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Congrains A, Niemann FS, Duarte ADSS, Ferro KPV, Olalla-Saad ST. Novel Non-Coding Transcript in NR4A3 Locus, LncNR4A3, Regulates RNA Processing Machinery Proteins and NR4A3 Expression. Front Oncol 2020; 10:569668. [PMID: 33330042 PMCID: PMC7719789 DOI: 10.3389/fonc.2020.569668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/19/2020] [Indexed: 11/30/2022] Open
Abstract
NR4A3 is a key tumor suppressor in myeloid malignancy, mice lacking both NR4A1 and family member NR4A3 rapidly develop lethal acute myeloid leukemia (AML). We identified a long non-coding transcript in the NR4A3 locus and pursued the characterization of this anonymous transcript and the study of its role in leukemogenesis. We characterized this novel long non-coding transcript as a sense polyadenylated transcript. Bone marrow cells from AML patients expressed significantly reduced levels of lncNR4A3 compared to healthy controls (controls = 15, MDS= 20, p=0.05., AML= 21, p<0.01). Expression of NR4A3, as previously reported, was also significantly reduced in AML. Interestingly, the expression of both coding and non-coding transcripts was highly correlated (Pearson R = 0.3771, P<0.01). Transient over-expression of LncNR4A3 by nucleofection led to an increase in the RNA and protein level of NR4A3, reduction of proliferation in myeloid cell lines K-562 and KG1 (n=3 and 2 respectively, p<0.05) and reduced colony formation capacity in primary leukemic cells. A mass spectrometry-based quantitative proteomics approach was used to identify proteins dysregulated after lncNR4A3 over-expression in K-562. Enrichment analysis showed that the altered proteins are biologically connected (n=4, p<0.001) and functionally associated to RNA binding, transcription elongation, and splicing. Remarkably, we were able to validate the most significant results by WB. We showed that this novel transcript, lncNR4A3 regulates NR4A3 and we hypothesize this regulatory mechanism is mediated by the modulation of the RNA processing machinery.
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Affiliation(s)
- Ada Congrains
- Hematology and Transfusion Medicine Center, University of Campinas, Campinas, Brazil
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Al-Raawi D, Kanhere A. Autoregulation of JARID2 through PRC2 interaction with its antisense ncRNA. BMC Res Notes 2020; 13:501. [PMID: 33126912 PMCID: PMC7602346 DOI: 10.1186/s13104-020-05348-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022] Open
Abstract
Objective JARID2 is a member of chromatin-modifying Polycomb Repressive Complex-2 or PRC2. It plays a role in recruiting PRC2 to developmental genes and regulating its activity. JARID2 along with PRC2 is indispensable for normal development. However, it remains unclear how JARID2 expression itself is regulated. Recently a number of non-protein-coding RNAs or ncRNAs are shown to regulate transcription. An antisense ncRNA, JARID2-AS1, is expressed from the first intron of JARID2 isoform-1 but its role in regulation of JARID2 expression has not been investigated. The objective of this study was to explore the role of JARID2-AS1 in regulating JARID2 and consequently PRC2. Results We found that JARID2-AS1 is localised in the nucleus and shows anti-correlated expression pattern to that of JARID2 isoform-1 mRNA. More interestingly, data mining approach strongly indicates that JARID2-AS1 binds to PRC2. These are important observations that provide insights into transcriptional regulation of JARID2, especially because they indicate that JARID2-AS1 by interacting and probably recruiting PRC2 participates in an auto-regulatory loop that controls levels of JARID2. This holds importance in regulation of developmental and differentiation processes. However, to support this hypothesis, further in-depth studies are needed which can verify JARID2-AS1-PRC2 interactions.
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Affiliation(s)
- Diaa Al-Raawi
- Tumour Biology Research Program, 57357 Children's Cancer Hospital, Cairo, Egypt.,School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Aditi Kanhere
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom. .,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3GE, United Kingdom.
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He H, Qin M. Long non-coding RNA LEF1-AS1 is involved in the progression of retinoblastoma through regulating the Wnt/β-catenin pathway. Clin Exp Pharmacol Physiol 2020; 47:886-891. [PMID: 31990064 DOI: 10.1111/1440-1681.13263] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 01/23/2020] [Accepted: 01/23/2020] [Indexed: 12/11/2022]
Abstract
The lymphoid enhancer binding factor 1 antisense RNA 1 (LEF1-AS1) has been suggested to function as a tumour-associated lncRNA in several types of human cancers, but there is no study to date about the role of LEF1-AS1 in retinoblastoma. In our study, LEF1-AS1 expression was increased in retinoblastoma tissues and cell lines compared with paired adjacent normal tissues and the retinal pigment epithelial cell line, respectively. Meanwhile, we found that patients with retinoblastoma with IIRC D-E or undifferentiated type had notably higher levels of LEF1-AS1 expression than those with IIRC A-C or differentiated type. High LEF1-AS1 expression predicted poor disease-free survival in patients with retinoblastoma. The in vitro assays suggested that silencing of LEF1-AS1 suppressed retinoblastoma cell proliferation, migration, and invasion through regulating the Wnt/β-catenin pathway. In conclusion, LEF1-AS1 functions as an oncogenic lncRNA in retinoblastoma.
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Affiliation(s)
- Hua He
- Department of Ophthalmology, The First Hospital of Yulin, Yulin, China
| | - Mu Qin
- Department of Ophthalmology, Affiliated Hospital of Xiangnan University, Chenzhou, China
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Swanson GM, Estill M, Diamond MP, Legro RS, Coutifaris C, Barnhart KT, Huang H, Hansen KR, Trussell JC, Coward RM, Zhang H, Goodrich R, Krawetz SA. Human chromatin remodeler cofactor, RNA interactor, eraser and writer sperm RNAs responding to obesity. Epigenetics 2020; 15:32-46. [PMID: 31354029 PMCID: PMC6961666 DOI: 10.1080/15592294.2019.1644880] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 12/23/2022] Open
Abstract
In the United States almost 33% of adults are considered obese (BMI > 30 kg/m2). Both animal models and to a lesser extent human studies, have associated BMI, a measure of obesity, with alterations in sperm DNA methylation and RNAs. Sperm RNAs from the Assessment of Multiple Gestations from Ovarian Stimulation trial, were isolated and sequenced. A Generalized Linear Model identified 487 BMI associated human sperm RNA elements (short exon-sized sequences). They partitioned into four patterns; a continual increase with BMI, increase once obese (BMI>30 kg/m2); a steady decrease with BMI; and decrease once overweight (BMI 25 - 30 kg/m2). Gene Ontology revealed a unique relationship between BMI and transcripts associated with chromosome organization, adipogenesis, cellular stress and obesity-related inflammation. Coregulatory networks linked by Chromatin remodeler cofactors, RNA interactors, Erasers and Writers (CREWs) were uncovered to reveal a hierarchical epigenetic response pathway.
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Affiliation(s)
- Grace M. Swanson
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, USA
| | - Molly Estill
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, USA
| | - Michael P. Diamond
- Department of Obstetrics and Gynecology, Augusta University, Augusta, USA
| | - Richard S. Legro
- Department of Obstetrics and Gynecology, Pennsylvania State University, Hershey, USA
| | - Christos Coutifaris
- Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, Philadelphia, USA
| | - Kurt T. Barnhart
- Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, Philadelphia, USA
| | - Hao Huang
- Department of Biostatistics, Yale University School of Public Health, New Haven, USA
| | - Karl R. Hansen
- Department of Obstetrics and Gynecology, University of Oklahoma College of Medicine, Oklahoma City, USA
| | - J. C. Trussell
- Urology Department, Upstate Medical University, Syracuse, USA
| | - R. Matthew Coward
- Department of Urology, University of North Carolina School of Medicine, Chapel Hill, USA
| | - Heping Zhang
- Department of Biostatistics, Yale University School of Public Health, New Haven, USA
| | - Robert Goodrich
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, USA
| | - Stephen A. Krawetz
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, USA
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Congrains-Castillo A, Niemann FS, Santos Duarte AS, Olalla-Saad ST. LEF1-AS1, long non-coding RNA, inhibits proliferation in myeloid malignancy. J Cell Mol Med 2019; 23:3021-3025. [PMID: 30770626 PMCID: PMC6433713 DOI: 10.1111/jcmm.14152] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 12/13/2018] [Accepted: 12/17/2018] [Indexed: 12/30/2022] Open
Abstract
LEF1 antisense RNA 1 (LEF1‐AS1) is an antisense long non‐coding RNA encoded in the lymphoid enhancer‐binding factor 1 (LEF1) locus. LEF1‐AS1 is a conserved transcript dysregulated in hematopoiesis. This study aimed to functionally characterize the role of this transcript in myeloid malignancy and explore a possible regulatory effect of LEF1‐AS1 upon LEF1. We show that LEF1‐AS1 is highly expressed in normal hematopoietic stem cells but barely detectable in myeloid malignant cell lines. Additionally, bone marrow cells from myelodysplastic syndrome (n=12) and acute myeloid malignancy patients (n=28) expressed significantly reduced levels of LEF1‐AS1 compared to healthy controls (n=15). Artificial LEF1‐AS1 over‐expression inhibited proliferation in HL60 and led to an upregulation of tumor suppressors p21 and p27, and reduced ERK1/2 activation. Unexpectedly, no underlying modulation of LEF1 was detected. Ectopic expression of LEF1‐AS1 also inhibited proliferation in HELA, a cell line lacking endogenous expression of LEF1, supporting a LEF1‐independent mechanism. Additionally, transient over‐expression of LEF1‐AS1 in AML patient cells also led to reduced proliferation and colony formation capacity. We used a mass spectrometry‐based proteomics approach. Proteomic quantification identified the modulation of an important metabolic regulator, Fumarase, and concomitant accumulation of the metabolite fumarate.
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Affiliation(s)
| | - Fernanda S Niemann
- Hematology and Hemotherapy Center, Hemocentro-Unicamp, São Paulo, Brazil
| | | | - Sara T Olalla-Saad
- Hematology and Hemotherapy Center, Hemocentro-Unicamp, São Paulo, Brazil
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Santiago L, Daniels G, Wang D, Deng FM, Lee P. Wnt signaling pathway protein LEF1 in cancer, as a biomarker for prognosis and a target for treatment. Am J Cancer Res 2017; 7:1389-1406. [PMID: 28670499 PMCID: PMC5489786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 04/08/2017] [Indexed: 06/07/2023] Open
Abstract
Transcription factors are regulatory proteins that either activate or repress the transcription of genes via binding to DNA regulatory sequences and regulating recruitment of transcriptional complexes. Lymphoid enhancer-binding factor 1 (LEF1), a member of the T-cell Factor (TCF)/LEF1 family of high-mobility group transcription factors, is a downstream mediator of the Wnt/β-catenin signaling pathway, but can also modulate gene transcription independently. LEF1 is essential in stem cell maintenance and organ development, especially in its role in epithelial-mesenchymal transition (EMT) by activating the transcription of hallmark EMT effectors including N-Cadherin, Vimentin, and Snail. Aberrant expression of LEF1 is implicated in tumorigenesis and cancer cell proliferation, migration, and invasion. LEF1's activity in particular cancer cell types, such as chronic lymphocytic leukemia (CLL), Burkitt lymphoma (BL), acute lymphoblastic leukemia (ALL), oral squamous cell carcinoma (OSCC), and colorectal cancer (CRC), makes it a valuable biomarker in predicting patient prognosis. Additionally, due to aberrant LEF1 activity resulting in cancer progression, knockdown and inhibition treatments designed to target LEF1 have proven effective in alleviating cancer growth, migration, and invasion in CLL, CRC, glioblastoma multiforme (GBM), and renal cell carcinoma (RCC). In prostate cancer cells, LEF1 promotes androgen receptor expression and activity in an androgen-independent manner, ultimately increasing prostate cancer growth regardless of androgen ablation therapy. In this review, we review LEF1 regulation, its role in tumorigenesis in several cancer types, and its clinical value as a biomarker for predicting prognoses and as a target for treatment.
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Affiliation(s)
- Larion Santiago
- Department of Pathology, School of Medicine, New York UniversityNew York, American
| | - Garrett Daniels
- Department of Pathology, School of Medicine, New York UniversityNew York, American
| | - Dongwen Wang
- Department of Urology, First Hospital of Shanxi Medical UniversityTaiyuan, Shanxi, China
| | - Fang-Ming Deng
- Department of Pathology, School of Medicine, New York UniversityNew York, American
- Association of Chinese American PhysiciansFlushing, New York, American
| | - Peng Lee
- Department of Pathology, School of Medicine, New York UniversityNew York, American
- Department of Urology, School of Medicine, New York UniversityNew York, American
- Department of NYU Cancer Institute, School of Medicine, New York UniversityNew York, American
- Department of New York Harbor Healthcare System, School of Medicine, New York UniversityNew York, American
- Association of Chinese American PhysiciansFlushing, New York, American
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Strategies to identify natural antisense transcripts. Biochimie 2017; 132:131-151. [DOI: 10.1016/j.biochi.2016.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/24/2016] [Indexed: 12/15/2022]
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Beltran M, García de Herreros A. Antisense non-coding RNAs and regulation of gene transcription. Transcription 2016; 7:39-43. [PMID: 26985653 DOI: 10.1080/21541264.2016.1148804] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Transcriptome analyses have revealed the existence of a large variety of non-coding RNAs (ncRNAs) that, although specifically expressed, are largely unknown in function. The best-studied role of ncRNAs is the regulation of gene expression, mostly participating in transcription. We report here the role of an antisense ncRNA that represses transcription of LEF1 by recruiting Polycomb repressive complex 2 (PRC2), which trimethylates H3K27. This antisense LEF1 transcript undergoes splicing losing its inhibitory function. We also discuss the possible general relevance of this finding.
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Affiliation(s)
- Manuel Beltran
- a UCL Cancer Institute, University College of London , London , United Kingdom
| | - Antonio García de Herreros
- b Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM) , Barcelona , Spain.,c Departament de Ciències Experimentals i de la Salut , Universitat Pompeu Fabra , Barcelona , Spain
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9
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Lin S, Zhang L, Luo W, Zhang X. Characteristics of Antisense Transcript Promoters and the Regulation of Their Activity. Int J Mol Sci 2015; 17:E9. [PMID: 26703594 PMCID: PMC4730256 DOI: 10.3390/ijms17010009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/23/2015] [Accepted: 12/16/2015] [Indexed: 02/07/2023] Open
Abstract
Recently, an increasing number of studies on natural antisense transcripts have been reported, especially regarding their classification, temporal and spatial expression patterns, regulatory functions and mechanisms. It is well established that natural antisense transcripts are produced from the strand opposite to the strand encoding a protein. Despite the pivotal roles of natural antisense transcripts in regulating the expression of target genes, the transcriptional mechanisms initiated by antisense promoters (ASPs) remain unknown. To date, nearly all of the studies conducted on this topic have focused on the ASP of a single gene of interest, whereas no study has systematically analyzed the locations of ASPs in the genome, ASP activity, or factors influencing this activity. This review focuses on elaborating on and summarizing the characteristics of ASPs to extend our knowledge about the mechanisms of antisense transcript initiation.
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Affiliation(s)
- Shudai Lin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
| | - Li Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
- Agricultural College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
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