The Non-histone Chromatin Protein HMG1 Protects Linker DNA on the Side Opposite to That Protected by Linker Histones

Abstract

Linker histones and HMG1/2 constitute the two major proteins that bind to linker DNA in chromatin. While the location of linker histones on the nucleosome has attracted considerable research effort, only a few studies have addressed the location of HMG1 in the particles. In this study, we use a procedure based on micrococcal nuclease digestion of reconstituted nucleosomal particles to which HMG1 has been bound, followed by analysis of the protected DNA by restriction nuclease digestion, to locate the HMG1 binding site. Nucleosomal particles were reconstituted on a 235-base pair DNA fragment, which is known to be a strong nucleosome positioning sequence. The results unequivocally show that HMG1 protects linker DNA on one side of the core particle. Importantly, and possibly of physiological relevance, the linker DNA site protected by HMG1 was located on the side opposite to that already shown to be protected by linker histone binding.Linker histones (H1, H5, and its cognates) and the nonhistone chromatin proteins HMG1 and HMG2 are the major proteins that bind to linker DNA between successive nucleosomes in the chromatin fiber (for recent reviews, See Refs. 1-4). The two proteins are believed to play roles in transcription regulation, the conventional view being that linker histones are general repressors of transcription, whereas HMG1/2 are considered general enhancers. Recent research shows that the situation is much more complex, and both proteins have been implicated in both positive and negative regulatory pathways (1-4). Exactly how the linker DNA binding proteins exert their regulatory function in transcription remains an enigma (e.g. Ref. 5). They may do so by affecting higher order chromatin structure; in addition, they may act at the level of individual nucleosomes, by creating particles of different stabilities and, hence, different accessibility to binding of general and genespecific transcription factors.The location of linker histones on the nucleosome has been studied for years, albeit with contradictory results (6). Recent studies performed on nucleosomes reconstituted on specific DNA fragments seem to indicate that the linker histone binds highly asymmetrically to the core particle, protecting linker DNA on only one side of the particle (7-9). The choice between two alternative binding sites is probably dictated by DNA sequences in the linker region (8). The location of HMG1, on the other hand, has been so far studied on reconstitutes on only one DNA sequence, the 5 S rDNA from Xenopus borealis (10,11). In this specific case, it was reported that HMG1 interacts with linker DNA in the same way as does histone H1, protecting ϳ5 bp 1 on one side of the nucleosome core and ϳ15 bp on the other side (10, 11).We have demonstrated recently that X. borealis 5 S DNA sequence is not suited for studies involving micrococcal nuclease (MNase) digestion, since results interpreted as "protection" by linker DNA-binding proteins could be obtained with naked DNA and with reconstituted core nucleosomes, in the absence...

HMGB1 in health and disease

“…These proteins share many features of DNA-binding behavior, although they are structurally unrelated (Zlatanova and van Holde, 1998b). An early study indicated that HMGB1 protects linker DNA on the side opposite to that protected by linker histones (An et al, 1998). We now know that they have opposing effects on nucleosome assembly and stability (Paull et al, 1993).…”

Yeast HMO1: Linker Histone Reinvented

“…Histone H1 binds linker DNA where it enters and exits the nucleosome ( Fig. 2) (23)(24)(25)(26). Unlike core histones, which have residency times on a time scale of hours, linker histones are quite mobile, with residency times being measured in minutes (16,27,28).…”

Functional interplay between histone H1 and HMG proteins in chromatin

“…Competition between HMGB1/-B2 proteins and linker histones for four-way junctions and cisplatin-modified DNA has been clearly demonstrated [41, 42]. Although their organization in isolated nucleosomes or in chromatin is not fully understood, HMGB1/B2 seems to preferentially bind to linker DNA at the entry/exit of nucleosomes, next to the nucleosome dyad axis [43, 44]. Since these are also major sites of H1-nucleosome interaction it is likely that this positional overlap plays an important role in the HMGB-H1 interplay in chromatin.…”