Packing of a specific gene into higher order structures following repression of RNA synthesis

A historical and evolutionary perspective on the biological significance of circulating DNA and extracellular vesicles

The discovery of quantitative and qualitative differences of the circulating DNA (cirDNA) between healthy and diseased individuals inclined researchers to investigate these molecules as potential biomarkers for non-invasive diagnosis and prognosis of various pathologies. However, except for some prenatal tests, cirDNA analyses have not been readily translated to clinical practice due to a lack of knowledge regarding its composition, function, and biological and evolutionary origins. We believe that, to fully grasp the nature of cirDNA and the extracellular vesicles (EVs) and protein complexes with which it is associated, it is necessary to probe the early and badly neglected work that contributed to the discovery and development of these concepts. Accordingly, this review consists of a schematic summary of the major events that developed and integrated the concepts of heredity, genetic information, cirDNA, EVs, and protein complexes. CirDNA enters target cells and provokes a myriad of gene regulatory effects associated with the messaging functions of various natures, disease progression, somatic genome variation, and transgenerational inheritance. This challenges the traditional views on each of the former topics. All of these discoveries can be traced directly back to the iconic works of Darwin, Lamarck, and their followers. The history of cirDNA that has been revisited here is rich in information that should be considered in clinical practice, when designing new experiments, and should be very useful for generating an empirically up-to-date view of cirDNA and EVs. Furthermore, we hope that it will invite many flights of speculation and stimulate further inquiry into its biological and evolutionary origins.

An H4K16 histone acetyltransferase mediates decondensation of the X chromosome in C. elegans males

Background

In C. elegans, in order to equalize gene expression between the sexes and balance X and autosomal expression, two steps are believed to be required. First, an unknown mechanism is hypothesized to upregulate the X chromosome in both sexes. This mechanism balances the X to autosomal expression in males, but creates X overexpression in hermaphrodites. Therefore, to restore the balance, hermaphrodites downregulate gene expression twofold on both X chromosomes. While many studies have focused on X chromosome downregulation, the mechanism of X upregulation is not known.

Results

To gain more insight into X upregulation, we studied the effects of chromatin condensation and histone acetylation on gene expression levels in male C. elegans. We have found that the H4K16 histone acetyltransferase MYS-1/Tip60 mediates dramatic decondensation of the male X chromosome as measured by FISH. However, RNA-seq analysis revealed that MYS-1 contributes only slightly to upregulation of gene expression on the X chromosome. These results suggest that the level of chromosome decondensation does not necessarily correlate with the degree of gene expression change in vivo. Furthermore, the X chromosome is more sensitive to MYS-1-mediated decondensation than the autosomes, despite similar levels of H4K16ac on all chromosomes, as measured by ChIP-seq. H4K16ac levels weakly correlate with gene expression levels on both the X and the autosomes, but highly expressed genes on the X chromosome do not contain exceptionally high levels of H4K16ac.

Conclusion

These results indicate that H4K16ac and chromosome decondensation influence regulation of the male X chromosome; however, they do not fully account for the high levels of gene expression observed on the X chromosomes.

Electronic supplementary material

The online version of this article (doi:10.1186/s13072-016-0097-x) contains supplementary material, which is available to authorized users.

The Balbiani Ring Story: Synthesis, Assembly, Processing, and Transport of Specific Messenger RNA-Protein Complexes

Eukaryotic gene expression is the result of the integrated action of multimolecular machineries. These machineries associate with gene transcripts, often already nascent precursor messenger RNAs (pre-mRNAs). They rebuild the transcript and convey properties allowing the processed transcript, the mRNA, to be exported to the cytoplasm, quality controlled, stored, translated, and degraded. To understand these integrated processes, one must understand the temporal and spatial aspects of the fate of the gene transcripts in relation to interacting molecular machineries. Improved methodology is necessary to study gene expression in vivo for endogenous genes. A complementary approach is to study biological systems that provide exceptional experimental possibilities. We describe such a system, the Balbiani ring (BR) genes in polytene cells in the dipteran Chironomus tentans. The BR genes, along with their pre-mRNA-protein complexes (pre-mRNPs) and mRNA-protein complexes (mRNPs), allow the visualization of intact cell nuclei and enable analyses of where and when different molecular machineries associate with and act on the BR pre-mRNAs and mRNAs.

Evidence for short-range helical order in the 30-nm chromatin fibers of erythrocyte nuclei

Chromatin folding in eukaryotes fits the genome into the limited volume of the cell nucleus. Formation of higher-order chromatin structures attenuates DNA accessibility, thus contributing to the control of essential genome functions such as transcription, DNA replication, and repair. The 30-nm fiber is thought to be the first hierarchical level of chromatin folding, but the nucleosome arrangement in the compact 30-nm fiber was previously unknown. We used cryoelectron tomography of vitreous sections to determine the structure of the compact, native 30-nm fiber of avian erythrocyte nuclei. The predominant geometry of the 30-nm fiber revealed by subtomogram averaging is a left-handed two-start helix with approximately 6.5 nucleosomes per 11 nm, in which the nucleosomes are juxtaposed face-to-face but are shifted off their superhelical axes with an axial translation of approximately 3.4 nm and an azimuthal rotation of approximately 54°. The nucleosomes produce a checkerboard pattern when observed in the direction perpendicular to the fiber axis but are not interdigitated. The nucleosome packing within the fibers shows larger center-to-center internucleosomal distances than previously anticipated, thus excluding the possibility of core-to-core interactions, explaining how transcription and regulation factors can access nucleosomes.

Close coupling between transcription and exit of mRNP from the cell nucleus

Transcription is intimately coupled to co-transcriptional formation of mRNP particles and their preparation for export. In the dipteran Chironomus tentans we have now investigated whether on-going transcription is closely linked also to the ensuing transfer of the mRNPs from genes to cytoplasm. The assembly and nucleocytoplasmic transport of a specific mRNP particle, the Balbiani ring (BR) RNP granule, were visualized in larval salivary glands by electron microscopy. When transcription was inhibited with DRB or actinomycin D (AMD), the growing BR mRNPs disappeared from the genes. The two inhibitors affected the distribution of BR mRNPs in the nucleoplasm and in the nuclear pores in essentially the same way. At the nuclear pore complexes (NPCs) the basket-associated and translocating mRNPs were substantially reduced in number, the translocating RNPs being essentially absent after 90 min treatment. Remarkably, the amount of BR mRNPs in the nucleoplasm did not change. We conclude that on-going transcription is required for the mRNPs to exit from the cell nucleus. Interruption of transcription seems to primarily affect the intranuclear movement of BR mRNPs and/or prevent the binding of mRNPs to the NPCs rather than to directly interfere with translocation per se.

Splicing factors SF1 and U2AF associate in extraspliceosomal complexes

Splicing factors SF1 and U2AF associate cooperatively with pre-mRNA and play a crucial role in 3' splice site recognition during early steps of spliceosome assembly. Formation of the active spliceosome subsequently displaces SF1 in a remodeling process that stabilizes the association of U2 snRNP with pre-mRNA. Fluorescence microscopy shows SF1 and U2AF distributed throughout the nucleoplasm, where transcription occurs, with additional concentration in nuclear speckles, where splicing factors accumulate when not engaged in splicing. Fluorescence recovery after photobleaching analysis in live cells shows that the mobilities of SF1 and the two subunits of U2AF (U2AF(65) and U2AF(35)) are correlated with the abilities of these proteins to interact with each other. Direct binding of SF1 to U2AF(65) was demonstrated by fluorescence resonance energy transfer in both the nucleoplasm and nuclear speckles. This interaction persisted after transcription inhibition, suggesting that SF1 associates with U2AF in a splicing-independent manner. We propose that SF1 and U2AF form extraspliceosomal complexes before and after taking part in the assembly of catalytic spliceosomes.

Gene expression in polytene nuclei

Gene expression in eukaryotic cells is a multi-step process. Many of the steps are both co-ordinated and quality controlled. For example, transcription is closely coupled to pre-messenger RNA (mRNA)-protein assembly, pre-mRNA processing, surveillance of the correct synthesis of messenger ribonucleoprotein (mRNP), and export. The coordination appears to be exerted through dynamic interactions between components of the transcription, processing, surveillance, and export machineries. Our knowledge is so far incomplete about these molecular interactions and where in the nucleus they take place. It is therefore essential to analyze the intranuclear steps of gene expression in vivo. Polytene nuclei are exceptionally large and contain chromosomes and individual genes that can be structurally analyzed in situ during ongoing transcription. Furthermore, they contain gene-specific pre-mRNPs/mRNPs that can be visualised and analyzed as they are synthesised on the gene and then followed on their path to the cytoplasm. We describe methods for investigating the structure and composition of active chromatin and gene-specific pre-mRNPs/mRNPs in the context of analyses of gene expression processes in the nuclei of polytene cells.

Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone

Background

Complexes of nucleosomes, which often occur in the gene promoter areas, are one of the fundamental levels of chromatin organization and thus are important for transcription regulation. Investigating the dynamic structure of a single nucleosome as well as nucleosome complexes is important for understanding transcription within chromatin. In a previous work, we highlighted the influence of histone variants on the functional dynamics of a single nucleosome using normal mode analysis developed by Bahar et al. The present work further analyzes the dynamics of nucleosome complexes (nucleosome oligomers or oligonucleosomes) such as dimer, trimer and tetramer (beads on a string model) with conventional core histones as well as with the H2A.Z histone variant using normal mode analysis.

Results

The global dynamics of oligonucleosomes reveal larger amplitude of motion within the nucleosomes that contain the H2A.Z variant with in-planar and out-of-planar fluctuations as the common mode of relaxation. The docking region of H2A.Z and the L1:L1 interactions between H2A.Z monomers of nucleosome (that are responsible for the highly stable nucleosome containing variant H2A.Z-histone) are highly dynamic throughout the first two dynamic modes.

Conclusion

Dissection of the dynamics of oligonucleosomes discloses in-plane as well as out-of-plane fluctuations as the common mode of relaxation throughout the global motions. The dynamics of individual nucleosomes and the combination of the relaxation mechanisms expressed by the individual nucleosome are quite interesting and highly dependent on the number of nucleosome fragments present in the complexes. Distortions generated by the non-planar dynamics influence the DNA conformation, and hence the histone-DNA interactions significantly alter the dynamics of the DNA. The variant H2A.Z histone is a major source of weaker intra- and inter-molecular correlations resulting in more disordered motions.

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.

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.

Considering nuclear compartmentalization in the light of nuclear dynamics

Many proteins are concentrated in compartments within the nucleus. Chromatin is also compartmentalized at different nuclear sites. However, nuclear proteins have now been shown to be highly mobile. This review considers the formation and function of nuclear compartments in a situation in which proteins are rapidly moving through the nuclear volume.

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.

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

We have examined the relationship between transcription and chromatin structure using a tandem array of the mouse mammary tumor virus (MMTV) promoter driving a ras reporter. The array was visualized as a distinctive fluorescent structure in live cells stably transformed with a green fluorescent protein (GFP)-tagged glucocorticoid receptor (GR), which localizes to the repeated MMTV elements after steroid hormone treatment. Also found at the array by immunofluorescence were two different steroid receptor coactivators (SRC1 and CBP) with acetyltransferase activity, a chromatin remodeler (BRG1), and two transcription factors (NFI and AP-2). Within 3 h after hormone addition, arrays visualized by GFP-GR or DNA fluorescent in situ hybridization (FISH) decondensed to varying degrees, in the most pronounced cases from a approximately 0.5-microm spot to form a fiber 1-10 microm long. Arrays later recondensed by 3-8 h of hormone treatment. The degree of decondensation was proportional to the amount of transcript produced by the array as detected by RNA FISH. Decondensation was blocked by two different drugs that inhibit polymerase II, 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) and alpha-amanitin. These observations demonstrate a role for polymerase in producing and maintaining decondensed chromatin. They also support fiber-packing models of higher order structure and suggest that transcription from a natural promoter may occur at much higher DNA-packing densities than reported previously.

Increased tenascin expression in melanocytic tumors

Tenascin is a large extracellular matrix glycoprotein which is widely distributed in normal, hyperplastic and neoplastic tissues. Its function is unknown but it has been associated with the epithelial-stromal interactions, such as cell adhesion and movement which take place, e.g. in morphogenesis, cellular proliferation and neoplasia. In this study, we investigated tenascin expression in 70 benign, dysplastic and malignant melanocytic tumors by using immunohistochemistry and monoclonal anti-tenascin 143DB7C8 antibody on paraffin sections. In all types of benign nevi, both intradermal, compound and junctional, there was a moderate expression of tenascin at the dermoepidermal junction and in the papillary dermis. In dysplastic nevi, the fibrotic areas in the papillary dermis also showed a moderate staining for tenascin. Invasive malignant melanomas showed the strongest expression of tenascin. In addition to the staining at the dermo-epidermal junction and in the papillary dermis, there was a variable expression of tenascin in the reticular dermis. Intracytoplasmic tenascin was detected both in primary melanomas and melanoma metastases. In conclusion, we have shown that tenascin expression is moderately increased in benign and dysplastic melanocytic tumors and greatly increased in malignant melanomas and melanoma metastases. The function of tenascin may be related to the cellular-stromal interactions and it is possibly associated with the proliferation and spread of the melanocytic tumors.

Androgen ablation induces tenascin expression in the rat prostate

Tenascin is a glycoprotein of the extracellular matrix of mesenchymal derived tissue compartments. Although the DNA sequences that code for tenascin production are known and the protein structure is well characterized, little is known about regulation of tenascin expression. Therefore, we are interested in hormonal aspects of tenascin expression. In this study, we addressed the question if androgen deprivation and prostatic involution would influence tenascin expression in the prostate. Methodologically, in two series of experiments, intact and orchiectomized testosterone propionate substituted male rats were subjected to one of the following hormonal treatments: a) flutamide, b) the antiandrogen casodex, and c) cyproterone acetate (CPA). As controls in each series, we used untreated controls and orchiectomized rats. After a period of 14 days of treatment, prostates were removed. Tenascin immunostaining of the sectioned specimen from the control and the hormonally treated animals demonstrated the following: 1) Little, if any tenascin immunoreactivity was detectable in prostates of untreated animals. 2) Androgen deprivation with either treatment resulted in tenascin expression in the stroma of the prostates. 3) Tenascin expression appeared to be variable both semiquantitatively and in the staining pattern detectable except in prostates treated with CPA, in which we observed the most uniform and most widespread staining pattern. From these results, we conclude that androgen deprivation induces tenascin expression in the stroma of the involuting prostate. Remodelling of the extracellular matrix of the stroma, known to appear in the process of prostate involution by androgen ablation, represents a process which has not been discussed with tenascin expression so far.

The borderline: basement membranes and the transition from premalignant to malignant neoplasia

In this paper, the use of immunohistochemistry for the analysis of basement membrane components and related extracellular matrix proteins in human cancer is reviewed. Basement membranes in cancer are dynamic structures that are constantly degraded but also deposited, in close collaboration between tumor cells and stromal cells. Basement membrane immunohistochemistry, using antibodies against type IV collagen and laminin, appears to be a useful tool in the analysis of lesions on the borderline between premalignant and malignant. Basement membrane interruptions, however, cannot be used as the only criterion for the diagnosis of malignancy. Type VII collagen is often degraded prior to type IV collagen and laminin in early invasion. This protein also tends to be expressed in carcinomas when it is not found in the corresponding normal tissue. Tenascin seems to play a complex role in the development of human tumors, including promotion of cell growth and differentiation, cell migration during invasion, and tissue remodeling during the development of primary and metastatic lesions. Further systemic exploration of extracellular matrix molecules in neoplasms should yield new information relevant for cancer biologists and useful in cancer diagnosis.

RNA polymerase: structural determinant of the chromatin loop and the chromosome

Current models for RNA synthesis involve an RNA polymerase that tracks along a static template. However, research on chromatin loops suggests that the template slides past a stationary polymerase; individual polymerases tie the chromatin fibre into loops and clusters of polymerases determine the basic structure of the interphase and metaphase chromosome. RNA polymerase is then both a player and a manager of the chromosome loop.

Expression of human tenascin in synovitis and its regulation by interleukin-1

OBJECTIVE

Tenascin is an extracellular matrix glycoprotein with effects on cell adhesion, cell migration, and lymphocyte activation. We proposed to identify the expression of human tenascin messenger RNA (mRNA) and protein in inflammatory synovitis and in normal synovium, and to identify potential regulatory cytokines.

METHODS

Immunohistochemistry and in situ hybridization were used to identify the expression of tenascin in synovium. Northern blot analysis of RNA and both immunoblot analysis and enzyme-linked immunosorbent assay of proteins were used to identify tenascin in synovial cell cultures.

RESULTS

Tenascin was found along the synovial lining layer and in perivascular areas of normal synovium. In inflammatory synovitis, tenascin protein and mRNA expression were shown to be increased in the synovial lining layer, in perivascular areas, in lymphoid aggregates, and in areas of fibrosis. Interleukin-1, a major mediator of tissue injury in inflammatory synovitis, induced tenascin expression and deposition in primary synovial fibroblast cultures.

CONCLUSION

Tenascin mRNA and protein are increased in inflammatory synovitis, and interleukin-1 is an inducer of tenascin in synovial fibroblasts. This identifies a new pathway by which interleukin-1 alters the extracellular matrix composition in synovitis. Since tenascin has effects on lymphocyte activation and cell adhesion, the induction of tenascin in inflammatory synovitis may play a role in the pathophysiology of arthritis.

A unified model of eukaryotic chromosomes

A revised model of DNA packaging into chromosomes is presented. Its features are consistent with observed structural dimensions and the molecular periodicities related to transcription, replication and matrix attachment domains. The transitions between euchromatic, heterochromatic and metaphase states are explained simply. Molecular and physical properties of chromosomal bands, and their correlation with specific DNA sequence motifs are discussed.

The ultrastructure of upstream and downstream regions of an active Balbiani ring gene

When active, the 37 kb Balbiani ring genes are known to form transcription loops with an almost fully extended chromatin axis. Here we examine the upstream and downstream regions of such transcription loops by electron microscopy. We demonstrate that a loop starts and ends in tightly packed chromatin; the two anchoring sites are clearly separated from each other in space. The upstream, nontranscribed region consists of a thin, extended, apparently flexible and nucleosome-free fiber corresponding to about 0.5 kb DNA. The downstream, nontranscribed region appears as a 200 nm long nucleofilament loosely coiled into a short, thick chromatin fiber and estimated to contain about 3 kb DNA.

Low degree of ubiquitination of histone 2A in the dipteran Chironomus tentans

A polyclonal antibody to ubiquitin has been prepared and shown to react with both ubiquitin and ubiquitinated histone 2A (uH2A). Applying this antibody in Western blotting experiments, we have observed that the salivary glands of Chironomus tentans contain an unusually low amount of uH2A (1% of histone 2A), while the amount of free ubiquitin is as abundant as in other animal cells, e.g. HeLa cells. The same low content of uH2A was also found in diploid epidermal cells of Chironomus origin suggesting that the low amount is not a characteristic of the polytene state of chromatin in salivary gland cells but rather a property of C. tentans as a species. The significance of the low degree of ubiquitination is discussed in relation to the information available on the organization of Chironomus chromatin into unusually large chromomeric entities.

A BR 1 gene in Chironomus tentans has a composite structure: a large repetitive core block is separated from a short unrelated 3'-terminal domain by a small intron

The large Balbiani ring (BR) genes in the dipteran genus Chironomus have been considered to be homogeneous repetitive structures. Analysis of a genomic DNA segment now reveals that a BR 1 gene in C. tentans is a composite gene, consisting of two different types of sequences. A 15-20 kb core block of tandemly arranged repeat units extends close to the 3' end of the BR 1 gene and ends in repetitive structures partly different from the repeat units in the core block. A 55 bp long intron separates the core block, which probably constitutes a single exon, from a non-related 3'-exon, comprising the final 332 bp of the translated part of the gene. According to hydrophobicity and secondary structure predictions, the 3'-exon encoded peptide is distinctly different from the repetitive core block domain and attains a globular structure. The carboxyl-terminal peptide domain is likely to be a general feature of BR encoded proteins and may have important functions in the excretion and polymerisation of the secretory proteins.

Correlations between prostate chromatin structure and transcriptional activity and acceptor site distribution

Androgen-receptor complexes are intimately involved in the maintenance of rat ventral prostate chromatin in a transcriptionally active structure. The presence or absence of androgens influenced the quantity of transcriptionally active chromatin and the distribution of acceptor sites for androgen-receptor complexes as probed by endonucleolytic cleavage. After castration, changes in the sedimentation rates of nucleosome oligomers were consistent with the absence of androgen-receptor complexes and elongating polyribonucleotide chains. These changes were accompanied by decreases in the ability of chromatin released under conditions of minimal nuclease digestion to bind androgen-receptor complexes and to support incorporation of RNA precursors responsive to androgenic stimulation. Saturation analyses of chromatin and nuclear fractions with partially purified androgen-receptor complexes revealed two affinity classes of acceptor sites. After castration, alterations in the intrachromatin distribution of acceptor sites were consistent with their redeployment into areas of decreased nuclease sensitivity, as previously shown for androgen-responsive genes.