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Mofayezi A, Jadaliha M, Zangeneh FZ, Khoddami V. Poly(A) tale: From A to A; RNA polyadenylation in prokaryotes and eukaryotes. Wiley Interdiscip Rev RNA 2024; 15:e1837. [PMID: 38485452 DOI: 10.1002/wrna.1837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024]
Abstract
Most eukaryotic mRNAs and different non-coding RNAs undergo a form of 3' end processing known as polyadenylation. Polyadenylation machinery is present in almost all organisms except few species. In bacteria, the machinery has evolved from PNPase, which adds heteropolymeric tails, to a poly(A)-specific polymerase. Differently, a complex machinery for accurate polyadenylation and several non-canonical poly(A) polymerases are developed in eukaryotes. The role of poly(A) tail has also evolved from serving as a degradative signal to a stabilizing modification that also regulates translation. In this review, we discuss poly(A) tail emergence in prokaryotes and its development into a stable, yet dynamic feature at the 3' end of mRNAs in eukaryotes. We also describe how appearance of novel poly(A) polymerases gives cells flexibility to shape poly(A) tail. We explain how poly(A) tail dynamics help regulate cognate RNA metabolism in a context-dependent manner, such as during oocyte maturation. Finally, we describe specific mRNAs in metazoans that bear stem-loops instead of poly(A) tails. We conclude with how recent discoveries about poly(A) tail can be applied to mRNA technology. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Ahmadreza Mofayezi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
- ReNAP Therapeutics, Tehran, Iran
| | - Mahdieh Jadaliha
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Vahid Khoddami
- ReNAP Therapeutics, Tehran, Iran
- Pediatric Cell and Gene Therapy Research Center, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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2
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Tariq A, Hao Q, Sun Q, Singh DK, Jadaliha M, Zhang Y, Chetlangia N, Ma J, Holton SE, Bhargava R, Lal A, Prasanth SG, Prasanth KV. LncRNA-mediated regulation of SOX9 expression in basal subtype breast cancer cells. RNA 2020; 26:175-185. [PMID: 31690584 PMCID: PMC6961546 DOI: 10.1261/rna.073254.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 10/30/2019] [Indexed: 05/08/2023]
Abstract
Triple-negative breast cancer (TNBC) is one of the most aggressive breast cancer (BC) subtypes with a poor prognosis and high recurrence rate. Recent studies have identified vital roles played by several lncRNAs (long noncoding RNAs) in BC pathobiology. Cell type-specific expression of lncRNAs and their potential role in regulating the expression of oncogenic and tumor suppressor genes have made them promising cancer drug targets. By performing a transcriptome screen in an isogenic TNBC/basal subtype BC progression cell line model, we recently reported ∼1800 lncRNAs that display aberrant expression during breast cancer progression. Mechanistic studies on one such nuclear-retained lncRNA, linc02095, reveal that it promotes breast cancer proliferation by facilitating the expression of oncogenic transcription factor, SOX9. Both linc02095 and SOX9 display coregulated expression in BC patients as well in basal subtype BC cell lines. Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase II occupancy at the SOX9 gene body as well as defective SOX9 mRNA export, implying that linc02095 positively regulates SOX9 transcription and mRNA export. Finally, we identify a positive feedback loop in BC cells that controls the expression of both linc02095 and SOX9 Thus, our results unearth tumor-promoting activities of a nuclear lncRNA linc02095 by facilitating the expression of key oncogenic transcription factor in BC.
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Affiliation(s)
- Aamira Tariq
- Department of Biosciences, Comsats Institute of Information Technology, Islamabad 45550, Pakistan
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Qinyu Hao
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Qinyu Sun
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Deepak K Singh
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Mahdieh Jadaliha
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yang Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Neha Chetlangia
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Sarah E Holton
- Department of Bioengineering and Beckman Institute of Advanced Science and Technology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Rohit Bhargava
- Department of Bioengineering and Beckman Institute of Advanced Science and Technology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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3
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Fei J, Jadaliha M, Harmon TS, Li ITS, Hua B, Hao Q, Holehouse AS, Reyer M, Sun Q, Freier SM, Pappu RV, Prasanth KV, Ha T. Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution. J Cell Sci 2017; 130:4180-4192. [PMID: 29133588 DOI: 10.1242/jcs.206854] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 11/01/2017] [Indexed: 12/30/2022] Open
Abstract
Nuclear speckles are self-assembled organelles composed of RNAs and proteins. They are proposed to act as structural domains that control distinct steps in gene expression, including transcription, splicing and mRNA export. Earlier studies identified differential localization of a few components within the speckles. It was speculated that the spatial organization of speckle components might contribute directly to the order of operations that coordinate distinct processes. Here, by performing multi-color structured illumination microscopy, we characterized the multilayer organization of speckles at a higher resolution. We found that SON and SC35 (also known as SRSF2) localize to the central region of the speckle, whereas MALAT1 and small nuclear (sn)RNAs are enriched at the speckle periphery. Coarse-grained simulations indicate that the non-random organization arises due to the interplay between favorable sequence-encoded intermolecular interactions of speckle-resident proteins and RNAs. Finally, we observe positive correlation between the total amount of RNA present within a speckle and the speckle size. These results imply that speckle size may be regulated to accommodate RNA accumulation and processing. Accumulation of RNA from various actively transcribed speckle-associated genes could contribute to the observed speckle size variations within a single cell.
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Affiliation(s)
- Jingyi Fei
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA .,Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Mahdieh Jadaliha
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tyler S Harmon
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Isaac T S Li
- Department of Chemistry, University of British Columbia Okanagan, Kelowna, British Columbia, Canada, V1V 1V7
| | - Boyang Hua
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Qinyu Hao
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alex S Holehouse
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Matthew Reyer
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Qinyu Sun
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Taekjip Ha
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21205, USA
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4
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Singh DK, Gholamalamdari O, Jadaliha M, Ling Li X, Lin YC, Zhang Y, Guang S, Hashemikhabir S, Tiwari S, Zhu YJ, Khan A, Thomas A, Chakraborty A, Macias V, Balla AK, Bhargava R, Janga SC, Ma J, Prasanth SG, Lal A, Prasanth KV. PSIP1/p75 promotes tumorigenicity in breast cancer cells by promoting the transcription of cell cycle genes. Carcinogenesis 2017. [PMID: 28633434 DOI: 10.1093/carcin/bgx062] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Breast cancer (BC) is a highly heterogeneous disease, both at the pathological and molecular level, and several chromatin-associated proteins play crucial roles in BC initiation and progression. Here, we demonstrate the role of PSIP1 (PC4 and SF2 interacting protein)/p75 (LEDGF) in BC progression. PSIP1/p75, previously identified as a chromatin-adaptor protein, is found to be upregulated in basal-like/triple negative breast cancer (TNBC) patient samples and cell lines. Immunohistochemistry in tissue arrays showed elevated levels of PSIP1 in metastatic invasive ductal carcinoma. Survival data analyses revealed that the levels of PSIP1 showed a negative association with TNBC patient survival. Depletion of PSIP1/p75 significantly reduced the tumorigenicity and metastatic properties of TNBC cell lines while its over-expression promoted tumorigenicity. Further, gene expression studies revealed that PSIP1 regulates the expression of genes controlling cell-cycle progression, cell migration and invasion. Finally, by interacting with RNA polymerase II, PSIP1/p75 facilitates the association of RNA pol II to the promoter of cell cycle genes and thereby regulates their transcription. Our findings demonstrate an important role of PSIP1/p75 in TNBC tumorigenicity by promoting the expression of genes that control the cell cycle and tumor metastasis.
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Affiliation(s)
- Deepak K Singh
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Omid Gholamalamdari
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mahdieh Jadaliha
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Xiao Ling Li
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Yo-Chuen Lin
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Yang Zhang
- Department of Bioengineering, Beckman Institute of Advanced Science and Technology, UIUC, Urbana, IL 61801, USA
| | - Shuomeng Guang
- Department of Bioengineering, Beckman Institute of Advanced Science and Technology, UIUC, Urbana, IL 61801, USA
| | - Seyedsasan Hashemikhabir
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202,USA
| | - Saumya Tiwari
- Department of Bioengineering, Beckman Institute of Advanced Science and Technology, UIUC, Urbana, IL 61801, USA
| | - Yuelin J Zhu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Abid Khan
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Arindam Chakraborty
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Virgilia Macias
- Department of Pathology, College of Medicine, University of Illinois at Chicago,Chicago, IL 60612, USA
| | - Andre K Balla
- Department of Pathology, College of Medicine, University of Illinois at Chicago,Chicago, IL 60612, USA
| | - Rohit Bhargava
- Department of Bioengineering, Beckman Institute of Advanced Science and Technology, UIUC, Urbana, IL 61801, USA.,Departments of Electrical and Computer Engineering, Mechanical Science and Engineering, Chemical and Biomolecular Engineering and Chemistry, UIUC, Urbana, IL, USA
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202,USA
| | - Jian Ma
- Department of Bioengineering, Beckman Institute of Advanced Science and Technology, UIUC, Urbana, IL 61801, USA.,School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ashish Lal
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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5
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Jangravi Z, Alikhani M, Arefnezhad B, Sharifi Tabar M, Taleahmad S, Karamzadeh R, Jadaliha M, Mousavi SA, Ahmadi Rastegar D, Parsamatin P, Vakilian H, Mirshahvaladi S, Sabbaghian M, Mohseni Meybodi A, Mirzaei M, Shahhoseini M, Ebrahimi M, Piryaei A, Moosavi-Movahedi AA, Haynes PA, Goodchild AK, Nasr-Esfahani MH, Jabbari E, Baharvand H, Sedighi Gilani MA, Gourabi H, Salekdeh GH. A fresh look at the male-specific region of the human Y chromosome. J Proteome Res 2012; 12:6-22. [PMID: 23253012 DOI: 10.1021/pr300864k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Chromosome-centric Human Proteome Project (C-HPP) aims to systematically map the entire human proteome with the intent to enhance our understanding of human biology at the cellular level. This project attempts simultaneously to establish a sound basis for the development of diagnostic, prognostic, therapeutic, and preventive medical applications. In Iran, current efforts focus on mapping the proteome of the human Y chromosome. The male-specific region of the Y chromosome (MSY) is unique in many aspects and comprises 95% of the chromosome's length. The MSY continually retains its haploid state and is full of repeated sequences. It is responsible for important biological roles such as sex determination and male fertility. Here, we present the most recent update of MSY protein-encoding genes and their association with various traits and diseases including sex determination and reversal, spermatogenesis and male infertility, cancers such as prostate cancers, sex-specific effects on the brain and behavior, and graft-versus-host disease. We also present information available from RNA sequencing, protein-protein interaction, post-translational modification of MSY protein-coding genes and their implications in biological systems. An overview of Human Y chromosome Proteome Project is presented and a systematic approach is suggested to ensure that at least one of each predicted protein-coding gene's major representative proteins will be characterized in the context of its major anatomical sites of expression, its abundance, and its functional relevance in a biological and/or medical context. There are many technical and biological issues that will need to be overcome in order to accomplish the full scale mapping.
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Affiliation(s)
- Zohreh Jangravi
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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Jadaliha M, Lee HJ, Pakzad M, Fathi A, Jeong SK, Cho SY, Baharvand H, Paik YK, Salekdeh GH. Quantitative proteomic analysis of human embryonic stem cell differentiation by 8-plex iTRAQ labelling. PLoS One 2012; 7:e38532. [PMID: 22723866 PMCID: PMC3377673 DOI: 10.1371/journal.pone.0038532] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 05/07/2012] [Indexed: 12/24/2022] Open
Abstract
Analysis of gene expression to define molecular mechanisms and pathways involved in human embryonic stem cells (hESCs) proliferation and differentiations has allowed for further deciphering of the self-renewal and pluripotency characteristics of hESC. Proteins associated with hESCs were discovered through isobaric tags for relative and absolute quantification (iTRAQ). Undifferentiated hESCs and hESCs in different stages of spontaneous differentiation by embryoid body (EB) formation were analyzed. Using the iTRAQ approach, we identified 156 differentially expressed proteins involved in cell proliferation, apoptosis, transcription, translation, mRNA processing, and protein synthesis. Proteins involved in nucleic acid binding, protein synthesis, and integrin signaling were downregulated during differentiation, whereas cytoskeleton proteins were upregulated. The present findings added insight to our understanding of the mechanisms involved in hESC proliferation and differentiation.
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Affiliation(s)
- Mahdieh Jadaliha
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Hyoung-Joo Lee
- Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Yonsei University, Sudaemoon-Ku, Seoul, Korea
| | - Mohammad Pakzad
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Ali Fathi
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Seul-Ki Jeong
- Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Yonsei University, Sudaemoon-Ku, Seoul, Korea
| | - Sang-Yun Cho
- Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Yonsei University, Sudaemoon-Ku, Seoul, Korea
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran
| | - Young-Ki Paik
- Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Yonsei University, Sudaemoon-Ku, Seoul, Korea
- * E-mail: (GSH); (Y-KP)
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
- * E-mail: (GSH); (Y-KP)
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