Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells

Epigenetics, nervous system tumors, and cancer stem cells

Recent advances have begun to elucidate how epigenetic regulatory mechanisms are responsible for establishing and maintaining cell identity during development and adult life and how the disruption of these processes is, not surprisingly, one of the hallmarks of cancer. In this review, we describe the major epigenetic mechanisms (i.e., DNA methylation, histone and chromatin modification, non-coding RNA deployment, RNA editing, and nuclear reorganization) and discuss the broad spectrum of epigenetic alterations that have been uncovered in pediatric and adult nervous system tumors. We also highlight emerging evidence that suggests epigenetic deregulation is a characteristic feature of so-called cancer stem cells (CSCs), which are thought to be present in a range of nervous system tumors and responsible for tumor maintenance, progression, treatment resistance, and recurrence. We believe that better understanding how epigenetic mechanisms operate in neural cells and identifying the etiologies and consequences of epigenetic deregulation in tumor cells and CSCs, in particular, are likely to promote the development of enhanced molecular diagnostics and more targeted and effective therapeutic agents for treating recalcitrant nervous system tumors.

Correlation of expression of Nanog, Oct-4 and SOX-2 with tumor metastasis in colonic cancer

AIM: To investigate the expression of Nanog, Oct-4 and SOX-2 in colonic carcinoma and to analyze their relationship with tumor metastasis.

METHODS: Immunohistochemistry was used to evaluate the expression of Nanog, Oct-4 and SOX-2 in 80 colonic cancer surgical specimens. The correlation of Nanog, Oct-4 and SOX-2 expression with tumor histological differentiation, T stage, N stage and metastasis was analyzed.

RESULTS: Thirty-five patients had metastasis. The positive rates of SOX-2, Oct-4 and Nanog expression were significantly higher in the metastasis group than in the non-metastasis group (48.57% vs 17.78%, 51.43% vs 13.33%, 60% vs 26.67%, all P < 0.05). Nanog expression was significantly correlated with differentiation (P = 0.001), but expression of Nanog, Oct-4 and SOX-2 was not associated with T stage or N stage. Metastatic rate was higher in patients with positive expression of the three markers than in those with negative expression. Survival analysis showed that the time to develop metastasis was significant different among patients with differential expression of the three markers (P = 0.0001).

CONCLUSION: The expression of Nanog, Oct-4 and SOX-2 in tumor tissue can predict the postoperative metastasis of colonic cancer. Nanog, Oct-4 and SOX-2 are promising predictors for metastasis of colonic cancer.

Chromatin connections to pluripotency and cellular reprogramming

The pluripotent state of embryonic stem cells (ESCs) provides a unique perspective on regulatory programs that govern self-renewal and differentiation and somatic cell reprogramming. Here, we review the highly connected protein and transcriptional networks that maintain pluripotency and how they are intertwined with factors that affect chromatin structure and function. The complex interrelationships between pluripotency and chromatin factors are illustrated by X chromosome inactivation, regulatory control by noncoding RNAs, and environmental influences on cell states. Manipulation of cell state through the process of transdifferentiation suggests that environmental cues may direct transcriptional programs as cells enter a transiently "plastic" state during reprogramming.

RNA-mediated silencing mechanisms in mammalian cells

Noncoding RNAs are a structural component of the nuclear scaffold and have been implicated in controlling gene expression. In mammals, long noncoding RNAs contribute to the regulation of imprinted gene expression, dosage compensation, development, and tumorigenesis. RNA is also a component of pericentric heterochromatin, and transcripts have been identified at the chromosomal telomeres. The functions of noncoding RNAs are likely diverse, and their underlying mechanisms are just beginning to be understood. Several noncoding RNAs interact with chromatin-modifying complexes and might have a role in targeting chromatin modifications to specific regions of the genome. This suggests a prominent function of RNA in establishing histone modification and DNA methylation patterns in development. Studies on model systems such as X inactivation, the regulation of the Hox clusters, and genomic imprinting have begun to shed light on the role of noncoding RNAs in chromosomal organization and regulation of gene expression. Well-studied examples of noncoding RNAs include Xist, Air, Kcnq1ot1, HOTAIR, and Tsix. Here, a concise review of noncoding RNA function in mammals is given, and the present understanding and future directions of the field are summarized.

Non-coding RNA and antisense RNA. Nature's trash or treasure?

Although control of cellular function has classically been considered the responsibility of proteins, research over the last decade has elucidated many roles for RNA in regulation of not only the proteins that control cellular functions but also for the cellular functions themselves. In parallel to this advancement in knowledge about the regulatory roles of RNA there has been an explosion of knowledge about the role that epigenetics plays in controlling not only long-term cellular fate but also the short-term regulatory control of genes. Of particular interest is the crossover between these two worlds, a world where RNA can act out its part and subsequently elicit chromatin modifications that alter cellular function. Two main categories of RNA are examined here, non-coding RNA and antisense RNA both of which perform vital functions in controlling numerous genes, proteins and RNA itself. As the activities of non-coding and antisense RNA in both normal and aberrant cellular function are elucidated, so does the number of possible targets for pharmacopeic intervention.

Clinical implications of stem cell gene Oct-4 expression in breast cancer

PURPOSE

To explore the expression of stem cell genes in breast cancer and the relationship between stem cell gene expression and clinical and pathological characteristics and prognosis of breast cancer.

BACKGROUND

By now, stem cell differentiation-related genes and the relationship between the genes and clinic-pathological characteristics and prognosis of breast cancer are still unclear.

MATERIALS AND METHODS

CD44+/CD24- tumor cells were selected by Flow cytometry. The differential expression of genes between CD44+/CD24- tumor cells and non-CD44+/CD24- tumor cells were detected by RT(2) Profiler™ PCR Array. The expression of stem cell gene Octamer-4 (Oct-4) was analyzed by immunohistochemistry staining and the relationship between Oct-4 and clinicopathological parameters of breast cancer was determined.

RESULTS

Seven different genes including stem cell differentiation-related factors (CD44, Oct-4, and nestin), cell cycle regulators (APC and CDC2), and growth factors (HGF and TGF) were detected as significantly differently expressed between CD44+/CD24- tumor cells and non-CD44+/CD24- tumor cells. Oct-4 protein expressed significantly higher in cancerous tissues than adjacent-tumor tissues (P = 0.001). Moreover, we observed that the expression of Oct-4 protein was related to histological type, lymph node status and molecular type of breast cancer (P = 0.001, 0.006, and 0.001, respectively). After survival analysis, the cases with highly expressed Oct-4 protein attained a significantly poorer postoperative disease-specific survival than those with none/low expressed Oct-4 protein (P = 0.001). In the Cox regression test, tumor size, histological type, disease stage, lymph node metastasis, Her-2 and Oct-4 were detected as the independent prognostic factors (P = 0.031, 0.012, 0.001, 0.002, 0.030, and 0.003, respectively).

CONCLUSIONS

Oct-4 was highly expressed in CD44+/CD24- tumor cells, and may be a potential biomarker for the initiation, progression, and differentiation of breast cancer.

Competition between a noncoding exon and introns: Gomafu contains tandem UACUAAC repeats and associates with splicing factor-1

Gomafu (also referred to as RNCR2/MIAT) was originally identified as a noncoding RNA expressed in a particular set of neurons. Unlike protein-coding mRNAs, the Gomafu RNA escapes nuclear export and stably accumulates in the nucleus, making a unique nuclear compartment. Although recent studies have revealed the functional relevance of Gomafu in a series of physiological processes, the underlying molecular mechanism remains largely uncharacterized. In this report, we identified a chicken homologue of Gomafu using a comparative genomic approach to search for functionally important and conserved sequence motifs among evolutionarily distant species. Unexpectedly, we found that all Gomafu RNA examined shared a distinctive feature: tandem repeats of UACUAAC, a sequence that has been identified as a conserved intron branch point in the yeast Saccharomyces cerevisiae. The tandem UACUAAC Gomafu RNA repeats bind to the SF1 splicing factor with a higher affinity than the divergent branch point sequence in mammals, which affects the kinetics of the splicing reaction in vitro. We propose that the Gomafu RNA regulates splicing efficiency by changing the local concentration of splicing factors within the nucleus.

RNA-protein interactions in human health and disease

It is now clear that the genomes of many organisms encode thousands of large and small non-coding (nc)RNAs. However, relative to the discovery of ncRNAs the functions and mechanisms of ncRNAs remain disproportionately understood. One intriguing observation is that many ncRNAs are found to be associated with protein complexes including those involved in transcription regulation, post-transcriptional silencing, and epigentic regulation. These observations suggest that the functions and mechanisms of many of these ncRNAs may depend on their interactions with various protein complexes within the cell. In this review we discuss well known examples as well as newly emerging evidence of a widespread RNA-protein interactions in distinct biological processes in a wide range of organisms, and highlight the importance of developing new technologies to dissect these interactions. Finally, we propose that mis-regulation of ncRNAs interactions with their protein partners may contribute to human disease, and open up a novel approach to therapeutic interventions.

Non-coding RNAs as regulators of embryogenesis

Non-coding RNAs (ncRNAs) are emerging as key regulators of embryogenesis. They control embryonic gene expression by several means, ranging from microRNA-induced degradation of mRNAs to long ncRNA-mediated modification of chromatin. Many aspects of embryogenesis seem to be controlled by ncRNAs, including the maternal-zygotic transition, the maintenance of pluripotency, the patterning of the body axes, the specification and differentiation of cell types and the morphogenesis of organs. Drawing from several animal model systems, we describe two emerging themes for ncRNA function: promoting developmental transitions and maintaining developmental states. These examples also highlight the roles of ncRNAs in ensuring a robust commitment to one of two possible cell fates.

Epigenetic regulation of gene expression in human cells by noncoding RNAs

Emerging evidence has begun to suggest that a vast array of noncoding RNAs is operative in human cells, with some containing the ability to directly modulate gene transcription. While observations of noncoding-RNA-based epigenetic regulation of gene expression were in the past relegated to imprinted or X-linked genes, it is now becoming apparent that several different genes in differentiated cells may be under some form of RNA-based regulatory control. Studies have begun to discern certain aspects of an underlying mechanism of action whereby noncoding RNAs modulate gene transcription. Much of the evidence suggests that noncoding RNAs are functional in controlling gene transcription by the targeted recruitment of epigenetic silencing complexes to homology-containing loci in the genome. The results of these studies, as well as the implications that a vast array of noncoding-RNA-based regulatory networks may be operative in human cells, are discussed. Knowledge of this emerging RNA-based epigenetic regulatory network has implications in cellular evolution as well as in an entirely new area of pharmacopeia.

RNA interactions

Noncoding RNAs form an indispensible component of the cellular information processing networks, a role that crucially depends on the specificity of their interactions among each other as well as with DNA and protein. Patterns of intramolecular and intermolecular base pairs govern most RNA interactions. Specific base pairs dominate the structure formation of nucleic acids. Only little details distinguish intramolecular secondary structures from those cofolding molecules. RNA-protein interactions, on the other hand, are strongly dependent on the RNA structure as well since the sequence content of helical regions is largely unreadable, so that sequence specificity is mostly restricted to unpaired loop regions. Conservation of both sequence and structure thus this can give indications of the functioning of the diversity of ncRNAs.

Role of Oct4 in maintaining and regaining stem cell pluripotency

Pluripotency, a characteristic of cells in the inner cell mass of the mammalian preimplantation blastocyst as well as of embryonic stem cells, is defined as the ability of a cell to generate all of the cell types of an organism. A group of transcription factors is essential for the establishment and maintenance of the pluripotent state. Recent studies have demonstrated that differentiated somatic cells could be reverted to a pluripotent state by the overexpression of a set of transcription factors, further highlighting the significance of transcription factors in the control of pluripotency. Among these factors, a member of the POU transcription factor family, Oct4, is central to the machinery governing pluripotency. Oct4 is highly expressed in pluripotent cells and becomes silenced upon differentiation. Interestingly, the precise expression level of Oct4 determines the fate of embryonic stem cells. Therefore, to control the expression of Oct4 precisely, a variety of regulators function at multiple levels, including transcription, translation of mRNA and post-translational modification. Additionally, in cooperation with Sox2, Nanog and other members of the core transcriptional regulatory circuitry, Oct4 activates both protein-coding genes and noncoding RNAs necessary for pluripotency. Simultaneously, in association with transcriptional repressive complexes, Oct4 represses another set of targets involved in developmental processes. Importantly, Oct4 can re-establish pluripotency in somatic cells, and proper reprogramming of Oct4 expression is indispensable for deriving genuine induced pluripotent stem cell lines. In the past several years, genome-wide identification of Oct4 target genes and Oct4-centered protein interactomes has been reported, indicating that Oct4 exerts tight control over pluripotency regulator expression and protects embryonic stem cells in an undifferentiated state. Nevertheless, further investigation is required to fully elucidate the underlying molecular mechanisms through which Oct4 maintains and reinitiates pluripotency. Systemic and dynamic exploration of the protein complexes and target genes associated with Oct4 will help to elucidate the role of Oct4 more comprehensively.

REST and CoREST are transcriptional and epigenetic regulators of seminal neural fate decisions

Complementary transcriptional and epigenetic regulatory factors (e.g., histone and chromatin modifying enzymes and non-coding RNAs) regulate genes responsible for mediating neural stem cell maintenance and lineage restriction, neuronal and glial lineage specification, and progressive stages of lineage maturation. However, an overall understanding of the mechanisms that sense and integrate developmental signals at the genomic level and control cell type-specific gene network deployment has not emerged. REST and CoREST are central players in the transcriptional and epigenetic regulatory circuitry that is responsible for modulating neural genes, and they have been implicated in establishing cell identity and function, both within the nervous system and beyond it. Herein, we discuss the emerging context-specific roles of REST and CoREST and highlight our recent studies aimed at elucidating their neural developmental cell type- and stage-specific actions. These observations support the conclusion that REST and CoREST act as master regulators of key neural cell fate decisions.

MacroRNA underdogs in a microRNA world: evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA

The central dogma of molecular biology relegates RNAs to the role of "messengers" of genetic information, with proteins as the end products that perform key roles as regulators and effectors of biological processes. Notable exceptions include non-protein-coding RNAs, which function as adaptors (tRNAs) and ribosomal components (rRNAs) during translation, as well as in splicing (snRNAs) and RNA maturation including editing (snoRNAs). Genome and transcriptome projects have revealed, however, a significant number, rivaling the protein-coding transcripts, of non-protein-coding RNAs not related to these previously characterized transcript classes. Non-protein-coding RNA research has primarily focused on microRNAs, a small subclass of non-protein-coding RNAs, and their regulatory roles in gene expression, and these findings have been reviewed extensively. Here, we turn our attention to the larger, in number and size, long non-coding RNAs (lncRNAs), and review their evolutionary complexity and the growing evidence for their diverse mechanisms of action and functional roles in basic molecular and cellular biology and in human disease. In contrast to the focus on in-silico and expression studies in existing lncRNA literature, we emphasize direct evidence for lncRNA function, presenting experimental approaches and strategies for systematic characterization of lncRNA activities, with applications to known gene regulatory networks and diseases.

Impact of nuclear organization and dynamics on epigenetic regulation in the central nervous system: implications for neurological disease states

Epigenetic mechanisms that are highly responsive to interoceptive and environmental stimuli mediate the proper execution of complex genomic programs, such as cell type-specific gene transcription and posttranscriptional RNA processing, and are increasingly thought to be important for modulating the development, homeostasis, and plasticity of the central nervous system (CNS). These epigenetic processes include DNA methylation, histone modifications, and chromatin remodeling, all of which play roles in neural cellular diversity, connectivity, and plasticity. Further, large-scale transcriptomic analyses have revealed that the eukaryotic genome is pervasively transcribed, forming interleaved protein-coding RNAs and regulatory nonprotein-coding RNAs (ncRNAs), which act through a broad array of molecular mechanisms. Most of these ncRNAs are transcribed in a cell type- and developmental stage-specific manner in the CNS. A broad array of posttranscriptional processes, such as RNA editing and transport, can modulate the functions of both protein-coding RNAs and ncRNAs. Additional studies implicate nuclear organization and dynamics in mediating epigenetic regulation. The compartmentalization of DNA sequences and other molecular machinery into functional nuclear domains, such as transcription factories, Cajal bodies, promyelocytic leukemia nuclear bodies, nuclear speckles, and paraspeckles, some of which are found prominently in neural cells, is associated with regulation of transcriptional activity and posttranscriptional RNA processing. These observations suggest that genomic architecture and RNA biology in the CNS are much more complex and nuanced than previously appreciated. Increasing evidence now suggests that most, if not all, human CNS diseases are associated with either primary or secondary perturbations in one or more aspects of the epigenome. In this review, we provide an update of our emerging understanding of genomic architecture, RNA biology, and nuclear organization and highlight the interconnected roles that deregulation of these factors may play in diverse CNS disorders.

Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5

Long non-coding RNAs (lncRNAs) have been shown to epigenetically regulate certain genes in human cells. Here we report evidence for the involvement of an antisense lncRNA in the transcriptional regulation of the pluripotency-associated factor Oct4. When an lncRNA antisense to Oct4-pseudogene 5 was suppressed, transcription of Oct4 and Oct4 pseudogenes 4 and 5 was observed to increase. This increase correlated with a loss of silent state epigenetic marks and the histone methyltransferase Ezh2 at the Oct4 promoter. We observed this lncRNA to interact with nucleolin and PURA, a 35 kD single-stranded DNA and RNA binding protein, and found that these proteins may act to negatively regulate this antisense transcript.

Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes

BACKGROUND

Long considered to be the building block of life, it is now apparent that protein is only one of many functional products generated by the eukaryotic genome. Indeed, more of the human genome is transcribed into noncoding sequence than into protein-coding sequence. Nevertheless, whilst we have developed a deep understanding of the relationships between evolutionary constraint and function for protein-coding sequence, little is known about these relationships for non-coding transcribed sequence. This dearth of information is partially attributable to a lack of established non-protein-coding RNA (ncRNA) orthologs among birds and mammals within sequence and expression databases.

RESULTS

Here, we performed a multi-disciplinary study of four highly conserved and brain-expressed transcripts selected from a list of mouse long intergenic noncoding RNA (lncRNA) loci that generally show pronounced evolutionary constraint within their putative promoter regions and across exon-intron boundaries. We identify some of the first lncRNA orthologs present in birds (chicken), marsupial (opossum), and eutherian mammals (mouse), and investigate whether they exhibit conservation of brain expression. In contrast to conventional protein-coding genes, the sequences, transcriptional start sites, exon structures, and lengths for these non-coding genes are all highly variable.

CONCLUSIONS

The biological relevance of lncRNAs would be highly questionable if they were limited to closely related phyla. Instead, their preservation across diverse amniotes, their apparent conservation in exon structure, and similarities in their pattern of brain expression during embryonic and early postnatal stages together indicate that these are functional RNA molecules, of which some have roles in vertebrate brain development.

Long non-coding RNAs in nervous system function and disease

Central nervous system (CNS) development, homeostasis, stress responses, and plasticity are all mediated by epigenetic mechanisms that modulate gene expression and promote selective deployment of functional gene networks in response to complex profiles of interoceptive and environmental signals. Thus, not surprisingly, disruptions of these epigenetic processes are implicated in the pathogenesis of a spectrum of neurological and psychiatric diseases. Epigenetic mechanisms involve chromatin remodeling by relatively generic complexes that catalyze DNA methylation and various types of histone modifications. There is increasing evidence that these complexes are directed to their sites of action by long non-protein-coding RNAs (lncRNAs), of which there are tens if not hundreds of thousands specified in the genome. LncRNAs are transcribed in complex intergenic, overlapping and antisense patterns relative to adjacent protein-coding genes, suggesting that many lncRNAs regulate the expression of these genes. LncRNAs also participate in a wide array of subcellular processes, including the formation and function of cellular organelles. Most lncRNAs are transcribed in a developmentally regulated and cell type specific manner, particularly in the CNS, wherein over half of all lncRNAs are expressed. While the numerous biological functions of lncRNAs are yet to be characterized fully, a number of recent studies suggest that lnRNAs are important for mediating cell identity. This function seems to be especially important for generating the enormous array of regional neuronal and glial cell subtypes that are present in the CNS. Further studies have also begun to elucidate additional roles played by lncRNAs in CNS processes, including homeostasis, stress responses and plasticity. Herein, we review emerging evidence that highlights the expression and function of lncRNAs in the CNS and suggests that lncRNA deregulation is an important factor in various CNS pathologies including neurodevelopmental, neurodegenerative and neuroimmunological disorders, primary brain tumors, and psychiatric diseases.