The 33 kb transcript of the chicken ?-globin gene domain is part of the nuclear matrix

Is RNA the working genome in eukaryotes ? The 60 year evolution of a conceptual challenge

About 80 years ago, in 1943, after a century of biochemical and genetic research, DNA was established as the carrier of genetic information. At the onset of Molecular Biology around 1960, the genome of living organisms embodied 3 basic, still unknown paradigms: its composition, organisation and expression. Between 1980 and 1990, its replication was understood, and ideas about its 3D-organisation were suggested and finally confirmed by 2010. The basic mechanisms of gene expression in higher organisms, the synthesis of precursor RNAs and their processing into functional RNAs, were also discovered about 60 years ago in 1961/62. However, some aspects were then, and are still now debated, although the latest results in post-genomic research have confirmed the basic principles. When my history-essay was published in 2003, describing the discovery of RNA processing 40 years earlier, the main facts were not yet generally confirmed or acknowledged. The processing of pre-rRNA to 28 S and 18 S rRNA was clearly demonstrated, confirmed by others and generally accepted as a fact. However, the "giant" size of pre-mRNA 10-100 kb-long and pervasive DNA transcription were still to be confirmed by post-genomic methods. It was found, surprisingly, that up to 90% of DNA is transcribed in the life cycle of eukaryotic organisms thus showing that pervasive transcription was the general rule. In this essay, we shall take a journey through the 60-year history of evolving paradigms of gene expression which followed the emergence of Molecular Biology, and we will also evoke some of the "folklore" in research throughout this period. Most important was the growing recognition that although the genome is encoded in DNA, the Working Genome in eukaryotic organisms is RNA.

Primary transcripts: From the discovery of RNA processing to current concepts of gene expression - Review

The main purpose of this review is to recall for investigators - and in particular students -, some of the early data and concepts in molecular genetics and biology that are rarely cited in the current literature and are thus invariably overlooked. There is a growing tendency among editors and reviewers to consider that only data produced in the last 10-20 years or so are pertinent. However this is not the case. In exact science, sound data and lucid interpretation never become obsolete, and even if forgotten, will resurface sooner or later. In the field of gene expression, covered in the present review, recent post-genomic data have indeed confirmed many of the earlier results and concepts developed in the mid-seventies, well before the start of the recombinant DNA revolution. Human brains and even the most powerful computers, have difficulty in handling and making sense of the overwhelming flow of data generated by recent high-throughput technologies. This was easier when low throughput, more integrative methods based on biochemistry and microscopy dominated biological research. Nowadays, the need for organising concepts is ever more important, otherwise the mass of available data can generate only "building ruins" - the bricks without an architect. Concepts such as pervasive transcription of genomes, large genomic domains, full domain transcripts (FDTs) up to 100 kb long, the prevalence of post-transcriptional events in regulating eukaryotic gene expression, and the 3D-genome architecture, were all developed and discussed before 1990, and are only now coming back into vogue. Thus, to review the impact of earlier concepts on later developments in the field, I will confront former and current data and ideas, including a discussion of old and new methods. Whenever useful, I shall first briefly report post-genomic developments before addressing former results and interpretations. Equally important, some of the terms often used sloppily in scientific discussions will be clearly defined. As a basis for the ensuing discussion, some of the issues and facts related to eukaryotic gene expression will first be introduced. In chapter 2 the evolution in perception of biology over the last 60 years and the impact of the recombinant DNA revolution will be considered. Then, in chapter 3 data and theory concerning the genome, gene expression and genetics will be reviewed. The experimental and theoretical definition of the gene will be discussed before considering the 3 different types of genetic information - the "Triad" - and the importance of post-transcriptional regulation of gene expression in the light of the recent finding that 90% of genomic DNA seems to be transcribed. Some previous attempts to provide a conceptual framework for these observations will be recalled, in particular the "Cascade Regulation Hypothesis" (CRH) developed in 1967-85, and the "Gene and Genon" concept proposed in 2007. A knowledge of the size of primary transcripts is of prime importance, both for experimental and theoretical reasons, since these molecules represent the primary units of the "RNA genome" on which most of the post-transcriptional regulation of gene expression occurs. In chapter 4, I will first discuss some current post-genomic topics before summarising the discovery of the high Mr-RNA transcripts, and the investigation of their processing spanning the last 50 years. Since even today, a consensus concerning the real form of primary transcripts in eukaryotic cells has not yet been reached, I will refer to the viral and specialized cellular models which helped early on to understand the mechanisms of RNA processing and differential splicing which operate in cells and tissues. As a well-studied example of expression and regulation of a specific cellular gene in relation to differentiation and pathology, I will discuss the early and recent work on expression of the globin genes in nucleated avian erythroblasts. An important concept is that the primary transcript not only embodies protein-coding information and regulation of its expression, but also the 3D-structure of the genomic DNA from which it was derived. The wealth of recent post-genomic data published in this field emphasises the importance of a fundamental principle of genome organisation and expression that has been overlooked for years even though it was already discussed in the 1970-80ties. These issues are addressed in chapter 5 which focuses on the involvement of the nuclear matrix and nuclear architecture in DNA and RNA biology. This section will make reference to the Unified Matrix Hypothesis (UMH), which was the first molecular model of the 3D organisation of DNA and RNA. The chapter on the "RNA-genome and peripheral memories" discusses experimental data on the ribonucleoprotein complexes containing pre-mRNA (pre-mRNPs) and mRNA (mRNPs) which are organised in nuclear and cytoplasmic spaces respectively. Finally, "Outlook " will enumerate currently unresolved questions in the field, and will propose some ideas that may encourage further investigation, and comprehension of available experimental data still in need of interpretation. In chapter 8, some propositions and paradigms basic to the authors own analysis are discussed. "In conclusion" the raison d'être of this review is recalled and positioned within the overall framework of scientific endeavour.

Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure

BACKGROUND

In homeotherms, the alpha-globin gene clusters are located within permanently open genome regions enriched in housekeeping genes. Terminal erythroid differentiation results in dramatic upregulation of alpha-globin genes making their expression comparable to the rRNA transcriptional output. Little is known about the influence of the erythroid-specific alpha-globin gene transcription outburst on adjacent, widely expressed genes and large-scale chromatin organization. Here, we have analyzed the total transcription output, the overall chromatin contact profile, and CTCF binding within the 2.7 Mb segment of chicken chromosome 14 harboring the alpha-globin gene cluster in cultured lymphoid cells and cultured erythroid cells before and after induction of terminal erythroid differentiation.

RESULTS

We found that, similarly to mammalian genome, the chicken genomes is organized in TADs and compartments. Full activation of the alpha-globin gene transcription in differentiated erythroid cells is correlated with upregulation of several adjacent housekeeping genes and the emergence of abundant intergenic transcription. An extended chromosome region encompassing the alpha-globin cluster becomes significantly decompacted in differentiated erythroid cells, and depleted in CTCF binding and CTCF-anchored chromatin loops, while the sub-TAD harboring alpha-globin gene cluster and the upstream major regulatory element (MRE) becomes highly enriched with chromatin interactions as compared to lymphoid and proliferating erythroid cells. The alpha-globin gene domain and the neighboring loci reside within the A-like chromatin compartment in both lymphoid and erythroid cells and become further segregated from the upstream gene desert upon terminal erythroid differentiation.

CONCLUSIONS

Our findings demonstrate that the effects of tissue-specific transcription activation are not restricted to the host genomic locus but affect the overall chromatin structure and transcriptional output of the encompassing topologically associating domain.

A long non-coding RNA promotes full activation of adult gene expression in the chicken α-globin domain

Long non-coding RNAs (lncRNAs) were recently shown to regulate chromatin remodelling activities. Their function in regulating gene expression switching during specific developmental stages is poorly understood. Here we describe a nuclear, non-coding transcript responsive for the stage-specific activation of the chicken adult α(D) globin gene. This non-coding transcript, named α-globin transcript long non-coding RNA (lncRNA-αGT) is transcriptionally upregulated in late stages of chicken development, when active chromatin marks the adult α(D) gene promoter. Accordingly, the lncRNA-αGT promoter drives erythroid-specific transcription. Furthermore, loss of function experiments showed that lncRNA-αGT is required for full activation of the α(D) adult gene and maintenance of transcriptionally active chromatin. These findings uncovered lncRNA-αGT as an important part of the switching from embryonic to adult α-globin gene expression, and suggest a function of lncRNA-αGT in contributing to the maintenance of adult α-globin gene expression by promoting an active chromatin structure.

Information theory, gene expression, and combinatorial regulation: a quantitative analysis

According to a functional definition of the term "gene", a protein-coding gene corresponds to a polypeptide and, hence, a coding sequence. It is therefore as such not yet present at the DNA level, but assembled from possibly heterogeneous pieces in the course of RNA processing. Assembly and regulation of genes require, thus, information about when and in which quantity specific polypeptides are to be produced. To assess this, we draw upon precise biochemical data. On the basis of our conceptual framework, we also develop formal models for the coordinated expression of specific sets of genes through the interaction of transcripts and mRNAs and with proteins via a precise putative regulatory code. Thus, the nucleotides in transcripts and mRNA are not only arranged into amino acid-coding triplets, but at the same time may participate in regulatory oligomotifs that provide binding sites for specific proteins. We can then quantify and compare product and regulatory information involved in gene expression and regulation.

Regulation of gene expression and the transcription factor cycle hypothesis

Post-genomic data show unexpected extent of the transcribed genome and the size of individual primary transcripts. Hence, most cis-regulatory modules (CRMs) binding transcription factors (TFs) at promotor, enhancer and other sites are actually transcribed within full domain transcripts (FDTs). The ensemble of these CRMs placed way upstream of exon clusters, downstream and in intronic or intergenic positions represent a program of gene expression which has been formally analysed within the Gene and Genon concept [1,2]. This concept has emphasised the necessity to separate product information from regulative information to allow information-theoretic analysis of gene expression. Classically, TFs have been assumed to act at DNA level exclusively but evidence has accumulated indicating eventual post-transcriptional functions. The transcription factor cycle (TFC) hypothesis suggests the transfer of DNA-bound factors to nascent RNA. Exerting downstream functions in RNA processing and transport, these factors would be liberated by RNA processing and cycle back to the DNA maintaining active transcription. Sequestered on RNA in absence of processing they would constitute a negative feedback loop. The TFC concept may explain epigenetic regulation in mitosis and meiosis. In mitosis control factors may survive as single proteins but also attached to FDTs as organised complexes. This process might perpetuate in cell division conditioning of chromatin for transcription. As observed on lampbrush chromosomes formed in avian and amphibian oogenesis, in meiosis the genome is fully transcribed and oocytes conserve high Mr RNA of high sequence complexity. When new interphase chromosomes form in daughter cells and early embryogenesis, TFs and other factors attached to RNA might be reinserted onto the DNA.

Enhancer-promoter interference and its prevention in transgenic plants

Biotechnology has several advantages over conventional breeding for the precise engineering of gene function and provides a powerful tool for the genetic improvement of agronomically important traits in crops. In particular, it has been exploited for the improvement of multiple traits through the simultaneous introduction or stacking of several genes driven by distinct tissue-specific promoters. Since transcriptional enhancer elements have been shown to override the specificity of nearby promoters in a position- and orientation-independent manner, the co-existence of multiple enhancers/promoters within a single transgenic construct could be problematic as it has the potential to cause the mis-expression of transgene product(s). In order to develop strategies with, which to prevent such interference, a clear understanding of the mechanisms underlying enhancer-mediated activation of target promoters, as well as the identification of DNA sequences that function to block these interactions in plants, will be necessary. To date, little is known concerning enhancer function in plants and only a very limited number of enhancer-blocking insulators that operate in plant species have been identified. In this review, we discuss the current knowledge surrounding enhancer-promoter interactions, as well as possible means of minimizing such interference during plant transformation experiments.

Both the constitutive cauliflower mosaic virus 35S and tissue-specific AGAMOUS enhancers activate transcription autonomously in Arabidopsis thaliana

The expression of eukaryotic genes from their cognate promoters is often regulated by the action of transcriptional enhancer elements that function in an orientation-independent manner either locally or at a distance within a genome. This interactive nature often provokes unexpected interference within transgenes in plants, as reflected by misexpression of the introduced gene and undesired phenotypes in transgenic lines. To gain a better understanding of the mechanism underlying enhancer/promoter interactions in a plant system, we analyzed the activation of a β-glucuronidase (GUS) reporter gene by enhancers contained within the AGAMOUS second intron (AGI) and the Cauliflower Mosaic Virus (CaMV) 35S promoter, respectively, in the presence and absence of a target promoter. Our results indicate that both the AGI and 35S enhancers, which differ significantly in their species of origin and in the pattern of expression that they induce, have the capacity to activate the expression of a nearby gene through the promoter-independent initiation of autonomous transcriptional events. Furthermore, we provide evidence that the 35S enhancer utilizes a mechanism resembling animal- and yeast-derived scanning or facilitated tracking models of long-distance enhancer action in its activation of a remote target promoter.

In embryonic chicken erythrocytes actively transcribed alpha globin genes are not associated with the nuclear matrix

The spatial organization of a 250 Kb region of chicken chromosome 14, which includes the alpha globin gene cluster, was studied using in situ hybridization of a corresponding BAC probe with nuclear halos. It was found that in non-erythroid cells (DT40) and cultured erythroid cells of definite lineage (HD3) the genomic region under study was partially (DT40 cells) or fully (HD3 cells) associated with the nuclear matrix. In contrast, in embryonic red blood cells (10-day RBC) the same area was located in the crown of DNA loops surrounding the nuclear matrix, although both globin genes and surrounding house-keeping genes were actively transcribed in these cells. This spatial organization was associated with the virtual absence of RNA polymerase II in nuclear matrices prepared from 10-day RBC. In contrast, in HD3 cells a significant portion of RNA polymerase II was present in nuclear matrices. Taken together, these observations suggest that in embryonic erythroid cells transcription does not occur in association with the nuclear matrix.

Noncoding RNA in development

Non-protein-coding sequences increasingly dominate the genomes of multicellular organisms as their complexity increases, in contrast to protein-coding genes, which remain relatively static. Most of the mammalian genome and indeed that of all eukaryotes is expressed in a cell- and tissue-specific manner, and there is mounting evidence that much of this transcription is involved in the regulation of differentiation and development. Different classes of small and large noncoding RNAs (ncRNAs) have been shown to regulate almost every level of gene expression, including the activation and repression of homeotic genes and the targeting of chromatin-remodeling complexes. ncRNAs are involved in developmental processes in both simple and complex eukaryotes, and we illustrate this in the latter by focusing on the animal germline, brain, and eye. While most have yet to be systematically studied, the emerging evidence suggests that there is a vast hidden layer of regulatory ncRNAs that constitutes the majority of the genomic programming of multicellular organisms and plays a major role in controlling the epigenetic trajectories that underlie their ontogeny.

Spatial configuration of the chicken alpha-globin gene domain: immature and active chromatin hubs

The spatial configuration of the chicken α-globin gene domain in erythroid and lymphoid cells was studied by using the Chromosome Conformation Capture (3C) approach. Real-time PCR with TaqMan probes was employed to estimate the frequencies of cross-linking of different restriction fragments within the domain. In differentiated cultured erythroblasts and in 10-day chick embryo erythrocytes expressing ‘adult’ α^A and α^D globin genes the following elements of the domain were found to form an ‘active’ chromatin hub: upstream Major Regulatory Element (MRE), −9 kb upstream DNase I hypersensitive site (DHS), −4 kb upstream CpG island, α^D gene promoter and the downstream enhancer. The α^A gene promoter was not present in the ‘active’ chromatin hub although the level of α^A gene transcription exceeded that of the α^D gene. Formation of the ‘active’ chromatin hub was preceded by the assembly of multiple incomplete hubs containing MRE in combination with either −9 kb DHS or other regulatory elements of the domain. These incomplete chromatin hubs were present in proliferating cultured erythroblasts which did not express globin genes. In lymphoid cells only the interaction between the α^D promoter and the CpG island was detected.

Gene and genon concept: coding versus regulation. A conceptual and information-theoretic analysis of genetic storage and expression in the light of modern molecular biology

We analyse here the definition of the gene in order to distinguish, on the basis of modern insight in molecular biology, what the gene is coding for, namely a specific polypeptide, and how its expression is realized and controlled. Before the coding role of the DNA was discovered, a gene was identified with a specific phenotypic trait, from Mendel through Morgan up to Benzer. Subsequently, however, molecular biologists ventured to define a gene at the level of the DNA sequence in terms of coding. As is becoming ever more evident, the relations between information stored at DNA level and functional products are very intricate, and the regulatory aspects are as important and essential as the information coding for products. This approach led, thus, to a conceptual hybrid that confused coding, regulation and functional aspects. In this essay, we develop a definition of the gene that once again starts from the functional aspect. A cellular function can be represented by a polypeptide or an RNA. In the case of the polypeptide, its biochemical identity is determined by the mRNA prior to translation, and that is where we locate the gene. The steps from specific, but possibly separated sequence fragments at DNA level to that final mRNA then can be analysed in terms of regulation. For that purpose, we coin the new term "genon". In that manner, we can clearly separate product and regulative information while keeping the fundamental relation between coding and function without the need to introduce a conceptual hybrid. In mRNA, the program regulating the expression of a gene is superimposed onto and added to the coding sequence in cis - we call it the genon. The complementary external control of a given mRNA by trans-acting factors is incorporated in its transgenon. A consequence of this definition is that, in eukaryotes, the gene is, in most cases, not yet present at DNA level. Rather, it is assembled by RNA processing, including differential splicing, from various pieces, as steered by the genon. It emerges finally as an uninterrupted nucleic acid sequence at mRNA level just prior to translation, in faithful correspondence with the amino acid sequence to be produced as a polypeptide. After translation, the genon has fulfilled its role and expires. The distinction between the protein coding information as materialised in the final polypeptide and the processing information represented by the genon allows us to set up a new information theoretic scheme. The standard sequence information determined by the genetic code expresses the relation between coding sequence and product. Backward analysis asks from which coding region in the DNA a given polypeptide originates. The (more interesting) forward analysis asks in how many polypeptides of how many different types a given DNA segment is expressed. This concerns the control of the expression process for which we have introduced the genon concept. Thus, the information theoretic analysis can capture the complementary aspects of coding and regulation, of gene and genon.

A facilitated tracking and transcription mechanism of long-range enhancer function

In the human ε−globin gene locus, the HS2 enhancer in the Locus Control Region regulates transcription of the embryonic ε-globin gene located over 10 kb away. The mechanism of long-range HS2 enhancer function was not fully established. Here we show that the HS2 enhancer complex containing the enhancer DNA together with RNA polymerase II (pol II) and TBP tracks along the intervening DNA, synthesizing short, polyadenylated, intergenic RNAs to ultimately loop with the ε-globin promoter. Guided by this facilitated tracking and transcription mechanism, the HS2 enhancer delivers pol II and TBP to the cis-linked globin promoter to activate mRNA synthesis from the target gene. An insulator inserted in the intervening DNA between the enhancer and the promoter traps the enhancer DNA and the associated pol II and TBP at the insulator site, blocking mid-stream the facilitated tracking and transcription mechanism of the enhancer complex, thereby blocking long-range enhancer function.

Mechanisms controlling activation of the alpha-globin gene domain in chicken erythroid cells

In this review we consider the organization of the chicken alpha-globin gene domain and mechanisms regulating the activity of this tissue-specific gene domain located in a potentially active (characterized by an increased sensitivity to nucleases) chromatin configuration in cells of all lineages. Both regulatory mechanisms ensuring repression of alpha-globin genes in non-erythroid cells and mechanisms responsible for activation of transcription of these genes during erythroid cell differentiation are discussed. The analysis of the structure-function organization of the chicken alpha-globin gene domain presented in this review is based mainly on the authors' own results obtained over the last 20 years. On discussing the hypotheses explaining the mechanisms controlling the functional activity of chicken alpha-globin gene domain, data obtained in studies of alpha-globin gene domains of other vertebrates are also analyzed.

Chromatin domains and regulation of transcription

Compartmentalization and compaction of DNA in the nucleus is the characteristic feature of eukaryotic cells. A fully extended DNA molecule has to be compacted 100,000 times to fit within the nucleus. At the same time it is critical that various DNA regions remain accessible for interaction with regulatory factors and transcription/replication factories. This puzzle is solved at the level of DNA packaging in chromatin that occurs in several steps: rolling of DNA onto nucleosomes, compaction of nucleosome fiber with formation of the so-called 30 nm fiber, and folding of the latter into the giant (50-200 kbp) loops, fixed onto the protein skeleton, the nuclear matrix. The general assumption is that DNA folding in the cell nucleus cannot be uniform. It has been known for a long time that a transcriptionally active chromatin fraction is more sensitive to nucleases; this was interpreted as evidence for the less tight compaction of this fraction. In this review we summarize the latest results on structure of transcriptionally active chromatin and the mechanisms of transcriptional regulation in the context of chromatin dynamics. In particular the significance of histone modifications and the mechanisms controlling dynamics of chromatin domains are discussed as well as the significance of spatial organization of the genome for functioning of distant regulatory elements.

The gene and the genon concept: a functional and information-theoretic analysis

'Gene' has become a vague and ill-defined concept. To set the stage for mathematical analysis of gene storage and expression, we return to the original concept of the gene as a function encoded in the genome, basis of genetic analysis, that is a polypeptide or other functional product. The additional information needed to express a gene is contained within each mRNA as an ensemble of signals, added to or superimposed onto the coding sequence. To designate this programme, we introduce the term 'genon'. Individual genons are contained in the pre-mRNA forming a pre-genon. A genomic domain contains a proto-genon, with the signals of transcription activation in addition to the pre-genon in the transcripts. Some contain several mRNAs and hence genons, to be singled out by RNA processing and differential splicing. The programme in the genon in cis is implemented by corresponding factors of protein or RNA nature contained in the transgenon of the cell or organism. The gene, the cis programme contained in the individual domain and transcript, and the trans programme of factors, can be analysed by information theory.

Globin genes transcriptional switching, chromatin structure and linked lessons to epigenetics in cancer: a comparative overview

At the present time research situates differential regulation of gene expression in an increasingly complex scenario based on interplay between genetic and epigenetic information networks, which need to be highly coordinated. Here we describe in a comparative way relevant concepts and models derived from studies on the chicken alpha- and beta-globin group of genes. We discuss models for globin switching and mechanisms for coordinated transcriptional activation. A comparative overview of globin genes chromatin structure, based on their genomic domain organization and epigenetic components is presented. We argue that the results of those studies and their integrative interpretation may contribute to our understanding of epigenetic abnormalities, from beta-thalassemias to human cancer. Finally we discuss the interdependency of genetic-epigenetic components and the need of their mutual consideration in order to visualize the regulation of gene expression in a more natural context and consequently better understand cell differentiation, development and cancer.

Non-coding transcripts far upstream of the epsilon-globin gene are distinctly expressed in human primary tissues and erythroleukemia cell lines

Non-coding exons of epsilon-globin mRNA originating within the 236 kb upstream region of the epsilon-globin gene were identified in human primary tissues and K562 cells. One predominant type of upstream epsilon mRNA, which originated in the -76 kb region 5' to the epsilon gene, was present in human primary tissues, whereas 11 other isoforms were identified in K562 cells. Fragment from the -76 kb region possessed promoter activity and a prominent DNase I hypersensitive site was formed in the region approximately 2 kb 5' to the -76 kb promoter in human fetal liver, but not in K562 cells. The promoter activity in the -236 kb region resided in a retrotransposon in K562 cells. A DNase I hypersensitive site was formed at the -236 kb promoter in K562 cells, but not in human fetal liver. We discussed these results in the context of intergenic transcription and chromatin opening in the beta-globin gene cluster.

Distal enhancer elements transcribe intergenic RNA in the IL-10 family gene cluster

The IL-10 gene and homologs IL-19, IL-20, and IL-24 are expressed within a highly conserved 145-kb cytokine gene cluster. Like the Th2 IL-4 cytokine gene cluster, it is feasible that there is coordinate regulation of these cytokines by distal regulatory elements spanning the locus. We initiated a search to characterize regulatory elements within the IL-10 family locus and present data herein on a conserved 40-kb region between the IL-19 and IL-10 genes. We map the location of 17 DNase I-hypersensitive sites in different murine T cell populations and identify three enhancer elements, which function in T cells in vitro. Two of these enhancer elements, located 9 kb upstream and 6.45 kb downstream of IL-10, display cell-specific function in the Th1-Th2 cell clones AE7 and D10 and also exhibit basic promoter activity. The downstream element, IL-10CNS+6.45, binds AP-1 in the absence of NFAT and expresses intergenic RNA in a Th2-specific manner, further validating its role as a Th2-specific enhancer/promoter element. We show that the five most highly conserved noncoding sequences in the 40-kb region transcribe intergenic RNA; four of these regions possess promoter activity in vitro that could account for the expression of these transcripts. Hence, we speculate that these novel regulatory elements in the IL-10 family gene locus function via an intermediate regulatory RNA.

The HS2 enhancer of the beta-globin locus control region initiates synthesis of non-coding, polyadenylated RNAs independent of a cis-linked globin promoter

The HS2 enhancer in the beta-globin locus control region (LCR) regulates transcription of the globin genes 10-50 kb away. Earlier studies show that a transcription mechanism initiated by the HS2 enhancer through the intervening DNA in the direction of the cis-linked promoter and gene mediates long-range enhancer function. Here, we further analyzed the enhancer-initiated RNAs and their mode of transcription from the HS2 enhancer in the endogenous genome of erythroid K562 cells, in plasmids integrated into K562 cells and in purified DNA used as template in in vitro transcription reactions. We found that the HS2 enhancer was able to initiate transcription autonomously in the absence of a cis-linked globin promoter. The enhancer-initiated, intergenic RNAs were different from the mRNA synthesized at the promoter in several aspects. The enhancer RNAs were synthesized not from a defined site but from multiple sites both within and as far as 1 kb downstream of the enhancer. The enhancer RNAs did not appear to contain a normal cap structure at the 5' ends. They were polyadenylated at multiple sites within 3 kb downstream of their initiation sites and were therefore shorter than 3 kb in lengths. The enhancer RNAs remained in discrete spots within the nucleus and were not processed into mRNA or translated into proteins. These particular features of enhancer-initiated transcription indicate that the transcriptional complex assembled by the enhancer was different from the basal transcription complex assembled at the promoter. The results suggest that in synthesizing non-coding, intergenic RNAs, the enhancer-assembled transcription complex could track through the intervening DNA to reach the basal promoter complex and activate efficient mRNA synthesis from the promoter.

RNA-dependent nuclear matrix contains a 33 kb globin full domain transcript as well as prosomes but no 26S proteasomes

Previously, we have shown that in murine myoblasts prosomes are constituents of the nuclear matrix; a major part of the latter was found to be RNase sensitive. Here, we further define the RNA-dependent matrix in avian erythroblastosis virus (AEV) transformed erythroid cells in relation to its structure, presence of specific RNA, prosomes and/or proteasomes. These cells transcribe but do not express globin genes prior to induction. Electron micrographs show little difference in matrices treated with DNase alone or with both, DNase and RNase. In situ hybridization with alpha globin riboprobes shows that this matrix includes globin transcripts. Of particular interest is that, apparently, a nearly 35 kb long globin full domain transcript (FDT), including genes, intergenic regions and a large upstream domain is a part of the RNA-dependent nuclear matrix. The 23K-type of prosomes, previously shown to be co-localized with globin transcripts in the nuclear RNA processing centers, were found all over the nuclear matrix. Other types of prosomes show different distributions in the intact cell but similar distribution patterns on the matrix. Globin transcripts and at least 80% of prosomes disappear from matrices upon RNase treatment. Interestingly, the 19S proteasome modulator complex is insensitive to RNase treatment. Only 20S prosomes but not 26S proteasomes are thus part of the RNA-dependent nuclear matrix. We suggest that giant pre-mRNA and FDTs in processing, aligning prosomes and other RNA-binding proteins are involved in the organization of the dynamic nuclear matrix. It is proposed that the putative function of RNA within the nuclear matrix and, thus, the nuclear dynamic architecture, might explain the giant size and complex organization of primary transcripts and their introns.

The upstream area of the chicken α-globin gene domain is transcribed in both directions in the same cells

It was demonstrated previously that in erythroid chicken cells an extended upstream area of the alpha-globin gene domain is transcribed in both directions as a part of ggPRX gene and a part of a full domain transcript of the alpha-globin gene domain. Here, we show that both DNA chains of the above-mentioned region are transcribed in the same cells and that the corresponding transcripts coexist in nuclei. The data obtained suggest that cells possess a molecular mechanism which in some cases prevents the formation of dsRNA and subsequent destruction of both transcripts in spite of the presence of complementary RNA chains in the cell nucleus.

Specific radial positions of centromeres of human chromosomes X, 1, and 19 remain unchanged in chromatin-depleted nuclei of primary human fibroblasts: Evidence for the organizing role of the nuclear matrix

Radial positions of centromeres of human chromosomes X, 1, and 19 were determined in the nuclei of primary fibroblasts before and after removal of 60%-80% of chromatin. It has been demonstrated that the specific radial positions of these centromeres (more central for the chromosome 19 centromere and more peripheral for the centromeres of chromosomes 1 and X) remain unchanged in chromatin-depleted nuclei. Additional digestion of nuclear RNA did not influence this specific distribution. These results strongly suggest that the characteristic organization of interphase chromosomes is supported by the proteinous nuclear matrix and is not maintained by simple repulsing of negatively charged chromosomes.