Regulation Of Genome Expression Research Articles

Switching G-quadruplex to parallel duplex by molecular rotor clustering.

Switching of G-quadruplex (G4) structures between variant types of folding has been proved to be a versatile tool for regulation of genomic expression and development of nucleic acid-based constructs. Various specific ligands have been developed to target G4s in K+ solution with therapeutic prospects. Although G4 structures have been reported to be converted by sequence modification or a unimolecular ligand binding event in K+-deficient conditions, switching G4s towards non-G4 folding continues to be a great challenge due to the stability of G4 in physiological K+ conditions. Herein, we first observed the G4 switching towards parallel-stranded duplex (psDNA) by multimolecular ligand binding (namely ligand clustering) to overcome the switching barrier in K+. Purine-rich sequences (e.g. those from the KRAS promoter region) can be converted from G4 structures to dimeric psDNAs using molecular rotors (e.g. thioflavin T and thiazole orange) as initiators. The formed psDNAs provided multiple binding sites for molecular rotor clustering to favor subsequent structures with stability higher than the corresponding G4 folding. Our finding provides a clue to designing ligands with the competency of molecular rotor clustering to implement an efficient G4 switching.

Genome-Wide Association Mapping of Salinity Tolerance at the Seedling Stage in a Panel of Vietnamese Landraces Reveals New Valuable QTLs for Salinity Stress Tolerance Breeding in Rice.

Rice tolerance to salinity stress involves diverse and complementary mechanisms, such as the regulation of genome expression, activation of specific ion-transport systems to manage excess sodium at the cell or plant level, and anatomical changes that avoid sodium penetration into the inner tissues of the plant. These complementary mechanisms can act synergistically to improve salinity tolerance in the plant, which is then interesting in breeding programs to pyramidize complementary QTLs (quantitative trait loci), to improve salinity stress tolerance of the plant at different developmental stages and in different environments. This approach presupposes the identification of salinity tolerance QTLs associated with different mechanisms involved in salinity tolerance, which requires the greatest possible genetic diversity to be explored. To contribute to this goal, we screened an original panel of 179 Vietnamese rice landraces genotyped with 21,623 SNP markers for salinity stress tolerance under 100 mM NaCl treatment, at the seedling stage, with the aim of identifying new QTLs involved in the salinity stress tolerance via a genome-wide association study (GWAS). Nine salinity tolerance-related traits, including the salt injury score, chlorophyll and water content, and K+ and Na+ contents were measured in leaves. GWAS analysis allowed the identification of 26 QTLs. Interestingly, ten of them were associated with several different traits, which indicates that these QTLs act pleiotropically to control the different levels of plant responses to salinity stress. Twenty-one identified QTLs colocalized with known QTLs. Several genes within these QTLs have functions related to salinity stress tolerance and are mainly involved in gene regulation, signal transduction or hormone signaling. Our study provides promising QTLs for breeding programs to enhance salinity tolerance and identifies candidate genes that should be further functionally studied to better understand salinity tolerance mechanisms in rice.

Epigenetic Contribution and Genomic Imprinting Dlk1-Dio3 miRNAs in Systemic Lupus Erythematosus.

Systemic lupus erythematosus (SLE) is a multifactorial autoimmune disease that afflicts multiple organs, especially kidneys and joints. In addition to genetic predisposition, it is now evident that DNA methylation and microRNAs (miRNAs), the two major epigenetic modifications, are critically involved in the pathogenesis of SLE. DNA methylation regulates promoter accessibility and gene expression at the transcriptional level by adding a methyl group to 5′ cytosine within a CpG dinucleotide. Extensive evidence now supports the importance of DNA hypomethylation in SLE etiology. miRNAs are small, non-protein coding RNAs that play a critical role in the regulation of genome expression. Various studies have identified the signature lupus-related miRNAs and their functional contribution to lupus incidence and progression. In this review, the mutual interaction between DNA methylation and miRNAs regulation in SLE is discussed. Some lupus-associated miRNAs regulate DNA methylation status by targeting the DNA methylation enzymes or methylation pathway-related proteins. On the other hand, DNA hyper- and hypo-methylation are linked with dysregulated miRNAs expression in lupus. Further, we specifically discuss the genetic imprinting Dlk1-Dio3 miRNAs that are subjected to DNA methylation regulation and are dysregulated in several autoimmune diseases, including SLE.

Regulation of Virulence Gene Expression in Bacteria: A Review

Bacterial diseases are the leading cause of death worldwide through the involvement of virulence determinants. Virulence genes encode virulence factors which are essential for pathogenesis and infectious disease development in bacteria. The virulence factor concept helps for further investigations in the fields of microbial pathogenesis. The objective of this paper is to review regulation of virulence gene expression in bacteria. Virulence genes can be acquired via spontaneous mutations or through horizontal gene transfer mechanisms. Bacteria sense and respond to environmental stimuli in the host during infection. Successful host infection can be possible by coordinated expression of multitude of virulence genes. They adapt in the host by modulating its gene expression. Pathogenic bacteria possess many regulatory networks that control the production of virulence factors which enable the bacteria to survive and proliferate in the host. The most common forms of regulation of genome expression are by involvement of transcription factors, post-transcriptional modifications, ribo-regulation, environmental flux sensing, stress response and biofilm formation through quorum sensing. Virulence gene expression is carefully controlled to ensure correct spatiotemporal production of virulence factors. Regulation of virulence gene expression is very complex and influenced by environmental factors. Major regulatory control mechanisms used by pathogenic bacteria are alternative sigma factors and the two component regulatory systems. They do not always express virulence factors because it is energetically costly and reduces bacterial fitness. Therefore, they need to regulate their virulence properly in order to maximize their fitness and it is a key invasion strategy of pathogens. Keywords: Bacteria, Expression, Regulation, Virulence gene DOI: 10.7176/JBAH/11-3-02 Publication date: February 28 th 2021

RNA-SEQ IN THE STUDY OF VIRUS-ASSOCIATED TUMORS: CERVICAL CANCER (REVIEW)

For the last few years Next Generation Sequencing technique and its applications has took the leading position in the arsenal of analytical methods that are used for studying the mechanisms of neoplastic progression. Among various experimental opportunities Next Generation Sequencing provides, RNA-sequencing (RNA-Seq) is of great importance as it makes possible unraveling the highest levels of genome expression regulation, which define the molecular phenotype of cells in composition of a tumor. Considerable amount of current studies carried out with the use of RNA-Seq method are designed as pan-cancer integrated research, in which special attention is payed to virus-associated tumors, including papillomavirus-dependent cervical cancer. This review paper summarizes the results of RNA-Seq studies published world-wide within 2017-2019 years and carried out using clinical samples from cervical cancer patients. New facts concerning such hot topics as genomic and transcriptomic instability, neoantigen load, cellular and molecular heterogeneity, tumor epigenetics, antitumor and antiviral immune response, chronic inflammation, immune exhaustion, phenotypic plasticity and tumor cell resistance, are considered. The whole spectrum of issues that are actively discussed in published literature is systematized according to three levels of organization: «molecular», «cellular» and «organismal». The findings reviewed in the paper convincingly illustrate that wide usage of RNA-Seq technology for profiling primary tumors does facilitate moving to a new level of our understanding of the mechanisms of carcinogenesis and emergence of new directions in cancer treatment, namely targeted and immune-therapy.

Modulation of Histone Deacetylases (HDACs) Expression in Patients with and without Systemic Lupus Erythematosus: Possible Drug Targets for Treatment

The difficulties in designing an effective pharmacological therapy for Systemic Lupus Erythematosus (SLE) are due in part to the complexities of its pathophysiology. However, recently researchers have begun to look at the role chromatin modification plays in SLE. Chromatin modification is important in the regulation of genomic expression.

Analysis of alternative splicing in chicken embryo fibroblasts in response to reticuloendotheliosis virus infection

ABSTRACTAlternative splicing (AS) plays a significant role in regulation of genomic expression at the transcriptional level and is involved in many important biological functions of cells, thus a gene can be spliced into distinct transcript variants then translated to many different kinds of protein. Reticuloendotheliosis virus (REV) is a kind of retrovirus that can infect multiple avian species, leading to runting syndrome, immunosuppression and oncogenesis. In this present study, we analyzed AS in REV-infected chicken embryo fibroblasts (CEFs) which were inoculated with the second generation of REV (group VB) and compared with normal CEFs (group C) by high-throughput RNA sequencing technology. A total of 6,939 genes which were alternatively spliced were detected, among them, skipped exon (SE) was the most common pattern. Moreover, 5,607 AS genes were detected as differentially expressed; compared with group C, group VB has 2,825 genes upregulated significantly and 2,782 genes downregulated significantly. These 5,607 differentially expressed AS genes are involved in many important biological processes. Many of them are involved in apoptosis and tumourigenesis. We also proved, by agarose gel electrophoresis, that AS events predicted by our study are authentic and AS is closely related with apoptosis and tumourigenesis in REV-infected CEFs. Our study provides the best analysis to date of the potential link between AS and CEFs in response to REV infection.Research highlightsTranscriptomics analysis of REV-infected CEFs using high-throughput sequencing.Potential link between alternative splicing and CEFs in response to REV infection.Skipped exon is the most common spliced pattern in REV-infected CEFs.Differentially expressed genes mainly involved in apoptosis and tumourigenesis.

Can Reprogramming of Overall Epigenetic Memory and Specific Parental Genomic Imprinting Memory within Donor Cell-Inherited Nuclear Genome be a Major Hindrance for the Somatic Cell Cloning of Mammals? – A Review

Abstract Successful cloning of animals by somatic cell nuclear transfer (SCNT) requires epigenetic transcriptional reprogramming of the differentiated state of the donor cell nucleus to a totipotent embryonic ground state. It means that the donor nuclei must cease its own program of gene expression and restore a particular program of the embryonic genome expression regulation that is necessary for normal development. Transcriptional activity of somatic cell-derived nuclear genome during embryo pre- and postimplantation development as well as foetogenesis is correlated with the frequencies for spatial remodeling of chromatin architecture and reprogramming of cellular epigenetic memory. This former and this latter process include such covalent modifications as demethylation/re-methylation of DNA cytosine residues and acetylation/deacetylation as well as demethylation/re-methylation of lysine residues of nucleosomal core-derived histones H3 and H4. The main cause of low SCNT efficiency in mammals turns out to be an incomplete reprogramming of transcriptional activity for donor cell-descended genes. It has been ascertained that somatic cell nuclei should undergo the wide DNA cytosine residue demethylation changes throughout the early development of cloned embryos to reset their own overall epigenetic and parental genomic imprinting memories that have been established by re-methylation of the nuclear donor cell-inherited genome during specific pathways of somatic and germ cell lineage differentiation. A more extensive understanding of the molecular mechanisms and recognition of determinants for epigenetic transcriptional reprogrammability of somatic cell nuclear genome will be helpful to solve the problems resulting from unsatisfactory SCNT effectiveness and open new possibilities for common application of this technology in transgenic research focused on human biomedicine.

Distribution of heterochromatin markers in lampbrush chromosomes in birds

Changes in functional gene activity not affecting primary DNA structure can be inherited by a cell and in total represent epigenetic mechanisms of the genome expression regulation. Epigenetic genome modifications include DNA methylation, histone modifications, and binding of the proteins and noncoding RNA. The distribution of heterochromatin markers (such as methylated cytosine, HP1 heterochromatin protein, and modifications of H3, H4, and H2A histones) was analyzed by example of lampbrush chromosomes typical for growing bird oocytes. On the lampbrush chromosomes of domesticated chicken (Gallus gallus domesticus), Japanese quail (Coturnix japonica), and chaffinch (Fringilla coelebs), methylated cytosine was mainly detected in chromomeres, as well as in unextended regions of lateral loop axes. The largest accumulation of methylated cytosine was demonstrated by chromosome W and dense chromomeres of macro- and microchromosomes. The HP1β protein distribution in the lampbrush chromosomes corresponded in general to the distribution of methylated cytosine. Chromomeres of chromosome W as well as centromeric and terminal chromomeres of macro- and microchromosomes accumulated the highest amount of the HP1β protein as compared with the remaining chromomeres. The character of distribution of the H3K9 me3 and H3K27 me3 histone modifications, as well as phosphorylated H4 and H2A histones, was different. Phosphorylated H4 and H2A histones were distributed proportionally to the staining by DNA specific dyes and were accumulated in all chromosomes, while trimethylated H3K9 histone was enriched in the regions of constitutive heterochromatin. We assume that the HP1β heterochromatin protein is involved in compaction and transcriptional inactivation of the chromatin in chromomeres of the lampbrush chromosomes.

The Nucleoskeleton.

SUMMARYThe nucleoskeleton is an important structural feature of the metazoan nucleus and is involved in the regulation of genome expression and maintenance. The nuclear lamins are intermediate filament proteins that form a peripheral nucleoskeleton in concert with other lamin-associated proteins. Several other proteins normally found in the cytoskeleton have also been identified in the nucleus, but, as will be discussed here, their roles in forming a nucleoskeleton have not been elucidated. Nevertheless, mutations in lamins and lamin-associated proteins cause a spectrum of diseases, making them interesting targets for future research.

Mechanobiology of Chromatin and the Nuclear Interior

The view of the cell nucleus has evolved from an isolated, static organelle to a dynamic structure integrated with other mechanical elements of the cell. Both dynamics and integration appear to contribute to a mechanical regulation of genome expression. Here, we review physical structures inside the nucleus at different length scales and the dynamic reorganization modulated by cellular forces. First, we discuss nuclear organization focusing on self-assembly and disassembly of DNA structures and various nuclear bodies. We then discuss the importance of connections from the chromatin fiber through the nuclear envelope to the rest of the cell as they relate to mechanobiology. Finally, we discuss how cell stimulation, both chemical and physical, can alter nuclear structures and ultimately cellular function in healthy cells and in some model diseases. The view of chromatin and nuclear bodies as mechanical entities integrated with force generation from the cytoskeleton combines polymer physics with cell biology and medicine.

Long Noncoding RNA Ceruloplasmin Promotes Cancer Growth by Altering Glycolysis.

Long noncoding RNAs (lncRNAs) significantly influence the development and regulation of genome expression in cells. Here, we demonstrate the role of lncRNA ceruloplasmin (NRCP) in cancer metabolism and elucidate functional effects leading to increased tumor progression. NRCP was highly upregulated in ovarian tumors, and knockdown of NRCP resulted in significantly increased apoptosis, decreased cell proliferation, and decreased glycolysis compared with control cancer cells. In an orthotopic mouse model of ovarian cancer, siNRCP delivered via a liposomal carrier significantly reduced tumor growth compared with control treatment. We identified NRCP as an intermediate binding partner between STAT1 and RNA polymerase II, leading to increased expression of downstream target genes such as glucose-6-phosphate isomerase. Collectively, we report a previously unrecognized role of the lncRNA NRCP in modulating cancer metabolism. As demonstrated, DOPC nanoparticle-incorporated siRNA-mediated silencing of this lncRNA in vivo provides therapeutic avenue toward modulating lncRNAs in cancer.

Genome expression control during the photoperiodic response of aphids

AbstractAphids are major crop pests and show a high level of phenotypic plasticity. They display a seasonal, photoperiodically‐controlled polyphenism during their life cycle. In spring and summer, they reproduce efficiently by parthenogenesis. At the end of summer, parthenogenetic individuals detect the transition from short nights to long nights, which initiates the production of males and oviparous females within their offspring. These are the morphs associated with the autumn season. Deciphering the physiological and molecular events associated with this switch in reproductive mode in response to photoperiodic conditions is thus of key interest for understanding and explaining the remarkable capacity of aphids to adapt to fluctuations in their environment. The present review aims to compile earlier physiological studies, focussing on the neuroendocrine control of seasonal photoperiodism, as well as a series of large‐scale transcriptomic approaches made possible by the recent development of genomic resources for the model aphid species: the pea aphid Acyrthosiphon pisum. These analyses identify genetic programmes putatively involved in the control of the initial steps of detection and transduction of the photoperiodic signal, as well as in the regulation of the switch between asexual and sexual oogenesis within embryonic ovaries. The contribution of small RNAs pathways (and especially microRNAs) in the post‐transcriptional control of gene expression, as well as the role of epigenetic mechanisms in the regulation of genome expression associated with the photoperiodic response, is also summarized.

Déficits de remodelage de la chromatine et cancer: l’exemple du complexe SWI/SNF

The SWI/SNF complex is a multiprotein complex essential for chromatin remodelling. As such, it plays a key role in the epigenetic regulation of genome expression. This complex is composed of a dozen of proteins, some of which are constant and ubiquitous, especially SMARCB1and SMARCA4. Mutations in these genes are now described in an increasing number of tumors. Mutations in SMARCB1characterize the majority of rhabdoid tumors, an aggressive malignancy that exquisitely depends on this single genetic event. Rare rhabdoid tumors have mutation in SMARCA4, a genetic abnormality also found in some medulloblastomas. Many other tumor types, of variable aggressiveness, show an abnormal loss of expression of SMARCB1, but the genetic underlying cause most often remains elusive. The recent sequencings of whole exomes have described frequent mutations in other genes of the SWI/SNF complex: mutations in ARID1A in liver, gastric or bladder carcinomas, and PBRM1 mutations in renal cancers. These data establish the wide role of SWI/SNF complex in cancers and justify that major efforts should now be devoted to this common mechanism of human oncogenesis.

La génomique: un outil performant pour une gestion intégrée de l'élevage, de l'entraînement et de la santé des chevaux

La génomique étudie la structure, le fonctionnement et l’évolution des génomes par des approches globales et systématiques. Elle se subdivise en deux disciplines : la génomique structurale qui étudie l’architecture et l’évolution des génomes et la génomique fonctionnelle qui vise à caractériser la régulation de l’expression du génome. Les connaissances et les outils technologiques qui en découlent peuvent aujourd’hui trouver de multiples applications dans la filière équine, qu’il s’agisse du dépistage d’affections génétiques, de l’identification d’individus prédisposés à diverses maladies, de la gestion de l’entraînement ou de l’amélioration génétique de la population. Dans tous les cas, les vétérinaires équins ont évidemment un rôle essentiel à jouer pour mettre en place et promouvoir ces recherches dont ils seront par ailleurs les principaux bénéficiaires. En effet, qui mieux que les vétérinaires sont capables de tirer pleinement parti de ces informations génomiques pour prodiguer un conseil génétique, proposer des adaptations pertinentes de la conduite des élevages ou élaborer des stratégies de traitement novatrices ?

Similarity and distinction between organ-specific gibberellin-modulated genome expression between Arabidopsis and rice

Gibberellins (GAs) regulate plant growth and development, at least in part, by modulating downstream gene expression. Different plant species and plant organs are differentially responsive to GAs, though it remains unclear whether there exist organ and species specificities of GA responses at the genome expression level. Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) are model dicot and monocot plants. Microarray analyses indicate that in different organs of both species, small portions of the genomes are affected by GA3 or paclobutrazol (PAC), a gibberellin biosynthetic inhibitor. Gene Ontology analyses reveal that GA3 regulates genes in almost all major functional categories of both species. Functional categorization of GA3-responsive homologous genes suggests that some features of GA3 regulation of genome expression are conserved between the two species. Venn diagrams and cluster display analyses show that only a small gene portion is shared between each pair of rice and Arabidopsis organs, strongly supporting the presence of organ specificity of GA3-regulated gene expression in both species.

Analysis of porcine MHC using microarrays

The major histocompatibility complex (MHC) in Mammals is one of the most gene dense regions of the genome and contains the polymorphic histocompatibility gene families known to be involved in pathogen response and control of auto-immunity. The MHC is a complex genetic system that provides an interesting model system to study genome expression regulation and genetic diversity at the megabase scale. The pig MHC or SLA (Swine Leucocyte Antigen) complex spans 2.4 megabases and 151 loci have been annotated. We will review key results from previous RNA expression studies using microarrays containing probes specific to annotated loci within SLA and in addition present novel data obtained using high-density tiling arrays encompassing the whole SLA complex. We have focused on transcriptome modifications of porcine peripheral blood mononuclear cells stimulated with a mixture of phorbol myristate acetate and ionomycin known to activate B and T cell proliferation. Our results show that numerous loci mapping to the SLA complex are affected by the treatment. A general decreased level of expression for class I and II genes and an up-regulation of genes involved in peptide processing and transport were observed. Tiling array-based experiments contributed to refined gene annotations as presented for one SLA class I gene referred to as SLA-11. In conclusion, high-density tiling arrays can serve as an excellent tool to draw comprehensive transcription maps, and improve genome annotations for the SLA complex. We are currently studying their relevance to characterize SLA genetic diversity in combination with high throughput next generation sequencing.

CYTO 2010—Overview of the XXV ISAC Congress Proceedings Issue of Cytometry Part A

issue of Cytometry Part A presents the second occasionon which a call has been issued to encourage authors to sub-mit their best work to the Journal for publication in a specialCongress Proceedings Issue of Cytometry. The incentive forsubmission was that accepted papers would be guaranteed anoral presentation at the XXV ISAC Congress in Seattle—CYTO 2010. The manuscripts submitted for the call werereviewed via the normal Cytometry Part A review process andthen by a second level of review by the Congress OrganizingCommittee. The outcome of this strict peer-review processwas that nine papers were accepted for the Proceedings Issueof Cytometry Part A. The research articles provide excellentexamples of some of the latest trends in the field of cytometryand we highlight them here in this editorial review. The topicsof the accepted papers range from application of 12-color flowcytometry through characterization of new probes and investi-gation of cytoskeleton elements to analysis of nuclear structurefrom histopathology images.Modern polychromatic flow cytometry can providehigher resolution approaches for the dissection and identifica-tion of cell subpopulations (1,2). In this issue, the paper byAutissier et al. (page 410) describes how 12-color flow cytome-try can be used for studying the phenotypes of lymphocyte,monocyte, and dendritic cell subsets. The authors developed asingle flow cytometry panel that allows for simultaneousdetection of the lymphocyte and monocyte cell populationsand all known DC subsets. Studying these crucial subpopula-tions of the immune system in one single panel may give abroader view of the immune response during HIV infectionand can be used for monitoring AIDS pathogenesis.Polychromatic cytometry has become increasingly impor-tant in slide-based applications with the drive to increase thenumber of measurable fluorochromes for multiparametricanalysis. New fluorochromes have been introduced where thefluorescent dyes possess different optical characteristicsincluding spectral range, lifetime signatures, and improvedphotostability (3–5). The special feature of slide-based cyto-metry is that analyzed fields can be revisited, providing a basisfor the application of sequential photobleaching of fluoro-chromes next to very photostable dyes to increase the numberof parameters captured. In this issue, Wessels et al. (page 420)analyzed the newly available NorthernLights secondary anti-bodies for use in slide-based cytometry and microscopy. Theypointed out that since the NorthernLights are bright, resistantto photobleaching, stable in alcohols and xylene, these dyesare promising candidates for use with most laser- and HBO/XBA-based fluorescence microscopy techniques. It is antici-pated that combination of NorthernLights with laser scanningcytometry could provide a better methodology for analysis oftumor dissemination to bone marrow and lymph node (6).The other group of fluorescent probes aims to stain cellorganelles with high specificity. Development of fluorescent,organelle-targeted probes has been driven by an interest in dis-covering new probes that excite and emit in the visible spec-

Structure–Activity Analysis of Semisynthetic Nucleosomes: Mechanistic Insights into the Stimulation of Dot1L by Ubiquitylated Histone H2B

Post-translational modification of histones plays an integral role in regulation of genomic expression through modulation of chromatin structure and function. Chemical preparations of histones bearing these modifications allows for comprehensive in vitro mechanistic investigation into their action to deconvolute observations from genome-wide studies in vivo. Previously, we reported the semisynthesis of ubiquitylated histone H2B (uH2B) using two orthogonal expressed protein ligation reactions. Semisynthetic uH2B, when incorporated into nucleosomes, directly stimulates methylation of histone H3 lysine 79 (K79) by the methyltransferase, disruptor of telomeric silencing-like (Dot1L). Although recruitment of Dot1L to the nucleosomal surface by uH2B could be excluded, comprehensive mechanistic analysis was precluded by systematic limitations in the ability to generate uH2B in large scale. Here we report a highly optimized synthesis of ubiquitylated H2B bearing a G76A point mutation u(G76A)H2B, yielding tens of milligrams of ubiquitylated protein. u(G76A)H2B is indistinguishable from the native uH2B by Dot1L, allowing for detailed studies of the resultant trans-histone crosstalk. Kinetic and structure-activity relationship analyses using u(G76A)H2B suggest a noncanonical role for ubiquitin in the enhancement of the chemical step of H3K79 methylation. Furthermore, titration of the level of uH2B within the nucleosome revealed a 1:1 stoichiometry of Dot1L activation.

Functional analysis and quantitative determination of the expression profile of human parvovirus B19

Comprehension of the pathogenetic potential of human parvovirus B19 requires the definition of the complete spectrum of cellular tropism and a functional analysis of the viral genome in infected cells. In this study, we carried out a systematic functional analysis of B19 virus genome in the course of infection of susceptible bone marrow mononuclear cells and myeloblastoid UT7/EpoS1 cells, in terms of dynamics of nucleic acid synthesis. A PCR array was designed and a comprehensive analysis was performed by quantitative PCR and RT-PCR, yielding extended information on the presence and abundance of the diverse classes of viral nucleic acids, on the temporal regulation of genome expression and on its relationship with the cell cycle. The analysis performed indicate that the synthesis of viral nucleic acids is correlated to the progression through the S phase of the cell cycle, that an extended pattern of transcriptional activity occurs throughout the course of infection, with a maximal rate of transcription preceding the onset of S-phase dependent replication of the viral genome, and that utilization of transcript processing signals is relatively constant throughout the course of infection. The information obtained led to the definition of a unified model of functional and expression profiling of parvovirus B19 genome.