Regulate Target Gene Expression Research Articles

Secreted miR-34a in astrocytic shedding vesicles enhanced the vulnerability of dopaminergic neurons to neurotoxins by targeting Bcl-2.

MicroRNAs (miRNAs) are a class of noncoding RNAs that regulates target gene expression at posttranscriptional level, leading to further biological functions. We have demonstrated that microvesicles (MVs) can deliver miRNAs into target cells as a novel way of intercellular communication. It is reported that in central nervous system, glial cells release MVs, which modulate neuronal function in normal condition. To elucidate the potential role of glial MVs in disease, we evaluated the effects of secreted astrocytic MVs on stress condition. Our results demonstrated that after Lipopolysaccharide (LPS) stimulation, astrocytes released shedding vesicles (SVs) that enhanced vulnerability of dopaminergic neurons to neurotoxin. Further investigation showed that increased astrocytic miR-34a in SVs was involved in this progress via targeting anti-apoptotic protein Bcl-2 in dopaminergic neurons. We also found that inhibition of astrocytic miR-34a after LPS stimulation can postpone dopaminergic neuron loss under neurotoxin stress. These data revealed a novel mechanism underlying astrocyte-neuron interaction in disease.Electronic supplementary materialThe online version of this article (doi:10.1007/s13238-015-0168-y) contains supplementary material, which is available to authorized users.

MiR-212/132 downregulates SMAD2 expression to suppress the G1/S phase transition of the cell cycle and the epithelial to mesenchymal transition in cervical cancer cells.

MicroRNAs (miRNAs), a class of small noncoding RNAs that regulate target gene expression, play an important role in cancer initiation, progression, and metastasis. However, the role of many miRNAs in cervical cancer is not fully understood. In this study, we found that miR-212 and miR-132 from the same gene cluster are downregulated in human cervical cancer tissues when compared with adjacent noncancerous tissues. The overexpression of miR-212/132 not only led to a delay in the G1/S phase transition and repressed cell proliferation but also resulted in an increase in E-cadherin expression and a decrease in vimentin, suppressing the epithelial to mesenchymal transition and migration and invasion in cervical cancer cells. Subsequently, SMAD2 was identified as a common target of miR-212/132 and was found to be negatively regulated by miR-212/132 at the mRNA and protein levels. Furthermore, SMAD2 silencing led to the same effect on cervical cancer cells as miR-212/132 overexpression. Importantly, SMAD2 overexpression partially reversed the cellular phenotypes induced by miR-212/132 overexpression. In conclusion, our study indicated that miR-212/132 functions as tumor suppressor by targeting SMAD2 in cervical cancer.

Modelling Bacterial Quorum Sensing and Effects of Nutrient Availability

Many bacteria developed a possibility to recognise aspects of their environment or to communicate with each other by chemical signals. The so-called Quorum sensing (QS) is a special case for such a communication, a regulatory system for gene expression.Such an extracellular signalling via small diffusible compounds (called autoinducers) is known for an increasing number of bacterial species, including pathogens and beneficials. Briefly, bacteria release autoinducers and simultaneously regulate target gene expression dependent on the environmental autoinducer concentration. Regulated behaviour often induces critical life style switches, thus mechanistic understanding of autoinducer regulation and its ecological significance is of high relevance for the development of treatment strategies. Typical bacterial species using QS are Vibrio fischeri (a marine, luminescent bacterium) and Pseudomonas aeruginosa (a pathogenic bacterium). ...

Fastigial nucleus stimulation regulates neuroprotection via induction of a novel microRNA, rno-miR-676-1, in middle cerebral artery occlusion rats.

Previous studies have shown that fastigial nucleus stimulation (FNS) reduces tissue damage resulting from focal cerebral ischemia. Although the mechanisms of neuroprotection induced by FNS are not entirely understood, important data have been presented in the past two decades. MicroRNAs (miRNAs) are a newly discovered group of non-coding small RNA molecules that negatively regulate target gene expression and are involved in the regulation of cell proliferation and cell apoptosis. To date, no studies have demonstrated whether miRNAs can serve as mediators of the brain's response to FNS, which leads to endogenous neuroprotection. Therefore, this study investigated the profiles of FNS-mediated miRNAs. Using a combination of deep sequencing and microarray with computational analysis, we identified a novel miRNA in the rat ischemic cortex after 1 h of FNS. This novel miRNA (PC-3p-3469_406), herein referred to as rno-miR-676-1, was upregulated in rats with cerebral ischemia after FNS. In vivo observations indicate that this novel miRNA may have antiapoptotic effects and contribute to neuroprotection induced by FNS. Our study provides a better understanding of neuroprotection induced by FNS. MicroRNA (miRNA) is defined as a small non-coding RNA that fulfills both the expression and biogenesis criteria. Here, we describe a novel miRNA in the rat ischemic cortex expressed after 1 h of fastigial nucleus stimulation (FNS). The miRNA was functionally characterized by secondary structure, quantitative expression, the conservation analysis, target gene analysis, and biological functions. We consider rno-miR-676-1 to be a true microRNA and present evidence for its neuroprotective effects exerted after induction by FNS.

Altered levels of circulating miRNAs are associated Schistosoma japonicum infection in mice

BackgroundDioecious flatworms of the genus Schistosoma causes schistosomiasis, which is a major public health problem in developing countries. Acquiring detailed knowledge of schistosome-host interactions may aid in the development of novel strategies for schistosomiasis control. MicroRNAs (miRNAs) are involved in processes such as development, cell proliferation, metabolism, and signal transduction. Circulating miRNAs not only serve as a novel class of biomarkers of many diseases but also regulate target gene expression in recipient cells, which are similar to hormones.MethodsIn the present study, we used miRNA microarrays to determine the profile of circulating miRNAs associated with S. japonicum infection of mice. The biological functions of the altered levels of miRNAs and their target genes were predicted using bioinformatics. Expression levels of selected miRNAs and their target genes were further analyzed by quantitative RT-PCR.ResultsOur study identified 294 and 189 miRNAs in infected mice that were expressed in two independent experiments at levels ≥ 2-fold higher or ≤ 0.5-fold lower, respectively, compared with uninfected mice. Thirty-six of the same miRNAs were detected in these analyses. Moreover, pathway analyses indicated that most of these miRNAs are putatively involved in signaling pathways associated with pathogenesis, such as Wnt and MAPK signaling. Further, we show an inverse correlation between the circulating levels of these miRNAs and their target genes, suggesting that changes in miRNA expression may cause aberrant expression of genes such as Creb1 and Caspase-3 in mice infected with S. japonicum.ConclusionsOur study shows significant differences in the levels of circulating miRNAs between S. japonicum infected mice and uninfected mice. In particular, the altered levels of miR-706 and miR-134-5p were associated with altered levels of expression of the Caspase-3 and Creb1 genes, respectively, suggesting that circulating miRNAs may serve as important mediators of the pathology of hepatic schistosomiasis. Additionally, our results are expected to provide new insights for further understanding the mechanisms of schistosome-host interaction that may facilitate in the development of novel interventions for alleviating the symptom of S. japonicum infection as well as for preventing and treating schistosomiasis.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-015-0806-5) contains supplementary material, which is available to authorized users.

Regulation of mouse liver chromatin accessibility and associated early gene responses by CAR

Many xenobiotics are metabolized in mammalian liver by pathways regulated by constitutive androstane receptor (CAR). Here, we identify early gene targets of mouse liver CAR and investigate their associated, CAR‐induced changes in local chromatin accessibility and transcription factor (TF) recruitment. Genes induced or repressed by the CAR agonist TCPOBOP were identified by RNA‐Seq after 3 or 27 hr. Chromatin sites that dynamically open or close following CAR activation (changes in DNase I hypersensitive sites, ΔDHS) were identified by DNase‐Seq. Genes dysregulated in 3 hr TCPOBOP‐treated mouse liver were enriched in KEGG pathways for retinol and drug metabolism (DAVID analysis; p<E‐15). IPA identified activated CAR and its agonists as the top predicted upstream regulators of these gene responses. After 27 hr TCPOBOP treatment, many more genes were identified and the predicted upstream regulators expanded to include cyclin D and vitamin D, indicating significant secondary transcriptional regulation. DNase‐Seq identified ~3,600 ΔDHS that were opened or closed by 3 hr TCPOBOP treatment. These ΔDHS were not randomly distributed: mapping to their putative gene targets (i.e., nearest gene within 10 kb) revealed enrichment (12.4‐fold, p<E‐45) of the TCPOBOP‐induced DHS for genes inducible by CAR. Thus, chromatin opening is associated with activation of nearby CAR target genes. Genomic sequences in the 3 hr TCPOBOP‐inducible DHS regions were enriched for TF binding motifs for CAR and for CCAAT‐enhancer binding protein (CEBP), suggesting that CEBPs cooperate with CAR to open chromatin and up regulate target gene expression. Studies designed to test this hypothesis are in progress and will be reported. Grant support: NIH ES024421.

MicroRNAs: heralds of the noncoding RNA revolution.

MicroRNAs: heralds of the noncoding RNA revolution.

High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea

Among legumes, chickpea (Cicer arietinum L.) is the second most important crop after soybean. MicroRNAs (miRNAs) play important roles by regulating target gene expression important for plant development and tolerance to stress conditions. Additionally, recently discovered phased siRNAs (phasiRNAs), a new class of small RNAs, are abundantly produced in legumes. Nevertheless, little is known about these regulatory molecules in chickpea. The small RNA population was sequenced from leaves and flowers of chickpea to identify conserved and novel miRNAs as well as phasiRNAs/phasiRNA loci. Bioinformatics analysis revealed 157 miRNA loci for the 96 highly conserved and known miRNA homologs belonging to 38 miRNA families in chickpea. Furthermore, 20 novel miRNAs belonging to 17 miRNA families were identified. Sequence analysis revealed approximately 60 phasiRNA loci. Potential target genes likely to be regulated by these miRNAs were predicted and some were confirmed by modified 5′ RACE assay. Predicted targets are mostly transcription factors that might be important for developmental processes, and others include superoxide dismutases, plantacyanin, laccases and F-box proteins that could participate in stress responses and protein degradation. Overall, this study provides an inventory of miRNA–target gene interactions for chickpea, useful for the comparative analysis of small RNAs among legumes.

Pluripotency Transcription Factor Oct4 Mediates Stepwise Nucleosome Demethylation and Depletion

The mechanisms whereby the crucial pluripotency transcription factor Oct4 regulates target gene expression are incompletely understood. Using an assay system based on partially differentiated embryonic stem cells, we show that Oct4 opposes the accumulation of local H3K9me2 and subsequent Dnmt3a-mediated DNA methylation. Upon binding DNA, Oct4 recruits the histone lysine demethylase Jmjd1c. Chromatin immunoprecipitation (ChIP) time course experiments identify a stepwise Oct4 mechanism involving Jmjd1c recruitment and H3K9me2 demethylation, transient FACT (facilitates chromatin transactions) complex recruitment, and nucleosome depletion. Genome-wide and targeted ChIP confirms binding of newly synthesized Oct4, together with Jmjd1c and FACT, to the Pou5f1 enhancer and a small number of other Oct4 targets, including the Nanog promoter. Histone demethylation is required for both FACT recruitment and H3 depletion. Jmjd1c is required to induce endogenous Oct4 expression and fully reprogram fibroblasts to pluripotency, indicating that the assay system identifies functional Oct4 cofactors. These findings indicate that Oct4 sequentially recruits activities that catalyze histone demethylation and depletion.

Toward a New Twist in Hox and TALE DNA-Binding Specificity

Hox proteins gain specificity by interacting with TALE-class cofactors. In a recent issue of Cell and in this issue of Developmental Cell, Crocker et al. (2015) and Amin et al. (2015), respectively, demonstrate that non-canonical Hox/TALE binding sequences play a major role in the regionalized regulation of target gene expression in vivo.

DNA methyltransferase inhibition accelerates the immunomodulation and migration of human mesenchymal stem cells.

DNA methyltransferase (DNMT) inhibitors regulate target gene expression through epigenetic modifications, and these compounds have primarily been studied for cancer therapy or reprogramming. However, the effect of DNMT inhibitors on the immunomodulatory capacity of human mesenchymal stem cells (hMSCs) has not been investigated. In the present study, we treated hMSCs with 5-azacytidine (5-aza), a DNMT inhibitor, and confirmed that the inhibitory effects on mononuclear cell proliferation and cell migration toward activated T cells were increased. To identify the immunomodulatory factors stimulated through 5-aza treatment, we investigated the changes in promoter methylation patterns using methylation arrays and observed that the promoters of immunomodulatory factors, COX2 and PTGES, and migration-related factors, CXCR2 and CXCR4, were hypomethylated after 5-aza treatment. In addition, we observed that the COX2-PGE2 pathway is one of the main pathways for the enhanced immunosuppressive activity of hMSCs through 5-aza treatment. We also determined that the migration of hMSCs toward ligands for CXCR2/CXCR4 was increased after 5-aza treatment. Moreover, using an experimental colitis model, we showed that 5-aza pre-treatment could enhance the therapeutic effect of MSCs against immune-related diseases.

WEE1 is a validated target of the microRNA miR-17-92 cluster in leukemia

MicroRNAs are short single-stranded RNAs that regulate target gene expression by binding to complementary sites in the 3' untranslated region (UTR) of their mRNA targets. The polycistronic miR-17-92 cluster, which encodes miR-17, miR-18a, miR-19a, miR-20a, miR-19b, and miR-92a, was previously shown to be overexpressed in multiple types of cancer. In this study, target gene prediction algorithms were used to predict potential targets of the miR-17-92 cluster. WEE1, a kinase that inhibits cell cycle progression, was identified as a possible target of five of the six miRNAs in the cluster. Luciferase reporter assays were used to determine that miR-17, miR-20a, and miR-18a specifically target nucleotides 465-487 of the 3' UTR of WEE1, whereas miR-19a and miR-19b exert control on WEE1 by targeting nucleotides 1069-1091. A negative correlation was determined between endogenous miR-17 or miR-19a expression and endogenous WEE1 protein expression in the same panel of cell lines. We conclude that WEE1 is a valid target of the miR-17-92 cluster in leukemia.

Impaired Hippo signaling promotes Rho1–JNK-dependent growth

The Hippo and c-Jun N-terminal kinase (JNK) pathway both regulate growth and contribute to tumorigenesis when dysregulated. Whereas the Hippo pathway acts via the transcription coactivator Yki/YAP to regulate target gene expression, JNK signaling, triggered by various modulators including Rho GTPases, activates the transcription factors Jun and Fos. Here, we show that impaired Hippo signaling induces JNK activation through Rho1. Blocking Rho1-JNK signaling suppresses Yki-induced overgrowth in the wing disk, whereas ectopic Rho1 expression promotes tissue growth when apoptosis is prohibited. Furthermore, Yki directly regulates Rho1 transcription via the transcription factor Sd. Thus, our results have identified a novel molecular link between the Hippo and JNK pathways and implicated the essential role of the JNK pathway in Hippo signaling-related tumorigenesis.

MicroRNA-26b inhibits osteosarcoma cell migration and invasion by down-regulating PFKFB3 expression.

MicroRNAs regulate target gene expression and are involved in cell proliferation, apoptosis, differentiation, tumor invasion, and cancer stem cell regulation, among other processes. MicroRNA-26b (miR-26b) is closely related to tumor occurrence and development. In this study, we analyzed miR-26b expression in osteosarcoma tissue, its effect on Saos-2 osteosarcoma cell proliferation and invasion, and its relationship with 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) expression. Osteosarcoma tissue was obtained from surgical patients and normal tissue adjacent to the tumor was used as a control. Real-time polymerase chain reaction was applied to detect miR-26b expression in cancer tissue and normal tissue. A vector expressing miR-26b was constructed and transfected into Saos-2. An MTT assay, cell invasion assay, and scratch experiment were used to analyze the effect of miR-26b on Saos-2 cell proliferation, invasion, and migration abilities. Western blotting analysis was performed to investigate the role of miR-26b on PFKFB3 expression. miR-26b expression in normal tissue was 7.55-fold higher than in osteosarcoma tissue (t = 10.20, P = 0.006). Compared with control tissue, miR-26b significantly inhibited osteosarcoma proliferation, migration, and invasion (P < 0.05). Western blotting results revealed that PFKFB3 protein expression decreased in Saos-2 cells after transfection with miR-26b. miR-26b was down-regulated in osteosarcoma tissue. miR- 26b may inhibit osteosarcoma cell proliferation, migration, and invasion by regulating PFKFB3 protein expression. miR-26b may have a tumor suppressor role in tumor occurrence and development.

MicroRNAs: New Players in Anesthetic-Induced Developmental Neurotoxicity.

Growing evidence demonstrates that prolonged exposure to general anesthetics during brain development induces widespread neuronal cell death followed by long-term memory and learning disabilities in animal models. These studies have raised serious concerns about the safety of anesthetic use in pregnant women and young children. However, the underlying mechanisms of anesthetic-induced neurotoxicity are complex and are not well understood. MicroRNAs are endogenous, small, non-coding RNAs that have been implicated to play important roles in many different disease processes by negatively regulating target gene expression. A possible role for microRNAs in anesthetic-induced developmental neurotoxicity has recently been identified, suggesting that microRNA-based signaling might be a novel target for preventing the neurotoxicity. Here we provide an overview of anesthetic-induced developmental neurotoxicity and focus on the role of microRNAs in the neurotoxicity observed in both human stem cell-derived neuron and animal models. Aberrant expression of some microRNAs has been shown to be involved in anesthetic-induced developmental neurotoxicity, revealing the potential of microRNAs as therapeutic or preventive targets against the toxicity.

Identification of Bexarotene as a PPARγ Antagonist with HDX.

The retinoid x receptors (RXRs) are the pharmacological target of Bexarotene, an antineoplastic agent indicated for the treatment of cutaneous T cell lymphoma (CTCL). The RXRs form heterodimers with several nuclear receptors (NRs), including peroxisome proliferator-activated receptor gamma (PPARγ), to regulate target gene expression through cooperative recruitment of transcriptional machinery. Here we have applied hydrogen/deuterium exchange (HDX) mass spectrometry to characterize the effects of Bexarotene on the conformational plasticity of the intact RXRα:PPARγ heterodimer. Interestingly, addition of Bexarotene to PPARγ in the absence of RXRα induced protection from solvent exchange, suggesting direct receptor binding. This observation was confirmed using a competitive binding assay. Furthermore, Bexarotene functioned as a PPARγ antagonist able to alter rosiglitazone induced transactivation in a cell based promoter:reporter transactivation assay. Together these results highlight the complex polypharmacology of lipophilic NR targeted small molecules and the utility of HDX for identifying and characterizing these interactions.

DNA Demethylation By Activation-Induced Cytidine Deaminase in B Cell Lymphoma

DNA methylation and demethylation at cytosine residues are epigenetic modifications that regulate gene expression associated with early cell development, somatic cell differentiation, cellular reprogramming and malignant transformation. While the process of DNA methylation and maintenance by DNA methyltransferases is well described, the nature of DNA demethylation remains poorly understood. The current model of DNA demethylation proposes modification of 5-methylcytosine followed by DNA repair-dependent cytosine substitution. Although there is debate on the extent of its involvement in DNA demethylation, activation-induced cytidine deaminase (AID) has recently emerged as an enzyme that is capable of deaminating 5-methylcytosine to thymine, creating a T:G mismatch which can be repaired back to cytosine through DNA repair pathways. AID is expressed at low levels in many tissue types but is most highly expressed in germinal center B cells where it deaminates cytidine to uracil during somatic hypermutation and class switch recombination of the immunoglobulin genes. In addition to this critical role in immune diversification, aberrant targeting of AID contributes to oncogenic point mutations and chromosome translocations associated with B cell malignancies. Thus, to explore a role for AID in DNA demethylation in B cell lymphoma, we performed genome-wide methylation profiling in BL2 and AID-deficient (AID-/-) BL2 cell lines (Burkitt lymphoma that can be induced to express high levels of AID). Using Illumina’s Infinium II DNA Methylation assay combined with the Infinium Human Methylation 450 Bead Chip, we analyzed over 450,000 methylation (CpG) sites at single nucleotide resolution in each line. BL2 AID-/- cells had a median average beta value (ratio of the methylated probe intensity to overall intensity) of 0.76 compared with 0.73 in AID-expressing BL2 cells (P < 0.00001), indicating a significant reduction in global methylation in the presence of AID. Using a delta average beta value of ≥ 0.3 (high stringency cut-off whereby a difference of 0.3 or more defines a CpG site as hypomethylated), we identified 5883 CpG sites in 3347 genes that were hypomethylated in BL2 versus BL2 AID-/- cells. Using the Illumina HumanHT-12 v4 Expression BeadChip and Genome Studio software, we then integrated gene expression and methylation profiles from both lines to generate a list of genes that met the following criteria: 1) contained at least 4 methylation sites within the first 1500 bases downstream of the primary transcriptional start site (TSS 1500; AID is most active in this region during somatic hypermutation); 2) average beta value increased by >0.1 in the TSS 1500 region in BL2 compared with BL2 AID-/- cells; and 3) down-regulated by >50% in BL2 compared with BL2 AID-/- cells. This analysis identified 31 candidate genes targeted for AID-dependent demethylation with consequent changes in gene expression. Interestingly, 15 of these genes have been reported to be bound by AID in association with stalled RNA polymerase II in activated mouse B cells. After validating methylation status in a subset of genes (APOBEC3B, BIN1, DEM1, GRN, GNPDA1) through bisulfite sequencing, we selected DEM1 for further analysis. DEM1 encodes an exonuclease involved in DNA repair and contains 16 CpG sites within its TSS1500, with only one site >50% methylated in BL2 cells compared with 8 of 16 in BL2 AID-/- cells. To assess a direct role for AID in DEM1 methylation status, a retroviral construct (AIDΔL189-L198ER) driving tamoxifen-inducible expression of a C-terminal deletion mutant of AID (increases time spent in the nucleus) was introduced into BL2 AID-/- cells. BL2, BL2 AID-/-, and BL2 AIDΔL189-L198ER cells were cultured continuously for 21 days in the presence of tamoxifen, 100 nM. Bisulfite sequencing of DEM1 TSS 1500 did not demonstrate any significant changes in methylation at day 7. However, at day 21, 13 of the 16 DEM1 TSS 1500 methylation sites in BL2 AIDΔL189-L198ER cells were found to have an increase in the ratio of unmethylated to methylated clones ~10-25% above that of BL2 AID-/- cells. By qPCR, this correlated with a 1.75-fold increase in DEM1 gene expression to levels that were equivalent to that seen in BL2 cells (P = 0.003). Although further investigations are needed, this data supports the notion that AID is able to regulate target gene expression in B cell malignancy through active DNA demethylation. DisclosuresNo relevant conflicts of interest to declare.

Computational identification and experimental validation of microRNAs binding to the fragile X syndrome gene Fmr1.

MicroRNAs (miRNAs) usually bind to their target mRNAs through imperfect base pairing in the 3'-untranslated regions (3' UTRs) and regulate target gene expression via post-transcriptional suppression. In recent years, computational approaches to predict miRNA targets have facilitated the identification of potential target sites. In this study, we used three programs TargetScan, miRDB and miRanda to predict potential miRNA binding sites to the fragile X gene Fmr1 and picked out 61 miRNAs which were predicted by all three programs for further investigation. Excitingly, 5 out of these miRNAs, miR-23a, miR-32, miR-124, miR-335-5p and miR-350, were experimentally verified by luciferase reporter assays. Furthermore, overexpression of miR-124 in mouse embryonic neural progenitor cells (eNPC) could not only significantly reduce Fmr1 level, but also increase Cdk4 and cyclin D1 levels which coincidently promoted eNPC proliferation. Our results imply that miR-124 plays an important role in the proliferation of mouse embryonic stem cells by promoting Cdk4 and cyclin D1 expression through directly inhibiting Fmr1 expression.

ULTRAPETALA trxG genes interact with KANADI transcription factor genes to regulate Arabidopsis gynoecium patterning.

Organ formation relies upon precise patterns of gene expression that are under tight spatial and temporal regulation. Transcription patterns are specified by several cellular processes during development, including chromatin remodeling, but little is known about how chromatin-remodeling factors contribute to plant organogenesis. We demonstrate that the trithorax group (trxG) gene ULTRAPETALA1 (ULT1) and the GARP transcription factor gene KANADI1 (KAN1) organize the Arabidopsis thaliana gynoecium along two distinct polarity axes. We show that ULT1 activity is required for the kan1 adaxialized polarity defect, indicating that ULT1 and KAN1 act oppositely to regulate the adaxial-abaxial axis. Conversely, ULT1 and KAN1 together establish apical-basal polarity by promoting basal cell fate in the gynoecium, restricting the expression domain of the basic helix-loop-helix transcription factor gene SPATULA. Finally, we show that ult alleles display dose-dependent genetic interactions with kan alleles and that ULT and KAN proteins can associate physically. Our findings identify a dual role for plant trxG factors in organ patterning, with ULT1 and KAN1 acting antagonistically to pattern the adaxial-abaxial polarity axis but jointly to pattern the apical-basal axis. Our data indicate that the ULT proteins function to link chromatin-remodeling factors with DNA binding transcription factors to regulate target gene expression.

MicroRNA-mediated regulation of extracellular matrix formation modulates somatic cell reprogramming.

Somatic cells can be reprogrammed to reach an embryonic stem cell-like state by overexpression of defined factors. Recent studies have greatly improved the efficiency of the reprogramming process but the underlying mechanisms regulating the transition from a somatic to a pluripotent state are still relatively unknown. MicroRNAs (miRs) are small noncoding RNAs that primarily regulate target gene expression post-transcriptionally. Here we present a systematic and comprehensive study of microRNAs in mouse embryonic fibroblasts (MEFs) during the early stage of cell fate decisions and reprogramming to a pluripotent state, in which significant transcriptional and epigenetic changes occur. One microRNA found to be highly induced during this stage of reprogramming, miR-135b, targeted the expression of extracellular matrix (ECM) genes including Wisp1 and Igfbp5. Wisp1 was shown to be a key regulator of additional ECM genes that serve as barriers to reprogramming. Regulation of Wisp 1 is likely mediated through biglycan, a glycoprotein highly expressed in MEFs that is silenced in reprogrammed cells. Collectively, this report reveals a novel link between microRNA-mediated regulation of ECM formation and somatic cell reprogramming, and demonstrates that microRNAs are powerful tools to dissect the intracellular and extracellular molecular mechanisms of reprogramming.