Dinucleosome DNA of Human K562 Cells: Experimental and Computational Characterizations

Kato, Megumi; Onishi, Yoshiaki; Wada‐Kiyama, Yuko; Abe, Takashi; Ikemura, Toshimichi; Kogan, Simon; Bolshoy, Alexander; Trifonov, Edward N.; Kiyama, Ryoiti

doi:10.1016/s0022-2836(03)00838-6

Cited by 30 publications

(29 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The window size was set to 42 nucleotides (approximately 4 nucleosome DNA periods). This size corresponds to estimated earlier periodical segments of the nucleosome DNA patterns [Boffelli, De Santis et al 1991;Kato, Onishi et al 2003;Cohanim, Yechezkel et al 2004].…”

Section: Window Fourier Transformsupporting

confidence: 81%

“…The data indicate that while the nucleosome sequences of C. elegans are AA(TT) periodical, as well as of SV40 virus in an early work [Trifonov and Sussman 1980] and of S. cerevisiae , in more recent studies [Herzel, Weiss et al 1999;Tomita, Wada et al 1999;Cohanim, Yechezkel et al 2004], other organisms, like human and mouse, display nucleosome sequence periodicity in form of oscillating GG and CC, as well as AG(CT) dinucleotides in smaller proportions, see also [Kato, Onishi et al 2003]. …”

Section: Discussionmentioning

confidence: 93%

“…In our recent work with human nucleosome DNA sequences [Kato, Onishi et al 2003] the AA(TT) dinucleotides failed to show expected dominance, while RR(YY) dinucleotides as a group did display the periodicity. This points to possible speciesspecificity of the nucleosome sequence pattern.…”

Section: Species Specificity Of Rr(yy) Oscillationsmentioning

confidence: 96%

“…1 are marked. The window center position was fixed for certainty at 40 nucleotides from splice junction, to span altogether 122 bases that is close to the estimated nucleosome core DNA size, 125 nucleotides [Kato, Onishi et al 2003, and references therein].…”

Section: Dinucleotide Periodicity In the Vicinity Of Splice Sitementioning

confidence: 99%

“…Nucleosome DNA has been shown to display AA(TT) and, more generally, RR(YY) dinucleotide periodicity with the period close to the pitch of the DNA double helix [Trifonov and Sussman 1980;Mengeritsky and Trifonov 1983;Uberbacher, Harp et al 1988;Kato, Onishi et al 2003]. The dinucleotide distribution obtained by alignment of 4000 splice site sequences [Denisov, Shpigelman et al 1997] did not show the periodicity, apparently, because of the small size of the data set.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Gene splice sites correlate with nucleosome positions

Kogan

Trifonov

2005

Gene

Self Cite

View full text Add to dashboard Cite

Gene sequences in the vicinity of splice sites are found to possess dinucleotide periodicities, especially RR and YY, with the period close to the pitch of nucleosome DNA. This confirms previously reported finding about preferential positioning of splice junctions within the nucleosomes. The RR and YY dinucleotides oscillate counterphase, i.e., their respective preferred positions are shifted about half-period one from another, as it was observed earlier for AA and TT dinucleotides. Species specificity of nucleosome positioning DNA pattern is indicated by predominant use of the periodical GG(CC) dinucleotides in human and mouse genes, as opposed to predominant AA(TT) dinucleotides in Arabidopsis and C.elegans.

show abstract

Section: Window Fourier Transformsupporting

confidence: 81%

Section: Discussionmentioning

confidence: 93%

Section: Species Specificity Of Rr(yy) Oscillationsmentioning

confidence: 96%

Section: Dinucleotide Periodicity In the Vicinity Of Splice Sitementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Gene splice sites correlate with nucleosome positions

Kogan

Trifonov

2005

Gene

Self Cite

View full text Add to dashboard Cite

show abstract

A Conserved Regulatory Element in the Mammalian β-Globin Promoters

Kiyama

Wada‐Kiyama

2011

J Mol Evol

View full text Add to dashboard Cite

We provide here evidence for a conserved regulatory element for transcription of the β-family globin genes based on a comparative study of 32 genes from 16 mammals. The element is characterized by the appearance of AA or TT dinucleotides in the A + T-rich region located 200-400 bp upstream of the cap sites. G-tracts 3-5 nucleotides long exist between the A + T-rich region and the conserved transcription factor binding sites (GATA-1 site and the CACCC, CCAAT, and ATA boxes) apparently dividing the regions. The average periodicity of AA or TT dinucleotides in the region from a total of 18 β-family globin genes from four species was approximately 10 bp, suggesting that the DNA in these regions shows right-handed superhelicity. The proposed biological function of this element is to adjust the spatial positions for the first interaction of the transcription factor(s) which can recognize specific DNA sequences in the presence of packed chromatin.

show abstract

The Cooperative Assembly of IFI16 Filaments on dsDNA Provides Insights into Host Defense Strategy

Sohn

Morrone

Wang

et al. 2015

Biophysical Journal

View full text Add to dashboard Cite

Whether host DNA-receptors have any capacity to distinguish self from nonself at the molecular level is one of the foremost questions in the innate immunity of mammals. By using quantitative assays and electron microscopy, we show that cooperatively assembling into filaments on dsDNA may serve an integral mechanism by which human interferon inducible protein 16 (IFI16) engages foreign DNA. IFI16 is essential for defense against a number of different pathogens, and its aberrant activity is also implicated in several autoimmune disorders such as Sjögren's syndrome. IFI16 cooperatively binds dsDNA in a length-dependent manner and clusters into distinct protein filaments even in the presence of excess dsDNA. Consequently, the assembled IFI16dsDNA oligomers are clearly different from the previously proposed noninteracting entities resembling beads on a string. The isolated DNAbinding domains of IFI16 engage dsDNA without forming filaments and with weak affinity, and it is the non-DNA binding pyrin domain (PYD) of IFI16 that drives the cooperative filament assembly. The surface residues on the PYD that mediate the cooperative DNA-binding are conserved, suggesting that related receptors use a common mechanism. These results suggest that IFI16 clusters into signaling complexes in a switch-like manner, and that it may use the size of naked dsDNA as molecular ruler to distinguish self from nonself. Gram-negative pathogenic bacteria, like Salmonella typhimurium and Shigella flexneri, employ the Type III Secretion System (T3SS) to infect human cells. The T3SS is a large protein secretion channel that assembles to span ã 50nm gap between the bacterial and target cell walls. A key component of the S. typhimurium SPI-1 T3SS is the 80 residue needle subunit PrgI which polymerizes to form a 25 Å wide channel through which proteins are transported. During needle assembly, the PrgI subunits pass through the nascent channel before attaching to the tip. We have studied the mechanism of PrgI transport using near-atomistic molecular dynamics simulations. We found that the channel's inward facing amino acids and its helical symmetry direct PrgI diffusion along a helical pathway (the iþ1 crystallographic axis) with 2.4nm axial displacement per 360 degrees rotation. In vivo assays have shown that mutations of channel residues inhibit the subunit secretion required for needle self-assembly. Our combined studies evidence that the channel surface plays an active role in substrate secretion, rather than being a passive corridor for linear diffusion. Our evidence of rotation-translation coupling suggests the that the T3S needle might rotate during effector secretion. 195-PlatUnraveling the Link between Nonlinear Mechanics, Microstructure, and Molecular Packing of Fibrin When we cut ourselves, our body's immediate response is to stop the bleeding by repairing the damage to the wall of the blood vessel_forming a ''blood clot''. This is physically carried out by forming a network of semiflexible fibrin fibers, which bind together red blood cells ...

show abstract

Dinucleosome DNA of Human K562 Cells: Experimental and Computational Characterizations

Cited by 30 publications

References 43 publications

Gene splice sites correlate with nucleosome positions

Gene splice sites correlate with nucleosome positions

A Conserved Regulatory Element in the Mammalian β-Globin Promoters

The Cooperative Assembly of IFI16 Filaments on dsDNA Provides Insights into Host Defense Strategy

Contact Info

Product

Resources

About