Molecular biology. Chromatin higher order folding--wrapping up transcription

Gene activation and deactivation related changes in the three-dimensional structure of chromatin

Chromatin in the interphase nucleus is dynamic, decondensing where genes are activated and condensing where they are silenced. Local chromatin remodelling to a more open structure during gene activation is followed by changes in nucleosome distribution through the action of the transcriptional machinery. This leads to chromatin expansion and looping out of whole genomic regions. Such chromatin loops can extend beyond the chromosome territory. As several studies point to the location of transcription sites inside chromosome territories as well as at their periphery, extraterritorial loops cannot simply be a mechanism for making transcribed genes accessible to the transcriptional machinery and must occur for other reasons. The level of decondensation within an activated region varies greatly and probably depends on the density of activated genes and the number of engaged RNA polymerases. Genes that are silenced during development form a more closed chromatin structure. Specific histone modifications are correlated with gene activation and silencing, and silenced genes may become associated with heterochromatin protein 1 homologues or with polycomb group complexes. Several levels of chromatin packaging are found in the nucleus relating to the different functions of and performed by active genes; euchromatic and heterochromatic regions and the models explaining higher-order chromatin structure are still disputed.

In vivo HP1 targeting causes large-scale chromatin condensation and enhanced histone lysine methylation

Changes in chromatin structure are a key aspect in the epigenetic regulation of gene expression. We have used a lac operator array system to visualize by light microscopy the effect of heterochromatin protein 1 (HP1) alpha (HP1alpha) and HP1beta on large-scale chromatin structure in living mammalian cells. The structure of HP1, containing a chromodomain, a chromoshadow domain, and a hinge domain, allows it to bind to a variety of proteins. In vivo targeting of an enhanced green fluorescent protein-tagged HP1-lac repressor fusion to a lac operator-containing, gene-amplified chromosome region causes local condensation of the higher-order chromatin structure, recruitment of the histone methyltransferase SETDB1, and enhanced trimethylation of histone H3 lysine 9. Polycomb group proteins of both the HPC/HPH and the EED/EZH2 complexes, which are involved in the heritable repression of gene activity, are not recruited to the amplified chromosome region by HP1alpha and HP1beta in vivo targeting. HP1alpha targeting causes the recruitment of endogenous HP1beta to the chromatin region and vice versa, indicating a direct interaction between the two HP1 homologous proteins. Our findings indicate that HP1alpha and HP1beta targeting is sufficient to induce heterochromatin formation.

The core histone N-terminal tail domains function independently and additively during salt-dependent oligomerization of nucleosomal arrays

Salt-dependent oligomerization of nucleosomal arrays is related to fiber-fiber interactions and global chromosome structure. Previous studies have shown that the H2A/H2B and H3/H4 N-terminal domain (NTD) pairs are able to mediate array oligomerization. However, because of technical barriers, the function(s) of the individual core histone NTDs have not been investigated. To address this question, all possible combinations of "tailless" nucleosomal arrays were assembled from native and NTD-deleted recombinant Xenopus core histones and tandemly repeated 5 S rDNA. The recombinant arrays were characterized by differential centrifugation over the range of 0-50 mm MgCl2 to determine how each NTD affects salt-dependent oligomerization. Results indicate that all core histone NTDs participate in the oligomerization process and that the NTDs function additively and independently. These observations provide direct biochemical evidence linking all four core histone NTDs to the assembly and maintenance of global chromatin structures.

LPS induces CD40 gene expression through the activation of NF-kappaB and STAT-1alpha in macrophages and microglia

CD40 is expressed on various immune cells, including macrophages and microglia. Aberrant expression of CD40 is associated with autoimmune inflammatory diseases such as multiple sclerosis and rheumatoid arthritis. Interaction of Toll-like receptor-4 (TLR4) with the Gram-negative bacteria endotoxin lipopolysaccharide (LPS) results in the induction of an array of immune response genes. In this study, we describe that LPS is a strong inducer of CD40 expression in macrophages and microglia, which occurs at the transcriptional level and involves the activation of the transcription factors nuclear factor-kappaB (NF-kappaB) and signal transducer and activator of transcription 1alpha (STAT-1alpha). LPS-induced CD40 expression involves the endogenous production of the cytokine interferon-beta (IFN-beta), which contributes to CD40 expression by the activation of STAT-1alpha. Blocking IFN-beta-induced activation of STAT-1alpha by IFN-beta-neutralizing antibody reduces LPS-induced CD40 gene expression. Furthermore, LPS induces acetylation and phosphorylation of histones H3 and H4 and the recruitment of NF-kappaB, STAT-1alpha, and RNA polymerase II on the CD40 promoter in vivo in a time-dependent manner, all events important for CD40 gene transcription. These results indicate that both LPS-induced NF-kappaB activation and endogenous production of IFN-beta that subsequently induces STAT-1alpha activation play critical roles in the transcriptional activation of the CD40 gene by LPS.

Role of high mobility group (HMG) chromatin proteins in DNA repair

While the structure and composition of chromatin not only influences the type and extent of DNA damage incurred by eukaryotic cells, it also poses a major obstacle to the efficient repair of genomic lesions. Understanding how DNA repair processes occur in the context of nuclear chromatin is a current experimental challenge, especially in mammalian cells where the powerful tools of genetic analysis that have been so successful in elucidating repair mechanisms in yeast have seen only limited application. Even so, work over the last decade with both yeast and mammalian cells has provided a rather detailed description of how nucleosomes, the basic subunit of chromatin, influence both DNA damage and repair in all eukaryotic cells. The picture that has emerged is, nonetheless, incomplete since mammalian chromatin is far more complex than simply consisting of vast arrays of histone-containing nucleosome core particles. Members of the "High Mobility Group" (HMG) of non-histone proteins are essential, and highly dynamic, constituents of mammalian chromosomes that participate in all aspects of chromatin structure and function, including DNA repair processes. Yet comparatively little is known about how HMG proteins participate in the molecular events of DNA repair in vivo. What information is available, however, indicates that all three major families of mammalian HMG proteins (i.e., HMGA, HMGB and HMGN) participate in various DNA repair processes, albeit in different ways. For example, HMGN proteins have been shown to stimulate nucleotide excision repair (NER) of ultraviolet light (UV)-induced cyclobutane pyrimidine dimer (CPD) lesions of DNA in vivo. In contrast, HMGA proteins have been demonstrated to preferentially bind to, and inhibit NER of, UV-induced CPDs in stretches of AT-rich DNA both in vitro and in vivo. HMGB proteins, on the other hand, have been shown to both selectively bind to, and inhibit NER of, cisplatin-induced DNA intrastrand cross-links and to bind to misincorporated nucleoside analogs and, depending on the biological circumstances, either promote lesion repair or induce cellular apoptosis. Importantly, from a medical perspective, the ability of the HMGA and HMGB proteins to inhibit DNA repair in vivo suggests that they may be intimately involved with the accumulation of genetic mutations and chromosome instabilities frequently observed in cancers. Not surprisingly, therefore, the HMG proteins are being actively investigated as potential new therapeutic drug targets for the treatment of cancers and other diseases.

The transcription machinery and the molecular toolbox to control gene expression in Toxoplasma gondii and other protozoan parasites

The phylum of Apicomplexa groups a large variety of obligate intracellular protozoan parasites that exhibit complicated life cycles, involving transmission and differentiation within and between different hosts. Little is known about the level of regulation and the nature of the factors controlling gene expression throughout their life stages. Unravelling the mechanisms that govern gene regulation is critical for the development of adequate tools to manipulate these parasites and modulate gene expression, in order to study their function in molecular terms in vivo. A comparative analysis of the transcriptional machinery of several apicomplexan genomes and other protozoan parasites has revealed the existence of a primitive eukaryotic transcription apparatus consisting only of a subset of the general transcription factors found in higher eukaryotes. These findings have some direct implications on development of tools.

The H1 phosphorylation state regulates expression of CDC2 and other genes in response to starvation in Tetrahymena thermophila

In Tetrahymena thermophila, highly phosphorylated histone H1 of growing cells becomes partially dephosphorylated when cells are starved in preparation for conjugation. To determine the effects of H1 phosphorylation on gene expression, PCR-based subtractive hybridization was used to clone cDNAs that were differentially expressed during starvation in two otherwise-isogenic strains differing only in their H1s. H1 in A5 mutant cells lacked phosphorylation, and H1 in E5 cells mimicked constitutive H1 phosphorylation. Sequences enriched in A5 cells included genes encoding proteases. Sequences enriched in E5 cells included genes encoding cdc2 kinase and a Ser/Thr kinase. These results indicate that H1 phosphorylation plays an important role in regulating the pattern of gene expression during the starvation response and that its role in transcription regulation can be either positive or negative. Treatment of starved cells with a phosphatase inhibitor caused CDC2 gene overexpression. Expression of the E5 version of H1 in starved cells containing endogenous, wild-type H1 caused the wild-type H1 to remain highly phosphorylated. These results argue that Cdc2p is the kinase that phosphorylates Tetrahymena H1, establish a positive feedback mechanism between H1 phosphorylation and CDC2 expression, and indicate that CDC2 gene expression is regulated by an H1 phosphatase.

Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle

Gene expression in eukaryotes depends upon positioning, mobility and packaging of nucleosomes; thus, we need the detailed information of the human nucleosome core particle (NCP) structure, which could clarify chromatin properties. Here, we report the 2.5 A crystal structure of a human NCP. The overall structure is similar to those of other NCPs reported previously. However, the DNA path of human NCP is remarkably different from that taken within other NCPs with an identical DNA sequence. A comparison of the structural parameters between human and Xenopus laevis DNA reveals that the DNA path of human NCP consecutively shifts by 1 bp in the regions of superhelix axis location -5.0 to -2.0 and 5.0 to 7.0. This alteration of the human DNA path is caused predominantly by tight DNA-DNA contacts within the crystal. It is also likely that the conformational change in the human H2B tail induces the local alteration of the DNA path. In human NCP, the region with the altered DNA path lacks Mn2+ ions and the B-factors of the DNA phosphate groups are substantially high. Therefore, in contrast to the histone octamer, the nucleosomal DNA is sufficiently flexible and mobile and can undergo drastic conformational changes, depending upon the environment.

Class I histone deacetylase Thd1p affects nuclear integrity in Tetrahymena thermophila

Class I histone deacetylases (HDACs) participate in the regulation of DNA-templated processes such as transcription and replication. Members of this class can act locally at specific sites, or they can act more globally, contributing to a baseline acetylation state, both of which actions may be important for genome maintenance and organization. We previously identified a macronuclear-specific class I HDAC in Tetrahymena thermophila called Thd1p, which is expressed early in the development of the macronucleus when it initially becomes transcriptionally active. To test the idea that Thd1p is important for global chromatin integrity in an active macronucleus, Tetrahymena cells reduced in expression of Thd1p were generated. We observed phenotypes that indicated loss of chromatin integrity in the mutant cells, including DNA fragmentation and extrusion of chromatin from the macronucleus, variable macronuclear size and shape, enlarged nucleoli, and reduced phosphorylation of histone H1 from bulk chromatin. Macronuclei in mutant cells also contained more DNA. This observation suggests a role for Thd1p in the control of nuclear DNA content, a previously undescribed role for class I HDACs. Together, these phenotypes implicate Thd1p in the maintenance of macronuclear integrity in multiple ways, probably through site-specific changes in histone acetylation since no change in the acetylation levels of bulk histones was detected in mutant cells.

Hyperacetylated chromatin domains: lessons from heterochromatin

A small but growing number of loci that exhibit covalent histone modifications, such as hyperacetylation, over broad regions of 10 kb or more have been characterized. These hyperacetylated domains occur exclusively at loci containing highly expressed, tissue-specific genes, and the available evidence suggests that they are involved in the activation of these genes. Although to date little is known concerning the formation or function of these domains, rather more is known concerning repressive, heterochromatic domains, and the example provided by heterochromatin may be instructive in considering mechanisms of active domain formation.

Gene expression analysis reveals that histone deacetylation sites may serve as partitions of chromatin gene expression domains

Background

It has been a long-term puzzle whether chromatin can be further divided into distinct gene expression domains. Because histone deacetylation affects chromatin structure, that in turn may affect the expression of nearby genes, histone deacetylation sites may act to partition chromatin into different gene expression domains. In this article, we explore the relationship between histone deacetylation sites and gene expression patterns on the genome scale using different data sources, including microarray data measuring gene expression levels, microarray data measuring histone deacetylation sites, and information on regulatory targets of transcription factors.

Results

Using 269 Saccharomyces cerevisiae microarray datasets, histone deacetylation datasets, and regulatory targets of transcription factors assembled from the Yeast Proteome Database and ChIP-chip data, we found that histone deacetylation sites can reduce the level of co-expression of neighboring genes.

Conclusion

Histone deacetylation sites may serve as possible partition sites for chromatin domains and affect gene expression.

Semirandom sampling to detect differentiation-related and age-related epigenome remodeling

With completion of the human genome project, patterns of higher order chromatin structure can be easily related to other features of genome organization. A well-studied aspect of chromatin, histone H4 acetylation, is examined here on the basis of its role in setting competence for gene activation. Three applications of a new hybrid genome sampling-chromatin immunoprecipitation strategy are described. The first explores aspects of epigenome architecture in human fibroblasts. A second focuses on chromatin from HL-60 promyelocytic leukemia cells before and after differentiation into macrophage-like cells. A third application explores age-related epigenome change. In the latter, acetylation patterns are compared in human skin fibroblast chromatin from donors of various ages. Two sites are reported at which observed histone H4 acetylation differences suggest decreasing acetylation over time. The sites, located in chromosome 4p16.1 and 4q35.2 regions, appear to remodel during late fetal-early child development and from preadolescence through adult life, respectively.

NAD+-dependent modulation of chromatin structure and transcription by nucleosome binding properties of PARP-1

PARP-1 is the most abundantly expressed member of a family of proteins that catalyze the transfer of ADP-ribose units from NAD+ to target proteins. Herein, we describe previously uncharacterized nucleosome binding properties of PARP-1 that promote the formation of compact, transcriptionally repressed chromatin structures. PARP-1 binds in a specific manner to nucleosomes and modulates chromatin structure through NAD+-dependent automodification, without modifying core histones or promoting the disassembly of nucleosomes. The automodification activity of PARP-1 is potently stimulated by nucleosomes, causing the release of PARP-1 from chromatin. The NAD+-dependent activities of PARP-1 are reversed by PARG, a poly(ADP-ribose) glycohydrolase, and are inhibited by ATP. In vivo, PARP-1 incorporation is associated with transcriptionally repressed chromatin domains that are spatially distinct from both histone H1-repressed domains and actively transcribed regions. Thus, PARP-1 functions both as a structural component of chromatin and a modulator of chromatin structure through its intrinsic enzymatic activity.

Mediator Requirement for Both Recruitment and Postrecruitment Steps in Transcription Initiation

Mediator complexes are required for activators to stimulate Pol II preinitiation complex assembly on an associated promoter. We show here that for the mouse Egr1 gene, controlled largely by MAP kinase phosphorylation of the ELK1 transcription factor, the MED23 Mediator subunit that interacts with phospho-ELK1 is also required to stimulate Pol II initiation at a step subsequent to preinitiation complex assembly. In Med23-/- cells, histone acetylation, methylation, and chromatin remodeling complex association at the Egr1 promoter were equivalent to that of wild-type cells, yet Egr1 induction was greatly reduced. MAP kinase activation stimulated Pol II and GTF promoter binding. However, the difference in factor binding between wild-type and mutant cells was much less than the difference in transcription, and Pol II remained localized to the promoter in mutant cells. These results indicate that an interaction with MED23 stimulates initiation by promoter bound Pol II in addition to Pol II and GTF recruitment.

Redundant roles for histone H3 N-terminal lysine residues in subtelomeric gene repression in Saccharomyces cerevisiae

The transcription of genes located in subtelomeric regions of yeast chromosomes is repressed relative to the rest of the genome. This repression requires wild-type nucleosome levels but not the telomere silencing factors Sir2, Sir3, Sir4, and Rap1. Subtelomeric heterochromatin is characterized by the absence of acetylation or methylation of histone H3 lysine residues, but it is not known whether histone H3 hypoacetylation or hypomethylation is a prerequisite for the establishment of subtelomeric heterochromatin. We have systematically mutated the N-terminal tails of histone H3 and H4 in Saccharomyces cerevisiae and characterized the effects each mutant has on genome-wide expression. Our results show that subtelomeric transcriptional repression is dependent on the histone H3 N-terminal domain, but not the histone H4 N-terminal domain. Mutating lysine-4, lysine-9, lysine-14, lysine-18, lysine-23, and lysine-27 to glycine in histone H3 is also sufficient to significantly reduce subtelomeric gene repression. Individual histone H3 lysine mutations, however, have little effect on subtelomeric gene repression or genome-wide expression, indicating that these six lysine residues have redundant functions. We propose that acetylation and methylation of histone H3 N-terminal lysine residues act as redundant mechanisms to demarcate regions of euchromatin from heterochromatin.

Noncoding DNA, isochores and gene expression: nucleosome formation potential

The nucleosome formation potential of introns, intergenic spacers and exons of human genes is shown here to negatively correlate with among-tissues breadth of gene expression. The nucleosome formation potential is also found to negatively correlate with the GC content of genomic sequences; the slope of regression line is steeper in exons compared with noncoding DNA (introns and intergenic spacers). The correlation with GC content is independent of sequence length; in turn, the nucleosome formation potential of introns and intergenic spacers positively (albeit weakly) correlates with sequence length independently of GC content. These findings help explain the functional significance of the isochores (regions differing in GC content) in the human genome as a result of optimization of genomic structure for epigenetic complexity and support the notion that noncoding DNA is important for orderly chromatin condensation and chromatin-mediated suppression of tissue-specific genes.

Prothymosin alpha associates with the oncoprotein SET and is involved in chromatin decondensation

Prothymosin alpha (ProTalpha) is a histone H1-binding protein that interacts with the transcription coactivator CREB-binding protein and potentiates transcription. Based on coimmunoprecipitation and mammalian two-hybrid assays, we show here that ProTalpha forms a complex with the oncoprotein SET. ProTalpha efficiently decondenses human sperm chromatin, while overexpression of GFP-ProTalpha in mammalian cells results in global chromatin decondensation. These results indicate that decondensation of compacted chromatin fibers is an important step in the mechanism of ProTalpha function.

Topoisomerase inhibitor induced dephosphorylation of H1 and H3 histones as a consequence of cell cycle arrest

Posttranslational modifications of histones have an integral function in the structural and functional organization of chromatin. Several changes in the modification state of histones could be observed after induction of apoptosis with topoisomerase inhibitors and other inducers. Most of these studies include the analysis of the state of phosphorylation of histones, and the results are to some extent controversial, depending on cell lines and agents used. In the present study we compared the kinetics of the dephosphorylation of H1 and H3 histones with apoptosis markers after treatment of leukemic cell lines with topoisomerase inhibitors. In parallel, we determined cell cycle parameters in detail. Dephosphorylation of both histone classes started within 1 h of induction, and no direct correlation with timing and intensity of the investigated apoptotic features could be observed. In contrast, we show that the effect of topoisomerase inhibitors on the state of H1 and H3 phosphorylation is not directly related to apoptosis, but reflects the changes in the cell cycle distribution of cells treated with these inducers.

Generic features of tertiary chromatin structure as detected in natural chromosomes

Knowledge of tertiary chromatin structure in mammalian interphase chromosomes is largely derived from artificial tandem arrays. In these model systems, light microscope images reveal fibers or beaded fibers after high-density targeting of transactivators to insertional domains spanning several megabases. These images of fibers have lent support to chromonema fiber models of tertiary structure. To assess the relevance of these studies to natural mammalian chromatin, we identified two different approximately 400-kb regions on human chromosomes 6 and 22 and then examined light microscope images of interphase tertiary chromatin structure when the regions were transcriptionally active and inactive. When transcriptionally active, these natural chromosomal regions elongated, yielding images characterized by a series of adjacent puncta or "beads", referred to hereafter as beaded images. These elongated structures required transcription for their maintenance. Thus, despite marked differences in the density and the mode of transactivation, the natural and artificial systems showed similarities, suggesting that beaded images are generic features of transcriptionally active tertiary chromatin. We show here, however, that these images do not necessarily favor chromonema fiber models but can also be explained by a radial-loop model or even a simple nucleosome affinity, random-chain model. Thus, light microscope images of tertiary structure cannot distinguish among competing models, although they do impose key constraints: chromatin must be clustered to yield beaded images and then packaged within each cluster to enable decondensation into adjacent clusters.

The Transcriptional Corepressor, PELP1, Recruits HDAC2 and Masks Histones Using Two Separate Domains

PELP1 (proline-, glutamic acid-, and leucine-rich protein 1) has been recognized as a coactivator of estrogen receptor (ER)-recruiting p300/CREB-binding protein histone acetyltransferase to the target chromosome. The present study shows that PELP1 does indeed coactivate ER-mediated transcription but also serves as a corepressor of other nuclear hormone receptors (NR)- and non-NR sequence-specific transcription factors tested, including GR, Nur77, AP1, NF-kappaB, and TCF/SRF. PELP1 expression also retarded the proliferation of mouse fibroblast cell lines in which there was no detectable ER. This was due, at least in part, to the suppressed activation of serum-response genes such as c-fos that in turn resulted from the blocked histone hyperacetylation of nucleosomes containing the c-fos promoter region. The N-terminal leucine-abundant region of PELP1 was observed to interact with HDAC2 and exhibited repressive activity when tethered to the chromatin. In addition, the C-terminal glutamic acid-abundant region bound to the hypoacetylated histones H3 and H4 and prevented them from becoming substrates of histone acetyltransferase. Thus PELP1 promotes and maintains the hypoacetylated state of histones at the target genomic site, and ER binding reverses its role to hyperacetylate histones through an as yet unidentified mechanism.

Lysine acetylation and the bromodomain: a new partnership for signaling

Lysine acetylation has been shown to occur in many protein targets, including core histones, about 40 transcription factors and over 30 other proteins. This modification is reversible in vivo, with its specificity and level being largely controlled by signal-dependent association of substrates with acetyltransferases and deacetylases. Like other covalent modifications, lysine acetylation exerts its effects through "loss-of-function" and "gain-of-function" mechanisms. Among the latter, lysine acetylation generates specific docking sites for bromodomain proteins. For example, bromodomains of Gcn5, PCAF, TAF1 and CBP are able to recognize acetyllysine residues in histones, HIV Tat, p53, c-Myb or MyoD. In addition to the acetyllysine moiety, the flanking sequences also contribute to efficient recognition. The relationship between acetyllysine and bromodomains is reminiscent of the specific recognition of phosphorylated residues by phospho-specific binding modules such as SH2 domains and 14-3-3 proteins. Therefore, lysine acetylation forges a novel signaling partnership with bromodomains to govern the temporal and spatial regulation of protein functions in vivo.

Sequential histone modifications at Hoxd4 regulatory regions distinguish anterior from posterior embryonic compartments

Hox genes are differentially expressed along the embryonic anteroposterior axis. We used chromatin immunoprecipitation to detect chromatin changes at the Hoxd4 locus during neurogenesis in P19 cells and embryonic day 8.0 (E8.0) and E10.5 mouse embryos. During Hoxd4 induction in both systems, we observed that histone modifications typical of transcriptionally active chromatin occurred first at the 3' neural enhancer and then at the promoter. Moreover, the sequential distribution of histone modifications between E8.0 and E10.5 was consistent with a spreading of open chromatin, starting with the enhancer, followed by successively more 5' intervening sequences, and culminating at the promoter. Neither RNA polymerase II (Pol II) nor CBP associated with the inactive gene. During Hoxd4 induction, CBP and RNA Pol II were recruited first to the enhancer and then to the promoter. Whereas the CBP association was transient, RNA Pol II remained associated with both regulatory regions. Histone modification and transcription factor recruitment occurred in posterior, Hox-expressing embryonic tissues, but never in anterior tissues, where such genes are inactive. Together, our observations demonstrate that the direction of histone modifications at Hoxd4 mirrors colinear gene activation across Hox clusters and that the establishment of anterior and posterior compartments is accompanied by the imposition of distinct chromatin states.

Unexpected binding motifs for subnucleosomal particles revealed by atomic force microscopy

The structure of individual nucleosomes organized within reconstituted 208-12 arrays at different levels of compaction was examined by tapping mode atomic force microscopy in air and liquid. Reconstitution at lower histone octamer to DNA weight ratios showed an extended beads-on-a-string morphology with less than the expected maximum of 12 nucleosome core particles per array, each particle located in the most favored positioning site. A correlation of the contour lengths of these arrays with the number of observed particles revealed two distinct populations of particles, one with approximately 50 nm of bound DNA and a second population with approximately 25 nm. The measured nucleosome center-to-center distances indicate that this approximately 25 nm is not necessarily symmetrically bound about the dyad axis, but can also correspond to DNA bound from either the entry or exit point of the particle to a location at or close to the dyad axis. An assessment of particle heights suggests that particles wrapping approximately 25 nm of DNA are most likely to be subnucleosomal particles, which lack either one or both H2A-H2B dimers. At a higher reconstitution ratio, folded compact arrays fully populated with 12 nucleosome core particles, were observed. Liquid measurements demonstrated dynamic movements of DNA loops protruding from these folded arrays.

Opening the chromatin for transcription

Eukaryotic genomes are packaged into a dynamic hierarchy chromatin structure. In such a particular context, the transition from a repressed compacted chromatin to a rather extended fiber is necessary for transcription. The chromatin opening includes three events, the initial factor getting access to nucleosome DNA, local chromatin opening mediated by activator/coactivator, and transcription associated with extensive chromatin opening. Chromatin dynamics, which is DNA sequence dependent, and also occurs in condensed fiber, provides the opportunity for activators binding to DNA. Coactivators recruited by the activator open the chromatin locally. However, it appears that genes adopt distinct chromatin opening mechanisms according to whether the gene is induced expression, developmental and tissue-specific expression, or constitutive expression. In contrast to transcription initiation-related local chromatin opening, large scale of chromatin opening is associated with a functional enhancer as well as high transcription rate. How the transcription initiated from an enhancer or enhancer like modules, i.e. intergenic transcription, conducts the extensive chromatin opening is discussed. A model for long-range interaction that non-coding transcripts from enhancers may promote efficient communication with promoters is proposed.

Mapping global histone acetylation patterns to gene expression

Histone acetyltransferases and deacetylases with specificities for different sites of acetylation affect common chromatin regions. This could generate unique patterns of acetylation that may specify downstream biological processes. To search for existence of these patterns and their relationship to gene activity, we analyzed the genome-wide acetylation profiles for eleven lysines in the four core histones of Saccharomyces cerevisiae. We find that both hyper- and hypoacetylation of individual lysines are associated with transcription, generating distinct patterns of acetylation that define groups of biologically related genes. The genes within these groups are significantly coexpressed, mediate similar physiological processes, share unique cis-regulatory DNA motifs, and are enriched for binding of specific transcription factors. Our data also indicate that the in vivo binding of the transcription factor Bdf1 is associated with acetylation on most lysines but relative deacetylation on H4 lysine 16. Thus, certain acetylation patterns may be used as surfaces for specific protein-histone interactions, providing one mechanism for coordinate regulation of chromatin processes that are biologically related.

Nucleosome interactions in chromatin: fiber stiffening and hairpin formation

We use Monte Carlo simulations to study attractive and excluded volume interactions between nucleosome core particles in 30-nm chromatin fibers. The nucleosomes are treated as disklike objects having an excluded volume and short-range attraction modeled by a variant of the Gay-Berne potential. The nucleosomes are connected via bendable and twistable linker DNA in the crossed linker fashion. We investigate the influence of the nucleosomal excluded volume on the stiffness of the fiber. For parameter values that correspond to chicken erythrocyte chromatin, we find that the persistence length is governed to a large extent by that excluded volume whereas the soft linker backbone elasticity plays only a minor role. We further find that internucleosomal attraction can induce the formation of hairpin configurations. Tension-induced opening of such configurations into straight fibers manifests itself in a quasiplateau in the force-extension curve that resembles results from recent micromanipulation experiments. Such hairpins may play a role in the formation of higher-order structures in chromosomes like chromonema fibers.

Are major defects in children conceived in vitro due to innate problems in patients or to induced genetic damage?

Birth anomalies recently detected in epidemiological studies indicate greater risks following assisted human reproduction than with natural conception. Some of these conclusions and assumptions are questioned in this paper, and the effects of specific causative factors unique to some infertile couples are analysed. Other recent studies have identified imprinting defects as causes of birth disorders following IVF or intracytoplasmic sperm injection. While few in numbers, they apparently involve unusual factors in conception such as aberrant responses among preimplantation embryos to culture medium or serum. Various genetic and developmental factors in infertile couples influencing the origin of such birth outcomes are assessed, and the significance of imprinting and its embryological roles are discussed.

Transcription factories: quantitative studies of nanostructures in the mammalian nucleus

Transcription by the three nuclear RNA polymerases is carried out in transcription factories. This conclusion has been drawn from estimates of the total number of nascent transcripts or active polymerase molecules and the number of transcription sites within a cell. Here we summarise the variety of methods used to determine these parameters, discuss their associated problems and outline future prospects.

Transcription Factors and Nuclear Receptors Interact with the SWI/SNF Complex through the BAF60c Subunit

Transcriptional activity relies on coregulators that modify chromatin structure or serve as bridging factors between transcription factors and the basal transcription machinery. We identified a new coregulator of peroxisome proliferator-activated receptor gamma, BRG1/Brm-associated factor of 60 kDa, subunit c2 (BAF60c2), in a yeast two-hybrid screen of a human adipose tissue cDNA library. BAF60c2 represents a new isoform of BAF60c, a component of the SWI/SNF (mating type switching/sucrose non-fermenting) chromatin remodeling complex. This new isoform as well as the previously identified protein, renamed BAF60c1, is localized primarily in the cell nucleus and is expressed in a wide variety of tissues. Both BAF60c isoforms bind to several nuclear receptors and transcription factors of various families. BAF60c proteins interact in a ligand-independent manner with peroxisome proliferator-activated receptor gamma and enhance its transcriptional activity. Both isoforms are enriched in the central nervous system and also modulate the transcriptional activity of retinoic acid-related orphan receptor alpha1. In conclusion, BAF60c represents a new coregulator that constitutes an important anchoring point by which the SWI/SNF complex is recruited to nuclear receptors and other transcription factors.

Basal chromatin modification at the IL-4 gene in helper T cells

Chromatin immunoprecipitations in naive CD4, but not CD8, T cells, demonstrated association of the IL-4 promoter with acetylated histone. Histone modifications and rapid IL-4 transcription were absent in conserved noncoding sequence 1 (CNS-1)(-/-) cells lacking an 8-kb-distant enhancer in the IL-4/IL-13 intergenic region, but also in CD4(-/-) and Itk(-/-) cells, which have similar Th2 deficiencies. Histones associated with the IL-13 promoter were not similarly acetylated in naive T cells, but became acetylated in differentiated Th2 cells. Conversely, Th1 differentiation induced histone methylation at the type 2 cytokine locus. Like CD4(-/-) and Itk(-/-) mice, CNS-1(-/-) BALB/c mice were highly resistant to the Th2-inducing protozoan, Leishmania major. CNS-1 deficiency led to failure of IL-4 gene repositioning to heterochromatin after Th1 polarization, possibly related to the presence of reiterative Ikaros binding sites in the intergenic element. Hyperacetylation of nonexpressed genes may serve to mark lineage-specific loci for rapid expression and further modification.

The linker histone homolog Hho1p from Saccharomyces cerevisiae represents a winged helix-turn-helix fold as determined by NMR spectroscopy

Hho1p is assumed to serve as a linker histone in Saccharomyces cerevisiae and, notably, it possesses two putative globular domains, designated HD1 (residues 41-118) and HD2 (residues 171-252), that are homologous to histone H5 from chicken erythrocytes. We have determined the three-dimensional structure of globular domain HD1 with high precision by heteronuclear magnetic resonance spectroscopy. The structure had a winged helix-turn-helix motif composed of an alphabetaalphaalphabetabeta fold and closely resembled the structure of the globular domain of histone H5. Interestingly, the second globular domain, HD2, in Hho1p was unstructured under physiological conditions. Gel mobility assay demonstrated that Hho1p preferentially binds to supercoiled DNA over linearized DNA. Furthermore, NMR analysis of the complex of a deletion mutant protein (residues 1-118) of Hho1p with a linear DNA duplex revealed that four regions within the globular domain HD1 are involved in the DNA binding. The above results suggested that Hho1p possesses properties similar to those of linker histones in higher eukaryotes in terms of the structure and binding preference towards supercoiled DNA.

Topography of genetic loci in the nuclei of cells of colorectal carcinoma and adjacent tissue of colonic epithelium

To determine the influence of increased gene expression and amplification in colorectal carcinoma on chromatin structure, the nuclear distances between pairs of bacterial artificial chromosome (BAC) clones with genomic separation from 800 to 29,000 kb were measured and compared between the tumor and parallel epithelial cells of six patients. The nuclear distances were measured between the loci in chromosomal bands 7p22.3-7p21.3; 7q35-7q36.3; 11p15.5-11p15.4; 20p13; 20p12.2; 20q11.21 and 20q12 where increased expression had been found in all types of colorectal carcinoma. The loci were visualized by three-dimensional fluorescence in situ hybridization using 22 BAC clones. Our results show that for short genomic separations, mean nuclear distance increases linearly with increased genomic separation. The results for some pairs of loci fell outside this linear slope, indicating the existence of different levels of chromatin folding. For the same genomic separations the nuclear distances were frequently shorter for tumor as compared with epithelial cells. Above the initial growing phase of the nuclear distances, a plateau phase was observed in both cell types where the increase in genomic separation was not accompanied by an increase in nuclear distance. The ratio of the mean nuclear distances between the corresponding loci in tumor and epithelium cells decreases with increasing amplification of loci. Our results further show that the large-scale chromatin folding might differ for specific regions of chromosomes and that it is basically preserved in tumor cells in spite of the amplification of many loci.

Nuclear Receptor Recruitment of Histone-Modifying Enzymes to Target Gene Promoters

Nuclear receptors (NRs) compose one of the largest known families of eukaryotic transcription factors and, as such, serve as a paradigm for understanding the fundamental molecular mechanisms of eukaryotic transcriptional regulation. The packaging of eukaryotic genomic DNA into a higher ordered chromatin structure, which generally acts as a barrier to transcription by inhibiting transcription factor accessibility, has a major influence on the mechanisms by which NRs activate or repress gene expression. A major breakthrough in the field's understanding of these mechanisms comes from the recent identification of NR-associated coregulatory factors (i.e., coactivators and corepressors). Although several of these NR cofactors are involved in chromatin remodeling and facilitating the recruitment of the basal transcription machinery, the focus of this chapter is on NR coactivators and corepressors that act to covalently modify the amino-terminal tails of core histones. These modifications (acetylation, methylation, and phosphorylation) are thought to directly affect chromatin structure and?or serve as binding surfaces for other coregulatory proteins. This chapter presents the most current models for NR recruitment of histone-modifying enzymes and then summarizes their functional importance in NR-associated gene expression.

ATP-dependent chromatin remodeling

The study of chromatin and how this dynamic structure modulates events in the eukaryotic nucleus has become an increasingly important topic in biomedical research. A large number of enzymes have been discovered that are responsible for modifying and altering chromatin structure, either globally or specifically at particular gene promoters or regions of the chromosome. This chapter provides an introduction to the structure of chromatin and then describes how special classes of enzymes modulate chromatin structure to allow access to DNA.

Nuclear phosphoinositides and their functions

Phosphoinositides are minor components of biological membranes, which have emerged as essential regulators of a variety of cellular processes, both on the plasma membrane and on several intracellular organelles. The versatility of these lipids stems from their ability to function either as substrates for the generation of second messengers, as membrane-anchoring sites for cytosolic proteins or as regulators of the actin cytoskeleton. Despite a vast literature demonstrating the presence of phosphoinositides in the nucleus, only recently has the function(s) of the nuclear pool of these lipids and their soluble analogues, inositol polyphosphates, started to emerge. These compounds have been shown to serve as essential co-factors for several nuclear processes, including DNA repair, transcription regulation and RNA dynamics. In this light, phosphoinositides and inositol polyphosphates might represent high turnover activity switches for nuclear complexes responsible for these processes. The regulation of these large machineries would be linked to the phosphorylation state of the inositol ring and limited temporally and spatially based on the synthesis and degradation of these molecules.

Corepressor Recruitment by Agonist-Bound Nuclear Receptors

Members of the nuclear receptor superfamily are ligand-regulated transcription factors that are composed of a series of conserved domains. These receptors are targets of a wide range of lipophilic signaling molecules that modulate many aspects of physiology and metabolism. Binding of cognate ligands to receptors induces a conformational change in the ligand binding domain (LBD) that creates a pocket for recruitment of coregulatory proteins, which are essential for ligand-dependent regulation of transcription. Several coregulatory proteins that interact with hormone-bound receptors contain characteristic helical LXXLL motifs, known as nuclear receptor (NR) boxes. Generally, ligand binding to receptors is associated with activation of transcription, and most of the NR box-containing proteins characterized to date are coactivators. However, a full understanding of the function of hormone-bound receptors must also incorporate their recruitment of corepressors. The recent identification of ligand-dependent corepressor (LCoR) is a case in point. LCoR contains a single NR box that mediates its hormone-dependent interaction with several nuclear receptors. It functions as a molecular scaffold that recruits several proteins that function in transcriptional repression. Remarkably, although the two proteins share only very limited homology, LCoR and another NR box-containing corepressor RIP140 recruit similar cofactors implicated in transcriptional repression, suggesting many parallels in their mechanisms of action. Corepressors such as LCoR and RIP140 may function in negative feedback loops to attenuate hormone-induced transactivation, act more transiently as part of a cycle of cofactors recruited to target promoters by ligand-bound receptors, or function in hormone-induced target gene repression.

Adenovirus core protein VII contains distinct sequences that mediate targeting to the nucleus and nucleolus, and colocalization with human chromosomes

During adenovirus infection, following capsid dissociation, core protein VII enters the host cell nucleus complexed with adenovirus DNA. In order to determine whether protein VII may have an active role in this nuclear import, regions of the preVII gene were amplified by PCR, and further oligonucleotide mutants were designed with site-directed mutation of codons for the basic amino acids arginine and lysine. Fragments were cloned into a mammalian expression plasmid to express the peptides as N-terminal fusions to enhanced green fluorescent protein. Results demonstrate that preVII protein contains both nuclear and nucleolar targeting sequences. Such signals may be important in the delivery of adenovirus DNA to the host cell nucleus during adenovirus infection. Furthermore, the data suggest that protein VII may bind to human chromosomes by means of two distinct domains, one sharing homology with the N-terminal regulatory tail of histone H3.

SET domains and histone methylation

The realisation that SET domains, which are found in numerous proteins involved in chromatin regulation, catalyse the methylation of lysine residues has led to intense interest in their cellular, biochemical and structural properties. The structures of five SET domain proteins have been reported over the past year. SET domains possess a novel fold, and use adjacent domains for both structural stabilisation and the completion of their active sites. The cofactor S-adenosyl-L-methionine and peptide substrates bind on opposite faces of the SET domain. Remarkably, the sidechain of the target lysine approaches the transferred methyl group through a narrow channel that passes through the middle of the domain.

Chromatin history: our view from the bridge

Thirty years ago, our conception of chromatin structure underwent a total metamorphosis as the nucleosome era began. In Kurosawa's classic movie 'Rashomon' (1951), each participant had a different perspective of the same pivotal event. This review outlines our perception of history.

Role of the M-loop and reactive center loop domains in the folding and bridging of nucleosome arrays by MENT

MENT is a developmentally regulated heterochromatin-associated protein that condenses chromatin in terminally differentiated avian blood cells. Its homology to the serpin protein family suggests that the conserved serpin reactive center loop (RCL) and the unique M-loop are important for its function. To examine the role of these domains, we studied the interaction of wild-type and mutant MENT with naked DNA and biochemically defined nucleosome arrays reconstituted from 12-mer repeats containing nucleosome positioning sequences. Wild-type MENT folded the naked DNA duplexes into closely juxtaposed parallel structures ("tramlines"). Deletion of the M-loop, but not inactivation of the RCL, prevented tramline formation and the cooperative interaction of MENT with DNA. Reconstitution of wild-type MENT with nucleosome arrays caused their tight folding and self-association. M-loop deletion inhibited nucleosome array folding, whereas the inactive RCL mutant was competent to fold the nucleosome arrays, but had a significantly impaired ability to cause their self-association. Bifunctional chemical cross-linking of MENT revealed oligomerization of wild-type MENT in the presence of chromatin and DNA. This oligomerization was severely reduced in the RCL mutant. We propose that the mechanism of MENT-induced heterochromatin formation involves two independent events: bringing together nucleosome linkers within a chromatin fiber and formation of protein bridges between chromatin fibers. Ordered binding of MENT to linker DNA via its unique M-loop domain promotes the folding of chromatin, whereas bridging of chromatin fibers is facilitated by MENT oligomerization mediated by the RCL.

Activation domain-mediator interactions promote transcription preinitiation complex assembly on promoter DNA

The interaction of activators with mediator has been proposed to stimulate the assembly of RNA polymerase II (Pol II) preinitiation complexes, but there have been few tests of this model. The finding that the major adenovirus E1A and mitogen-activated protein kinase-phosphorylated Elk1 activation domains bind to Sur2 uniquely among the metazoan mediator subunits and the development of transcriptionally active nuclear extracts from WT and sur2-/- embryonic stem cells, reported here, allowed a direct test of the model. We found that whereas VP16, E1A, and phosphorylated Elk1 activation domains each stimulate binding of mediator, Pol II, and general transcription factors to promoter DNA in extracts from WT cells, only VP16 stimulated their binding in extracts from sur2-/- cells. This stimulation of mediator, Pol II, and general transcription factor binding to promoter DNA correlated with transcriptional activation by these activators in WT and mutant extracts. Because the mutant mediator was active in reactions with the VP16 activation domain, the lack of activity in response to the E1A and Elk1 activation domains was not due to loss of a generalized mediator function, but rather the inability of the mutant mediator to be bound by E1A and Elk1. These results directly demonstrate that the interaction of activation domains with mediator stimulates preinitiation complex assembly on promoter DNA.

Insulation of the chicken beta-globin chromosomal domain from a chromatin-condensing protein, MENT

Active genes are insulated from developmentally regulated chromatin condensation in terminally differentiated cells. We mapped the topography of a terminal stage-specific chromatin-condensing protein, MENT, across the active chicken beta-globin domain. We observed two sharp transitions of MENT concentration coinciding with the beta-globin boundary elements. The MENT distribution profile was opposite to that of acetylated core histones but correlated with that of histone H3 dimethylated at lysine 9 (H3me2K9). Ectopic MENT expression in NIH 3T3 cells caused a large-scale and specific remodeling of chromatin marked by H3me2K9. MENT colocalized with H3me2K9 both in chicken erythrocytes and NIH 3T3 cells. Mutational analysis of MENT and experiments with deacetylase inhibitors revealed the essential role of the reaction center loop domain and an inhibitory affect of histone hyperacetylation on the MENT-induced chromatin remodeling in vivo. In vitro, the elimination of the histone H3 N-terminal peptide containing lysine 9 by trypsin blocked chromatin self-association by MENT, while reconstitution with dimethylated but not acetylated N-terminal domain of histone H3 specifically restored chromatin self-association by MENT. We suggest that histone H3 modification at lysine 9 directly regulates chromatin condensation by recruiting MENT to chromatin in a fashion that is spatially constrained from active genes by gene boundary elements and histone hyperacetylation.

Selective up-regulation of the growth arrest DNA damage-inducible gene Gadd45 alpha in sensory and motor neurons after peripheral nerve injury

The growth arrest and DNA damage-inducible gene 45 alpha (Gadd45a) was one of 240 genes found previously by high density oligonucleotide microarray analysis to be regulated in the rat L4 and L5 dorsal root ganglia 3 days after transection of the sciatic nerve (>four-fold up-regulation). The Gadd45a mRNA expression profile investigated by northern blot, RNase protection assay and in situ hybridization in the rat shows negligible constitutive mRNA levels in embryonic, neonatal or adult intact dorsal root ganglia. Within 24 h of a sciatic nerve injury, a very large induction is found that persists for as long as regeneration of injured fibres is prevented by peripheral nerve ligation. When axons are allowed to regrow following sciatic nerve crush injury, Gadd45a expression is terminated at later time points, when levels of other markers of injury return towards normal. Colocalization with activating transcription factor 3-LI and c-jun mRNA implies that all peripherally injured primary sensory and motor neurons express Gadd45a mRNA. Injury to the central axons of dorsal root ganglion neurons produces only a minimal induction of Gadd45a while peripheral inflammation is without effect. Gadd45a is a specific marker of the presence of peripheral axonal injury in adult primary sensory and motor neurons.

Spurious spatial periodicity of co-expression in microarray data due to printing design

Global transcriptome data is increasingly combined with sophisticated mathematical analyses to extract information about the functional state of a cell. Yet the extent to which the results reflect experimental bias at the expense of true biological information remains largely unknown. Here we show that the spatial arrangement of probes on microarrays and the particulars of the printing procedure significantly affect the log-ratio data of mRNA expression levels measured during the Saccharomyces cerevisiae cell cycle. We present a numerical method that filters out these technology-derived contributions from the existing transcriptome data, leading to improved functional predictions. The example presented here underlines the need to routinely search and compensate for inherent experimental bias when analyzing systematically collected, internally consistent biological data sets.