Regulate Target Gene Expression Research Articles

Non-coding RNAs in the reprogramming of glucose metabolism in cancer

Proliferating cancer cells reprogram their metabolic circuitry to thrive in an environment deficient in nutrients and oxygen. Cancer cells exhibit a higher rate of glucose metabolism than normal somatic cells, which is achieved by switching from oxidative phosphorylation to aerobic glycolysis to meet the energy and metabolites demands of tumour progression. This phenomenon, which is known as the Warburg effect, has generated renewed interest in the process of glucose metabolism reprogramming in cancer cells. Several regulatory pathways along with glycolytic enzymes are responsible for the emergence of glycolytic dependence. Non-coding (nc)RNAs are a class of functional RNA molecules that are not translated into proteins but regulate target gene expression. NcRNAs have been shown to be involved in various biological processes, including glucose metabolism. In this review, we describe the regulatory role of ncRNAs–specifically, microRNAs and long ncRNAs–in the glycolytic switch and propose that ncRNA-based therapeutics can be used to inhibit the process of glucose metabolism reprogramming in cancer cells.

In Vitro Methods for Analyzing miRNA Roles in Cancer Cell Proliferation, Invasion, and Metastasis.

MicroRNAs (miRNAs) are small noncoding, single-stranded RNAs consisting of 20-24 nucleotides (Bartel, Cell 116:281-297, 2004), which regulate target genes expression by interacting with 3'-untranslated regions (3'-UTRs) of target mRNAs, leading to translation repression or mRNA degradation (Filipowicz et al., Nat Rev Genet 9:102-114, 2008; Nilsen, Trends Genet 23:243-249, 2007). Accumulating evidence has elucidated them as oncogenes or tumor suppressors in cancers such as hepatocellular carcinoma, breast cancer, and lung cancer (Liu et al., Gastroenterology 136:683-693, 2009; Yu et al., Cell 131:1109-1123, 2007; Zhou et al., Sci Rep 7:42680, 2017; Iorio and Croce, Carcinogenesis 33:1126-1133, 2012). MiRNAs are involved in various biological processes, including cell proliferation (Liu et al., Mol Cancer Res 11:1314-1325, 2013), differentiation (Liu et al., Mol Cancer Res 11:1314-1325, 2013), apoptosis (Pan et al., Oncol Res 24:429-435, 2016), invasion and metastasis (Liu et al., Nat Commun 8:14270, 2017). Understanding the role of miRNAs in tumor gives new perspective on cancer diagnosis and therapy (Rupaimoole and Slack, Nat Rev Drug Discov 16:203-222, 2017; Berindan-Neagoe et al., CA Cancer J Clin 64:311-336, 2014). This chapter will focus on the in vitro methods for identifying miRNAs roles in cell proliferation, invasion, and metastasis in tumor development, which includes CCK-8 assay, Wound Healing assay, and Transwell assay.

RNA Interference-Mediated Gene Silencing in Esophageal Adenocarcinoma.

RNA interference (RNAi) is a normal physiological mechanism in which a short effector antisense RNA molecule regulates target gene expression. It is a powerful tool to silence a particular gene of interest in a sequence-specific manner and can be used to target against various molecular pathways in esophageal adenocarcinoma by designing RNAi targeting key pathogenic genes. RNAi-based therapeutics against esophageal adenocarcinoma can be developed using different strategies including inhibition of overexpressed oncogenes, blocking cell division by interfering cyclins and related genes or enhancing apoptosis by suppressing anti-apoptotic genes. In addition, RNAi against multidrug resistance genes or chemo-resistance targets may provide promising cancer therapeutic options. Here, we describe RNAi technology using MET, a proto-oncogene in esophageal adenocarcinoma cells, as a model target. Lentiviral particles expressing MET shRNA was used to silence MET genes. Then, Western blot analysis was performed to confirm MET knockdown.

Integrated MicroRNA-mRNA Analysis Reveals miR-204 Inhibits Cell Proliferation in Gastric Cancer by Targeting CKS1B, CXCL1 and GPRC5A.

Gastric cancer (GC) is the second most frequent cause of cancer-related deaths worldwide. MicroRNAs are single-stranded RNA molecules of 21–23 nucleotides that regulate target gene expression through specific base-pairing interactions between miRNA and untranslated regions of targeted mRNAs. In this study, we generated a multistep approach for the integrated analysis of miRNA and mRNA expression. First, both miRNA and mRNA expression profiling datasets in gastric cancer from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) identified 79 and 1042 differentially expressed miRNAs and mRNAs, respectively, in gastric cancer. Second, inverse correlations between miRNA and mRNA expression levels identified 3206 miRNA–mRNA pairs combined with 79 dysregulated miRNAs and their 774 target mRNAs predicted by three prediction tools, miRanda, PITA, and RNAhybrid. Additionally, miR-204, which was found to be down-regulated in gastric cancer, was ectopically over-expressed in the AGS gastric cancer cell line and all down-regulated targets were identified by RNA sequencing (RNA-seq) analysis. Over-expression of miR-204 reduced the gastric cancer cell proliferation and suppressed the expression of three targets which were validated by qRT-PCR and luciferase assays. For the first time, we identified that CKS1B, CXCL1, and GPRC5A are putative targets of miR-204 and elucidated that miR-204 acted as potential tumor suppressor and, therefore, are useful as a promising therapeutic target for gastric cancer.

Cap‐seq reveals complicated miRNA transcriptional mechanisms in C. elegans and mouse

BackgroundMicroRNAs (miRNAs) regulate target gene expression at post‐transcriptional level. Intense research has been conducted for miRNA identification and the target finding. However, much less is known about the transcriptional regulation of miRNA genes themselves. Recently, a special group of pre‐miRNAs that are produced directly by transcription without Drosha processing were validated in mouse, indicating the complexity of miRNA biogenesis.MethodsIn this work, we detect clusters of aligned Cap‐seq reads to find the transcription start sites (TSSs) for intergenic miRNAs and study their transcriptional regulation in Caenorhabditis elegans and mouse.ResultsIn both species, we have identified a class of special pre‐miRNAs whose 5′ ends are capped, and are most probably generated directly by transcription. Furthermore, we distinguished another class of special pre‐miRNAs that are 5′‐capped but are also part of longer primary miRNAs, suggesting they may have more than one transcription mechanism. We detected multiple cap reads peaks within miRNA clusters in C. elegans. We surmised that the miRNAs in a cluster may either be transcribed independently or be re‐capped during the microprocessor cleavage process. We also observed that H3K4me3 and Pol II are enriched at those identified miRNA TSSs.ConclusionsThe Cap‐seq datasets enabled us to annotate the primary TSSs for miRNA genes with high resolution. Special class of 5′‐capped pre‐miRNAs have been identified in both C. elegans and mouse. The capping patter of miRNAs in a cluster indicate t hat clustered miRNA transcripts probably undergo a re‐capping procedure during the microprocessor cleavage process.

Horizontal transfer of miR-23a from hypoxic tumor cell colonies can induce angiogenesis.

Neo vessel formation by angiogenesis is an important event during many pathological conditions including cancer, where it is indispensable for tumor growth and survival. Although, various pro-angiogenic cytokines and soluble factors, secreted by tumor cells, have been reported to promote angiogenesis, recent studies have shown regulatory role of exosomes, secreted by tumor cells in the process of angiogenesis. These exosomes are capable of carrying nucleic acids, proteins, etc., as their cargo. Under the light of these facts and considering the presence of miRNAs, the non-coding RNAs capable of regulating target gene expression, as one of the major cargos in the exosomes, we investigated, whether exosomes derived from normoxic and hypoxic tumor cell colonies exhibit difference in levels of miR-23∼27∼24 cluster members and if so, to check the significance of their horizontal transfer on the process of angiogenesis. Results of our study showed that exosomes secreted by hypoxic tumor cell colonies possess significantly higher levels of miR23a and can induce angiogenesis. Further, we have shown that exosomes secreted by cells that ectopically over express miR23a is capable of inducing angiogenesis in different angiogenic model systems such as CAM, in ovo Xenograft and HUVEC models systems. Further, mechanistic analysis revealed that miR23a driven regulation of angiogenesis is brought about by down regulation of SIRT1 in the recipient cells. Collectively, the results presented here suggest that exosomal transfer of miR23a from tumor cell colonies can induce the process of angiogenesis by targeting SIRT1 in the recipient endothelial cells.

Optogenetic regulation of artificial microRNA improves H2 production in green alga Chlamydomonas reinhardtii

BackgroundChlamydomonas reinhardtii is an ideal model organism not only for the study of basic metabolic processes in both plants and animals but also the production of biofuels including hydrogen. Transgenic analysis of C. reinhardtii is now well established and very convenient, but inducible exogenous gene expression systems remain under-studied. The most commonly used heat shock-inducible system has serious effects on algal cell growth and is difficult and costly to control in large-scale culture. Previous studies of hydrogen photoproduction in Chlamydomonas also use this heat-inducible system to activate target gene transcription and hydrogen synthesis.ResultsHere we describe a blue light-inducible system with which we achieved optogenetic regulation of target gene expression in C. reinhardtii. This light-inducible system was engineered in a photosynthetic organism for the first time. The photo-inducible heterodimerizing proteins CRY2 and CIB1 were fused to VP16 transcription activation domain and the GAL4 DNA-binding domain, respectively. This scheme allows for transcription activation of the target gene downstream of the activation sequence in response to blue light. Using this system, we successfully engineered blue light-inducible hydrogen-producing transgenic alga. The transgenic alga was cultured under red light and grew approximately normally until logarithmic phase. When illuminated with blue light, the transgenic alga expressed the artificial miRNA targeting photosynthetic system D1 protein, and altered hydrogen production was observed.ConclusionsThe light-inducible system successfully activated the artificial miRNA and, consequently, regulation of its target gene under blue light. Moreover, hydrogen production was enhanced using this system, indicating a more convenient and efficient approach for gene expression regulation in large-scale microalgae cultivation. This optogenetic gene control system is a useful tool for gene regulation and also establishes a novel way to improve hydrogen production in green algae.

Identification of two types of GGAA-microsatellites and their roles in EWS/FLI binding and gene regulation in Ewing sarcoma.

Ewing sarcoma is a bone malignancy of children and young adults, frequently harboring the EWS/FLI chromosomal translocation. The resulting fusion protein is an aberrant transcription factor that uses highly repetitive GGAA-containing elements (microsatellites) to activate and repress thousands of target genes mediating oncogenesis. However, the mechanisms of EWS/FLI interaction with microsatellites and regulation of target gene expression is not clearly understood. Here, we profile genome-wide protein binding and gene expression. Using a combination of unbiased genome-wide computational and experimental analysis, we define GGAA-microsatellites in a Ewing sarcoma context. We identify two distinct classes of GGAA-microsatellites and demonstrate that EWS/FLI responsiveness is dependent on microsatellite length. At close range “promoter-like” microsatellites, EWS/FLI binding and subsequent target gene activation is highly dependent on number of GGAA-motifs. “Enhancer-like” microsatellites demonstrate length-dependent EWS/FLI binding, but minimal correlation for activated and none for repressed targets. Our data suggest EWS/FLI binds to “promoter-like” and “enhancer-like” microsatellites to mediate activation and repression of target genes through different regulatory mechanisms. Such characterization contributes valuable insight to EWS/FLI transcription factor biology and clarifies the role of GGAA-microsatellites on a global genomic scale. This may provide unique perspective on the role of non-coding DNA in cancer susceptibility and therapeutic development.

Paracrine and autocrine regulation of gene expression by Wnt-inhibitor Dickkopf in wild-type and mutant hepatocytes

BackgroundCells are able to communicate and coordinate their function within tissues via secreted factors. Aberrant secretion by cancer cells can modulate this intercellular communication, in particular in highly organised tissues such as the liver. Hepatocytes, the major cell type of the liver, secrete Dickkopf (Dkk), which inhibits Wnt/ β-catenin signalling in an autocrine and paracrine manner. Consequently, Dkk modulates the expression of Wnt/ β-catenin target genes. We present a mathematical model that describes the autocrine and paracrine regulation of hepatic gene expression by Dkk under wild-type conditions as well as in the presence of mutant cells.ResultsOur spatial model describes the competition of Dkk and Wnt at receptor level, intra-cellular Wnt/ β-catenin signalling, and the regulation of target gene expression for 21 individual hepatocytes. Autocrine and paracrine regulation is mediated through a feedback mechanism via Dkk and Dkk diffusion along the porto-central axis. Along this axis an APC concentration gradient is modelled as experimentally detected in liver. Simulations of mutant cells demonstrate that already a single mutant cell increases overall Dkk concentration. The influence of the mutant cell on gene expression of surrounding wild-type hepatocytes is limited in magnitude and restricted to hepatocytes in close proximity. To explore the underlying molecular mechanisms, we perform a comprehensive analysis of the model parameters such as diffusion coefficient, mutation strength and feedback strength.ConclusionsOur simulations show that Dkk concentration is elevated in the presence of a mutant cell. However, the impact of these elevated Dkk levels on wild-type hepatocytes is confined in space and magnitude. The combination of inter- and intracellular processes, such as Dkk feedback, diffusion and Wnt/ β-catenin signal transduction, allow wild-type hepatocytes to largely maintain their gene expression.

Silencing messages in a unique way.

A global analysis of translation efficiency and RNA accumulation revealed that microRNAs in the unicellular green alga Chlamydomonas regulate target gene expression via RNA destabilization and translational repression like land plants and metazoans, yet in a different way.

Down-regulation of genes coding for core RNAi components and disease resistance proteins via corresponding microRNAs might be correlated with successful Soybean mosaic virus infection in soybean.

Plants protect themselves from virus infections by several different defence mechanisms. RNA interference (RNAi) is one prominent antiviral mechanism, which requires the participation of AGO (Argonaute) and Dicer/DCL (Dicer-like) proteins. Effector-triggered immunity (ETI) is an antiviral mechanism mediated by resistance (R) genes, most of which encode nucleotide-binding site-leucine-rich repeat (NBS-LRR) family proteins. MicroRNAs (miRNAs) play important regulatory roles in plants, including the regulation of host defences. Soybean mosaic virus (SMV) is the most common virus in soybean and, in this work, we identified dozens of SMV-responsive miRNAs by microarray analysis in an SMV-susceptible soybean line. Amongst the up-regulated miRNAs, miR168a, miR403a, miR162b and miR1515a predictively regulate the expression of AGO1, AGO2, DCL1 and DCL2, respectively, and miR1507a, miR1507c and miR482a putatively regulate the expression of several NBS-LRR family disease resistance genes. The regulation of target gene expression by these seven miRNAs was validated by both transient expression assays and RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) experiments. Transcript levels for AGO1, DCL1, DCL2 and five NBS-LRR family genes were repressed at different time points after SMV infection, whereas the corresponding miRNA levels were up-regulated at these same time points. Furthermore, inhibition of miR1507a, miR1507c, miR482a, miR168a and miR1515a by short tandem target mimic (STTM) technology compromised SMV infection efficiency in soybean. Our results imply that SMV can counteract soybean defence responses by the down-regulation of several RNAi pathway genes and NBS-LRR family resistance genes via the induction of the accumulation of their corresponding miRNA levels.

Interleukin 1 β-induced SMAD2/3 linker modifications are TAK1 dependent and delay TGFβ signaling in primary human mesenchymal stem cells

BackgroundChondrogenic differentiation of mesenchymal stem cells (MSC) requires transforming growth factor beta (TGFβ) signaling. TGFβ binds to the type I receptor activin-like kinase (ALK)5 and results in C-terminal SMAD2/3 phosphorylation (pSMAD2/3C). In turn pSMAD2/3C translocates to the nucleus and regulates target gene expression. Inflammatory mediators are known to exert an inhibitory effect on MSC differentiation. In this study we investigated the effect of interleukin 1 β (IL1β) on SMAD2/3 signaling dynamics and post-translational modifications. ResultsCo-stimulation of MSC with TGFβ and IL1β did not affect peak pSMAD2C levels at 1h post-stimulation. Surprisingly, SMAD3 transcriptional activity, as determined by the CAGA12-luciferase reporter construct, was enhanced by co-stimulation of TGFβ and IL1β compared to TGFβ alone. Furthermore, IL1β stimulation induced CAGA12-luciferase activity in a SMAD dependent way. As SMAD function can be modulated independent of canonical TGFβ signaling through the SMAD linker domain, we studied SMAD2 linker phosphorylation at specific threonine and serine residues. SMAD2 linker threonine and serine modifications were observed within 1h following TGFβ, IL1β or TGFβ and IL1β stimulation. Upon co-stimulation linker modified SMAD2 accumulated in the cytoplasm and SMAD2/3 target gene transcription (ID1, JUNB) at 2–4h was inhibited. A detailed time course analysis of IL1β-induced SMAD2 linker modifications revealed a distinct temperospatial pattern compared to TGFβ. Co-stimulation with both factors resulted in a similar kinetic profile as TGFβ alone. Nevertheless, IL1β did subtly alter TGFβ-induced pSMAD2C levels between 8 and 24h post-stimulation, which was reflected by TGFβ target gene expression (PAI1, JUNB). Direct evidence for the importance of SMAD3 linker modifications for the effect of IL1β on TGFβ signaling was obtained by over-expression of SMAD3 or a SMAD3 linker phospho-mutant. Finally, an inhibitor screening was performed to identify kinases involved in SMAD2/3 linker modifications. We identified TAK1 kinase activity as crucial for IL1β-induced SMAD2 linker modifications and CAGA12-luciferase activity. ConclusionsTGFβ and IL1β signaling interact at the SMAD2/3 level in human primary MSC. Down-stream TGFβ target genes were repressed by IL1β independent of C-terminal SMAD2 phosphorylation. We demonstrate that SMAD2/3 linker modifications are required for this interplay and identified TAK1 as a crucial mediator of IL1β-induced TGFβ signal modulation.

Thyroid Hormone Signaling in the Development of the Endochondral Skeleton.

Thyroid hormone (TH) is an established regulator of skeletal growth and maintenance both in clinical studies and in laboratory models. The clinical consequences of altered thyroid status on the skeleton during development and in adulthood are well known, and genetic mouse models in which elements of the TH signaling axis have been manipulated illuminate the mechanisms which underlie TH regulation of the skeleton. TH is involved in the regulation of the balance between proliferation and differentiation in several skeletal cell types including chondrocytes, osteoblasts, and osteoclasts. The effects of TH are mediated primarily via the thyroid hormone receptors (TRs) α and β, ligand-inducible nuclear receptors which act as transcription factors to regulate target gene expression. Both TRα and TRβ signaling are important for different stages of skeletal development. The molecular mechanisms of TH action in bone are complex and include interaction with a number of growth factor signaling pathways. This review provides an overview of the regulation and mechanisms of TH action in bone, focusing particularly on the role of TH in endochondral bone formation during postnatal growth.

Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism.

In phylogenetically diverse bacteria, the conserved protein RapZ plays a central role in RNA-mediated regulation of amino-sugar metabolism. RapZ contributes to the control of glucosamine phosphate biogenesis by selectively presenting the regulatory small RNA GlmZ to the essential ribonuclease RNase E for inactivation. Here, we report the crystal structures of full length Escherichia coli RapZ at 3.40 Å and 3.25 Å, and its isolated C-terminal domain at 1.17 Å resolution. The structural data confirm that the N-terminal domain of RapZ possesses a kinase fold, whereas the C-terminal domain bears closest homology to a subdomain of 6-phosphofructokinase, an important enzyme in the glycolytic pathway. RapZ self-associates into a domain swapped dimer of dimers, and in vivo data support the importance of quaternary structure in RNA-mediated regulation of target gene expression. Based on biochemical, structural and genetic data, we suggest a mechanism for binding and presentation by RapZ of GlmZ and the closely related decoy sRNA, GlmY. We discuss a scenario for the molecular evolution of RapZ through re-purpose of enzyme components from central metabolism.

Abnormal expression of the vitamin D receptor in keloid scars

Keloids are abnormal fibroproliferative scars that pose a significant challenge to patients and clinicians. The molecular basis for keloid formation remains incompletely understood, and currently no universally effective treatments exist. It is well recognized that keloids are more prevalent in populations with darkly pigmented skin, such as African Americans, but the basis for the link between skin color and keloid risk is not known. Pigmentation reduces vitamin D production in the skin. Because most of the body’s vitamin D is produced in the skin, rates of vitamin D deficiency are higher in populations with darker skin pigmentation. In addition to regulation of calcium homeostasis, vitamin D plays important roles in cell proliferation, differentiation, cancer progression, inflammation, and fibrosis. The activities of vitamin D are dependent on the vitamin D receptor (VDR), a member of the steroid nuclear receptor superfamily. The ligand-bound VDR acts as a transcription factor; thus, nuclear localization is required for ligand-dependent regulation of target gene expression. The current study investigated expression and nuclear localization of VDR in keloid scars (N=24) and biopsies of normal skin (N=24). Immunohistochemistry with two different antibodies demonstrated reduced VDR protein levels in a majority of keloid scars. Further, the percentage of epidermal cells displaying nuclear VDR localization was significantly lower in keloid scars compared with normal skin samples. Interestingly, analysis of VDR-positive nuclei among different normal skin samples showed a significant reduction in nuclear localization in epidermis of black donors compared with white donors. The results suggest that VDR may play a role in keloid pathology, and hint at a possible role for VDR in the increased susceptibility to keloid scarring in individuals with darkly pigmented skin.

Regulatory 3' Untranslated Regions of Bacterial mRNAs.

The untranslated regions (UTRs) of mRNA contain important features that are relevant to the post-transcriptional and translational regulation of gene expression. Most studies of bacterial UTRs have focused on the 5′regions; however, 3′UTRs have recently emerged as a new class of post-transcriptional regulatory elements. 3′UTRs were found to regulate the decay and translation initiation in their own mRNAs. In addition, 3′UTRs constitute a rich reservoir of small regulatory RNAs, regulating target gene expression. In the current review, we describe several recently discovered examples of bacterial regulatory 3′UTRs, discuss their modes of action, and illustrate how they facilitate gene regulation in various environments.

MicroRNA Profiling and Target Genes Related to Metastasis of Salivary Adenoid Cystic Carcinoma.

Perineural invasion and distant metastasis lead to a poor prognosis of adenoid cystic carcinoma and there is no effective therapy available. MicroRNAs (miRNAs) are small non-coding RNAs that regulate target gene expression, which can be biomarkers or therapeutic targets for certain cancer types. We aimed to identify miRNAs and their target genes possibly involved in metastasis of salivary gland adenoid cystic carcinoma (SACC). Using Nanostring nCounter analysis, we examined miRNA expression in two SACC cell lines: SACC-83 and SACC-LM, with low and high lung metastasis rates, respectively. We then verified the differentially expressed miRNAs with real-time polymerase chain reaction in the cell lines and in tumor samples from patients with SACC. miRNA target-gene expression was also analyzed. SACC-83 showed higher gene expression of miR-130a, miR-342, and miR-205; SACC-LM showed higher gene expression of miR-99a and miR-155. In human tissue, miR-205 was highly expressed in the primary SACC, while miR-155 and miR-342 were highly expressed in recurrent SACC. Six predicted target genes of miRNA-155 and miR-99a linked to tumorigenesis were further analyzed and RNA expression of ubiquitin-like modifier activating enzyme 2 (UBA2) was higher in SACC than normal salivary gland tissue, and higher in primary compared to recurrent SACC (p<0.05). RNA expression of retinoic acid receptors (RARS) was higher in tissue from primary than recurrent SACC and normal salivary gland (p<0.05), but that in recurrent SACC was not significantly higher than normal salivary gland tissue. RNA expression of minichromosome maintenance 8 homologous recombination repair factor (MCM8) and 24-dehydrocholesterol reductase (DHCR24) was higher in primary SACC than normal salivary gland tissue (p<0.05). miR-99a, miR-155, miR-130a, miR-342, and miR-205 may play a role in metastasis of SACC. MiR-155 may be involved in SACC metastasis through UBA2 pathways, and UBA2 may function as a biomarker/mediator of SACC metastasis.

Functional role of SETD2, BAP1, PARP-3 and PBRM1 candidate genes on the regulation of hTERT gene expression.

Narrowing the search for the critical hTERT repressor sequence(s) has identified three regions on chromosome 3p (3p12-p21.1, 3p21.2 and 3p21.3-p22). However, the precise location and identity of the sequence(s) responsible for hTERT transcriptional repression remains elusive. In order to identify critical hTERT repressor sequences located within human chromosome 3p12-p22, we investigated hTERT transcriptional activity within 21NT microcell hybrid clones containing chromosome 3 fragments. Mapping of chromosome 3 structure in a single hTERT-repressed 21NT-#3fragment hybrid clone, revealed a 490kb region of deletion localised to 3p21.3 and encompassing the histone H3, lysine 36 (H3K36) trimethyltransferase enzyme SETD2; a putative tumour suppressor gene in breast cancer. Three additional genes, BAP1, PARP-3 and PBRM1, were also selected for further investigation based on their location within the 3p21.1-p21.3 region, together with their documented role in the epigenetic regulation of target gene expression or hTERT regulation. All four genes (SETD2, BAP1, PARP-3 and PBRM1) were found to be expressed at low levels in 21NT. Gene copy number variation (CNV) analysis of SETD2, BAP1, PARP-3 and PBRM1 within a panel of nine breast cancer cell lines demonstrated single copy number loss of all candidate genes within five (56%) cell lines (including 21NT cells). Stable, forced overexpression of BAP1, but not PARP2, SETD2 or PBRM1, within 21NT cells was associated with a significant reduction in hTERT expression levels relative to wild-type controls. We propose that at least two sequences exist on human chromosome 3p, that function to regulate hTERT transcription within human breast cancer cells.

Evolutionary Footprints Reveal Insights into Plant MicroRNA Biogenesis.

MicroRNAs (miRNAs) are endogenous small RNAs that recognize target sequences by base complementarity and play a role in the regulation of target gene expression. They are processed from longer precursor molecules that harbor a fold-back structure. Plant miRNA precursors are quite variable in size and shape, and are recognized by the processing machinery in different ways. However, ancient miRNAs and their binding sites in target genes are conserved during evolution. Here, we designed a strategy to systematically analyze MIRNAs from different species generating a graphical representation of the conservation of the primary sequence and secondary structure. We found that plant MIRNAs have evolutionary footprints that go beyond the small RNA sequence itself, yet their location along the precursor depends on the specific MIRNA We show that these conserved regions correspond to structural determinants recognized during the biogenesis of plant miRNAs. Furthermore, we found that the members of the miR166 family have unusual conservation patterns and demonstrated that the recognition of these precursors in vivo differs from other known miRNAs. Our results describe a link between the evolutionary conservation of plant MIRNAs and the mechanisms underlying the biogenesis of these small RNAs and show that the MIRNA pattern of conservation can be used to infer the mode of miRNA biogenesis.

MicroRNA-195 inhibits the behavior of cervical cancer tumors by directly targeting HDGF.

MicroRNAs (miRNAs/miRs) are a class of conserved non-coding endogenous small regulatory RNAs that regulate target gene expression by binding to the 3′-untranslated region of target mRNAs in a base-pairing manner, resulting in repression of transcription or degradation of target mRNAs. It has been demonstrated previously that the abnormal expression of miRNAs is involved in the carcinogenesis and progression of cervical cancer. The aim of the present study was to investigate the expression, biological functions and underlying molecular mechanisms of miR-195 in cervical cancer. The reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to detect the expression level of miR-195 in cervical cancer tissues and cell lines. Following transfection, an MTT assay, cell migration and invasion assays, western blot analysis and a dual-luciferase reporter assay were performed in human cervical cancer cells. In the present study, it was identified that miR-195 was downregulated in cervical cancer tissues and cell lines. Additionally, upregulation of miR-195 and knockdown of hepatoma-derived growth factor (HDGF) inhibited proliferation, migration and invasion of cervical cancer cells. Furthermore, a dual-luciferase reporter assay identified that HDGF was a direct target gene of miR-195. RT-qPCR and western blot analysis demonstrated that miR-195 mimic inhibited HDGF expression at the mRNA and protein levels, whereas miR-195 inhibitor enhanced HDGF expression at the mRNA and protein levels. These results indicated that miR-195 targeted HDGF to inhibit the behavior of tumors in cervical cancer. These results also suggested that miR-195 was a potential therapeutic biomarker of cervical cancer.