Large-scale chromatin decondensation and recondensation regulated by transcription from a natural promoter

Fluctuation of chromatin unfolding associated with variation in the level of gene expression

We examined whether spontaneous alteration of chromatin structure, if any, correlates with variation in gene expression. Gene activation is associated with changes in chromatin structure at different levels. Large-scale chromatin unfolding is one such change detectable under the light microscope. We established cell clones carrying tandem repeats (more than 50 copies spanning several hundred kb) of the GFP (green fluorescent protein)-ASK reporter genes driven by a tetracycline responsive promoter. These clones constitutively express the transcriptional transactivator. Flow cytometry and live-recording fluorescence microscopy revealed that, although fully activated by a saturating amount of doxycycline, GFP-ASK expression fluctuated in individual cell clones, regardless of the cell cycle stage. The GFP-ASK expression changed from lower to higher levels and vice versa within a few cell cycles. Furthermore, the levels of GFP-ASK expression were correlated with the degrees of chromatin unfolding of the integrated array as detected by FISH (fluorescent in situ hybridization). The chromatin unfolding was not coupled to a mitotic event; around one-third of the daughter-pairs exhibited dissimilar degrees of chromatin unfolding. We concluded that fluctuation of chromatin unfolding was likely to result in variation in gene expression, although the source of the fluctuation of chromatin unfolding remains to be studied.

Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription

The colinearity of genes in Hox clusters suggests a role for chromosome structure in gene regulation. We reveal programmed changes in chromatin structure and nuclear organization upon induction of Hoxb expression by retinoic acid. There is an early increase in the histone modifications that are marks of active chromatin at both the early expressed gene Hoxb1, and also at Hoxb9 that is not expressed until much later. There is also a visible decondensation of the chromatin between Hoxb1 and Hoxb9 at this early stage. However, a further change in higher-order chromatin structure, looping out of genes from the chromosome territory, occurs in synchrony with the execution of the gene expression program. We suggest that higher-order chromatin structure regulates the expression of the HoxB cluster at several levels. Locus-wide changes in chromatin structure (histone modification and chromatin decondensation) may establish a transcriptionally poised state but are not sufficient for the temporal program of gene expression. The choreographed looping out of decondensed chromatin from chromosome territories may then allow for activation of high levels of transcription from the sequence of genes along the cluster.

Analysis of binding reactions by fluorescence recovery after photobleaching

Fluorescence recovery after photobleaching (FRAP) is now widely used to investigate binding interactions in live cells. Although various idealized solutions have been identified for the reaction-diffusion equations that govern FRAP, there has been no comprehensive analysis or systematic approach to serve as a guide for extracting binding information from an arbitrary FRAP curve. Here we present a complete solution to the FRAP reaction-diffusion equations for either single or multiple independent binding interactions, and then relate our solution to the various idealized cases. This yields a coherent approach to extract binding information from FRAP data which we have applied to the question of transcription factor mobility in the nucleus. We show that within the nucleus, the glucocorticoid receptor is transiently bound to a single state, with each molecule binding on average 65 sites per second. This rapid sampling is likely to be important in finding a specific promoter target sequence. Further we show that this predominant binding state is not the nuclear matrix, as some studies have suggested. We illustrate how our analysis provides several self-consistency checks on a FRAP fit. We also define constraints on what can be estimated from FRAP data, show that diffusion should play a key role in many FRAP recoveries, and provide tools to test its contribution. Overall our approach establishes a more general framework to assess the role of diffusion, the number of binding states, and the binding constants underlying a FRAP recovery.

Rapid glucocorticoid receptor exchange at a promoter is coupled to transcription and regulated by chaperones and proteasomes

Exchange of the glucocorticoid receptor (GR) at promoter target sites provides the only known system in which transcription factor cycling at a promoter is fast, occurring on a time scale of seconds. The mechanism and function of this rapid exchange are unknown. We provide evidence that proteasome activity is required for rapid GR exchange at a promoter. We also show that chaperones, specifically hsp90, stabilize the binding of GR to the promoter, complicating models in which the associated chaperone, p23, has been proposed to induce GR removal. Our results are the first to connect chaperone and proteasome functions in setting the residence time of a transcription factor at a target promoter. Moreover, our results reveal that longer GR residence times are consistently associated with greater transcriptional output, suggesting a new paradigm in which the rate of rapid exchange provides a means to tune transcriptional levels.

From silencing to gene expression: real-time analysis in single cells

We have developed an inducible system to visualize gene expression at the levels of DNA, RNA and protein in living cells. The system is composed of a 200 copy transgene array integrated into a euchromatic region of chromosome 1 in human U2OS cells. The condensed array is heterochromatic as it is associated with HP1, histone H3 methylated at lysine 9, and several histone methyltransferases. Upon transcriptional induction, HP1alpha is depleted from the locus and the histone variant H3.3 is deposited suggesting that histone exchange is a mechanism through which heterochromatin is transformed into a transcriptionally active state. RNA levels at the transcription site increase immediately after the induction of transcription and the rate of synthesis slows over time. Using this system, we are able to correlate changes in chromatin structure with the progression of transcriptional activation allowing us to obtain a real-time integrative view of gene expression.

Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter

Transcriptional activation of a gene involves an orchestrated recruitment of components of the basal transcription machinery and intermediate factors, concomitant with an alteration in local chromatin structure generated by posttranslational modifications of histone tails and nucleosome remodeling. We provide here a comprehensive picture of events resulting in transcriptional activation of a gene, through evaluating the estrogen receptor-alpha (NR3A1) target pS2 gene promoter in MCF-7 cells. This description integrates chromatin remodeling with a kinetic evaluation of cyclical networks of association of 46 transcription factors with the promoter, as determined by chromatin immunoprecipitation assays. We define the concept of a "transcriptional clock" that directs and achieves the sequential and combinatorial assembly of a transcriptionally productive complex on a promoter. Furthermore, the unanticipated findings of key roles for histone deacetylases and nucleosome-remodeling complexes in limiting transcription implies that transcriptional activation is a cyclical process that requires both activating and repressive epigenetic processes.

Progesterone receptor deficient in chromatin binding has an altered cellular state

Our previous work has shown that the progesterone receptor (PR) can exist in two distinct functional states in mammary adenocarcinoma cells. The differences in function included the ability to activate a promoter in organized chromatin, sensitivity to ligand, and ligand-independent activation. To determine whether these functional differences were because of altered cellular processing, we carried out biochemical analyses of the functionally distinct PRs. Although the majority of PR is localized to the nucleus, biochemical partitioning resulted in a loosely bound (cytosolic) fraction, and a tightly bound (nuclear) fraction. In the absence of progestins, the functionally distinct PRs differed significantly in partitioning between the two fractions. To characterize these fractions further, we analyzed interactions of unliganded PR with chaperones by coimmunoprecipitation. We determined that PR in the cytosolic fraction associated with hsp90 and p23. In contrast, PR in the nuclear fraction consisted of complexes containing hsp90, p23, and FKBP51 as well as PR that was dimerized and highly phosphorylated. Hormone treatment significantly reduced the formation of all PR-chaperone complexes. The hsp90 inhibitor, geldanamycin, similarly blocked transcriptional activity of both functionally distinct receptors. However, the two forms of the PR differed in their ability to associate with the mouse mammary tumor virus promoter in organized chromatin. These findings provide new information about the composition and distribution of mature progesterone receptor complexes in mammary adenocarcinoma cells, and suggest that differences in receptor subcellular distribution have a significant impact on their function. These findings also reveal that transiently expressed steroid receptors may not always be processed like their endogenous counterparts.

Chromatin organization in the mammalian nucleus

Mammalian cells package their DNA into chromatin and arrange it in the nucleus as chromosomes. In interphase cells chromosomes are organized in a radial distribution with the most gene-dense chromosomes toward the center of the nucleus. Gene transcription, replication, and repair are influenced by the underlying chromatin architecture, which in turn is affected by the formation of chromosome territories. This arrangement in the nucleus presumably facilitates cellular functions to occur in an efficient and ordered fashion and exploring the link between transcription and nuclear organization will be an exciting area of further research.

Linker histone-dependent organization and dynamics of nucleosome entry/exit DNAs

A DNA sequence-dependent nucleosome structural and dynamic polymorphism was recently uncovered through topoisomerase I relaxation of mononucleosomes on two homologous approximately 350-370 bp DNA minicircle series, one originating from pBR322, the other from the 5S nucleosome positioning sequence. Whereas both pBR and 5S nucleosomes had access to the closed, negatively crossed conformation, only the pBR nucleosome had access to the positively crossed conformation. Simulation suggested this discrepancy was the result of a reorientation of entry/exit DNAs, itself proposed to be the consequence of specific DNA untwistings occurring in pBR nucleosome where H2B N-terminal tails pass between the two gyres. The present work investigates the behavior of the same two nucleosomes after binding of linker histone H5, its globular domain, GH5, and engineered H5 C-tail deletion mutants. Nucleosome access to the open uncrossed conformation was suppressed and, more surprisingly, the ability of 5S nucleosome to positively cross was largely restored. This, together with the paradoxical observation of a less extensive crossing in the negative conformation with GH5 than without, favored an asymmetrical location of the globular domain in interaction with the central gyre and only entry (or exit) DNA, and raised the possibility of the domain physical rotation as a mechanism assisting nucleosome fluctuation from one conformation to the other. Moreover, both negative and positive conformations showed a high degree of loop conformational flexibility in the presence of the full-length H5 C-tail, which the simulation suggested to reflect the unique feature of the resulting stem to bring entry/exit DNAs in contact and parallel. The results point to the stem being a fundamental structural motif directing chromatin higher order folding, as well as a major player in its dynamics.

Estrogen receptor-dependent proteasomal degradation of the glucocorticoid receptor is coupled to an increase in mdm2 protein expression

Glucocorticoids and estrogens regulate a number of vital physiological processes. We developed a model breast cancer cell line, MCF-7 M, to examine potential mechanisms by which the ligand-bound estrogen receptor (ER) regulates glucocorticoid receptor (GR)-mediated transcription. MCF-7 cells, which endogenously express ERalpha, were stably transfected with mouse mammary tumor virus promoter-luciferase (MMTV-LUC) reporter and GR expression constructs. Our results demonstrate that treatment with estrogen agonists (17beta-estradiol [E2], diethylstilbestrol, genistein), but not antagonists (tamoxifen or raloxifene), for 48 h inhibits GR-mediated MMTV-LUC transcription and chromatin remodeling. Furthermore, estrogen agonists inhibit glucocorticoid induction of p21 mRNA and protein levels, suggesting that the repressive effect applies to other GR-regulated genes and proteins in MCF-7 cells. Importantly, GR transcriptional activity is compromised because treatment with estrogen agonists down regulates GR protein levels. The protein synthesis inhibitor cycloheximide and the proteasome inhibitor MG132 block E2-mediated decrease in GR protein levels, suggesting that estrogen agonists down regulate the GR via the proteasomal degradation pathway. In support of this, we demonstrate that E2-mediated GR degradation is coupled to an increase in p53 and its key regulator protein Mdm2 (murine double minute 2), an E3 ubiquitin ligase shown to target the GR for degradation. Using the chromatin immunoprecipitation assay, we demonstrate an E2-dependent recruitment of ERalpha to the Mdm2 promoter, suggesting a role of ER in the regulation of Mdm2 protein expression and hence the enhanced GR degradation in the presence of estrogen agonists. Our study shows that cross talk between the GR and ER involves multiple signaling pathways, indicative of the mechanistic diversity within steroid receptor-regulated transcription.

Steroid receptor coactivator-1 is not required for androgen-mediated sexual differentiation of spinal motoneurons

Steroid receptor coactivator-1 (SRC-1) amplifies genomic steroid hormone signal transduction and has been implicated in steroid-mediated sexual differentiation of the mammalian nervous system. We investigated the possible effect of an SRC-1 null mutation on 2 morphological endpoints of androgenic signaling: the number and size of motoneurons within the spinal nucleus of the bulbocavernosus (SNB). In wild-type C57/BL6 mice, SRC-1 immunoreactive nuclei were observed within the SNB and one of its target muscles, the levator ani. However, SRC-1 null mice were indistinguishable from sex-matched wild-type littermates in both SNB number and cross-sectional area of SNB motoneurons. Similarly, we found no difference between SRC-1 null and wildtype littermates in the number or size of motoneurons in the retrodorsolateral nucleus, a motor pool that is not typically sexually differentiated in either number or size. These results demonstrate that SRC-1 is not essential for the development and maintenance of a sexually dimorphic neuromuscular system.

Formation of higher-order secondary and tertiary chromatin structures by genomic mouse mammary tumor virus promoters

Agarose multigel electrophoresis has been used to characterize the structural features of isolated genomic mouse mammary tumor virus (MMTV) promoters. The mouse 3134 cells used for these studies contain approximately 200 stably integrated tandem repeats of a 2.4-kb MMTV promoter fragment. Inactive, basally active, and hormonally activated genomic promoters were liberated by restriction digestion of isolated nuclei, recovered in low-salt nuclear extracts, and electrophoresed in multigels consisting of nine individual agarose running gels. Specific bands were detected and characterized by Southern and Western blotting. We find that transcriptionally inactive promoters contain TBP and high levels of histone H1, and are present to varying extents in both untreated and dexamethasone (DEX)-treated 3134 cells. In contrast, the basally active promoter, present in untreated cells, is bound to RNA Pol II, TBP, and Oct1, contains acetylated H3 tail domains, and is depleted of histone H1. The DEX-activated promoter possessed similar composition as the basal promoter, but also contains stably bound Brg1. Strikingly, all forms of the MMTV promoter condense into higher-order secondary and/or tertiary chromatin structures in vitro in the presence of Mg2+. Thus, genomic MMTV promoter chromatin retains the ability to form classical higher-order structures under physiological salt conditions, even after dissociation of H1 and binding of several transcription factors and multiprotein complexes. These results suggest that transcriptionally active eukaryotic promoters may function in a locally folded chromatin environment in vivo.

The Dynamics of Chromosome Organization and Gene Regulation

With the sequence of the human genome now complete, studies must focus on how the genome is functionally organized within the confines of the cell nucleus and the dynamic interplay between the genome and its regulatory factors to effectively control gene expression and silencing. In this review I describe our current state of knowledge with regard to the organization of chromosomes within the nucleus and the positioning of active versus inactive genes. In addition, I discuss studies on the dynamics of chromosomes and specific genetic loci within living cells and its relationship to gene activity and the cell cycle. Furthermore, our current understanding of the distribution and dynamics of RNA polymerase II transcription factors is discussed in relation to chromosomal loci and other nuclear domains.

Genome function and nuclear architecture: from gene expression to nanoscience

Biophysical, chemical, and nanoscience approaches to the study of nuclear structure and activity have been developing recently and hold considerable promise. A selection of fundamental problems in genome organization and function are reviewed and discussed in the context of these new perspectives and approaches. Advancing these concepts will require coordinated networks of physicists, chemists, and materials scientists collaborating with cell, developmental, and genome biologists.

Nuclear choreography: interpretations from living cells

The advent of green fluorescent protein technology, its use in photobleaching experiments and the development of methods to rapidly acquire images and analyze complex datasets have opened the door to unraveling the mechanisms of nuclear functions in living cells. Studies over the past few years have characterized the movement of chromatin, nuclear proteins and nuclear bodies and, in some cases, correlated their dynamics with energy dependence, cell cycle progression, developmental changes, factor targeting and nuclear position. The mechanisms by which nuclear components move or are restrained have important implications for understanding not only the efficacy of nuclear functions but also the regulation of developmental programs and cellular growth.

Global chromosome positions are transmitted through mitosis in mammalian cells

We investigated positioning of chromosomes during the cell cycle in live mammalian cells with a combined experimental and computational approach. By non-invasive labeling of chromosome subsets and tracking by 4D imaging, we could show that no global rearrangements occurred in interphase. Using the same assay, we also observed a striking order of chromosomes throughout mitosis. By contrast, our computer simulation based on stochastic movements of individual chromosomes predicted randomization of chromosome order in mitosis. In vivo, a quantitative assay for single chromosome positioning during mitosis revealed strong similarities between daughter and mother cells. These results demonstrate that global chromosome positions are heritable through the cell cycle in mammalian cells. Based on tracking of labeled chromosomes and centromeres during chromosome segregation and experimental perturbations of chromosomal order, we propose that chromosome specific timing of sister chromatid separation transmits chromosomal positions from one cell generation to the next.

Nuclear factor 1 is required for both hormone-dependent chromatin remodeling and transcriptional activation of the mouse mammary tumor virus promoter

The mouse mammary tumor virus (MMTV) promoter has been used as a model to study how the glucocorticoid receptor (GR) remodels chromatin to allow other transcription factors to bind and activate transcription. To dissect the precise role of nuclear factor 1 (NF1) in chromatin remodeling and transcriptional activation, we used linker-scanning mutants of transcription factor binding sites on the MMTV promoter. We compared the NF1 mutant MMTV promoter in the context of transiently transfected templates (transient transfection) and templates organized as chromatin (stable transfection) to understand the effect of chromatin on factor binding and transcription. We show that on a transiently transfected template, mutation in the NF1 binding site reduces both basal and hormone-dependent transcription. This suggests that NF1 is required for transcription in the absence of organized chromatin. We also found that binding of NF1 on a transiently transfected template is independent of mutation in hormone response elements or the octamer transcription factor (OTF) binding site. In contrast, the binding of OTF proteins to a transiently transfected template was found to be dependent on the binding of NF1, which may imply that NF1 has a stabilizing effect on OTF binding. On a chromatin template, mutation in the NF1 binding site does not affect the positioning of nucleosomes on the promoter. We also show that in the absence of NF1 binding, GR-mediated chromatin remodeling of nucleosome B is reduced and hormone-dependent activation of transcription is abolished. Further, we demonstrate that NF1 is required for both the association of BRG1 chromatin remodeling complex and the GR on the promoter in vivo. These results suggest the novel possibility that NF1 may participate in chromatin remodeling activities in addition to directly enhancing transcription and that in the absence of its binding site the GR is unable to effectively bind the promoter and recruit the remodeling complex.

Chromatin structure of eukaryotic promoters: a changing perspective

Over the past few years, many studies have attempted to determine the role of nucleosomes as both positive and negative transcription regulators. The emphasis has mostly centered on chromatin remodeling activities and histone modifications, leaving the question of the influence of the higher-order structure out of the spotlight. Recent technical developments allowing direct measurements of size and mechanical properties of in vivo assembled chromatin may shed light on this poorly understood area. This article presents a brief summary of the current knowledge on transcription-dependent chromatin dynamics and how a rather simple agarose electrophoresis method may change the current view on structural changes linked to transcriptional activation of chromatin.

Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH

Genes can be transcribed from within chromosome territories; however, the major histocompatibilty complex locus has been reported extending away from chromosome territories, and the incidence of this correlates with transcription from the region. A similar result has been seen for the epidermal differentiation complex region of chromosome 1. These data suggested that chromatin decondensation away from the surface of chromosome territories may result from, and/or may facilitate, transcription of densely packed genes subject to coordinate regulation.To investigate whether localization outside of the visible confines of chromosome territories can also occur for regions that are not coordinately regulated, we have examined the spatial organization of human 11p15.5 and the syntenic region on mouse chromosome 7. This region is gene rich but its genes are not coordinately expressed, rather overall high levels of transcription occur in several cell types. We found that chromatin from 11p15.5 frequently extends away from the chromosome 11 territory. Localization outside of territories was also detected for other regions of high gene density and high levels of transcription. This is shown to be partly dependent on ongoing transcription. We suggest that local gene density and transcription, rather than the activity of individual genes, influences the organization of chromosomes in the nucleus.

The interdependence of nuclear structure and function

2001 was the year of the human genome, but the new information has had little immediate impact on the field of nuclear structure. Rather, functional studies - especially on transcription - are leading us to a better understanding of how genomes might organise themselves into structures we call nuclei.

Creating new fluorescent probes for cell biology

Fluorescent probes are one of the cornerstones of real-time imaging of live cells and a powerful tool for cell biologists. They provide high sensitivity and great versatility while minimally perturbing the cell under investigation. Genetically-encoded reporter constructs that are derived from fluorescent proteins are leading a revolution in the real-time visualization and tracking of various cellular events. Recent advances include the continued development of 'passive' markers for the measurement of biomolecule expression and localization in live cells, and 'active' indicators for monitoring more complex cellular processes such as small-molecule-messenger dynamics, enzyme activation and protein-protein interactions.

Dynamic behavior of transcription factors on a natural promoter in living cells

Through the use of photobleaching techniques, we examined the dynamic interaction of three members of the transcription apparatus with a target promoter in living cells. The glucocorticoid receptor (GR) interacting protein 1 (GRIP-1) exhibits a half maximal time for fluorescent recovery (tau(R)) of 5 s, reflecting the same rapid exchange as observed for GR. In contrast, the large subunit (RPB1) of RNA polymerase II (pol II) required 13 min for complete fluorescence recovery, consistent with its function as a processive enzyme. We also observe a complex induction profile for the kinetics of GR-stimulated transcription. Our results indicate that GR and GRIP-1 as components of the activating complex are in a dynamic equilibrium with the promoter, and must return to the template many times during the course of transcriptional activation.

Colocalization and ligand-dependent discrete distribution of the estrogen receptor (ER)alpha and ERbeta

To investigate the relationships between the loci expressing functions of estrogen receptor (ER)alpha and that of ERbeta, we analyzed the subnuclear distribution of ERalpha and ERbeta in response to ligand in single living cells using fusion proteins labeled with different spectral variants of green fluorescent protein. Upon activation with ligand treatment, fluorescent protein-tagged (FP)-ERbeta redistributed from a diffuse to discrete pattern within the nucleus, showing a similar time course as FP-ERalpha, and colocalized with FP-ERalpha in the same discrete cluster. Analysis using deletion mutants of ERalpha suggested that the ligand-dependent redistribution of ERalpha might occur through a large part of the receptor including at least the latter part of activation function (AF)-1, the DNA binding domain, nuclear matrix binding domain, and AF-2/ligand binding domain. In addition, a single AF-1 region within ERalpha homodimer, or a single DNA binding domain as well as AF-1 region within the ERalpha/ERbeta heterodimer, could be sufficient for the cluster formation. More than half of the discrete clusters of FP-ERalpha and FP-ERbeta were colocalized with hyperacetylated histone H4 and a component of the chromatin remodeling complex, Brg-1, indicating that ERs clusters might be involved in structural changes of chromatin.

Quantitation of GFP-fusion proteins in single living cells

The green fluorescent protein (GFP) has revolutionized cell biology. The ability to observe genetically encoded fluorescently tagged fusion proteins in intact cells has made virtually any biological process amenable to investigation in living cells. However, most in vivo imaging studies are qualitative and little information about the number of fluorescently labeled molecules observed in a cell or a cellular structure is available. This deficiency severely limits the interpretation of imaging experiments and it impedes the application of in vivo imaging methods for biophysical purposes. Here we describe a simple method for the quantitative determination of the number of GFP-tagged molecules in cellular structures in single living cells. The method is based on the use of rotavirus-like particles containing a known number of GFP molecules as an internal calibration standard during in vivo imaging. We have applied this method to estimate in single living cells the number of fluorescent transcription factor molecules on RNA polymerase I and polymerase II genes. In addition, we have estimated the number of molecules for several proteins in subnuclear compartments and in exocytic vesicles. VLP-GFP calibration is a simple, convenient, rapid, and noninvasive method for routine quantification of GFP-labeled molecules in single, living cells.

Transcript elongation on a nucleoprotein template

Chromatin forms a general, repeating barrier to elongation of transcripts by eukaryotic RNA polymerases. Recent studies of nucleosome structure and histone modifications reveal a set of likely mechanisms for control of elongation through chromatin. Genetic and biochemical studies of transcription have identified a set of accessory factors for transcript elongation by RNA polymerase II (Pol II) that appear to function in the context of chromatin. The C-terminal repeated domain (CTD) of Pol II may also play a role in regulating elongation through chromatin.

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

Eukaryotic genomes are organized into condensed, heterogeneous chromatin fibers throughout much of the cell cycle. Here we describe recent studies indicating that even transcriptionally active loci may be encompassed within 80- to 100-nanometer-thick chromonema fibers. These studies suggest that chromatin higher order folding may be a key feature of eukaryotic transcriptional control. We also discuss evidence suggesting that adenosine-5'-triphosphate-dependent chromatin-remodeling enzymes and histone-modifying enzymes may regulate transcription by controlling the extent and dynamics of chromatin higher order folding.

Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functions

Chromatin fibers are dynamic macromolecular assemblages that are intimately involved in nuclear function. This review focuses on recent advances centered on the molecular mechanisms and determinants of chromatin fiber dynamics in solution. Major points of emphasis are the functions of the core histone tail domains, linker histones, and a new class of proteins that assemble supramolecular chromatin structures. The discussion of important structural issues is set against a background of possible functional significance.

Topography of genetic elements of X-chromosome relative to the cell nucleus and to the chromosome X territory determined for human lymphocytes

Topography of three genetic elements--dystrophin (dmd) exons 5-7 (E(1)), 46-47 (E(2)), and centromere of chromosome X (N(X)) were studied relative to cell nuclei and to chromosome X territories of spatially fixed human lymphocytes. Repeated three-dimensional (3D) dual color fluorescence in situ hybridization combined with high-resolution cytometry was used. In addition, the nuclear location of fluorescence weight centers (FWC), spatial volume, and maximal area per one section of chromosome-X territories were investigated. The larger (X(L)) and smaller (X(S)) homologous X-chromosomes were distinguished for each nucleus according to the 3D volume of their territories. The distributions of the [center of nucleus]-to-[genetic element] distances (radial distributions) of dmd exons E(1), E(2), centromere N(X) and FWC were very similar for both homologous X-chromosomes of female lymphocytes as well as for the chromosome X of the human male. On the other hand, larger average mutual distances between all pairs of signals (E(1), E(2), N(X), FWC) and larger average maximal area were observed for the larger chromosome (X(L)) in comparison with the smaller one (X(S)). The territory of the larger homologue showed also more irregular surface. The most significant differences between homologous X-chromosomes were found for N(X)-E(1), N(X)-E(2) and E(1)-E(2) distances that were in average about twice longer for X(L) as compared with X(S). These parameters correlate to each other and can be used for the reliable determination of more (de)condensed X-chromosome territory. The longer E(1)-E(2) distances for X(L) indicate more open chromatin structure of the dystrophin gene on this chromosome in contrary to closed structure on X(S). Substantially shorter distances of the dystrophin exons from the centromeric heterochromatin in X(S) as compared to X(L) can be explained by silencing effect of centromeres as described in Nature 1 (2000) 137.

The viral transactivator E1A regulates the mouse mammary tumor virus promoter in an isoform- and chromatin-specific manner

Proteins encoded by the adenovirus E1A gene regulate both cellular and viral genes to mediate effects on cell cycle, differentiation, and cell growth control. We have identified the mouse mammary tumor virus (MMTV) promoter as a target of E1A action and investigated the role nucleoprotein structure plays in its response to E1A. Both 12 and 13 S forms target the MMTV promoter when it has a disorganized and accessible chromatin configuration. However, whereas the 13 S form is stimulatory, the 12 S form is repressive. When the MMTV promoter adopts an organized and repressed chromatin structure, it is targeted only by the 13 S form, which stimulates it. Although evidence indicates that E1A interacts with the SWI/SNF remodeling complex, E1A had no effect on chromatin remodeling at the MMTV promoter in organized chromatin. Analysis of E1A mutants showed that stimulation of the MMTV promoter is mediated solely through conserved region 3 and does not require interaction with Rb, p300/CBP-associated factor, or CBP/p300. Imaging analysis showed that E1A colocalizes with MMTV sequences in vivo, suggesting that it functions directly at the promoter. These results indicate that E1A stimulates the MMTV promoter in a fashion independent of chromatin conformation and through a direct mechanism involving interaction with the basal transcription machinery.

Alteration of large-scale chromatin structure by estrogen receptor

The estrogen receptor (ER), a member of the nuclear hormone receptor superfamily important in human physiology and disease, recruits coactivators which modify local chromatin structure. Here we describe effects of ER on large-scale chromatin structure as visualized in live cells. We targeted ER to gene-amplified chromosome arms containing large numbers of lac operator sites either directly, through a lac repressor-ER fusion protein (lac rep-ER), or indirectly, by fusing lac repressor with the ER interaction domain of the coactivator steroid receptor coactivator 1. Significant decondensation of large-scale chromatin structure, comparable to that produced by the approximately 150-fold-stronger viral protein 16 (VP16) transcriptional activator, was produced by ER in the absence of estradiol using both approaches. Addition of estradiol induced a partial reversal of this unfolding by green fluorescent protein-lac rep-ER but not by wild-type ER recruited by a lac repressor-SRC570-780 fusion protein. The chromatin decondensation activity did not require transcriptional activation by ER nor did it require ligand-induced coactivator interactions, and unfolding did not correlate with histone hyperacetylation. Ligand-induced coactivator interactions with helix 12 of ER were necessary for the partial refolding of chromatin in response to estradiol using the lac rep-ER tethering system. This work demonstrates that when tethered or recruited to DNA, ER possesses a novel large-scale chromatin unfolding activity.

BRCA1-induced large-scale chromatin unfolding and allele-specific effects of cancer-predisposing mutations

The breast cancer susceptibility gene BRCA1 encodes a protein that has been implicated in multiple nuclear functions, including transcription and DNA repair. The multifunctional nature of BRCA1 has raised the possibility that the polypeptide may regulate various nuclear processes via a common underlying mechanism such as chromatin remodeling. However, to date, no direct evidence exists in mammalian cells for BRCA1-mediated changes in either local or large-scale chromatin structure. Here we show that targeting BRCA1 to an amplified, lac operator-containing chromosome region in the mammalian genome results in large-scale chromatin decondensation. This unfolding activity is independently conferred by three subdomains within the transactivation domain of BRCA1, namely activation domain 1, and the two BRCA1 COOH terminus (BRCT) repeats. In addition, we demonstrate a similar chromatin unfolding activity associated with the transactivation domains of E2F1 and tumor suppressor p53. However, unlike E2F1 and p53, BRCT-mediated chromatin unfolding is not accompanied by histone hyperacetylation. Cancer-predisposing mutations of BRCA1 display an allele-specific effect on chromatin unfolding: 5' mutations that result in gross truncation of the protein abolish the chromatin unfolding activity, whereas those in the 3' region of the gene markedly enhance this activity. A novel cofactor of BRCA1 (COBRA1) is recruited to the chromosome site by the first BRCT repeat of BRCA1, and is itself sufficient to induce chromatin unfolding. BRCA1 mutations that enhance chromatin unfolding also increase its affinity for, and recruitment of, COBRA1. These results indicate that reorganization of higher levels of chromatin structure is an important regulated step in BRCA1-mediated nuclear functions.