1451
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A New Mechanism for Mendelian Dominance in Regulatory Genetic Pathways: Competitive Binding by Transcription Factors. Genetics 2016; 205:101-112. [PMID: 27866169 DOI: 10.1534/genetics.116.195255] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/04/2016] [Indexed: 12/11/2022] Open
Abstract
We report a new mechanism for allelic dominance in regulatory genetic interactions that we call binding dominance. We investigated a biophysical model of gene regulation, where the fractional occupancy of a transcription factor (TF) on the cis-regulated promoter site it binds to is determined by binding energy (-ΔG) and TF dosage. Transcription and gene expression proceed when the TF is bound to the promoter. In diploids, individuals may be heterozygous at the cis-site, at the TF's coding region, or at the TF's own promoter, which determines allele-specific dosage. We find that when the TF's coding region is heterozygous, TF alleles compete for occupancy at the cis-sites and the tighter-binding TF is dominant in proportion to the difference in binding strength. When the TF's own promoter is heterozygous, the TF produced at the higher dosage is also dominant. Cis-site heterozygotes have additive expression and therefore codominant phenotypes. Binding dominance propagates to affect the expression of downstream loci and it is sensitive in both magnitude and direction to genetic background, but its detectability often attenuates. While binding dominance is inevitable at the molecular level, it is difficult to detect in the phenotype under some biophysical conditions, more so when TF dosage is high and allele-specific binding affinities are similar. A body of empirical research on the biophysics of TF binding demonstrates the plausibility of this mechanism of dominance, but studies of gene expression under competitive binding in heterozygotes in a diversity of genetic backgrounds are needed.
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1452
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Xiao Y, Jiao C, Lin Y, Chen M, Zhang J, Wang J, Zhang Z. lncRNA UCA1 Contributes to Imatinib Resistance by Acting as a ceRNA Against miR-16 in Chronic Myeloid Leukemia Cells. DNA Cell Biol 2016; 36:18-25. [PMID: 27854515 DOI: 10.1089/dna.2016.3533] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Imatinib (IM) has been applied to the chronic phase of chronic myeloid leukemia (CML) and has great benefit on the prognosis of patients with CML. The function of drug efflux mediated by multidrug resistance protein-1 (MDR1) is considered as a main reason for IM drug resistance in CML cells. However, the exact mechanisms of MDR1 modulation in IM resistance of CML cells remain unclear. In the present study, long noncoding RNA (lncRNA) UCA1 was identified as an important modulator of MDR1 by a model system of leukemia cell lines with a gradual increase of MDR1 expression and IM resistance. Overexpression of UCA1 increased MDR1 expression to promote IM resistance of CML cells. Furthermore, for the first time, we demonstrated that UCA1 functions as a competitive endogenous (ceRNA) of MDR1 through completely binding the common miR-16. UCA1-MDR1 might be a novel target for enhancing the therapeutic efficacy of CML patients with IM resistance.
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Affiliation(s)
- Yun Xiao
- 1 Department of Clinical Laboratory, Zhongshan Hospital of Xiamen University , Xiamen, Fujian Province, China
| | - Changjie Jiao
- 2 Department of Cardiothoracic Surgery, The Affiliated Dongnan Hospital of Xiamen University , Xiamen, Fujian Province, China
| | - Yiqiang Lin
- 1 Department of Clinical Laboratory, Zhongshan Hospital of Xiamen University , Xiamen, Fujian Province, China
| | - Meijun Chen
- 1 Department of Clinical Laboratory, Zhongshan Hospital of Xiamen University , Xiamen, Fujian Province, China
| | - Jingwen Zhang
- 1 Department of Clinical Laboratory, Zhongshan Hospital of Xiamen University , Xiamen, Fujian Province, China
| | - Jiajia Wang
- 1 Department of Clinical Laboratory, Zhongshan Hospital of Xiamen University , Xiamen, Fujian Province, China
| | - Zhongying Zhang
- 1 Department of Clinical Laboratory, Zhongshan Hospital of Xiamen University , Xiamen, Fujian Province, China
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1453
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Freedman JE, Miano JM. Challenges and Opportunities in Linking Long Noncoding RNAs to Cardiovascular, Lung, and Blood Diseases. Arterioscler Thromb Vasc Biol 2016; 37:21-25. [PMID: 27856459 DOI: 10.1161/atvbaha.116.308513] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 11/04/2016] [Indexed: 01/16/2023]
Abstract
The new millennium heralds an unanticipated surge of genomic information, most notably an expansive class of long noncoding RNAs (lncRNAs). These transcripts, which now outnumber all protein-coding genes, often exhibit the same characteristics as mRNAs (RNA polymerase II-dependent, 5' methyl-capped, multiexonic, polyadenylated); yet, they do not encode for stable, well-conserved proteins. Elucidating the function of all relevant lncRNAs in heart, vasculature, lung, and blood is essential for generating a complete interactome in these tissues. This is particularly evident because an increasing number of investigators perform RNA-sequencing experiments where, typically, annotated lncRNAs exhibit impressive changes in gene expression. How does one go about evaluating an lncRNA when the sequence of the transcript lends no insight into how it may function within a cell type? Here, we provide a brief overview for the rational study of lncRNAs.
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Affiliation(s)
- Jane E Freedman
- From the Memorial Heart and Vascular Center, University of Massachusetts Medical School, Worcester (J.E.F.); and Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, NY (J.M.M.)
| | - Joseph M Miano
- From the Memorial Heart and Vascular Center, University of Massachusetts Medical School, Worcester (J.E.F.); and Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, NY (J.M.M.).
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1454
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STARD13 promotes hepatocellular carcinoma apoptosis by acting as a ceRNA for Fas. Biotechnol Lett 2016; 39:207-217. [PMID: 27844181 DOI: 10.1007/s10529-016-2253-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 11/02/2016] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To study the roles of STARD13 in cellular apoptosis of hepatocellular carcinoma (HCC). RESULTS Quantitative real-time PCR and immunohistochemistry analyses showed that the expression levels of STARD13 and Fas were lower in clinical HCC tissues than in normal tissues and were positively correlated, which is consistent with the results analyzed by The Cancer Genome Atlas (TCGA) data. Patients with higher STARD13 or Fas expression levels had longer overall survival. Additionally, STARD13 3'-UTR enhanced cellular apoptosis and the 3'-UTRs of STARD13 and Fas were predicted to harbor nine similar miRNA binding sites. And STARD13 3'-UTR promoted Fas expression in a 3'-UTR- and miRNA-dependent way and increased the sensitivity of HCC cells to chemotherapy. Importantly, the coding sequence of STARD13 did not increase Fas expression. CONCLUSIONS STARD13 3'-UTR promotes HCC apoptosis through acting as a ceRNA for Fas.
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1455
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Bracken CP, Scott HS, Goodall GJ. A network-biology perspective of microRNA function and dysfunction in cancer. Nat Rev Genet 2016; 17:719-732. [DOI: 10.1038/nrg.2016.134] [Citation(s) in RCA: 468] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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1456
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Bonizzato A, Gaffo E, te Kronnie G, Bortoluzzi S. CircRNAs in hematopoiesis and hematological malignancies. Blood Cancer J 2016; 6:e483. [PMID: 27740630 PMCID: PMC5098259 DOI: 10.1038/bcj.2016.81] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 08/11/2016] [Indexed: 12/12/2022] Open
Abstract
Cell states in hematopoiesis are controlled by master regulators and by complex circuits of a growing family of RNA species impacting cell phenotype maintenance and plasticity. Circular RNAs (circRNAs) are rapidly gaining the status of particularly stable transcriptome members with distinctive qualities. RNA-seq identified thousands of circRNAs with developmental stage- and tissue-specific expression corroborating earlier suggestions that circular isoforms are a natural feature of the cell expression program. CircRNAs are abundantly expressed also in the hematopoietic compartment. There are a number of studies on circRNAs in blood cells, a specific overview is however lacking. In this review we first present current insight in circRNA biogenesis discussing the relevance for hematopoiesis of the highly interleaved processes of splicing and circRNA biogenesis. Regarding molecular functions circRNAs modulate host gene expression, but also compete for binding of microRNAs, RNA-binding proteins or translation initiation and participate in regulatory circuits. We examine circRNA expression in the hematopoietic compartment and in hematologic malignancies and review the recent breakthrough study that identified pathogenic circRNAs derived from leukemia fusion genes. CircRNA high and regulated expression in blood cell types indicate that further studies are warranted to inform the position of these regulators in normal and malignant hematopoiesis.
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Affiliation(s)
- A Bonizzato
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - E Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - G te Kronnie
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - S Bortoluzzi
- Department of Molecular Medicine, University of Padova, Padova, Italy
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1457
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Murtha M, Esteller M. Extraordinary Cancer Epigenomics: Thinking Outside the Classical Coding and Promoter Box. Trends Cancer 2016; 2:572-584. [DOI: 10.1016/j.trecan.2016.08.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/17/2016] [Accepted: 08/23/2016] [Indexed: 12/23/2022]
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1458
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Sun J, Yan J, Yuan X, Yang R, Dan T, Wang X, Kong G, Gao S. A computationally constructed ceRNA interaction network based on a comparison of the SHEE and SHEEC cell lines. Cell Mol Biol Lett 2016; 21:21. [PMID: 28536623 PMCID: PMC5415789 DOI: 10.1186/s11658-016-0022-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 09/10/2016] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play critical and complicated roles in the regulation of various biological processes, including chromatin modification, transcription and post-transcriptional processing. Interestingly, some lncRNAs serve as miRNA "sponges" that inhibit interaction with miRNA targets in post-transcriptional regulation. We constructed a putative competing endogenous RNA (ceRNA) network by integrating lncRNA, miRNA and mRNA expression based on high-throughput RNA sequencing and microarray data to enable a comparison of the SHEE and SHEEC cell lines. Using Targetscan and miRanda bioinformatics algorithms and miRTarbase microRNA-target interactions database, we established that 51 miRNAs sharing 13,623 MREs with 2260 genes and 82 lncRNAs were involved in this ceRNA network. Through a biological function analysis, the ceRNA network appeared to be primarily involved in cell proliferation, apoptosis, the cell cycle, invasion and metastasis. Functional pathway analyses demonstrated that the ceRNA network potentially modulated multiple signaling pathways, such as the MAPK, Ras, HIF-1, Rap1, and PI3K/Akt signaling pathways. These results might provide new clues to better understand the regulation of the ceRNA network in cancer.
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Affiliation(s)
- Jiachun Sun
- Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Junqiang Yan
- Department of Neurology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Xiaozhi Yuan
- Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Ruina Yang
- Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Tanyou Dan
- Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Xinshuai Wang
- Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Guoqiang Kong
- Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Shegan Gao
- Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
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1459
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Sardina DS, Alaimo S, Ferro A, Pulvirenti A, Giugno R. A novel computational method for inferring competing endogenous interactions. Brief Bioinform 2016; 18:1071-1081. [DOI: 10.1093/bib/bbw084] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Indexed: 12/14/2022] Open
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1460
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Guo X, Hua Y. CCAT1: an oncogenic long noncoding RNA in human cancers. J Cancer Res Clin Oncol 2016; 143:555-562. [PMID: 27638771 DOI: 10.1007/s00432-016-2268-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 09/08/2016] [Indexed: 01/17/2023]
Abstract
PURPOSE Long noncoding RNAs (lncRNAs) are a new class of noncoding RNAs that participate in a variety of biological processes such as cell proliferation, cell cycle, differentiation and apoptosis, mainly by regulation of gene expression at various levels, including chromatin, splicing, transcriptional and post-transcriptional levels. CCAT1 is a recently identified oncogenic lncRNA, which has been reported to be consistently upregulated in multiple cancer tissues and closely correlated with initiation and progression of cancers. The aim of this paper is to provide an overview of various roles of CCAT1 in human cancers. METHODS AND RESULTS We searched studies in electronic databases. Studies have shown the high expression pattern and oncogenic role of CCAT1 in different types of cancer, and aberrant expression of CCAT1 is involved in several processes correlated with carcinogenesis such as cell proliferation, apoptosis, migration and invasion by regulating different target genes and pathways. CONCLUSION LncRNA CCAT1 promises to be a novel diagnostic biomarker, therapeutic target, as well as prognostic biomarker in human cancers.
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Affiliation(s)
- Xiaoqiang Guo
- Department of General Surgery, Wuxi No. 3 People's Hospital, Wuxi, 214002, Jiangsu, China
| | - Yuming Hua
- Department of General Surgery, Wuxi No. 3 People's Hospital, Wuxi, 214002, Jiangsu, China.
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1461
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Ulitsky I. Evolution to the rescue: using comparative genomics to understand long non-coding RNAs. Nat Rev Genet 2016; 17:601-14. [DOI: 10.1038/nrg.2016.85] [Citation(s) in RCA: 373] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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1462
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Lai X, Wolkenhauer O, Vera J. Understanding microRNA-mediated gene regulatory networks through mathematical modelling. Nucleic Acids Res 2016; 44:6019-35. [PMID: 27317695 PMCID: PMC5291278 DOI: 10.1093/nar/gkw550] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 06/06/2016] [Indexed: 12/19/2022] Open
Abstract
The discovery of microRNAs (miRNAs) has added a new player to the regulation of gene expression. With the increasing number of molecular species involved in gene regulatory networks, it is hard to obtain an intuitive understanding of network dynamics. Mathematical modelling can help dissecting the role of miRNAs in gene regulatory networks, and we shall here review the most recent developments that utilise different mathematical modelling approaches to provide quantitative insights into the function of miRNAs in the regulation of gene expression. Key miRNA regulation features that have been elucidated via modelling include: (i) the role of miRNA-mediated feedback and feedforward loops in fine-tuning of gene expression; (ii) the miRNA–target interaction properties determining the effectiveness of miRNA-mediated gene repression; and (iii) the competition for shared miRNAs leading to the cross-regulation of genes. However, there is still lack of mechanistic understanding of many other properties of miRNA regulation like unconventional miRNA–target interactions, miRNA regulation at different sub-cellular locations and functional miRNA variant, which will need future modelling efforts to deal with. This review provides an overview of recent developments and challenges in this field.
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Affiliation(s)
- Xin Lai
- Laboratory of Systems Tumour Immunology, Department of Dermatology, Erlangen University Hospital and Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, 91054, Germany
| | - Olaf Wolkenhauer
- Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, 18051, Germany Stellenbosch Institute for Advanced Study, Wallenberg Research Centre at Stellenbosch University, 7600, South Africa
| | - Julio Vera
- Laboratory of Systems Tumour Immunology, Department of Dermatology, Erlangen University Hospital and Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, 91054, Germany
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1463
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Hart RP, Goff LA. Long noncoding RNAs: Central to nervous system development. Int J Dev Neurosci 2016; 55:109-116. [PMID: 27296516 DOI: 10.1016/j.ijdevneu.2016.06.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 06/01/2016] [Accepted: 06/02/2016] [Indexed: 11/29/2022] Open
Abstract
The development of the central nervous system (CNS) is a complex orchestration of stem cells, transcription factors, growth/differentiation factors, and epigenetic control. Noncoding RNAs have been identified, classified, and studied for their functional roles in many systems including the CNS. In particular, the class of long noncoding RNAs (lncRNAs) has generated both enthusiasm and skepticism due to the unexpected discovery, the diversity of mechanisms, and the lower level of expression than found in protein-coding RNAs. Here we describe evidence supporting the role of lncRNAs in driving CNS-specific differentiation. It is clear that lncRNAs exhibit a functional diversity that makes their study and compartmentalization more challenging than other classes of noncoding RNAs. We predict, however, that lncRNAs will be essential for the characterization of discrete neuronal cell types in the age of single-cell transcriptomics and that these regulatory RNAs contribute to the multitude of functional mechanisms during CNS differentiation that will rival the diversities of protein-based mechanisms.
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Affiliation(s)
- Ronald P Hart
- Department of Cell Biology & Neuroscience, and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA.
| | - Loyal A Goff
- McKusick-Nathans Institute for Genetic Medicine & Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21025, USA
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