Histone H1 Binds to the Putative Nuclear Factor I Recognition Sequence in the Mouse α2(I) Collagen Promoter

The COL5A1 gene and Achilles tendon pathology

PURPOSE

There is an increase in the incidence of Achilles tendon injuries as a result of the participation in physical activity. It has been suggested that some individuals have a genetic predisposition to Achilles tendon pathology (ATP). The aim of this study was to determine whether the alpha 1 type V collagen (COL5A1) gene, which encodes for a tendon protein, is associated with the symptoms of ATP.

METHODS

One-hundred and eleven Caucasian subjects diagnosed with ATP and 129 Caucasian control (CON) subjects were genotyped for the BstUI and DpnII restriction fragment length polymorphisms (RFLPs) within the COL5A1 gene.

RESULTS

There was a significant difference in the allele frequencies of the COL5A1 BstUI RFLP between the ATP and CON subjects (P=0.006). The frequency of the A2 allele was significantly higher in the CON group (29.8%) than in the ATP group (18.0%) (odds ratio of 1.9; 95% confidence interval (CI) 1.3-3.0; P=0.004). This allele had a stronger protective role when only the 72 patients diagnosed with chronic Achilles tendinopathy were analyzed (odds ratio of 2.6; 95% CI 1.5-4.5).

CONCLUSIONS

The COL5A1 BstUI RFLP is associated with ATP and more specifically, chronic Achilles tendinopathy. Individuals with an A2 allele of this gene are less likely of developing symptoms of chronic Achilles tendinopathy.

Histone H1–like protein participates in endothelial cell–specific activation of the von Willebrand factor promoter

A region of the von Willebrand factor (VWF) promoter has been identified that is necessary to confer endothelial cell-specific activation to the VWF promoter. This region spans sequences +155 to +247 and contains binding sites for GATA6 and NFY transcription factors. To identify potential DNA binding transcription factors that directly interact with these sequences in an endothelial-specific manner, we have performed extensive gel mobility assays with use of 7 overlapping DNA probes that collectively span this entire region. An endothelial-specific protein DNA complex was formed with an oligonucleotide that corresponded to sequences +155 to +184 of the VWF gene. Mutation analysis identified a 6-nucleotide element corresponding to sequences +164 to +169 as the core-binding region for the formation of this complex. Transfection analysis demonstrated that the mutation, which abolished DNA-protein interaction, resulted in significant inhibition of the VWF promoter activity. DNA pull-down analysis, mass spectrometry, and Western blot analysis demonstrated that a 32-kDa polypeptide with homology to histone H1 constituted the endothelial-specific DNA binding protein, or a DNA binding subunit of this protein complex. On the basis of these results, we hypothesize that an H1-like protein functions as an endothelial cell-specific transcriptional activator of the VWF promoter. (Blood. 2004;104: 1725-1732)

Roles of the NFI/CTF gene family in transcription and development

The Nuclear Factor I (NFI) family of site-specific DNA-binding proteins (also known as CTF or CAAT box transcription factor) functions both in viral DNA replication and in the regulation of gene expression. The classes of genes whose expression is modulated by NFI include those that are ubiquitously expressed, as well as those that are hormonally, nutritionally, and developmentally regulated. The NFI family is composed of four members in vertebrates (NFI-A, NFI-B, NFI-C and NFI-X), and the four NFI genes are expressed in unique, but overlapping, patterns during mouse embryogenesis and in the adult. Transcripts of each NFI gene are differentially spliced, yielding as many as nine distinct proteins from a single gene. Products of the four NFI genes differ in their abilities to either activate or repress transcription, likely through fundamentally different mechanisms. Here, we will review the properties of the NFI genes and proteins and their known functions in gene expression and development.

Acetaldehyde-mediated collagen regulation in hepatic stellate cells

Alcohol-induced liver cirrhosis is one of the major causes of death worldwide. Strong evidence has established that ethanol's first metabolite, acetaldehyde, is highly fibrogenic and enhances the deposition of many extracellular matrix components by hepatic stellate cells. This article reviews our current knowledge of the molecular mechanisms whereby acetaldehyde induces these activities, with particular emphasis on those related to the upregulation of type I collagen.

Specific binding of glucosaminylmuramyl peptides to histones

Intracellular N-acetylglucosaminylmuramyl peptide-binding proteins of murine macrophages and myelomonocytic WEHI-3 cells were characterized. SDS-PAGE and Western blotting revealed proteins with molecular masses of 18, 32 and 34 kDa retaining the ability to specifically bind glucosaminylmuramyl dipeptide. The inhibition analysis demonstrated that only biologically active muramyl peptides but not inactive analogs or fragments of glucosaminylmuramyl dipeptide could inhibit glucosaminylmuramyl dipeptide-binding to these proteins. Purification of these proteins and sequencing of peptides obtained after in-gel trypsin digestion enabled us to identify the above mentioned proteins as histones H1 and H3. These findings suggest that nuclear histones might be target molecules for muramyl peptides.

A transient increase in c-myc precedes the transdifferentiation of hepatic stellate cells to myofibroblast-like cells

AIMS/BACKGROUND

Liver stellate cells are transdifferentiated to collagen-producing myofibroblast-like cells in vivo during liver injury or when placed in culture. The purpose of this study was to determine the presence of retinoids and the expression of the immediate early genes as they relate to the transdifferentiation of liver stellate cells in culture.

METHODS

Rat liver stellate cells were studied immediately after isolation or sequentially after culture for varying periods of time. RNA was isolated and specific messages were determined by RT-PCR. Cells were also isolated for determination of retinoid autofluorescence and immunofluorescent staining with specific antibodies by laser confocal microscopy.

RESULTS

c-fos message and immunoprotein were high in the freshly isolated cells prior to culture, while c-myc expression increased markedly after one day of culture. Both c-fos and c-myc gene expression decreased prior to the transdifferentiation of the cells to myofibroblast-like cells and to the increase in alpha 1(I) and alpha 2(I) collagen messages and collagen production. The presence of retinoid autofluorescence and retinoic acid receptor (RAR-alpha and RAR-beta) messages and RAR-beta immunoprotein persisted during initial transdifferentiation of the stellate cells.

CONCLUSIONS

This study shows a high initial level of c-fos expression and a transient increase in c-myc expression followed by a decrease to lower levels prior to transdifferentiation and collagen production by stellate cells. A total loss of retinoid autofluorescence or a decrease in RAR-alpha or RAR-beta are not required for initial transdifferentiation of stellate cells or collagen production.

Assembly of MMTV promoter minichromosomes with positioned nucleosomes precludes NF1 access but not restriction enzyme cleavage

To generate long arrays of nucleosomes within a topologically defined chromatin domain we have assembled minichromosomes on negatively supercoiled plasmid DNA with extracts from Drosophila preblastoderm embryos. These minichromosomes are dynamic substrates for energy-dependent nucleosome remodeling machines that facilitate the binding of various transcription factors but do not exhibit nucleosome positioning. In contrast, if such minichromosomes include the mouse mammary tumour virus (MMTV) promoter we find it wrapped around a nucleosome with similar translational and rotational position as in vivo . This structure precluded binding of NF1 to its cognate site at -75/-65 at salt concentrations between 60 and 120 mM, even in the presence of ATP, which rendered the NF1 site accessible to the restriction enzyme Hin fI. However, insertion of 30 bp just upstream of the NF1 site, which moves the site to the linker DNA, allowed ATP-dependent binding of NF1 to a fraction of the minichromosomes, even in the presence ofstoichiometric amounts of histone H1. The minichromosomes assembled in the Drosophila embryo extract reproduce important features of the native MMTV promoter chromatin and reveal differences in the ability of transcription factors and restriction enzymes to access their binding sites in positioned nucleosomes.

Transforming growth factor-beta 1 regulation of bone sialoprotein gene transcription: identification of a TGF-beta activation element in the rat BSP gene promoter

Transforming growth factor-beta (TGF-beta) increases steady-state mRNA levels of several extracellular matrix proteins in mineralized connective tissues. Bone sialoprotein (BSP) is a major constituent of the bone matrix, thought to initiate and regulate the formation of mineral crystals. To determine the molecular pathways of TGF-beta 1 regulation of bone proteins, we have analyzed the effects of the TGF-beta 1 on the expression of the BSP in the rat osteosarcoma cell line (ROS 17/2.8). TGF-beta 1 at 1 ng/ml, increased BSP mRNA levels in ROS 17/2.8 cells approximately 8-fold: the stimulation was first evident at 3 hr, reached maximal levels at 12 hr and slowly declined thereafter. Since the stability of the BSP mRNA was not significantly affected by TGF-beta 1, and nuclear "run-on" transcription analyses revealed only a approximately 2-fold increase in the transcription of the BSP gene, most of the increase in BSP mRNA appeared to involve a nuclear post-transcriptional mechanism. Moreover, the effects of TGF-beta 1 were indirect, since the increase in BSP mRNA was abrogated by cycloheximide (28 micrograms/ml). To identify the site of transcriptional regulation by TGF-beta 1, transient transfection analyses were performed using BSP gene promoter constructs linked to a luciferase reporter gene. Constructs that included nt -801 to -426 of the promoter sequence were found to enhance transcriptional activity approximately 1.8-fold in cells treated with TGF-beta 1. Within this sequence, approximately 500 nt upstream of the transcription start site, a putative TGF-beta activation element (TAE) was identified that contained the 5'-portion of the nuclear factor-1 (NF-1) canonical sequence (TTGGC) overlapping a consensus sequence for activator protein-2 (AP-2). The functionality of the TAE was shown by an increased binding of a nuclear protein from TGF-beta 1 stimulated cells in gel mobility shift assays and from the attenuation of TGF-beta 1-induced luciferase activity when cells were co-transfected with a double-stranded TAE oligonucleotide. Competition gel mobility shift analyses revealed that the nuclear protein that binds to the TAE has similar properties to, but is distinct from, NF-1 nuclear protein. These studies have therefore identified a TGF-beta activation element (TAE) in the rat BSP gene promoter that mediates the stimulatory effects of TGF-beta 1 on BSP gene transcription.

A mouse histone H1 variant, H1b, binds preferentially to a regulatory sequence within a mouse H3.2 replication-dependent histone gene

H1 histones, found in all multicellular eukaryotes, associate with linker DNA between adjacent nucleosomes, presumably to keep the chromatin in a compact, helical state. The identification of multiple histone H1 subtypes in vertebrates suggests these proteins have specialized roles in chromatin organization and thus influence the regulation of gene expression in the multicellular organism. The mechanism by which the association of H1 with nucleosomal DNA is regulated is not completely understood, but affinity for different DNA sequences may play a role. Here we report that a specific H1 subtype in the mouse, namely H1b, selectively binds to a regulatory element within the protein-encoding sequence of a replication-dependent mouse H3.2 gene. We have previously shown that this coding region element, Omega, is the target of very specific interactions in vitro with another nuclear factor called the Omega factor. This element is required for normal gene expression in stably transfected rodent cells. The mouse H1b protein interacts poorly (100-fold lower affinity) with the comparable "Omega" sequence of a replication-independent mouse H3.3 gene. This H3.3 sequence differs at only 4 out of 22 nucleotide positions from the H3.2 sequence. Our findings raise the possibility that this H1b protein plays a specific role in regulation of expression of the replication-dependent histone gene family.

Nucleotide and calcium-induced conformational changes in histone H1

The principal constituents of chromatin, histone H1 (H1) and the nucleosome have essential roles in regulation of eukaryotic gene expression. However, mechanisms for the H1-dependent inactivation and for the ATP-dependent chromatin remodeling upon activation are largely unelucidated. Using circular dichroism (CD) analysis we show that ATP and other nucleotides and Ca2+ induce structural changes in H1. ATP and Ca2+ also induce changes when H1 is interacting with DNA, and the changes in H1 are accompanied by alterations in its DNA interaction. These results suggest that nucleotide and Ca2+ binding may be important for H1-mediated chromatin changes.

An NF1-like protein functions as a repressor of the von Willebrand factor promoter

The expression of the von Willebrand factor (vWf) gene is restricted to endothelial cells and megakaryocytes. We have previously reported the identification of a region of the vWf gene that regulates its cell-type-specific expression in cell culture. This region (spanning nucleotides -487 to +247) consists of a core promoter (spanning nucleotides -90 to +22), a positive regulatory region (spanning nucleotides +155 to +247), and a negative regulatory region spanning nucleotides -312 to -487. To identify the trans-acting factor(s) that interacts with the negative regulatory region, we carried out gel mobility and DNase1 footprint analyses of sequences -312 to -487. These analyses demonstrated that an NF1-like protein interacts with DNA sequences spanning -440 to -470 nucleotides in the negative regulatory region of the vWf promoter. Base substitution mutations of the NF1 binding site abolished the NF1-DNA interaction. Furthermore, mutation of the NF1 binding site in the promoter fragment (-487 to +155) that contained the core and the negative regulatory region resulted in activation of the mutant promoter in both endothelial and nonendothelial cells. The wild type promoter fragment (-487 to +155) was not activated in either cell type. These results demonstrate that an NF1-like protein functions as a repressor of vWf promoter activity. In contrast, the mutation of the same NF1 binding site, but now in the context of the larger 734-base pair endothelial cell-specific promoter fragment (-487 to +247), did not result in promoter activation in nonendothelial cells. The data indicate that there are additional repressor elements within the vWf promoter region suppressing its activity specifically, in nonendothelial cells, and suggest that there is a secondary repressor element(s) that is located in the terminal region of the first exon of this gene.

Involvement of a protein distinct from transcription enhancer factor-1 (TEF-1) in mediating human chorionic somatomammotropin gene enhancer function through the GT-IIC enhanson in choriocarcinoma and COS cells

Previous studies suggested that transcription enhancer factor-1 (TEF-1) was involved in mediating the human chorionic somatomammotropin (hCS) gene enhancer (CSEn) function (Jiang, S.-W., and Eberhardt, N. L. (1994) J. Biol. Chem. 269, 10384-10392). We now show that an unrelated protein (CSEF-1) found in BeWo and COS-1 cells binds to the GT-IIC enhanson in CSEn and is correlated with CSEn activity in these cells. TEF-1 and CSEF-1 were distinguished by differential migration as GT-IIC complexes, thermal stability, molecular mass, and cross-reactivity with chicken TEF-1 antibodies. TEF-1 and CSEF-1 bound to the GT-IIC and Sph-I/Sph-II enhansons with identical binding properties, and in vitro generated TEF-1 competed with CSEF-1 binding to the GT-IIC motif, suggesting that their actions might be mutually exclusive. Up- and down-regulation of TEF-1 levels by expression systems and antisense oligonucleotides demonstrated that TEF-1 inhibited the hCS promoter in a manner independent of the enhancer or a known TEF-1 DNA binding site. The data suggest that TEF-1 may provide a counter-regulatory stimulus to the actions of CSEF-1, which may be involved in mediating enhancer stimulatory activity.

Acetaldehyde activates the promoter of the mouse alpha 2(I) collagen gene

The mechanism whereby ethanol ingestion results in hepatic fibrosis remains unknown. Acetaldehyde has been shown to increase alpha 1(I) collagen gene transcription in human fibroblasts and in rat myofibroblastlike cells (Ito cells) in culture. In this study, the effect of acetaldehyde was determined on the activation of the alpha 2(I) collagen promoter. A plasmid containing the mouse alpha 2(I) collagen promoter region (-2000 to 54), fused to the coding sequence of the reporter gene chloramphenicol acetyl transferase and similar plasmid constructs containing deletions in the collagen promoter, were transfected into NIH 3T3 fibroblasts in culture. Acetaldehyde (200 mumol/L) and transforming growth factor-beta 1 (5 ng/ml) activated the wild type promoter. The combination of acetaldehyde and transforming growth factor-beta 1 did not result in a greater effect than either alone. Acetaldehyde inhibited, whereas transforming growth factor-beta 1 did not activate, the promoter, with a -352 to -104 deletion. By contrast, acetaldehyde had no effect, whereas transforming growth factor-beta 1 resulted in a small decrease in the activity of the promoter, with a -501 to -352 deletion. This study shows that acetaldehyde and transforming growth factor-beta 1 independently activate the mouse alpha 2(I) collagen promoter and that this activation is mediated by the same proximal region of the promoter.

Ethanol increases ADP-ribosylation of histones in rat hepatocyte nuclei

Ethanol was shown previously to increase ADP-ribosylation of hepatocyte proteins. The purpose of this study was to determine the effect of ethanol on ADP-ribosylation of histones in hepatocyte nuclei. Freshly isolated hepatocytes were exposed to 100 mM ethanol for 2 h and ADP-ribosylated histones were separated from nonribosylated histones by phenylboronate agarose chromatography. Both histone factions were then separated into the individual histones by 12% acetic-urea-triton polyacrylamide gel electrophoresis. Ethanol did not change the amounts of outer histone H1 or amounts of core histones (H2A, H2B, H3.1, and H4) but increased the histone variants H3.2 and H3.3. The principal effect of ethanol was to increase the ADP-ribosylation of all the above histones. Exposure of hepatocytes in culture to 100 mM ethanol for 3 days did not increase the synthesis of histones as determined by the incorporation of 14C-L-lysine, but increased the ADP-ribosylation of histones, principally histone H2A, determined from the incorporation of 2, 8, 3H adenosine. These results show that ethanol increases the ADP-ribosylation of histones. This is a potential mechanism for effects of ethanol on the regulation of gene expression and cell differentiation.

Specific non-enzymatic glycation of the rat histone H1 nucleotide binding site in vitro in the presence of AlF4-. A putative mechanism for impaired chromatin function

We show here that an aluminium derivative, AlF4-, stimulates glycation of histone H1 selectively in the proximity of its nucleotide-binding site. This adduct formation interferes with nucleoside triphosphate hydrolysis by H1 and with nucleotide modulation of H1 DNA binding. The present mode of aluminium action may in part be responsible for its effects on the chromatin structure and expression of tissue-specific genes, and may constitute a mechanism in the pathogenesis of aluminium-induced encephalopathy and in that of Alzheimer's disease, for example.

Does histone H1 bind specifically to the nuclear factor I recognition sequence?

The issue of whether histone H1 possesses specificity of binding to certain nucleotide sequences in DNA is of fundamental importance to the suggested role of the linker histone in the regulation of gene transcription. The purpose of the present study was to reinvestigate the specificity of binding of histone H1 to the putative nuclear factor I (NFI) recognition sequence suggested by a previous report in the literature. The interaction of purified mouse liver histone H1 with a synthetic oligonucleotide representing the natural NFI binding site from the adenovirus 2 origin of replication cloned in pBR322 has been studied by filter binding and a solid-phase procedure performed on nitrocellulose filter-immobilized protein dots. No indication of specific interactions of the lysine-rich histone H1 with the NFI recognition sequence was obtained.

DNA binding of histone H1 is modulated by nucleotides

Histone H1 acts as a general repressor of transcription in eukaryotes by organizing nucleosomes into inaccessible condensed forms of chromatin. The capability of H1 to bind to DNA with some sequence specificity is likely to be critical in the control of these processes. We show here that ATP and several other nucleotides, including non-hydrolyzable derivatives, can inhibit DNA binding of H1. The results also show that ATP differentially affects binding of H1 to DNA in a fashion enhancing nucleotide sequence specificity of the binding. The study suggests a novel mechanism of modulation of H1 activity that has important implications for the role of H1 as a transcriptional regulator.

Homeotic protein binding sites, origins of replication, and nuclear matrix anchorage sites share the ATTA and ATTTA motifs

Nuclear matrix organizes the mammalian chromatin into loops. This is achieved by binding of nuclear matrix proteins to characteristic DNA landmarks in introns as well as proximal and distal sites flanking the 5' and 3' ends of genes. Matrix anchorage sites (MARs), origins of replication (ORIs), and homeotic protein binding sites share common DNA sequence motifs. In particular, the ATTA and ATTTA motifs, which constitute the core elements recognized by the homeobox domain from species as divergent as flies and humans, are frequently occurring in the matrix attachment sites of several genes. The human apolipoprotein B 3' MAR and a stretch of the Chinese hamster DHFR gene intron and human HPRT gene intron shown to anchor these genes to the nuclear matrix are mosaics of ATTA and ATTTA motifs. Several origins of replication also share these elements. This observation suggests that homeotic proteins which control the expression level of many genes and pattern formation during development are components of the nuclear matrix. Thus, the nuclear matrix, known as the site of DNA replication, might sculpture the crossroads of the differential activation of origins during development and S-phase and the control of gene expression and pattern formation in embryogenesis.

Induction of fibronectin gene expression by transforming growth factor beta-1 is attenuated in bronchial epithelial cells by ADP-ribosyltransferase inhibitors

Transforming growth factor-beta (TGF-beta) exerts several effects on cultured airway epithelial cells including inhibition of proliferation and stimulation of fibronectin gene expression. ADP-ribosylation is one potential regulatory mechanism of gene expression by TGF-beta. We tested this possibility by exposing cultured bovine bronchial epithelial cells to the chemical inhibitor of ADP-ribosyl transferase enzymes, 3-aminobenzamide (3-AB) and, for comparison, 3-aminobenzoic acid (3-ABA), which is structurally similar to 3-AB but which does not inhibit ADP-ribosyl transferases. Exponential cell growth rate (1.2 doublings/day) or cellular morphology observed by phase contrast microscopy were not affected by 3 mM 3-AB or 3-ABA. Neither compound antagonized inhibition of cell division or induction of squamous morphology by TGF-beta 1. In contrast, the sixfold stimulation of fibronectin production by exposure of cells to 30 pM TGF-beta 1 for 48 h was reduced by 50% in the presence of 3 mM 3-AB, whereas 3 mM 3-ABA had no effect. The antagonistic effect was augmented by administration of 3-AB 24 h prior to induction by TGF-beta 1. Northern blot hybridization analyses demonstrated that 3-AB, but not 3-ABA, attenuated the induction of fibronectin mRNA by TGF-beta 1 by up to 50%. These observations may implicate a role of cellular ADP-ribosylation in the regulation of some gene expression by TGF-beta.

Histone H1 interacts specifically with certain regions of the mouse alpha-globin gene

We used fragments of a cloned mouse alpha-globin gene to determine if histone H1 interacts selectively with defined regions of a eukaryotic gene. The use of intact plasmids instead of isolated fragments permitted study of relevant sequences in their superhelical form. Several independent experimental approaches (filter binding, precipitation, binding to protein immobilized on nitrocellulose membranes, and agarose gel electrophoresis of the protein-DNA complexes) were used and the histone-DNA interaction was investigated under both noncompetitive and competitive conditions. Binding to subclones encompassing the 5' end of the gene and the first half of the coding sequence is preferred over binding to other subclones. The expression of the sequence-specific selectivity depends on the ionic strength of the binding reaction; the selectivity is mainly expressed under conditions of non-cooperative binding of the histone to DNA. No correlation is observed between AT content and relative affinity of binding to H1. Evidently, other features of DNA structure are involved in the specific H1 binding.

Nucleoside triphosphate binding and hydrolysis by histone H1

We present here further evidence supporting that histone H1 contains a nucleotide binding site interacting e.g. with ADP, ATP, GDP and GTP. The finding is in accordance with the previous observation that nucleotides modulate recognition of DNA by H1. Most interestingly, H1 appears to be capable of hydrolyzing NTPs and incorporating phosphate to exogenous proteins. The mode of nucleotide action on H1 may be considered highly analogous to that of GTPases. Nuclear receptors may thus act through mechanisms similar to those for receptors on the plasma membrane.

Histone H1 and the regulation of transcription by nuclear receptors

Histone H1 is a eukaryotic repressor which recognizes specific DNA structures, and nucleotides regulate its interaction with DNA. Since their mode of action may be considered similar to that observed in the case of plasma membrane GTPases, H1 may be regarded as an ATP/GTPase involved in the action of nuclear receptors. A hypothesis is put forward here to suggest that transcriptional activators CTF/NF-I and AP-1 (fos/jun), for example, are effectors for H1. H1 and CTF/NF-I may be members of a stimulatory regulatory cascade for nuclear receptor action that ends with selective activation of chromatin through histone modification and the disruption or a more subtle structural change of a specific nucleosome, while an opposite effect may be obtained through modification of fos/jun by H1.

Interference of AlF4- with nucleotide and DNA binding of rat histone H1 in vitro. Implications for the pathogenesis of Alzheimer's disease

We demonstrate here that the H2PO4- analogue AlF4- binds to the nucleotide-binding site of rat liver histone H1 in vitro, and interferes with nucleotide recognition and H1 DNA binding. AlF4- may thus compromise the genetically determined pattern of protein synthesis through binding to H1, the general repressor. The present findings are of interest as a number of studies have implicated aluminium as a factor in the pathogenesis of Alzheimer's disease.

Histone H1-DNA interactions and their relation to chromatin structure and function

The belief that histone H1 interacts primarily with DNA in chromatin and much less with the protein component has led to numerous studies of artificial H1-DNA complexes. This review summarizes and discusses the data on different aspects of the interaction between the linker histone and naked DNA, including cooperativity of binding, preference for supercoiled DNA, selectivity with respect to base composition and nucleotide sequence, and effect of H1 binding on the conformation of the underlying DNA. The nature of the interaction, the structure of the complexes, and the role histone H1 exerts in chromatin are also discussed.

Multiple sets of adjacent mu E1 and oct-1 binding sites upstream of the pseudorabies virus immediate-early gene promoter

Binding of cellular proteins to specific motifs in the promoter region of the immediate-early gene of pseudorabies virus was studied. The region was dissected into several portions that were used with HeLa cell nuclear proteins in mobility shift assays, DNase I footprinting, and a methylation interference assay. Close to the transcription start site (nucleotide + 1) are a TATA-box (-26 to -29), an Sp 1-binding motif (GGGGCGGGC) (-45 to -54), a CCAAT motif (-66 to -70), and, further upstream, an NF-microE1-binding site (AAGATGGC) (-161 to -168). Binding of a protein to the Sp1 site was demonstrated. Competition experiments show that the CCAAT motif might bind the NF-microE1 factor, rather than any of the known CCAAT-specific factors. Four domains were identified further upstream (nucleotides -200 to -500) from this promoter, each of which contained closely associated motifs where cellular transcription factors NF-microE1 and oct-1 could bind. These domains comprise what we call the upstream element. The orientation of the four NF-microE1 motifs in the upstream element is opposite to the orientation of the two NF-microE1 motifs located closer to the transcription start site. Transient expression of reporter genes was used to study the activity of the upstream element after transfection into 3T3 and HeLa cells. The upstream element was necessary for efficient expression of the pseudorabies virus immediate-early gene and increased somewhat the efficiency of the herpes simplex virus thymidine kinase promoter.

DNA sequence specific interactions of histone H1

Histone H1 is know to play a role in the formation and maintenance of higher-order chromatin structure. It has been recently suggested that the linker histone might be also involved in the regulation of the activity of individual genes. If H1 is a regulatory factor in eukaryotic gene transcription, it should possess specificity of binding to defined DNA sequences. This review is an attempt to summarize and discuss the existing literature data on DNA sequence-specific interactions of histone H1.

A model for histone H5-DNA interaction: simultaneous minor and major groove binding

Using the tertiary structure of the globular domain of H5 (GH5) and based on an alternative sequence homology between GH5 and DNA-binding proteins containing the helix-turn-helix motif, a model for H5-DNA interaction is proposed. From molecular graphics it follows that helix II recognizes the major groove of the DNA, as does the second helix of the helix-turn-helix motif, while helix III makes minor groove contacts, in agreement with the hypothesis of Turnell et al. (FEBS letters 232, 263-268). In the resulting model GH5 makes contact with a full turn of DNA.

The histone H1-lacZ' fusion protein produced in Escherichia coli binds to the 5'-TTGGCAnnnTGCCAA-3' motif on DNA

The coding region of the chicken histone H1.03 gene was cloned to a bacterial expression vector, and the 291-amino acid H1-beta-galactosidase fusion protein was isolated after induction with IPTG. The fusion protein recognizes the 5'-TTGGCAnnnTGCCAA-3' motif on DNA. The H1 globular domain was initially shown to be responsible for the sequence-specific binding by functional deletion analysis. This function may be indispensable for the role of H1 as a determinant of nucleosome positioning and as a eukaryotic repressor.

Histone H1 and the regulation of transcription of eukaryotic genes

Histone H1 plays a role in the formation of chromatin structure, both at the level of the nucleosome particle itself and in the formation of the higher-order structures of the chromatin fibre. Histone H1 is regarded as a part of a general repressor mechanism that ensures a strong and stable repression of gene expression. In addition to serving as a general repressor for relatively large chromatin fragments, histone H1 might also be involved in controlling the transcriptional activity of individual genes.

A DNA-binding homeodomain in histone H1

The structure of the globular domain of chicken histone H1 was compared here with that of the DNA-binding homeodomain in the Drosophila Antp protein, and they were observed to display considerable similarity. Both of them consist of three or four alpha-helices separated by well-defined turns. Charged residues in the aminoterminal end of alpha 3 are therefore suggested to be responsible for sequence-specific recognition of DNA by the histone. In addition, alpha 2 of H1, with a short leucine zipper in it, may be capable of protein-protein interaction in a similar manner to the other homeodomains.

Impairment of histone H1 DNA binding by adduct formation with acetaldehyde

Incubation of histone H1 with pharmacologically relevant concentrations of acetaldehyde resulted in the formation of spontaneously stable acetaldehyde-protein linkages. The reaction of acetaldehyde and H1 purified from rat liver either by a DNA recognition site affinity chromatography or by perchloric acid extraction occurred primarily at the lysine residues in the carboxyterminal tail of H1, which is crucial for its function as a eukaryotic repressor. It was further shown using an H1-lacZ fusion protein produced in E. coli and the protein isolated from rat liver that the formation of acetaldehyde adducts with H1 impair its DNA binding properties. We propose that such a reaction may occur in vivo and lead to an inability to repress genes in the liver upon excessive alcohol consumption. This mechanism may play a role in acetaldehyde-induced collagen synthesis in alcoholics.

Homology of nuclear factor I with the protein kinase family

It is observed that a putative DNA binding domain in nuclear factor I (NF I) which is a eukaryotic sequence-specific DNA binding protein participating in both regulation of DNA replication and transcription displays sequence homology with catalytic domains in various protein kinases. In addition, hydropathy analysis reveals that the NF I polypeptide chain is likely to fold into similar secondary and tertiary structures to those of the protein kinases. Although it is not known whether NF I functions as a protein kinase in addition to recognizing a specific sequence on DNA, it is concluded that some of the eukaryotic DNA binding proteins and protein kinases may belong to a gene family, various members of which are evolutionarily related and responsible for the regulation of metabolism in diverse compartments of the cell. The present finding also suggests that a number of kinases may to varying extents be capable of direct interaction with DNA.