scholarly journals Understanding the Action of RARγ Agonists on Human Osteochondroma Explants

2020 ◽  
Vol 21 (8) ◽  
pp. 2686 ◽  
Author(s):  
Sonia A. Garcia ◽  
Hongying Tian ◽  
Yuka Imamura-Kawasawa ◽  
Aidan Fisher ◽  
Ashley Cellini ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Death ◽  
Target Genes ◽  
Retinoic Acid Receptor ◽  
Human Growth ◽  
Explant Culture ◽  
Cartilage Matrix ◽  
Sequencing Analysis ◽  
Matrix Degradation ◽  
Growth Plate Chondrocytes

Osteochondromas are cartilage-capped growths located proximate to the physis that can cause skeletal deformities, pain, limited motion, and neurovascular impingement. Previous studies have demonstrated retinoic acid receptor gamma (RARγ) agonists to inhibit ectopic endochondral ossification, therefore we hypothesize that RARγ agonists can target on established osteochondromas. The purpose of this study was to examine the action of RARγ agonist in human osteochondromas. Osteochondroma specimens were obtained during surgery, subjected to explant culture and were treated with RARγ agonists or vehicles. Gene expression analysis confirmed the up-regulation of RARγ target genes in the explants treated with NRX 204647 and Palovarotene and revealed strong inhibition of cartilage matrix and increased extracellular matrix proteases gene expression. In addition, immunohistochemical staining for the neoepitope of protease-cleaved aggrecan indicated that RARγ agonist treatment stimulated cartilage matrix degradation. Interestingly, cell survival studies demonstrated that RARγ agonist treatment stimulated cell death. Moreover, RNA sequencing analysis indicates changes in multiple molecular pathways due to RARγ agonists treatment, showing similarly to human growth plate chondrocytes. Together, these findings suggest that RARγ agonist may exert anti-tumor function on osteochondromas by inhibiting matrix synthesis, promoting cartilage matrix degradation and stimulating cell death.

scholarly journals Genome-Wide Analysis of Glucocorticoid-Responsive Transcripts in the Hypothalamic Paraventricular Region of Male Rats

Endocrinology ◽  
2018 ◽  
Vol 160 (1) ◽  
pp. 38-54 ◽  
Author(s):  
Keiichi Itoi ◽  
Ikuko Motoike ◽  
Ying Liu ◽  
Sam Clokie ◽  
Yasumasa Iwasaki ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Receptor Gene ◽  
Male Rats ◽  
Regulatory Mechanisms ◽  
High Dose ◽  
Sequencing Analysis ◽  
Reverse Transcription Pcr ◽  
Genome Wide ◽  
A Genome

Abstract Glucocorticoids (GCs) are essential for stress adaptation, acting centrally and in the periphery. Corticotropin-releasing factor (CRF), a major regulator of adrenal GC synthesis, is produced in the paraventricular nucleus of the hypothalamus (PVH), which contains multiple neuroendocrine and preautonomic neurons. GCs may be involved in diverse regulatory mechanisms in the PVH, but the target genes of GCs are largely unexplored except for the CRF gene (Crh), a well-known target for GC negative feedback. Using a genome-wide RNA-sequencing analysis, we identified transcripts that changed in response to either high-dose corticosterone (Cort) exposure for 12 days (12-day high Cort), corticoid deprivation for 7 days (7-day ADX), or acute Cort administration. Among others, canonical GC target genes were upregulated prominently by 12-day high Cort. Crh was upregulated or downregulated most prominently by either 7-day ADX or 12-day high Cort, emphasizing the recognized feedback effects of GC on the hypothalamic-pituitary-adrenal (HPA) axis. Concomitant changes in vasopressin and apelin receptor gene expression are likely to contribute to HPA repression. In keeping with the pleotropic cellular actions of GCs, 7-day ADX downregulated numerous genes of a broad functional spectrum. The transcriptome response signature differed markedly between acute Cort injection and 12-day high Cort. Remarkably, six immediate early genes were upregulated 1 hour after Cort injection, which was confirmed by quantitative reverse transcription PCR and semiquantitative in situ hybridization. This study may provide a useful database for studying the regulatory mechanisms of GC-dependent gene expression and repression in the PVH.

BCL6 Transcriptionally Reprograms the DLBCL Genome by Forming Distinct Biochemically Active Complexes on Genes Corresponding to Different Pathways.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2646-2646
Author(s):  
Jose M. Polo ◽  
Katerina Chatzi ◽  
Tania Dell’Oso ◽  
Paola Lev ◽  
Ari Melnick
Keyword(s):  
Gene Expression ◽  
Cell Death ◽  
Chromatin Structure ◽  
Transcriptional Control ◽  
Target Genes ◽  
Biological Effects ◽  
Hematologic Malignancies ◽  
Specific Gene ◽  
Control Mechanisms ◽  
Biochemical Mechanisms

Abstract Aberrant gene expression is a hallmark of cancer, and so it is not surprising that the most common category of oncogenes and tumor suppressors involved in hematologic malignancies are transcription factors. These factors mediate their effects by nucleating biochemically active cofactor complexes to modify the chromatin structure of their respective target genes. BCL6 is a transcriptional repressor and the most commonly involved oncogene in diffuse large B-cell lymphomas. BCL6 represses genes by recruiting several corepressor complexes including SMRT, N-CoR, BCoR; all of which bind to BCL6 through its BTB domain. Each of these complexes has different biochemical functions (e.g. BCoR forms a polycomb complex vs. SMRT which forms an HDAC3 complex). Moreover, our preliminary data suggested that BCL6 uses different sets of corepressors to mediate distinct biological effects, possibly by using different biochemical mechanisms at specific sets of target genes. Therefore, we hypothesized that BCL6 regulates its target genes using different biochemical tools, allowing it to exquisitely fine tune gene expression and provide specific control mechanisms for different biological functions. In order to test this hypothesis we first identified the direct target genes of BCL6 SMRT, N-CoR and BCoR by ChIP-on-chip in DLBCL cells (Ly1 cells) in multiple replicates, and examined whether the overlapping sets of genes corresponded to different gene pathways. We used a 24,000 promoter microarray representing 1.5 KB of sequence for each gene. The results show reproducible binding of BCL6 at 940 promoters, While BCoR bound to 770, SMRT to 545 and N-CoR to 487 promoters respectively. BCL6 and BCoR overlapped at 400 genes, preferentially involved in involve in cell cycle, cell death chromatin structure, ubiquitin dependent process and chemotaxis. BCL6 and SMRT overlapped on 376 genes, involved in immune response, cell motility and also as BCOR cell death, while N-CoR and BCL6 overlapped on 100 genes including transcriptional control and cell death pathways. The overlap between BCoR and SMRT was at 200 genes, BCoR and N-CoR at 60 genes and SMRT and N-CoR at 85 genes. All three overlapped at 50 genes. We also examined whether these corepressors were associated with specific combinations of histone modifications including H3K9 acetylation, H3K9 methylation, H3K4 methylation, H3K27 methylation, H4K16 acetylation and H3K36 acetylation. Taken together, the data indicate that specific subsets of BCL6 target genes are dependent on distinct biochemical mechanisms, suggesting that additional layers of biochemical complexity govern formation of gene repression complexes in DLBCL cells and providing opportunities for highly specific therapeutic targeting of specific gene programs.

scholarly journals Transcriptome and Small RNA Combined Sequencing Analysis of Cold Tolerance in Non-heading Chinese Cabbage

2021 ◽  
Vol 12 ◽  
Author(s):  
Jin Wang ◽  
Qinxue Zhang ◽  
Xiong You ◽  
Xilin Hou
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Small Rna ◽  
Target Genes ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Pak Choi ◽  
Expression Levels ◽  
Heading Chinese Cabbage ◽  
Gene Expression Levels

BackgroundNon-heading Chinese cabbage (Brassica rapa ssp. chinensis) is an important leaf vegetable grown worldwide. However, there has currently been not enough transcriptome and small RNA combined sequencing analysis of cold tolerance, which hinders further functional genomics research.ResultsIn this study, 63.43 Gb of clean data was obtained from the transcriptome analysis. The clean data of each sample reached 6.99 Gb, and the basic percentage of Q30 was 93.68% and above. The clean reads of each sample were sequence aligned with the designated reference genome (Brassica rapa, IVFCAASv1), and the efficiency of the alignment varied from 81.54 to 87.24%. According to the comparison results, 1,860 new genes were discovered in Pak-choi, of which 1,613 were functionally annotated. Among them, 13 common differentially expressed genes were detected in all materials, including seven upregulated and six downregulated. At the same time, we used quantitative real-time PCR to confirm the changes of these gene expression levels. In addition, we sequenced miRNA of the same material. Our findings revealed a total of 34,182,333 small RNA reads, 88,604,604 kinds of small RNAs, among which the most common size was 24 nt. In all materials, the number of common differential miRNAs is eight. According to the corresponding relationship between miRNA and its target genes, we carried out Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis on the set of target genes on each group of differentially expressed miRNAs. Through the analysis, it is found that the distributions of candidate target genes in different materials are different. We not only used transcriptome sequencing and small RNA sequencing but also used experiments to prove the expression levels of differentially expressed genes that were obtained by sequencing. Sequencing combined with experiments proved the mechanism of some differential gene expression levels after low-temperature treatment.ConclusionIn all, this study provides a resource for genetic and genomic research under abiotic stress in Pak-choi.

scholarly journals KDM7A Is Targeted By MiR-155 in Acute Myeloid Leukemia and Impacts Differentiation

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 3641-3641 ◽  
Author(s):  
Maya D. Hughes ◽  
Valerie A. Morris ◽  
Carrie Cummings ◽  
Soheil Meshinchi ◽  
Vivian G. Oehler
Keyword(s):  
Gene Expression ◽  
Cell Death ◽  
Acute Myeloid Leukemia ◽  
Cell Differentiation ◽  
Binding Sites ◽  
Myeloid Leukemia ◽  
Target Genes ◽  
K562 Cells ◽  
Erythroid Differentiation ◽  
Acute Myeloid

Abstract Acute myeloid leukemia (AML) is a heterogeneous disease that develops secondary to the acquisition of mutations that disrupt cell differentiation, proliferation and survival. MicroRNAs (miRNAs or miRs) are short non-coding RNA molecules that modulate post-transcriptional gene expression by either cleaving or repressing translation of target mRNA transcripts. Differential expression of miRNAs has been identified in AML and noted to correlate with specific disease characteristics, cytogenetic abnormalities and prognosis. MiR-155 expression is upregulated in both adult and pediatric patients with cytogenetically normal AML (CN-AML) and correlates with adverse clinical outcomes. Specifically, we have shown that high miR-155 expression is associated with an increased incidence of induction chemotherapy failure and inferior overall and event free survival. However, how miR-155 up-regulation contributes mechanistically to adverse clinical outcomes is poorly understood. In prior work, we correlated the expression of predicted or validated miR-155 target genes with miR-155 expression in a gene expression profiling (GEP) dataset of pediatric AML samples. We identified 22 candidates with inversely correlated expression by GEP for further validation in diagnostic bone marrow specimens from children with the highest miR-155 expression levels (n=9) vs. children with the lowest miR-155 expression levels (n=9). Although the expression of miR-155 inversely correlated with 9 target genes, only expression of the putative target KDM7A demonstrated a statistically significant difference in expression between low and high miR-155 expressing cases (p = 0.03). KDM7A is a lysine-specific histone demethylase enzyme that may play a role in regulating differentiation by impacting transcriptional elongation. Computational software programs, i.e. TargetScan, identified two predicted miR-155 binding sites in the KDM7A 3'UTR. To evaluate whether miR-155 directly binds to the KDM7A 3'UTR, we cloned two regions of the KDM7A 3'UTR containing predicted miR-155 binding sequences into luciferase reporter vectors and then mutated the binding sites by site-directed DNA mutagenesis. We validated that both predicted binding sites in KDM7A 3'UTR were direct miR-155 targets using HEK293T cells. Next, we examined the impact of miR-155 overexpression in K562 cells, an acute leukemia cell line that express very low levels of endogenous miR-155, and can be differentiated along the erythroid lineage after hemin exposure. KDM7A RNA expression was decreased 16-fold in miR-155 versus control lentivirally transduced K562 cells as detected by qPCR. KDM7A protein expression was also decreased in miR-155 versus control expressing K562 cells as measured via Western blot. These data demonstrate that KDM7A is a previously uncharacterized target of miR-155. Next, we explored the effect of differential KDM7A expression on cell differentiation, and cell death and apoptosis after exposure to daunorubicin chemotherapy. For this work we used GFP-labeled miR-155 and YFP-labeled KDM7A lentiviral constructs and labeled control constructs. To examine differentiation we used benzidine staining of hemin-exposed K562 cells transduced with empty control vector (ECV), miR-155, KDM7A, or both constructs. The lowest percentage of benzidine staining, consistent with limited erythroid differentiation, was seen in K562 cells with miR-155 overexpression compared to ECV (28.2% vs. 39.8% positive). This effect on blocked erythroid differentiation was fully reversed with overexpression of KDM7A in miR-155 overexpressing cells (41.4% positive). Confirming these observations, we also observed decreased benzidine staining in hemin exposed K562 cells that were transduced with KDM7A shRNA versus control (28.9% versus 42.7%). Together, these data support that KDM7A plays a role in cell differentiation that is in part controlled by miR-155 expression. Preliminary data also support that re-expression of KDM7A in miR-155 overexpressing cells promotes cell death after exposure to daunorubicin. Further work is ongoing. In conclusion, we have identified a new target of miR-155, KDM7A. Our data suggest that KDM7A plays a role in cell differentiation and that decreased KDM7A expression in AML cells that overexpress miR-155 contributes to blocked differentiation, and may also contribute to resistance to chemotherapy. Disclosures No relevant conflicts of interest to declare.

Abstract 121: Modulation of Apoptosis, Matrix Degradation and Matrix Synthesis Are the Primary Determinants for Intimal Hyperplasia in Response to Altered Shear

2012 ◽  
Vol 32 (suppl_1) ◽  
Author(s):  
Khayree Butler ◽  
Zhihua Jiang ◽  
Kerri O’Malley ◽  
Rongling Wu ◽  
Scott A Berceli
Keyword(s):  
Gene Expression ◽  
Cell Death ◽  
High Throughput ◽  
Intimal Hyperplasia ◽  
Biological Significance ◽  
Matrix Degradation ◽  
Matrix Synthesis ◽  
Bilateral Carotid ◽  
Morphologic Data ◽  
Low Shear

Introduction: The quantity of high throughput microarray data leads to unique challenges in understanding its biological significance. We have developed a novel statistical method of clustering dynamics to elucidate for the mapping of gene expression arcs. In the current study, we applied these techniques to the multifactorial process of vein graft intimal hyperplasia, where direct correlation of these patterns was integrated with detailed morphologic data to identify those pathways central to the disease process. Methods: NZW rabbits underwent bilateral carotid vein grafting and unilateral distal branch ligation to create high and low shear environments. Vein grafts were harvested at 2h, 1 d, 7 ds, 28 d, 90 d, and 180 d (n=4 per group), and mRNA expression analyzed using a rabbit Agilent microarray platform. Parallel experiments were used to determine wall morphology, cell proliferation, apoptosis, and matrix content at each time point. Results: Compared to high shear grafts, exposure to a low shear resulted in a 5-fold greater intimal thickness at 180 d. Although 3365 (out of 14,958) genes varied with either time or shear, no single gene was significantly different (at a false discovery rate <0.001) as a function of shear only. To analyze the broad-based modulation of gene expression, a novel clustering technique was used to identify temporal patterns of genes expression. Eight clusters (A through H) were identified, with five of these clusters demonstrating significant variation between high and low shear grafts (Table; A <0.0001, D <0.0001, F < 0.0001, G <0.001, H <0.0001). Ingenuity pathway analysis was used to map gene ontology groups within the clusters to the dominant biologic process observed on histologic analysis. Cell death (cluster D), matrix degradation (cluster G), and matrix synthesis (cluster H), and the associated gene network pathways, were identified being significantly different in the high and low shear grafts (Figure). Conclusions: Using high throughput genomics and detailed morphologic data, we identify cell death, matrix degradation, and matrix synthesis, and the specific pathways associated with these process, as the most critical components in the development of the intimal hyperplastic lesion.

The Functional Impact of PKCβ/PI3K/AKT Signalling on Translational Initiation in MCL

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 2624-2624
Author(s):  
Grit Hutter ◽  
Yvonne Zimmermann ◽  
Marc Weinkauf ◽  
Alina Postnikova ◽  
Tobias Weiglein ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Death ◽  
Cell Lines ◽  
Translation Initiation ◽  
Target Genes ◽  
Mtor Inhibitors ◽  
Potential Effect ◽  
Mtor Pathway ◽  
Akt Pathway ◽  
Mtor Signalling

Abstract Introduction: Mantle cell lymphoma (MCL) is an aggressive form of B-cell non-Hodgkin’s lymphoma (NHL). It is characterized by the t(11;14)(q13;q32) translocation, which results in the overexpression of cyclinD1, a cyclin regulated by the PI3K/AKT pathway. Activation of the PI3K/AKT pathway has been shown to be involved in the pathogenesis of MCL. In addition overexpression of the protein kinase C beta (PKCβ) has been described for most cases of MCL, inhibited by enzastaurin which in turn induces apoptosis and reduces proliferation through the PKCβ/PI3K/AKT pathways. 4EBP1 is described as one of the downstream targets of PI3K/mTOR pathway linking translation initiation with PI3K/mTOR signalling as a EIF4E binding protein and playing therefore critical role in the control of protein synthesis, survival and cell growth. Targeting 4EBP1 and/or EIF4E via the PI3K/AKt/mTOR signalling or directly will affect tumor tissue. Aim of the study: The aim of the study was to determine the functional impact of PKCβ/PI3K/AKt/mTOR signaling on the translation initiation factor EIF4E, its binding protein and regulated proteins in MCL cell lines. Methods: MCL cell lines were treated with inhibitors of the PKCβ/PI3K/AKt/mTOR pathways (enzastaurin, LY294002, rapamycin) for up to 48h.The impact of the drugs on the proliferation rate of the cells was accessed after 48h by WST-assay and/or cell count. mRNA expression levels were determined using Taqmanassays. Protein phosphorylation status and protein expression were identified by westernblot. For downregulation of EIF4E in the cells sodium arsenite was used. Specific silencing of EIF4E was achieved by transfection of cells with siRNA against EIF4E. Results: The MCL celllines (5) responded to the treatment with the inhibitors of the PI3K/AKt/mTOR pathway at a IC50 for rapamycin between 5nM-50nM and for the PI3Kinhibitor between 0,31μM-5μM. Treatment of the cells with the PI3K/AKt/mTOR inhibitors induced dephosphorylation of 4EBP1 in a time-and dosedependent manner while a potential effect of the PI3K and mTOR inhibitors on the EIF4E expression and its target genes (cyclinD1, BCL2) could not be shown consistently. 4 out of 5 MCL cell lines were susceptible to enzastaurin with an IC50 between 2μM-5μM. In the not responding to enzastaurin and most resistant to rapamycin cell line (Rec-1) no 4EBP1 proteinexpression was detectable. Dephosphorylation of 4EBP1 achieved by treatment of the cells with sodium arsenit was accompanied by downregulation of EIF4E, cyclinD1 and BCL2 proteins but also stop of proliferation. The potential involvement of eIF4E gene expression in the NaAsO2-induced cytotoxicity and cell death in MCL cell lines was shown by silencing the expression of the eIF4E gene by transfection with siRNA specifically targeting the eIF4E gene expression leading to downregulation of cyclinD1, 4EBP1 proteins and cell proliferation. Conclusion: Eventhough treatment of the cells with the PI3K/AKt/mTOR inhibitors induced dephosphorylation of 4EBP1 a potential effect of the PI3K and mTOR inhibitors on the EIF4E expression and its target genes (cyclinD1, BCL2) could not be shown consistently. Instead dephosphorylation of 4EBP1 accomponied by downregulation of EIF4E or targeted downregulation of eIF4E gene expression lead to downregulation of cyclinD1 and BCL2 proteins as well as cell death in MCL. Therefore targeting the downstream targets of the PI3K/AKt/mTOR signalling 4EBP1 and/or EIF4E directly seems to be a promising anticancer strategy.

Comprehensive Genomic Screens Reveal Multiple Modes of Action of the PLZF-RAR-α Oncoprotein

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 686-686
Author(s):  
Kim L. Rice ◽  
Itsaso Hormaeche ◽  
Melanie J. McConnell ◽  
Sergei Doulatov ◽  
Jared Flatow ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Retinoic Acid ◽  
Target Genes ◽  
Kinase Inhibitor ◽  
Retinoic Acid Receptor ◽  
Cyclin Dependent Kinase ◽  
Self Renewal ◽  
Acid Receptor ◽  
Cyclin Dependent Kinase Inhibitor

Abstract The t(11;17)(q23;q21) translocation is associated with a retinoic acid-insensitive form of acute promyelocytic leukemia (APL) involving the production of reciprocal fusion proteins PLZF-RARα and RARα-PLZF. These proteins mediate malignant transformation by binding to and dysregulating RARα/RXR and PLZF target genes, respectively. In order to investigate the molecular basis of PLZF-RARα induced leukemia, we performed a genome wide screen for PLZF-RARα direct target genes using a gain of function model in which PLZF-RARα was expressed in human U937 leukemia cells. Chromatin from U937/PLZF-RARα cells was immunoprecipitated using PLZF antibodies, amplified by ligation-mediated PCR and biological triplicates were hybridized to NimbleGen 2.7kB promoter arrays, which represent 24,659 human promoters. We identified 4916 genes directly bound by PLZF-RARα (2/3 biological replicates, FDR <0.2). These genes were highly enriched for ontological categories including immunity and defense (p<10-6), apoptosis (p<2×10-5), cell cycle (p<10-3) and oncogenesis (p<10-2). Gene expression profiling of U937/PLZF-RARα cells revealed that 34% of direct targets were also transcriptionally regulated in response to PLZF-RARα induction. Despite the established role of PLZF-RARα as a transcriptional repressor, 56% of genes bound by PLZF-RARα were upregulated and 44% repressed. Bioinformatic analysis of PLZF-RARα bound sequences using the MATRIXReduce algorithm identified the ‘-AGGTCA-‘ core sequence as the highest ranked position specific affinity matrix (PSAM). Comparison of this matrix with known transcription factor binding sites from the JASPAR core database revealed high similarity to the recognition sequence for the RAR-related orphan receptor A1 (RORA1) (E value: 5.2×10-3), RORA2 (3.5×10-2) and RXRA-VDR (4.4×10-2). This suggests that the natural binding site of PLZF-RARα is similar to that of other nuclear receptors. The ‘GTCA’ core sequence is frequently observed in canonical retinoic acid receptor response elements and this motif was only associated with genes repressed with binding by PLZF-RARα. Together these results are consistent with the idea that PLZF-RARα acts in large part as a dominant negative retinoic acid receptor. A comparison of genes bound directly by PLZF-RARα with gene expression profiles from 22 APL (4 PLZF-RARα, 18 PML-RARα) and 99 acute myeloid leukemias (AML) selected at random from the Erasmus University dataset, using gene set enrichment analysis, revealed that direct targets of PLZF-RARα were differentially repressed in APL when compared to other forms of AML. Overexpression of PLZF-RARα in murine hematopoietic progenitors and human CD34+ cord blood, blocked myeloid differentiation, an effect associated with the repression of C/EBP genes (α, β and ε), which were identified as direct targets of PLZF-RARα by ChIP-chip. Treatment of primary CD34+ cells with ATRA led to an increase in CEBPα and β, but repression of CEBPε was not relieved. Overexpression of PLZF-RARα in primary murine bone marrow led to an increase in the more primitive Sca1+ population, coincident with increased serial replating ability. Overexpression of PLZF-RARα in mouse and human progenitors led to increased proliferation with more cells in the S and G2/M phases of cell cycle. Correlating with this effect, genes with defined roles in hematopoietic stem cell self-renewal including HOXA9 and MPL were bound and activated by the induction of PLZF-RARα in U937 cells. Increased proliferation was also coincident with repressed expression of Cdkn2d (p19) a cyclin dependent kinase inhibitor, also directly bound by PLZF-RARα. PLZF-RARα appears to transform cells through three interlinked modes of action, inhibition of differentiation by direct repression of key myeloid transcription factors, stimulation of proliferation by repression of a cyclin dependent kinase inhibitor and activation of genes critical for self renewal.

scholarly journals Alterations of Rice (Oryza sativa L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf Virus

2020 ◽  
Vol 21 (16) ◽  
pp. 5753
Author(s):  
Linying Li ◽  
Yuqing He ◽  
Xueying Zhang ◽  
Hehong Zhang ◽  
Zongtao Sun ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Oryza Sativa ◽  
Methylation Level ◽  
Cytosine Methylation ◽  
Target Genes ◽  
Oryza Sativa L ◽  
Rna Virus ◽  
Dwarf Virus ◽  
Sequencing Analysis

Rice black-streaked dwarf virus (RBSDV) causes severe yield losses in rice (Oryza sativa L.) in China. Studies have shown that the mechanisms of DNA methylation-mediated plant defense against DNA viruses and RNA viruses are different. However, in rice its function in response to infection of RBSDV, a double-stranded RNA virus, remains unclear. In this study, high-throughput single-base resolution bisulfite sequencing (BS-Seq) was carried out to analyze the distribution pattern and characteristics of cytosine methylation in RBSDV-infected rice. Widespread differences were identified in CG and non-CG contexts between the RBSDV-infected and RBSDV-free rice. We identified a large number of differentially methylated regions (DMRs) along the genome of RBSDV-infected rice. Additionally, the transcriptome sequencing analysis obtained 1119 differentially expressed genes (DEGs). Correlation analysis of DMRs-related genes (DMGs) and DEGs filtered 102 genes with positive correlation and 71 genes with negative correlation between methylation level at promoter regions and gene expression. Key genes associated with maintaining DNA methylation in rice were analyzed by RT-qPCR and indicated that OsDMT702 might be responsible for the global increase of DNA methylation level in rice under RBSDV stress. Our results suggest important roles of rice DNA methylation in response to RBSDV and provide potential target genes for rice antiviral immunity.

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