How Human H1 Histone Recognizes DNA.

Olesya P Luzhetskaya,Sergey E Sedykh,Georgy A Nevinsky

doi:10.3390/molecules25194556

Olesya P Luzhetskaya, Sergey E Sedykh + Show 1 more

Open Access

https://doi.org/10.3390/molecules25194556

Copy DOI

Abstract

Linker H1 histone is one of the five main histone proteins (H1, H2A, H2B, H3, and H4), which are components of chromatin in eukaryotic cells. Here we have analyzed the patterns of DNA recognition by free H1 histone using a stepwise increase of the ligand complexity method; the affinity of H1 histone for various single- and double-stranded oligonucleotides (d(pN)n; n = 1–20) was evaluated using their competition with 12-mer [32P]labeled oligonucleotide and protein–oligonucleotide complex delaying on nitrocellulose membrane filters. It was shown that minimal ligands of H1 histone (like other DNA-dependent proteins and enzymes) are different mononucleotides (dNMPs; Kd = (1.30 ± 0.2) × 10−2 M). An increase in the length of single-stranded (ss) homo- and hetero-oligonucleotides (d(pA)n, d(pT)n, d(pC)n, and d(pN)n with different bases) by one nucleotide link regardless of their bases, leads to a monotonic increase in their affinity by a factor of f = 3.0 ± 0.2. This factor f corresponds to the Kd value = 1/f characterizing the affinity of one nucleotide of different ss d(pN)n for H1 at n = 2–6 (which are covered by this protein globule) is approximately 0.33 ± 0.02 M. The affinity of five out of six DNA nucleotide units is approximately 25 times lower than for one of the links. The affinity of duplexes of complementary homo- and hetero-d(pN)20 is only 1.3–3.3-fold higher in comparison with corresponding ss oligonucleotides. H1 histone forms mainly weak additive contacts with internucleoside phosphate groups of ssDNAs and one chain of double-stranded DNAs, but not with the bases.

Highlights

Genetic information encoded in DNA is packed as chromatin in the cell nuclei, the diameters of which do not exceed 10 μm [1,2,3,4]
A very high affinity of enzymes and proteins for specific sequences or nucleotide units of extended DNAs can be dangerous for living organisms
If such a high affinity is provided by the interaction of enzymes with only specific modified nucleotide units, after their removal from DNA, enzymes could be significantly inhibited by free mononucleotides

Summary

Introduction

Genetic information encoded in DNA is packed as chromatin in the cell nuclei, the diameters of which do not exceed 10 μm [1,2,3,4]. The first stage of DNA compaction is interaction with histones, leading to the formation of nucleosomes, the structure of which, after their discovery in. 1974, remained unclear for a long time. The exact crystal structures were determined after 1997 by X-ray diffractometry and have long been regarded as basic conformational states [1,2,3,4]. The variety of allowed crystal structures of nucleosomes has increased the intensity study in this area and led to the development of the concept of the nucleosome as a dynamic unit [5]. The scientific interest is due to the fact that many mechanisms of gene regulation are realized at the nucleosomal level. A well-known example is the "nucleosomal barrier"—a mechanism that prevents RNA polymerase from accessing

Methods

Results

Discussion

Conclusion