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Fan Z, Wu C, Chen M, Jiang Y, Wu Y, Mao R, Fan Y. The generation of PD-L1 and PD-L2 in cancer cells: From nuclear chromatin reorganization to extracellular presentation. Acta Pharm Sin B 2022; 12:1041-1053. [PMID: 35530130 PMCID: PMC9069407 DOI: 10.1016/j.apsb.2021.09.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/27/2021] [Accepted: 08/25/2021] [Indexed: 12/16/2022] Open
Abstract
The immune checkpoint blockade (ICB) targeting on PD-1/PD-L1 has shown remarkable promise in treating cancers. However, the low response rate and frequently observed severe side effects limit its broad benefits. It is partially due to less understanding of the biological regulation of PD-L1. Here, we systematically and comprehensively summarized the regulation of PD-L1 from nuclear chromatin reorganization to extracellular presentation. In PD-L1 and PD-L2 highly expressed cancer cells, a new TAD (topologically associating domain) (chr9: 5,400,000-5,600,000) around CD274 and CD273 was discovered, which includes a reported super-enhancer to drive synchronous transcription of PD-L1 and PD-L2. The re-shaped TAD allows transcription factors such as STAT3 and IRF1 recruit to PD-L1 locus in order to guide the expression of PD-L1. After transcription, the PD-L1 is tightly regulated by miRNAs and RNA-binding proteins via the long 3'UTR. At translational level, PD-L1 protein and its membrane presentation are tightly regulated by post-translational modification such as glycosylation and ubiquitination. In addition, PD-L1 can be secreted via exosome to systematically inhibit immune response. Therefore, fully dissecting the regulation of PD-L1/PD-L2 and thoroughly detecting PD-L1/PD-L2 as well as their regulatory networks will bring more insights in ICB and ICB-based combinational therapy.
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Key Words
- 3′-UTR, 3′-untranslated region
- ADAM17, a disintegrin and metalloprotease 17
- APCs, antigen-presenting cells
- AREs, adenylate and uridylate (AU)-rich elements
- ATF3, activating transcription factor 3
- CD273/274, cluster of differentiation 273/274
- CDK4, cyclin-dependent kinase 4
- CMTM6, CKLF like MARVEL transmembrane domain containing 6
- CSN5, COP9 signalosome subunit 5
- CTLs, cytotoxic T lymphocytes
- EMT, epithelial to mesenchymal transition
- EpCAM, epithelial cell adhesion molecule
- Exosome
- FACS, fluorescence-activated cell sorting
- GSDMC, Gasdermin C
- GSK3β, glycogen synthase kinase 3 beta
- HSF1, heat shock transcription factor 1
- Hi-C, high throughput chromosome conformation capture
- ICB, immune checkpoint blockade
- IFN, interferon
- IL-6, interleukin 6
- IRF1, interferon regulatory factor 1
- Immune checkpoint blockade
- JAK, Janus kinase 1
- NFκB, nuclear factor kappa B
- NSCLC, non-small cell lung cancer
- OTUB1, OTU deubiquitinase, ubiquitin aldehyde binding 1
- PARP1, poly(ADP-ribose) polymerase 1
- PD-1, programmed cell death-1
- PD-L1
- PD-L1, programmed death-ligand 1
- PD-L2
- PD-L2, programmed death ligand 2
- Post-transcriptional regulation
- Post-translational regulation
- SP1, specificity protein 1
- SPOP, speckle-type POZ protein
- STAG2, stromal antigen 2
- STAT3, signal transducer and activator of transcription 3
- T2D, type 2 diabetes
- TADs, topologically associating domains
- TFEB, transcription factor EB
- TFs, transcription factors
- TNFα, tumor necrosis factor-alpha
- TTP, tristetraprolin
- Topologically associating domain
- Transcription
- UCHL1, ubiquitin carboxy-terminal hydrolase L1
- USP22, ubiquitin specific peptidase 22
- dMMR, deficient DNA mismatch repair
- irAEs, immune related adverse events
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Affiliation(s)
- Zhiwei Fan
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong 226001, China
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China
| | - Changyue Wu
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China
- Department of Dermatology, Affiliated Hospital of Nantong University, Nantong University, Nantong 226001, China
| | - Miaomiao Chen
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China
| | - Yongying Jiang
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong 226001, China
| | - Yuanyuan Wu
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China
- Corresponding authors.
| | - Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong 226001, China
- Corresponding authors.
| | - Yihui Fan
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong 226001, China
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China
- Corresponding authors.
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Gao X, You J, Gong Y, Yuan M, Zhu H, Fang L, Zhu H, Ying M, He Q, Yang B, Cao J. WSB1 regulates c-Myc expression through β-catenin signaling and forms a feedforward circuit. Acta Pharm Sin B 2022; 12:1225-39. [PMID: 35530152 DOI: 10.1016/j.apsb.2021.10.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/20/2022] Open
Abstract
The dysregulation of transcription factors is widely associated with tumorigenesis. As the most well-defined transcription factor in multiple types of cancer, c-Myc can transform cells by transactivating various downstream genes. Given that there is no effective way to directly inhibit c-Myc, c-Myc targeting strategies hold great potential for cancer therapy. In this study, we found that WSB1, which has a highly positive correlation with c-Myc in 10 cancer cell lines and clinical samples, is a direct target gene of c-Myc, and can positively regulate c-Myc expression, which forms a feedforward circuit promoting cancer development. RNA sequencing results from Bel-7402 cells confirmed that WSB1 promoted c-Myc expression through the β-catenin pathway. Mechanistically, WSB1 affected β-catenin destruction complex-PPP2CA assembly and E3 ubiquitin ligase adaptor β-TRCP recruitment, which inhibited the ubiquitination of β-catenin and transactivated c-Myc. Of interest, the effect of WSB1 on c-Myc was independent of its E3 ligase activity. Moreover, overexpressing WSB1 in the Bel-7402 xenograft model could further strengthen the tumor-driven effect of c-Myc overexpression. Thus, our findings revealed a novel mechanism involved in tumorigenesis in which the WSB1/c-Myc feedforward circuit played an essential role, highlighting a potential c-Myc intervention strategy in cancer treatment.
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Key Words
- ATM, serine-protein kinase ATM
- CHIP, chromatin immunoprecipitation
- CK1, casein kinase 1
- Cancer treatment
- EBP2, probable rRNA-processing protein EBP2
- ESC complex, elongin B/C-cullin 2/5-SOCS box containing ubiquitin ligase protein complex
- Feedback loop
- GSK3β, glycogen synthase kinase 3β
- HCC, hepatocellular carcinoma
- HIF1-α, hypoxia induced factor 1-alpha
- IHC, immunohistochemistry
- PLK1, serine/threonine-protein kinase PLK1
- PP2A, serine/threonine protein phosphatase 2A
- PROTAC, proteolysis targeting chimaera
- RhoGDI2, Rho GDP dissociation inhibitor 2
- TFs, transcription factors
- Transcription factors
- Tumorigenesis
- Ubiquitination-proteasome pathway
- WSB1
- WSB1, WD repeat and SOCS box containing 1
- c-Myc
- c-Myc, proto-oncogene c-Myc
- eIF4F, eukaryotic translation initiation factor 4F
- β-Catenin destruction complex
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Lu Y, Li Q, Zheng K, Fu C, Jiang C, Zhou D, Xia C, Ma S. Development of a high efficient promoter finding method based on transient transfection. Gene 2019; 2:100008. [PMID: 32550544 PMCID: PMC7286058 DOI: 10.1016/j.gene.2019.100008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/23/2019] [Accepted: 02/08/2019] [Indexed: 01/19/2023]
Abstract
In metazoan genome, the mechanism of gene expression regulation between transcriptional regulatory elements and their target gene is spatiotemporal. Active promoters possess many specific chromosomal features, such as hypersensitive to DNaseI and enrichment of specific histone modifications. In this article, we proposed a novel method which possesses a high efficiency to find promoters in vitro. A promoter-trap library was constructed with totally 706 random mouse genomic DNA fragment clones, and 260 promoter-active fragments of the library were screened by transient transfection into 4T1 cells. To demonstrate the accuracy of this promoter finding method, 13 fragments with promoter activities were randomly selected for published DNase-seq and ChIP-seq data analysis, downstream transcripts prediction and expression confirmation. qRT-PCR results showed that six predicted transcription units were successfully amplified in different mouse tissues/cells or in reconstituted mouse mammary tumors. Our results indicate that this promoter finding method can successfully detect the promoter-active fragments and their downstream transcripts.
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Key Words
- ATAC-seq, Assay for transposase-accessible chromatin using sequencing
- Bioinformatics
- CAGE, cap analysis of gene expression
- CMV, Cytomegalovirus
- Cancer-specific promoter
- ChIP-seq, Chromatin immunoprecipitation followed by massively parallel DNA sequencing
- Ct, threshold
- DHS, DNaseI hypersensitive sites
- DNase-seq, DNase I hypersensitive sites sequencing
- EF1a1, eukaryotic translation elongation factor 1 alpha 1
- FBS, fetal bovine serum
- GRO-seq, global run-on sequencing
- Gene expression regulation
- Gene finding
- H3K4me3, histone H3 lysine 4 trimethylation
- Itpr2, inositol 1, 4, 5-triphosphate receptor 2
- LSINCT5, long stress-induced non-coding transcript 5
- MCS, multiple cloning site
- MPRA, Massively parallel reporter assays
- Mouse breast cancer
- PBS, phosphate buffered solution
- Promoter trap
- RNA-seq, RNA sequencing
- SD, standard deviation
- STARR-seq, Self-transcribing active regulatory region sequencing
- TFs, transcription factors
- TSS, transcription start sites
- dNTPs, deoxy-ribonucleoside triphosphate
- eRNAs, enhancer RNAs
- mSEAP, mouse synthetic secreted embryonic alkaline phosphatase
- pNPP, p-nitropheny-phosate
- qRT-PCR, quantitative RT-PCR
- tpk1, thiamine pyrophosphokinase
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Affiliation(s)
- Yao Lu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, PR China
| | - Qilong Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, PR China
| | - Kexin Zheng
- College of Food Science and Technology, Shenyang Agricultural University, Shenyang, Liaoning, PR China
| | - Chenghao Fu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, PR China
| | - Chunying Jiang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, PR China
| | - Dayu Zhou
- College of Food Science and Technology, Shenyang Agricultural University, Shenyang, Liaoning, PR China
| | - Chao Xia
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, PR China
| | - Shiliang Ma
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, PR China
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Pinweha P, Rattanapornsompong K, Charoensawan V, Jitrapakdee S. MicroRNAs and oncogenic transcriptional regulatory networks controlling metabolic reprogramming in cancers. Comput Struct Biotechnol J 2016; 14:223-33. [PMID: 27358718 PMCID: PMC4915959 DOI: 10.1016/j.csbj.2016.05.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/25/2016] [Accepted: 05/27/2016] [Indexed: 12/15/2022] Open
Abstract
Altered cellular metabolism is a fundamental adaptation of cancer during rapid proliferation as a result of growth factor overstimulation. We review different pathways involving metabolic alterations in cancers including aerobic glycolysis, pentose phosphate pathway, de novo fatty acid synthesis, and serine and glycine metabolism. Although oncoproteins, c-MYC, HIF1α and p53 are the major drivers of this metabolic reprogramming, post-transcriptional regulation by microRNAs (miR) also plays an important role in finely adjusting the requirement of the key metabolic enzymes underlying this metabolic reprogramming. We also combine the literature data on the miRNAs that potentially regulate 40 metabolic enzymes responsible for metabolic reprogramming in cancers, with additional miRs from computational prediction. Our analyses show that: (1) a metabolic enzyme is frequently regulated by multiple miRs, (2) confidence scores from prediction algorithms might be useful to help narrow down functional miR-mRNA interaction, which might be worth further experimental validation. By combining known and predicted interactions of oncogenic transcription factors (TFs) (c-MYC, HIF1α and p53), sterol regulatory element binding protein 1 (SREBP1), 40 metabolic enzymes, and regulatory miRs we have established one of the first reference maps for miRs and oncogenic TFs that regulate metabolic reprogramming in cancers. The combined network shows that glycolytic enzymes are linked to miRs via p53, c-MYC, HIF1α, whereas the genes in serine, glycine and one carbon metabolism are regulated via the c-MYC, as well as other regulatory organization that cannot be observed by investigating individual miRs, TFs, and target genes.
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Key Words
- 2-HG, 2-hydroxyglutarate
- ACC, acetyl-CoA carboxylase
- ACL, ATP-citrate lyase
- BRCA1, breast cancer type 1 susceptibility protein
- Cancer
- FAS, fatty acid synthase
- FH, fumarate hydratase
- G6PD, glucose-6-phosphate dehydrogenase
- GDH, glutamate dehydrogenase
- GLS, glutaminase
- GLUT, glucose transporter
- HIF1α, hypoxia inducible factor 1α
- HK, hexokinase
- IDH, isocitrate dehydrogenase
- MCT, monocarboxylic acid transporter
- ME, malic enzyme
- Metabolism
- MicroRNA
- Oncogene
- PC, pyruvate carboxylase
- PDH, pyruvate dehydrogenase
- PDK, pyruvate dehydrogenase kinase
- PEP, phosphoenolpyruvate
- PEPCK, phosphoenolpyruvate carboxykinase
- PFK, phosphofructokinase
- PGK, phosphoglycerate kinase (PGK)
- PHGDH, phosphoglycerate dehydrogenase
- PKM, muscle-pyruvate kinase
- PPP, pentose phosphate pathway
- PSAT, phosphoserine aminotransferase
- PSPH, phosphoserine phosphatase
- SDH, succinate dehydrogenase
- SHMT, serine hydroxymethyl transferase
- SREBP1, sterol regulatory element binding protein 1
- TCA, tricarboxylic acid
- TFs, transcription factors
- Transcriptional regulation network
- c-MYC, V-myc avian myelocytomatosis viral oncogene homolog
- miR/miRNA, LDH, lactate dehydrogenase micro RNA
- p53, tumor protein p53
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Affiliation(s)
- Pannapa Pinweha
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | | | - Varodom Charoensawan
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Sarawut Jitrapakdee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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Türei D, Földvári-Nagy L, Fazekas D, Módos D, Kubisch J, Kadlecsik T, Demeter A, Lenti K, Csermely P, Vellai T, Korcsmáros T. Autophagy Regulatory Network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy. Autophagy 2015; 11:155-65. [PMID: 25635527 PMCID: PMC4502651 DOI: 10.4161/15548627.2014.994346] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Autophagy is a complex cellular process having multiple roles, depending on tissue, physiological, or pathological conditions. Major post-translational regulators of autophagy are well known, however, they have not yet been collected comprehensively. The precise and context-dependent regulation of autophagy necessitates additional regulators, including transcriptional and post-transcriptional components that are listed in various datasets. Prompted by the lack of systems-level autophagy-related information, we manually collected the literature and integrated external resources to gain a high coverage autophagy database. We developed an online resource, Autophagy Regulatory Network (ARN; http://autophagy-regulation.org), to provide an integrated and systems-level database for autophagy research. ARN contains manually curated, imported, and predicted interactions of autophagy components (1,485 proteins with 4,013 interactions) in humans. We listed 413 transcription factors and 386 miRNAs that could regulate autophagy components or their protein regulators. We also connected the above-mentioned autophagy components and regulators with signaling pathways from the SignaLink 2 resource. The user-friendly website of ARN allows researchers without computational background to search, browse, and download the database. The database can be downloaded in SQL, CSV, BioPAX, SBML, PSI-MI, and in a Cytoscape CYS file formats. ARN has the potential to facilitate the experimental validation of novel autophagy components and regulators. In addition, ARN helps the investigation of transcription factors, miRNAs and signaling pathways implicated in the control of the autophagic pathway. The list of such known and predicted regulators could be important in pharmacological attempts against cancer and neurodegenerative diseases.
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Affiliation(s)
- Dénes Türei
- a Department of Genetics ; Eötvös Loránd University ; Budapest , Hungary
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6
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Abstract
DNA methylation is responsible for regulating gene expression and cellular differentiation and for maintaining genomic stability during normal human development. Furthermore, it plays a significant role in the regulation of hematopoiesis. In order to elucidate the influence of DNA methylation during B-cell development, genome-wide DNA methylation status of pro-B, pre-BI, pre-BII, and naïve-B-cells isolated from human umbilical cord blood was determined using the methylated CpG island recovery assay followed by next generation sequencing. On average, 182–200 million sequences were generated for each precursor B-cell subset in 10 biological replicates. An overall decrease in methylation was observed during the transition from pro-B to pre-BI, whereas no differential methylation was observed in the pre-BI to pre-BII transition or in the pre-BII to naïve B-cell transition. Most of the methylated regions were located within intergenic and intronic regions not present in a CpG island context. Putative novel enhancers were identified in these regions that were differentially methylated between pro-B and pre-BI cells. The genome-wide methylation profiles are publically available and may be used to gain a better understanding of the involvement of atypical DNA methylation in the pathogenesis of malignancies associated with precursor B-cells.
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Key Words
- CG dinucleotide
- CLP, common lymphoid progenitor cells
- CpGI, CpG island
- DMRs, differentially methylated regions
- DNA methylation
- FDR, false discovery rate.
- H3K27ac, histone H3 lysine 27 acetylation
- H3K4me1, histone H3 lysine 4 monomethylation
- HCB, human umbilical cord blood
- HSCs, haematopoietic stem cells
- MBDs, methyl CpG binding domains
- MIRA-seq, methylated CpG island recovery assay (MIRA) followed by next generation sequencing
- MeCP2, methyl CpG binding protein 2
- Pre-B, precursor B-cell; CD
- Pro-B, progenitor B-cell
- ROIs, regions of interest
- TFs, transcription factors
- acute lymphoblastic leukemia; CpG
- cluster of differentiation; ALL
- enhancer
- next-generation sequencing
- precursor B-cell
- umbilical cord blood
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Affiliation(s)
- Md Almamun
- a Department of Pathology and Anatomical Sciences ; University of Missouri-Columbia ; Columbia , MO USA
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Rao G, Sui J, Zeng Y, He C, Zhang J. Genome-wide analysis of the AP2/ERF gene family in Salix arbutifolia. FEBS Open Bio 2015; 5:132-7. [PMID: 25830086 PMCID: PMC4354408 DOI: 10.1016/j.fob.2015.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/15/2015] [Accepted: 02/18/2015] [Indexed: 01/08/2023] Open
Abstract
We identified 173 AP2/ERF superfamily genes in Salix arbutifolia. A comparative analysis of AP2/ERF superfamily genes was performed. The phylogenic trees of AP2/ERF superfamily have been constructed.
AP2/ERF genes encode transcriptional regulators with a variety of functions in plant growth and development and in response to biotic and abiotic stresses. To date, there are no detailed classification and expression profiles for AP2/ERF genes in Salix. In this study, a comprehensive computational analysis identified 173 AP2/ERF superfamily genes in willow (Salix arbutifolia), by using in silico cloning methods with the use of the AP2/ERF conserved domain amino acid sequence of Arabidopsis thaliana as a probe. Based on the results of phylogenetic analyses and the number of AP2/ERF domains, the AP2/ERF genes were classified into four groups: AP2, RAV, ERF and Soloist. The expression profile was analyzed using transcriptome data from different tissues. A comparative analysis of AP2/ERF superfamily genes among Salix, Populus and Arabidopsis was performed. The Salix DREB, AP2 and RAV groups had a similar number to those in Arabidopsis, and the size of the ERF subfamily in Salix was about 1.4-fold that of Arabidopsis. The Salix DREB subfamily was smaller compared to Populus, while the other families were similar in size to those in Populus. These results will be useful for future functional analyses of the ERF family genes.
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Affiliation(s)
- Guodong Rao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China ; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China ; Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jinkai Sui
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yanfei Zeng
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Caiyun He
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China ; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China ; Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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Fontemaggi G, Bellissimo T, Donzelli S, Iosue I, Benassi B, Bellotti G, Blandino G, Fazi F. Identification of post-transcriptional regulatory networks during myeloblast-to-monocyte differentiation transition. RNA Biol 2015; 12:690-700. [PMID: 25970317 PMCID: PMC4615388 DOI: 10.1080/15476286.2015.1044194] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/17/2015] [Accepted: 04/20/2015] [Indexed: 01/24/2023] Open
Abstract
Treatment of leukemia cells with 1,25-dihydroxyvitamin D3 may overcome their differentiation block and lead to the transition from myeloblasts to monocytes. To identify microRNA-mRNA networks relevant for myeloid differentiation, we profiled the expression of mRNAs and microRNAs associated to the low- and high-density ribosomal fractions in leukemic cells and in their differentiated monocytic counterpart. Intersection between mRNAs shifted across the fractions after treatment with putative target genes of modulated microRNAs showed a series of molecular networks relevant for the monocyte cell fate determination, as for example the post-transcriptional regulation of the Polo-like kinase 1 (PLK1) by miR-22-3p and let-7e-5p.
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Key Words
- AGO2, argonaute 2
- AML
- AML, acute myeloid leukemia
- ECL methods, enhanced chemiluminescence methods
- GAPDH, glyceraldehyde 3-phosphate dehydrogenase
- GFP, green fluorescent protein
- HPCs, haematopoietic progenitor cells
- KPNA2, karyopherin α, 2
- NBT assay, nitroblue tetrazolium assay
- PLK1
- PLK1, polo-like kinase 1
- PMSF, phenylmethylsulfonyl fluoride
- RAB10, member RAS oncogene family 10
- RAB5C, member RAS oncogene family 5C
- RT-qPCR, quantitative reverse transcription polymerase chain reaction
- SF2A1, splicing factor 2A1
- TFs, transcription factors
- VitD3, 1,25-dihydroxyvitamin D3
- miRNAs, microRNAs
- microRNAs
- myeloid differentiation
- ribosomal/polysomal fractions
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Affiliation(s)
- Giulia Fontemaggi
- Translational Oncogenomics Unit; “Regina Elena” National Cancer Institute; Rome, Italy
| | - Teresa Bellissimo
- Department of Anatomical, Histological, Forensic, and Orthopedic Sciences; Section of Histology & Medical Embryology; Sapienza University of Rome; Rome, Italy
| | - Sara Donzelli
- Translational Oncogenomics Unit; “Regina Elena” National Cancer Institute; Rome, Italy
| | - Ilaria Iosue
- Department of Anatomical, Histological, Forensic, and Orthopedic Sciences; Section of Histology & Medical Embryology; Sapienza University of Rome; Rome, Italy
| | - Barbara Benassi
- Unit of Radiation Biology and Human Health; ENEA-Casaccia; Rome, Italy
| | | | - Giovanni Blandino
- Translational Oncogenomics Unit; “Regina Elena” National Cancer Institute; Rome, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic, and Orthopedic Sciences; Section of Histology & Medical Embryology; Sapienza University of Rome; Rome, Italy
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Grob A, McStay B. Construction of synthetic nucleoli and what it tells us about propagation of sub-nuclear domains through cell division. Cell Cycle 2014; 13:2501-8. [PMID: 25486191 PMCID: PMC4614152 DOI: 10.4161/15384101.2014.949124] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/16/2014] [Accepted: 07/16/2014] [Indexed: 11/19/2022] Open
Abstract
The cell nucleus is functionally compartmentalized into numerous membraneless and dynamic, yet defined, bodies. The cell cycle inheritance of these nuclear bodies (NBs) is poorly understood at the molecular level. In higher eukaryotes, their propagation is challenged by cell division through an "open" mitosis, where the nuclear envelope disassembles along with most NBs. A deeper understanding of the mechanisms involved can be achieved using the engineering principles of synthetic biology to construct artificial NBs. Successful biogenesis of such synthetic NBs demonstrates knowledge of the basic mechanisms involved. Application of this approach to the nucleolus, a paradigm of nuclear organization, has highlighted a key role for mitotic bookmarking in the cell cycle propagation of NBs.
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Key Words
- 1°, primary
- 2°, secondary
- CBs, Cajal bodies
- CDK, cyclin-dependent kinase
- DFC, dense fibrillar component
- DJ, distal junction
- FCs, fibrillar centers
- GC, granular component
- HLBs, histone locus bodies
- HMG, high mobility group
- IGS, intergenic spacers
- NBs, nuclear bodies
- NORs, nucleolar organizer regions
- Nucleolar Organizer Region (NOR)
- PJ, proximal junction
- PML, promyelocytic leukemia
- PNBs, pre-nucleolar bodies
- TFs, transcription factors
- UBF
- UBF, Upstream binding factor
- XEn, Xenopus enhancer
- cell cycle
- mitotic bookmarking
- neo-NOR
- neonucleoli
- nuclear bodies
- nucleolus
- pol, RNA polymerase
- pre-rRNA, precursor rRNA
- pseudo-NOR
- rDNA, ribosomal genes
- rRNA, ribosomal RNA; RNP, ribonucleoprotein
- synthetic biology
- t-UTPs, transcription U 3 proteins
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Affiliation(s)
- Alice Grob
- Center for Chromosome Biology; School of Natural Sciences; National University of Ireland; Galway, Ireland
| | - Brian McStay
- Center for Chromosome Biology; School of Natural Sciences; National University of Ireland; Galway, Ireland
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