), and the transcription machinery (19)(20)(21)(22).The underlying mechanisms for the species-or cell typespecific nucleosome positioning features have not been well understood. The fission yeast Schizosaccharomyces pombe and the budding yeast Saccharomyces cerevisiae are two highly diverged model organisms widely used to study basic biological processes in eukaryotes (23). Although similar in siz...

“…This result, in light of the correlation between GapR ChIP-seq enrichment and local AT richness, suggests that the association of GapR with DNA is specified by local AT content rather than by an explicit consensus binding sequence. Indeed, DNA-associated proteins with generic affinity for AT-rich sequences have been described in various prokaryotic and eukaryotic organisms, including mammals (26)(27)(28)(29)(30)(31)(32).…”

Section: Gapr Is Essential For Normal Growth and Cell Division In Caumentioning

confidence: 99%

Cell cycle progression inCaulobacterrequires a nucleoid-associated protein with high AT sequence recognition

Ricci

Melfi

Lasker

et al. 2016

Faithful cell cycle progression in the dimorphic bacterium Caulobacter crescentus requires spatiotemporal regulation of gene expression and cell pole differentiation. We discovered an essential DNA-associated protein, GapR, that is required for Caulobacter growth and asymmetric division. GapR interacts with adenine and thymine (AT)-rich chromosomal loci, associates with the promoter regions of cell cycle-regulated genes, and shares hundreds of recognition sites in common with known master regulators of cell cycle-dependent gene expression. GapR target loci are especially enriched in binding sites for the transcription factors GcrA and CtrA and overlap with nearly all of the binding sites for MucR1, a regulator that controls the establishment of swarmer cell fate. Despite constitutive synthesis, GapR accumulates preferentially in the swarmer compartment of the predivisional cell. Homologs of GapR, which are ubiquitous among the α-proteobacteria and are encoded on multiple bacteriophage genomes, also accumulate in the predivisional cell swarmer compartment when expressed in Caulobacter. The Escherichia coli nucleoid-associated protein H-NS, like GapR, selectively associates with AT-rich DNA, yet it does not localize preferentially to the swarmer compartment when expressed exogenously in Caulobacter, suggesting that recognition of AT-rich DNA is not sufficient for the asymmetric accumulation of GapR. Further, GapR does not silence the expression of H-NS target genes when expressed in E. coli, suggesting that GapR and H-NS have distinct functions. We propose that Caulobacter has co-opted a nucleoid-associated protein with high AT recognition to serve as a mediator of cell cycle progression.