1
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Nemsick S, Hansen AS. Molecular models of bidirectional promoter regulation. Curr Opin Struct Biol 2024; 87:102865. [PMID: 38905929 DOI: 10.1016/j.sbi.2024.102865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/30/2024] [Accepted: 05/27/2024] [Indexed: 06/23/2024]
Abstract
Approximately 11% of human genes are transcribed by a bidirectional promoter (BDP), defined as two genes with <1 kb between their transcription start sites. Despite their evolutionary conservation and enrichment for housekeeping genes and oncogenes, the regulatory role of BDPs remains unclear. BDPs have been suggested to facilitate gene coregulation and/or decrease expression noise. This review discusses these potential regulatory functions through the context of six prospective underlying mechanistic models: a single nucleosome free region, shared transcription factor/regulator binding, cooperative negative supercoiling, bimodal histone marks, joint activation by enhancer(s), and RNA-mediated recruitment of regulators. These molecular mechanisms may act independently and/or cooperatively to facilitate the coregulation and/or decreased expression noise predicted of BDPs.
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Affiliation(s)
- Sarah Nemsick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA.
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2
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Ronchetti D, Traini V, Silvestris I, Fabbiano G, Passamonti F, Bolli N, Taiana E. The pleiotropic nature of NONO, a master regulator of essential biological pathways in cancers. Cancer Gene Ther 2024; 31:984-994. [PMID: 38493226 PMCID: PMC11257950 DOI: 10.1038/s41417-024-00763-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/18/2024]
Abstract
NONO is a member of the Drosophila behavior/human splicing (DBHS) family of proteins. NONO is a multifunctional protein that acts as a "molecular scaffold" to carry out versatile biological activities in many aspects of gene regulation, cell proliferation, apoptosis, migration, DNA damage repair, and maintaining cellular circadian rhythm coupled to the cell cycle. Besides these physiological activities, emerging evidence strongly indicates that NONO-altered expression levels promote tumorigenesis. In addition, NONO can undergo various post-transcriptional or post-translational modifications, including alternative splicing, phosphorylation, methylation, and acetylation, whose impact on cancer remains largely to be elucidated. Overall, altered NONO expression and/or activities are a common feature in cancer. This review provides an integrated scenario of the current understanding of the molecular mechanisms and the biological processes affected by NONO in different tumor contexts, suggesting that a better elucidation of the pleiotropic functions of NONO in physiology and tumorigenesis will make it a potential therapeutic target in cancer. In this respect, due to the complex landscape of NONO activities and interactions, we highlight caveats that must be considered during experimental planning and data interpretation of NONO studies.
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Affiliation(s)
- Domenica Ronchetti
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Valentina Traini
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Ilaria Silvestris
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Giuseppina Fabbiano
- Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Passamonti
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Niccolò Bolli
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elisa Taiana
- Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy.
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3
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Zheng Y, Wu S, Liu L, Guan Y, Sun W, Miao C, Li Q. Activation of HAND2-FGFR signaling pathway by lncRNA HAND2-AS1 in adenomyosis†. Biol Reprod 2024; 110:490-500. [PMID: 38084072 DOI: 10.1093/biolre/ioad171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 11/13/2023] [Accepted: 12/09/2023] [Indexed: 03/14/2024] Open
Abstract
Heart and neural crest derivatives expressed transcript 2 (HAND2) is a critical mediator of progesterone action in endometrial stromal cells. Silencing of Hand2 expression in mouse uterus leads to an unopposed FGFR-mediated action that causes female mice infertility. To investigate the involvement of HAND2-FGFR signaling in pathogenesis of adenomyosis, immunohistochemistry, in situ hybridization, and quantitative real-time PCR were employed to assess gene expression in the normal endometrium, the paired eutopic endometrium and ectopic lesions obtained from women with adenomyosis. DNA methylation in the regions of HAND2 promoter and the first exon was also monitored in these samples. Our results revealed that HAND2 expression were dramatically reduced, but FGF9 expression and FGFR-ERK1/2-mediated MAPK signaling pathway were enhanced in the eutopic endometrium and ectopic lesions of patients with adenomyosis compared to the normal controls. Interestingly, expression of HAND2-AS1, a long noncoding RNA that resides adjacent to HAND2 in genome, was also reduced in adenomyosis. DNA methylation analysis revealed that the bidirectional promoter between HAND2 and HAND2-AS1, and the first exon of HAND2 gene was heavily methylated in the eutopic endometrium and the ectopic lesions of adenomyosis. To investigate the regulation of gene expression by HAND2-AS1, HAND2-AS1 expression was silenced in human endometrial stromal cells. In contrast to the downregulation of HAND2 in response to HAND2-AS1 silencing, FGF9 expression was augmented significantly. Endometrial stromal cells lacking HAND2-AS1 exhibited enhanced proliferation and migration potentials. Collectively, our studies revealed a new molecular mechanism by which HAND2-AS1 is involved in the pathogenesis of adenomyosis via modulating HAND2-FGFR-mediated signaling.
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Affiliation(s)
- Ya Zheng
- Department of Gynecology, P.R. China
| | - Shuang Wu
- Department of Reproductive Genetics, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Heping Hospital of Changzhi Medical College, Changzhi, Shanxi 046000, P.R. China
| | - Lingli Liu
- Department of Reproductive Genetics, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Heping Hospital of Changzhi Medical College, Changzhi, Shanxi 046000, P.R. China
| | - Yining Guan
- Department of Reproductive Genetics, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Heping Hospital of Changzhi Medical College, Changzhi, Shanxi 046000, P.R. China
| | | | - Congxiu Miao
- Department of Reproductive Genetics, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Heping Hospital of Changzhi Medical College, Changzhi, Shanxi 046000, P.R. China
| | - Quanxi Li
- Department of Reproductive Genetics, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Heping Hospital of Changzhi Medical College, Changzhi, Shanxi 046000, P.R. China
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4
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Xin Q, Feng I, Yu G, Dean J. Stromal Pbrm1 mediates chromatin remodeling necessary for embryo implantation in the mouse uterus. J Clin Invest 2024; 134:e174194. [PMID: 38426493 PMCID: PMC10904057 DOI: 10.1172/jci174194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/09/2024] [Indexed: 03/02/2024] Open
Abstract
Early gestational loss occurs in approximately 20% of all clinically recognized human pregnancies and is an important cause of morbidity. Either embryonic or maternal defects can cause loss, but a functioning and receptive uterine endometrium is crucial for embryo implantation. We report that the switch/sucrose nonfermentable (SWI/SNF) remodeling complex containing polybromo-1 (PBRM1) and Brahma-related gene 1 (BRG1) is essential for implantation of the embryonic blastocyst on the wall of the uterus in mice. Although preimplantation development is unaffected, conditional ablation of Pbrm1 in uterine stromal cells disrupts progesterone pathways and uterine receptivity. Heart and neural crest derivatives expressed 2 (Hand2) encodes a basic helix-loop-helix (bHLH) transcription factor required for embryo implantation. We identify an enhancer of the Hand2 gene in stromal cells that requires PBRM1 for epigenetic histone modifications/coactivator recruitment and looping with the promoter. In Pbrm1cKO mice, perturbation of chromatin assembly at the promoter and enhancer sites compromises Hand2 transcription, adversely affects fibroblast growth factor signaling pathways, prevents normal stromal-epithelial crosstalk, and disrupts embryo implantation. The mutant female mice are infertile and provide insight into potential causes of early pregnancy loss in humans.
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Soukup J, Manethova M, Stejskal V, Novakova M, Duskova J, Hornychova H, Hacova M, Staniczkova-Zambo I, Zelinka T, Kosak M, Cesak T, Netuka D, Ryska A, Gabalec F. Hand2 Immunohistochemistry in the Diagnosis of Paragangliomas and Other Neuroendocrine Neoplasms. Endocr Pathol 2024; 35:14-24. [PMID: 38416360 DOI: 10.1007/s12022-024-09803-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/08/2024] [Indexed: 02/29/2024]
Abstract
Hand2 is a core transcription factor responsible for chromaffin cell differentiation. However, its potential utility in surgical pathology has not been studied. Thus, we aimed to investigate its expression in paragangliomas, other neuroendocrine neoplasms (NENs), and additional non-neuroendocrine tumors. We calibrated Hand2 immunohistochemistry on adrenal medulla cells and analyzed H-scores in 46 paragangliomas (PGs), 9 metastatic PGs, 21 cauda equina neuroendocrine tumors (CENETs), 48 neuroendocrine carcinomas (NECs), 8 olfactory neuroblastomas (ONBs), 110 well-differentiated NETs (WDNETs), 10 adrenal cortical carcinomas, 29 adrenal cortical adenomas, 8 melanomas, 41 different carcinomas, and 10 gastrointestinal stromal tumors (GISTs). Both tissue microarrays (TMAs) and whole sections (WSs) were studied. In 171 NENs, previously published data on Phox2B and GATA3 were correlated with Hand2. Hand2 was positive in 98.1% (54/55) PGs, but only rarely in WDNETs (9.6%, 10/104), CENETs (9.5%, 2/21), NECs (4.2%, 2/48), or ONBs (12.5%, 1/8). Any Hand2 positivity was 98.1% sensitive and 91.7% specific for the diagnosis of PG. The Hand2 H-score was significantly higher in primary PGs compared to Hand2-positive WDNETs (median 166.3 vs. 7.5; p < 0.0001). Metastatic PGs were positive in 88.9% (8/9). No Hand2 positivity was observed in any adrenal cortical neoplasm or other non-neuroendocrine tumors, with exception of 8/10 GISTs. Parasympathetic PGs showed a higher Hand2 H-score compared to sympathetic PGs (median H-scores 280 vs. 104, p < 0.0001). Hand2 positivity in NENs serves as a reliable marker of primary and metastatic PG, since other NENs only rarely exhibit limited Hand2 positivity.
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Affiliation(s)
- Jiri Soukup
- Department of Pathology, Military University Hospital Prague, U Vojenske Nemocnice 1200, Praha 6, 169 02, Prague, Czech Republic.
- The Fingerland Department of Pathology, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Sokolska 582, 500 05, Hradec Kralove, Czech Republic.
- Department of Pathology, Charles University, First Faculty of Medicine and General University Hospital in Prague, Studnickova, 2039, 128 00, Nové Mesto, Prague, Czech Republic.
| | - Monika Manethova
- The Fingerland Department of Pathology, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Sokolska 582, 500 05, Hradec Kralove, Czech Republic
| | - Vaclav Stejskal
- The Fingerland Department of Pathology, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Sokolska 582, 500 05, Hradec Kralove, Czech Republic
| | - Marie Novakova
- Department of Pathology, Military University Hospital Prague, U Vojenske Nemocnice 1200, Praha 6, 169 02, Prague, Czech Republic
| | - Jaroslava Duskova
- Department of Pathology, Charles University, First Faculty of Medicine and General University Hospital in Prague, Studnickova, 2039, 128 00, Nové Mesto, Prague, Czech Republic
| | - Helena Hornychova
- The Fingerland Department of Pathology, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Sokolska 582, 500 05, Hradec Kralove, Czech Republic
| | - Maria Hacova
- Department of Pathology, The Regional Hospital Pardubice, Pardubice, Czech Republic
| | - Iva Staniczkova-Zambo
- 1st Department of Pathology, St. Anne's University Hospital and Faculty of Medicine , Masaryk University, Pekarská 664/53, 602 00, Brno-stred, Brno, Czech Republic
| | - Tomas Zelinka
- Centre for Hypertension, 3rd Department of Medicine, Charles University, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Mikulas Kosak
- Department of Internal Medicine, First Faculty of Medicine, Charles University and Military University Hospital, Prague, Czech Republic
| | - Tomas Cesak
- Department of Neurosurgery, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Sokolska 582, 500 05, Hradec Kralove, Czech Republic
| | - David Netuka
- Department of Neurosurgery and Neurooncology, 1st Medical Faculty, Charles University, Military University Hospital Prague, U Vojenske Nemocnice 1200, Praha 6, 169 02, Prague, Czech Republic
| | - Ales Ryska
- The Fingerland Department of Pathology, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Sokolska 582, 500 05, Hradec Kralove, Czech Republic
| | - Filip Gabalec
- 4th Department of Internal Medicine, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Sokolska 582, 500 05, Hradec Kralove, Czech Republic
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Liu L, Dong H, Guan Y, Fan T, Sun W, Bagchi IC, Miao C, Li Q. Regulation of HAND2 Expression by LncRNA HAND2-AS1 in Ovarian Endometriosis Involving DNA Methylation. J Endocr Soc 2023; 7:bvad049. [PMID: 37153110 PMCID: PMC10161139 DOI: 10.1210/jendso/bvad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 05/09/2023] Open
Abstract
HAND2 is a critical mediator of progesterone receptor signaling in endometrium. Silencing of HAND2 expression is associated with female infertility and endometrial cancers. We recently observed that lncRNA HAND2-AS1 and HAND2 are expressed coordinately in human endometrial stromal cells. To investigate involvement of HAND2-AS1 and HAND2 in pathogenesis of endometriosis, we employed immunohistochemistry, in situ hybridization, and quantitative real-time PCR to assess their expression in normal endometrium and the ectopic lesions obtained from patients with ovarian endometriosis. HAND2 promoter methylation was also monitored in these samples. Our results revealed that HAND2 and HAND2-AS1 expression levels were reduced but promoter methylation was enhanced significantly in ectopic endometrium when compared with the normal controls. Fluorescence in situ hybridization showed that HAND-AS1 is predominantly localized in the nuclei of endometrial stromal cells in contrast to the cytoplasmic distribution in epithelial cell compartment. To further investigate regulation of HAND2 expression by HAND2-AS1, HAND2-AS1 was silenced or overexpressed in human endometrial stromal cells. Our studies showed that expression levels of HAND2 and its direct target IL15 were attenuated markedly in HAND2-AS1 silenced cells but enhanced significantly in the overexpressed human endometrial stromal cells. Silencing of HAND2-AS1 also impaired endometrial stromal cell decidualization as indicated by downregulation of decidual biomarkers IGFBP1 and PRL. In addition, HAND2 promoter methylation was also enhanced upon HAND2-AS1 silencing. RNA immunoprecipitation studies further revealed that HAND2-AS1 is capable of binding to DNA methyltransferase DNMT1, indicating that HAND2-AS1 governs HAND2 expression epigenetically involving DNA methylation.
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Affiliation(s)
- Lingli Liu
- Department of Reproductive Genetics, Heping Hospital of Changzhi Medical College, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Changzhi, Shanxi 046000, P.R. China
| | - Huijing Dong
- Department of Reproductive Genetics, Heping Hospital of Changzhi Medical College, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Changzhi, Shanxi 046000, P.R. China
| | - Yining Guan
- Department of Reproductive Genetics, Heping Hospital of Changzhi Medical College, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Changzhi, Shanxi 046000, P.R. China
| | - Tingting Fan
- Department of Reproductive Genetics, Heping Hospital of Changzhi Medical College, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Changzhi, Shanxi 046000, P.R. China
| | - Wenxia Sun
- Department of Gynecology, Heping Hospital, Changzhi Medical College, Changzhi, Shanxi 046000, P.R. China
| | - Indrani C Bagchi
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Congxiu Miao
- Department of Reproductive Genetics, Heping Hospital of Changzhi Medical College, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Changzhi, Shanxi 046000, P.R. China
| | - Quanxi Li
- Department of Reproductive Genetics, Heping Hospital of Changzhi Medical College, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Changzhi, Shanxi 046000, P.R. China
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7
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Zhang S, Cooper JAL, Chong YS, Naveed A, Mayoh C, Jayatilleke N, Liu T, Amos S, Kobelke S, Marshall AC, Meers O, Choi YS, Bond CS, Fox AH. NONO enhances mRNA processing of super-enhancer-associated GATA2 and HAND2 genes in neuroblastoma. EMBO Rep 2023; 24:e54977. [PMID: 36416237 PMCID: PMC9900351 DOI: 10.15252/embr.202254977] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
Abstract
High-risk neuroblastoma patients have poor survival rates and require better therapeutic options. High expression of a multifunctional DNA and RNA-binding protein, NONO, in neuroblastoma is associated with poor patient outcome; however, there is little understanding of the mechanism of NONO-dependent oncogenic gene regulatory activity in neuroblastoma. Here, we used cell imaging, biochemical and genome-wide molecular analysis to reveal complex NONO-dependent regulation of gene expression. NONO forms RNA- and DNA-tethered condensates throughout the nucleus and undergoes phase separation in vitro, modulated by nucleic acid binding. CLIP analyses show that NONO mainly binds to the 5' end of pre-mRNAs and modulates pre-mRNA processing, dependent on its RNA-binding activity. NONO regulates super-enhancer-associated genes, including HAND2 and GATA2. Abrogating NONO RNA binding, or phase separation activity, results in decreased expression of HAND2 and GATA2. Thus, future development of agents that target RNA-binding activity of NONO may have therapeutic potential in this cancer context.
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Affiliation(s)
- Song Zhang
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Jack AL Cooper
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Yee Seng Chong
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Alina Naveed
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Chelsea Mayoh
- Children's Cancer Institute AustraliaRandwickNSWAustralia
- Centre for Childhood Cancer ResearchUNSW SydneyKensingtonNSWAustralia
- School of Women's and Children's HealthUNSW SydneyKensingtonNSWAustralia
| | - Nisitha Jayatilleke
- Children's Cancer Institute AustraliaRandwickNSWAustralia
- Centre for Childhood Cancer ResearchUNSW SydneyKensingtonNSWAustralia
| | - Tao Liu
- Children's Cancer Institute AustraliaRandwickNSWAustralia
- Centre for Childhood Cancer ResearchUNSW SydneyKensingtonNSWAustralia
| | - Sebastian Amos
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Simon Kobelke
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Andrew C Marshall
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Oliver Meers
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Yu Suk Choi
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Charles S Bond
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Archa H Fox
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
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Rengel BD, Kowalski TW, Bremm JM, do Amaral Gomes J, Schüler-Faccini L, Vianna FSL, Fraga LR. Genetic evaluation of HAND2 gene and its effects on thalidomide embryopathy. Birth Defects Res 2022; 114:1354-1363. [PMID: 36177858 DOI: 10.1002/bdr2.2092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/28/2022] [Accepted: 09/04/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND HAND2 is a transcription factor important for embryonic development, required for limbs and cardiovascular development. Thalidomide is a drug responsible to a spectrum of congenital anomalies known as Thalidomide Embryopathy (TE), which includes mainly limb and heart defects. It is known that HAND2 interaction with TBX5, an important protein for limbs and heart development, is inhibited by Thalidomide. The aim of this study was to evaluate and characterize HAND2 in the context of TE, and to evaluate its variability in TE individuals. METHODS DNA from 35 TE subjects was extracted from saliva samples and PCR was performed for amplification and Sanger sequencing of HAND2 coding sequence. RESULTS The analysis showed only one variant; a synonymous variant p.P51 (rs59621536) in exon 1 found in three individuals. Further in silico evaluation confirmed highly HAND2 conservation, being the 3'UTR the most polymorphic region of the gene. Additional computational analyses classified the variant as neutral, without alteration in splicing and miRNA sites. In silico predictions pointed to alteration of two CpG islands adjacent to the variant; however, we did not observe any alterations on the methylation pattern of HAND2 gene in our sample. Moreover, alteration of the binding site of MeCP2, a nuclear protein involved in DNA methylation, was predicted along with alteration in HAND2 mRNA structure. CONCLUSIONS Considering HAND2 being a well conserved gene, further studies with a larger sample should be performed to evaluate the role this gene on genetic susceptibility to TE.
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Affiliation(s)
- Bruna Duarte Rengel
- Laboratory of Medical Genetics and Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Brazilian Teratogen Information Service (SIAT), Medical Genetics Service of Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Genomic Medicine Laboratory at Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Thayne Woycinck Kowalski
- Laboratory of Medical Genetics and Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Brazilian Teratogen Information Service (SIAT), Medical Genetics Service of Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Genomic Medicine Laboratory at Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil.,Bioinformatics Core, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil.,Centro Universitário CESUCA, Cachoeirinha, Brazil
| | - João Matheus Bremm
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Julia do Amaral Gomes
- Laboratory of Medical Genetics and Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Brazilian Teratogen Information Service (SIAT), Medical Genetics Service of Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Genomic Medicine Laboratory at Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil
| | - Lavínia Schüler-Faccini
- Laboratory of Medical Genetics and Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Brazilian Teratogen Information Service (SIAT), Medical Genetics Service of Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- Laboratory of Medical Genetics and Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Brazilian Teratogen Information Service (SIAT), Medical Genetics Service of Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Genomic Medicine Laboratory at Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil.,Postgraduate Program in Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Lucas Rosa Fraga
- Laboratory of Medical Genetics and Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Brazilian Teratogen Information Service (SIAT), Medical Genetics Service of Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Genomic Medicine Laboratory at Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,Postgraduate Program in Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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9
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Ahmad SS, Samia NSN, Khan AS, Turjya RR, Khan MAAK. Bidirectional promoters: an enigmatic genome architecture and their roles in cancers. Mol Biol Rep 2021; 48:6637-6644. [PMID: 34378109 DOI: 10.1007/s11033-021-06612-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022]
Abstract
Bidirectional promoters are the transcription regulatory regions of genes positioned head-to-head on opposite strands. Specific sequence signals, chromatin modifications and three-dimensional structures of the transcription site facilitate the unconventional yet tightly regulated transcription proceeding in both directions from these promoters. Mutations or aberrant epigenetic changes can lead to abnormal enhanced or reduced expression from either of the bidirectionally transcribed genes resulting in tumorigenesis. Moreover, bidirectionally transcribed genes might also contribute towards the immune regulation in tumor microenvironment. In this review, we aimed to expound the characteristic features of bidirectional promoters alongside their transcriptional regulations, and ultimately, the association of these enigmatic genomic elements in different cancers.
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Affiliation(s)
- Sheikh Shafin Ahmad
- Department of Mathematics and Natural Sciences, Brac University, Dhaka, Bangladesh
| | | | - Auroni Semonti Khan
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Rafeed Rahman Turjya
- Department of Mathematics and Natural Sciences, Brac University, Dhaka, Bangladesh
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Razavi ZS, Tajiknia V, Majidi S, Ghandali M, Mirzaei HR, Rahimian N, Hamblin MR, Mirzaei H. Gynecologic cancers and non-coding RNAs: Epigenetic regulators with emerging roles. Crit Rev Oncol Hematol 2020; 157:103192. [PMID: 33290823 DOI: 10.1016/j.critrevonc.2020.103192] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/24/2022] Open
Abstract
Gynecologic cancers involve the female genital organs, such as the vulva, vagina, cervix, endometrium, ovaries, and fallopian tubes. The occurrence and frequency of gynecologic cancer depends on personal lifestyle, history of exposure to viruses or carcinogens, genetics, body shape, and geographical habitat. For a long time, research into the molecular biology of cancer was broadly restricted to protein-coding genes. Recently it has been realized that non-coding RNAs (ncRNA), including long noncoding RNAs (LncRNAs), microRNAs, circular RNAs and piRNAs (PIWI-interacting RNAs), can all play a role in the regulation of cellular function within gynecological cancer. It is now known that ncRNAs are able to play dual roles, i.e. can exert both oncogenic or tumor suppressive functions in gynecological cancer. Moreover, several clinical trials are underway looking at the biomarker and therapeutic roles of ncRNAs. These efforts may provide a new horizon for the diagnosis and treatment of gynecological cancer. Herein, we summarize some of the ncRNAs that have been shown to be important in gynecological cancers.
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Affiliation(s)
| | - Vida Tajiknia
- Department of Surgery, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shahab Majidi
- Student Research Committee, Fasa University of Medical Sciences, Fasa, Iran
| | - Maryam Ghandali
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Neda Rahimian
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences (IUMS), Tehran, Iran.
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, 02114, USA; Department of Dermatology, Harvard Medical School, Boston, MA, 02115, USA; Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, 2028, South Africa.
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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Long Non-Coding RNA HAND2-AS1 Acts as a Tumor Suppressor in High-Grade Serous Ovarian Carcinoma. Int J Mol Sci 2020; 21:ijms21114059. [PMID: 32517089 PMCID: PMC7312972 DOI: 10.3390/ijms21114059] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/19/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are increasingly being identified as crucial regulators in pathologies like cancer. High-grade serous ovarian carcinoma (HGSC) is the most common subtype of ovarian cancer (OC), one of the most lethal gynecological malignancies. LncRNAs, especially in cancers such as HGSC, could play a valuable role in diagnosis and even therapy. From RNA-sequencing analysis performed between an OC cell line, SKOV3, and a Fallopian Tube (FT) cell line, FT194, an important long non-coding RNA, HAND2 Anti sense RNA 1 (HAND2-AS1), was observed to be significantly downregulated in OCs when compared to FT. Its downregulation in HGSC was validated in different datasets and in a panel of HGSC cell lines. Furthermore, this study shows that the downregulation of HAND2-AS1 is caused by promoter hypermethylation in HGSC and behaves as a tumor suppressor in HGSC cell lines. Since therapeutic relevance is of key importance in HGSC research, for the first time, HAND2-AS1 upregulation was demonstrated to be one of the mechanisms through which HDAC inhibitor Panobinostat could be used in a strategy to increase HGSC cells’ sensitivity to chemotherapeutic agents currently used in clinical trials. To unravel the mechanism by which HAND2-AS1 exerts its role, an in silico mRNA network was constructed using mRNAs whose expressions were positively and negatively correlated with this lncRNA in HGSC. Finally, a putative ceRNA network with possible miRNA targets of HAND2-AS1 and their mRNA targets was constructed, and the enriched Gene Ontology (GO) biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified.
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Xu Z, Lv H, Wang Y, Hu C, Chen S, Du Y, Shi C, Cheng X. HAND2-AS1 Inhibits Gastric Adenocarcinoma Cells Proliferation and Aerobic Glycolysis via miRNAs Sponge. Cancer Manag Res 2020; 12:3053-3068. [PMID: 32431548 PMCID: PMC7200253 DOI: 10.2147/cmar.s222878] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 02/09/2020] [Indexed: 01/14/2023] Open
Abstract
Objective To study the effect of lncRNA HAND2-AS1 on gastric adenocarcinoma (GA) cell property and explore its specific mechanism. Methods Data on stomach adenocarcinoma (STAD) were analyzed to screen differentially expressed lncRNA HAND2-AS1. RNA22-HAS database and dual luciferase reporter assay were applied to confirm the target relationship between HAND2-AS1/HIF3A and miR-184. The HAND2-AS1 and miR-184 expressions in tissue or cells were determined by qRT-PCR and Western blot. Besides, after GA cells (AGS) cultured in normoxic and hypoxic condition, phosphoenolpyruvate (PEP) and lactic acid were quantified by Phosphoenolpyruvate Fluorometric Assay Kit and Lactic Acid Detection kit, respectively. Additionally, colony formation assay, transwell invasion and migration assays were used to evaluate the abilities of cell invasion, migration, and proliferation in distinct conditions. Results The HAND2-AS1 and HIF3A expressions were down-regulated and miR-184 expression was up-regulated in GA tissues and cells. Dual luciferase reporter assay confirmed HAND2-AS1 and HIF3A were targeted by miR-184. AGS cell proliferation abilities were restrained by HAND2-AS1 and HIF3A overexpression and enhanced by miR-184, as well as migration and invasion abilities. In addition, HAND2-AS1 rescued enhanced AGS cell proliferation, cell migration, cell invasion abilities and glycolytic process caused by hypoxia via miR-184/HIF3A. Conclusion LncRNA HAND2-AS1 could inhibit GA cell proliferation, migration and invasion abilities and glycolytic process induced by hypoxia through miR-184/HIF3A signaling.
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Affiliation(s)
- Zhiyuan Xu
- Department of Gastric Surgery, Institute of Cancer and Basic Medicine, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, People's Republic of China
| | - Hang Lv
- Key Laboratory of Integrated Traditional Chinese and Western Medicine for Diagnosis and Treatment of Digestive System Tumor, Hangzhou 300020, Zhejiang, People's Republic of China
| | - Yiping Wang
- Key Laboratory of Integrated Traditional Chinese and Western Medicine for Diagnosis and Treatment of Digestive System Tumor, Hangzhou 300020, Zhejiang, People's Republic of China
| | - Can Hu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, Zhejiang, People's Republic of China
| | - Shangqi Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, Zhejiang, People's Republic of China
| | - Yian Du
- Department of Gastric Surgery, Institute of Cancer and Basic Medicine, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, People's Republic of China
| | - Chengwei Shi
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, Zhejiang, People's Republic of China
| | - Xiangdong Cheng
- Department of Gastric Surgery, Institute of Cancer and Basic Medicine, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, People's Republic of China
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13
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Han X, Zhang J, Liu Y, Fan X, Ai S, Luo Y, Li X, Jin H, Luo S, Zheng H, Yue Y, Chang Z, Yang Z, Tang F, He A, Shen X. The lncRNA Hand2os1/ Uph locus orchestrates heart development through regulation of precise expression of Hand2. Development 2019; 146:146/13/dev176198. [PMID: 31273086 DOI: 10.1242/dev.176198] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/09/2019] [Indexed: 12/30/2022]
Abstract
Exploration and dissection of potential actions and effects of long noncoding RNA (lncRNA) in animals remain challenging. Here, using multiple knockout mouse models and single cell RNA sequencing, we demonstrate that the divergent lncRNA Hand2os1/Uph has a key complex modulatory effect on the expression of its neighboring gene HAND2 and subsequently on heart development and function. Short deletion of the Hand2os1 promoter in mouse diminishes Hand2os1 transcription to ∼8-32%, but fails to affect HAND2 expression and yields no discernable heart phenotypes. Interestingly, full-length deletion of Hand2os1 in mouse causes moderate yet prevalent upregulation of HAND2 in hundreds of cardiac cells, leading to profound biological consequences, including dysregulated cardiac gene programs, congenital heart defects and perinatal lethality. We propose that the Hand2os1 locus dampens HAND2 expression to restrain cardiomyocyte proliferation, thereby orchestrating a balanced development of cardiac cell lineages. This study highlights the regulatory complexity of the lncRNA Hand2os1 on HAND2 expression, emphasizing the need for complementary genetic and single cell approaches to delineate the function and primary molecular effects of an lncRNA in animals.
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Affiliation(s)
- Xue Han
- Tsinghua Center for Life Sciences, School of Medicine, and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiejie Zhang
- Peking Center for Life Sciences, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Yaxi Liu
- Peking Center for Life Sciences, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Xiaoying Fan
- Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Peking University, Beijing 100871, China
| | - Shanshan Ai
- Peking Center for Life Sciences, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Yingjie Luo
- Peking Center for Life Sciences, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Xin Li
- Peking Center for Life Sciences, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Hengwei Jin
- Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Sai Luo
- Tsinghua Center for Life Sciences, School of Medicine, and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hui Zheng
- Tsinghua Center for Life Sciences, School of Medicine, and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yanzhu Yue
- Peking Center for Life Sciences, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Zai Chang
- Tsinghua Center for Life Sciences, School of Medicine, and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhongzhou Yang
- Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Peking University, Beijing 100871, China
| | - Aibin He
- Peking Center for Life Sciences, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Xiaohua Shen
- Tsinghua Center for Life Sciences, School of Medicine, and School of Life Sciences, Tsinghua University, Beijing 100084, China
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14
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Wang Y, Zhu P, Wang J, Zhu X, Luo J, Meng S, Wu J, Ye B, He L, Du Y, He L, Chen R, Tian Y, Fan Z. Long noncoding RNA lncHand2 promotes liver repopulation via c-Met signaling. J Hepatol 2018; 69:861-872. [PMID: 29653123 DOI: 10.1016/j.jhep.2018.03.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/14/2018] [Accepted: 03/24/2018] [Indexed: 01/20/2023]
Abstract
BACKGROUND & AIMS Long noncoding RNAs (lncRNAs) play important roles in various biological processes, regulating gene expression by diverse mechanisms. However, how lncRNAs regulate liver repopulation is unknown. Herein, we aimed to identify lncRNAs that regulate liver repopulation and elucidate the signaling pathways involved. METHODS Herein, we performed 70% partial hepatectomy in wild-type and gene knockout mice. We then performed transcriptomic analyses to identify a divergent lncRNA termed lncHand2 that is highly expressed during liver regeneration. RESULTS LncHand2 is constitutively expressed in the nuclei of pericentral hepatocytes in mouse and human livers. LncHand2 knockout abrogates liver regeneration and repopulation capacity. Mechanistically, lncHand2 recruits the Ino80 remodeling complex to initiate expression of Nkx1-2 in trans, which triggers c-Met (Met) expression in hepatocytes. Finally, knockout of both Nkx1-2 and c-Met causes more severe liver injury and poorer repopulation ability. Thus, lncHand2 promotes liver repopulation via initiating Nkx1-2-induced c-Met signaling. CONCLUSIONS Our findings reveal that lncHand2 acts as a critical mediator regulating liver repopulation. It does this by inducing Nkx1-2 expression, which in turn triggers c-Met signaling. LAY SUMMARY Long noncoding RNAs play important roles in various biological processes. While long noncoding RNAs do not directly code proteins, they can regulate gene expression by diverse mechanisms. We identified the long noncoding RNA, termed lncHand2 because of its proximity to the gene Hand2, to be an important determinant of liver regeneration through c-Met signaling.
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Affiliation(s)
- Yanying Wang
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingping Zhu
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Wang
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxiao Zhu
- CAS Key Laboratory of RNA Biology; Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianjun Luo
- CAS Key Laboratory of RNA Biology; Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shu Meng
- CAS Key Laboratory of RNA Biology; Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiayi Wu
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Buqing Ye
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Luyun He
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Du
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei He
- Department of Hepatobiliary Surgery, PLA General Hospital, Beijing 100853, China
| | - Runsheng Chen
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of RNA Biology; Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yong Tian
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of RNA Biology; Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zusen Fan
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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15
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Stephenson SEM, Aumann TD, Taylor JM, Riseley JR, Li R, Mann JR, Tomas D, Lockhart PJ. Generation and characterisation of a parkin-Pacrg knockout mouse line and a Pacrg knockout mouse line. Sci Rep 2018; 8:7528. [PMID: 29760428 PMCID: PMC5951884 DOI: 10.1038/s41598-018-25766-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/25/2018] [Indexed: 11/24/2022] Open
Abstract
Mutations in PARK2 (parkin) can result in Parkinson's disease (PD). Parkin shares a bidirectional promoter with parkin coregulated gene (PACRG) and the transcriptional start sites are separated by only ~200 bp. Bidirectionally regulated genes have been shown to function in common biological pathways. Mice lacking parkin have largely failed to recapitulate the dopaminergic neuronal loss and movement impairments seen in individuals with parkin-mediated PD. We aimed to investigate the function of PACRG and test the hypothesis that parkin and PACRG function in a common pathway by generating and characterizing two novel knockout mouse lines harbouring loss of both parkin and Pacrg or Pacrg alone. Successful modification of the targeted allele was confirmed at the genomic, transcriptional and steady state protein levels for both genes. At 18-20 months of age, there were no significant differences in the behaviour of parental and mutant lines when assessed by openfield, rotarod and balance beam. Subsequent neuropathological examination suggested there was no gross abnormality of the dopaminergic system in the substantia nigra and no significant difference in the number of dopaminergic neurons in either knockout model compared to wildtype mice.
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Affiliation(s)
- Sarah E M Stephenson
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Flemington Road, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Timothy D Aumann
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Juliet M Taylor
- Department of Pharmacology and Therapeutics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Jessica R Riseley
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Flemington Road, Parkville, Victoria, Australia
| | - Ruili Li
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
- Surgical Research, Murdoch Children's Research Institute, Flemington Road, Parkville, Victoria, Australia
| | - Jeffrey R Mann
- Monash Genome Modification Platform, Monash University, Clayton, Victoria, Australia
| | - Doris Tomas
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Flemington Road, Parkville, Victoria, Australia.
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia.
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16
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Chen J, Xu J, Li Y, Zhang J, Chen H, Lu J, Wang Z, Zhao X, Xu K, Li Y, Li X, Zhang Y. Competing endogenous RNA network analysis identifies critical genes among the different breast cancer subtypes. Oncotarget 2018; 8:10171-10184. [PMID: 28052038 PMCID: PMC5354650 DOI: 10.18632/oncotarget.14361] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/15/2016] [Indexed: 01/10/2023] Open
Abstract
Although competing endogenous RNAs (ceRNAs) have been implicated in many solid tumors, their roles in breast cancer subtypes are not well understood. We therefore generated a ceRNA network for each subtype based on the significance of both, positive co-expression and the shared miRNAs, in the corresponding subtype miRNA dys-regulatory network, which was constructed based on negative regulations between differentially expressed miRNAs and targets. All four subtype ceRNA networks exhibited scale-free architecture and showed that the common ceRNAs were at the core of the networks. Furthermore, the common ceRNA hubs had greater connectivity than the subtype-specific hubs. Functional analysis of the common subtype ceRNA hubs highlighted factors involved in proliferation, MAPK signaling pathways and tube morphogenesis. Subtype-specific ceRNA hubs highlighted unique subtype-specific pathways, like the estrogen response and inflammatory pathways in the luminal subtypes or the factors involved in the coagulation process that participates in the basal-like subtype. Ultimately, we identified 29 critical subtype-specific ceRNA hubs that characterized the different breast cancer subtypes. Our study thus provides new insight into the common and specific subtype ceRNA interactions that define the different categories of breast cancer and enhances our understanding of the pathology underlying the different breast cancer subtypes, which can have prognostic and therapeutic implications in the future.
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Affiliation(s)
- Juan Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yongsheng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jinwen Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hong Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jianping Lu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zishan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xueying Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kang Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yixue Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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Zhang J, Yuan Y, Wei Z, Ren J, Hou X, Yang D, Cai S, Chen C, Tan M, Chen GG, Wu K, He Y. Crosstalk between prognostic long noncoding RNAs and messenger RNAs as transcriptional hallmarks in gastric cancer. Epigenomics 2018; 10:433-443. [PMID: 29402138 DOI: 10.2217/epi-2017-0136] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
AIM Our study investigated the significance of the crosstalk between long noncoding RNAs (lncRNAs) and mRNAs in gastric cancer (GC). METHODS lncRNA and mRNA expression profiling data in 671 GC tumors and 77 nontumorous gastric tissues were retrieved from the gene expression omnibus database: GSE54129, GSE13911, GSE19826, GSE79973, GSE15459 and GSE66229. Differentially expressed analysis, RNA coexpression network construction, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were conducted in this study. RESULTS Using differentially expressed and prognostic lncRNAs or mRNAs in GC, we constructed the lncRNA-mRNA coexpression networks. This network involved with vital GO and KEGG pathways. CONCLUSION Our study reveals coexpressed lncRNAs and mRNAs as transcriptional hallmarks in GC patients which provide interesting information regarding the incidence and outcome of GC.
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Affiliation(s)
- Jian Zhang
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Yujie Yuan
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Zhewei Wei
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Jianwei Ren
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, PR China.,Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, PR China
| | - Xun Hou
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Dongjie Yang
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Sirong Cai
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Chuangqi Chen
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Min Tan
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - George Gong Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, PR China.,Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, PR China
| | - Kaiming Wu
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Yulong He
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
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Yang X, Wang CC, Lee WYW, Trovik J, Chung TKH, Kwong J. Long non-coding RNA HAND2-AS1 inhibits invasion and metastasis in endometrioid endometrial carcinoma through inactivating neuromedin U. Cancer Lett 2018; 413:23-34. [DOI: 10.1016/j.canlet.2017.10.028] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/19/2017] [Accepted: 10/19/2017] [Indexed: 11/17/2022]
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Catsper1 promoter is bidirectional and regulates the expression of a novel lncRNA. Sci Rep 2017; 7:13351. [PMID: 29042633 PMCID: PMC5645346 DOI: 10.1038/s41598-017-13867-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 10/03/2017] [Indexed: 11/10/2022] Open
Abstract
The Catsper1 gene, whose expression is restricted to male germ cells, has great importance in reproductive biology because of its function in sperm motility and fertilization. We previously reported that the promoter of this gene has transcriptional activity in either direction in a heterologous system. In the present study, we found that the Catsper1 promoter has in vitro transcriptional activity in either orientation in GC-1 spg mouse spermatogonial cells. The results also showed that this promoter regulates the expression of a new divergent Catsper1 gene named Catsper1au (Catsper1 antisense upstream transcript). Catsper1au is expressed in adult male mouse testis and liver tissues but not in female mouse liver or ovary tissues. In the testis, Catsper1au is expressed in embryos at 11.5 days post-coitum and from newborns to adults. This gene is also expressed in 1- to 3-week postnatal hearts and in 1-week to adult stage livers. The analysis of the 1402 bp whole genome sequence revealed that Catsper1au is an intronless and polyadenylated lncRNA, located in the nuclei of Sertoli and spermatogenic cells from adult testis. These data indicate that Catsper1au is divergently expressed from the Catsper1 promoter and could regulate gene expression during spermatogenesis.
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Chicken CCDC152 shares an NFYB-regulated bidirectional promoter with a growth hormone receptor antisense transcript and inhibits cells proliferation and migration. Oncotarget 2017; 8:84039-84053. [PMID: 29137403 PMCID: PMC5663575 DOI: 10.18632/oncotarget.21091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 09/04/2017] [Indexed: 12/11/2022] Open
Abstract
The chicken coiled-coil domain-containing protein 152 (CCDC152) recently has been identified as a novel one implicated in cell cycle regulation, cellular proliferation and migration by us. Here we demonstrate that CCDC152 is oriented in a head-to-head configuration with the antisense transcript of growth hormone receptor (GHR) gene. Through serial luciferase reporter assays, we firstly identified a minimal 102 bp intergenic region as a core bidirectional promoter to drive basal transcription in divergent orientations. And site mutation and transient transfected assays showed that nuclear transcription factor Y subunit beta (NFYB) could bind to the CCAAT box and directly transactivate this bidirectional promoter. SiRNA-mediated NFYB depletion could significantly down-regulate the expression of both GHR-AS-I6 and CCDC152. Additionally, the expression of GHR-AS-I6 was significantly up-regulated after CCDC152 overexpression. Overexpression of CCDC152 remarkably reduced cell proliferation and migration through JAK2/STAT signaling pathway. Thus, the GHR-AS-I6-CCDC152 bidirectional transcription unit, as a novel direct target of NFYB, is possibly essential for the accelerated proliferation and motility of different cells.
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Hua Y, Ma X, Liu X, Yuan X, Qin H, Zhang X. Abnormal expression of mRNA, microRNA alteration and aberrant DNA methylation patterns in rectal adenocarcinoma. PLoS One 2017; 12:e0174461. [PMID: 28350845 PMCID: PMC5370119 DOI: 10.1371/journal.pone.0174461] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 03/09/2017] [Indexed: 12/12/2022] Open
Abstract
Aim Rectal adenocarcinoma (READ) is a malignancy cancer with the high morbidity and motility worldwide. Our study aimed to explore the potential pathogenesis of READ through integrated analysis of gene expression profiling and DNA methylation data. Methods The miRNA, mRNA expression profiling and corresponding DNA methylation data were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed mRNAs/ miRNAs/methylated regions (DEmRNA/DEmiRNAs) were identified in READ. The negatively correlation of DEmiRNA-DEmRNAs and DNA methylation-DEmRNAs were obtained. DEmRNAs expression was validated through quantitative real-time polymerase chain reaction (qRT-PCR) and microarray expression profiling analyses. Results 1192 dysregulated DEmRNAs, 27 dysregulated DEmiRNAs and 6403 aberrant methylation CpG sites were screened in READ compared to normal controls. 1987 negative interaction pairs among 27 DEmiRNAs and 668 DEmRNAs were predicted. 446 genes with aberrant methylation were annotated. Eventually, 50 DEmRNAs (39 down- and 11 up-regulated DEmRNAs) with hypermethylation, synchronously negatively targeted by DEmiRNAs, were identified through the correlation analysis among 446 genes with aberrant methylation and 668 DEmRNAs. 50 DEmRNAs were significantly enriched in cAMP signaling pathway, circadian entrainment and glutamatergic synapse. The validation results of expression levels of DEmRNAs through qRT-PCR and microarray analyses were compatible with our study. Conclusion 7 genes of SORCS1, PDZRN4, LONRF2, CNGA3, HAND2, RSPO2 and GNAO1 with hypermethylation and negatively regulation by DEmiRNAs might contribute to the tumorigenesis of READ. Our work might provide valuable foundation for the READ in mechanism elucidation, early diagnosis and therapeutic target identification.
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Affiliation(s)
- Yang Hua
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China
| | - Xiukun Ma
- Department of Surgery, Sino-Singapore Eco-City Hospital of Tianjin Medical University, Tianjin, China
| | - Xianglong Liu
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China
| | - Xiangfei Yuan
- Tianjin Institute of Integrative Medicine for Acute Abdominal Diseases, Nankai Hospital, Tianjin, China
| | - Hai Qin
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China
| | - Xipeng Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China
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Transcription of the non-coding RNA upperhand controls Hand2 expression and heart development. Nature 2016; 539:433-436. [PMID: 27783597 DOI: 10.1038/nature20128] [Citation(s) in RCA: 260] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 09/29/2016] [Indexed: 12/28/2022]
Abstract
HAND2 is an ancestral regulator of heart development and one of four transcription factors that control the reprogramming of fibroblasts into cardiomyocytes. Deletion of Hand2 in mice results in right ventricle hypoplasia and embryonic lethality. Hand2 expression is tightly regulated by upstream enhancers that reside within a super-enhancer delineated by histone H3 acetyl Lys27 (H3K27ac) modifications. Here we show that transcription of a Hand2-associated long non-coding RNA, which we named upperhand (Uph), is required to maintain the super-enhancer signature and elongation of RNA polymerase II through the Hand2 enhancer locus. Blockade of Uph transcription, but not knockdown of the mature transcript, abolished Hand2 expression, causing right ventricular hypoplasia and embryonic lethality in mice. Given the substantial number of uncharacterized promoter-associated long non-coding RNAs encoded by the mammalian genome, the Uph-Hand2 regulatory partnership offers a mechanism by which divergent non-coding transcription can establish a permissive chromatin environment.
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Aliperti V, Donizetti A. Long Non-coding RNA in Neurons: New Players in Early Response to BDNF Stimulation. Front Mol Neurosci 2016; 9:15. [PMID: 26973456 PMCID: PMC4773593 DOI: 10.3389/fnmol.2016.00015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/18/2016] [Indexed: 12/28/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) is a neurotrophin family member that is highly expressed and widely distributed in the brain. BDNF is critical for neural survival and plasticity both during development and in adulthood, and dysfunction in its signaling may contribute to a number of neurodegenerative disorders. Deep understanding of the BDNF-activated molecular cascade may thus help to find new biomarkers and therapeutic targets. One interesting direction is related to the early phase of BDNF-dependent gene expression regulation, which is responsible for the activation of selective gene programs that lead to stable functional and structural remodeling of neurons. Immediate-early coding genes activated by BDNF are under investigation, but the involvement of the non-coding RNAs is largely unexplored, especially the long non-coding RNAs (lncRNAs). lncRNAs are emerging as key regulators that can orchestrate different aspects of nervous system development, homeostasis, and plasticity, making them attractive candidate markers and therapeutic targets for brain diseases. We used microarray technology to identify differentially expressed lncRNAs in the immediate response phase of BDNF stimulation in a neuronal cell model. Our observations on the putative functional role of lncRNAs provide clues to their involvement as master regulators of gene expression cascade triggered by BDNF.
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Affiliation(s)
- Vincenza Aliperti
- Department of Biology, University of Naples Federico II Naples, Italy
| | - Aldo Donizetti
- Department of Biology, University of Naples Federico II Naples, Italy
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Wang Y, Zhang Y, Zhang C, Weng H, Li Y, Cai W, Xie M, Long Y, Ai Q, Liu Z, Du G, Wang S, Niu Y, Song F, Ozaki T, Bu Y. The gene pair PRR11 and SKA2 shares a NF-Y-regulated bidirectional promoter and contributes to lung cancer development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1133-44. [PMID: 26162986 DOI: 10.1016/j.bbagrm.2015.07.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/03/2015] [Accepted: 07/06/2015] [Indexed: 12/21/2022]
Abstract
Head-to-head gene pairs represent a unique feature of gene organization in eukaryotes, accounting for >10% of genes in the human genome. Identification and functional analysis of such gene pairs is only in its infancy. Recently, we identified PRR11 as a novel cancer-related gene that is implicated in cell cycle and lung cancer. Here we demonstrate that PRR11 is oriented in a head-to-head configuration with its neighboring gene, SKA2. 5'-RACE assay revealed that the intergenic spacer region between the two genes is <500 bp. Serial luciferase reporter assays demonstrated that a minimal 80-bp intergenic region functions as a core bidirectional promoter to drive basal transcription in both the PRR11 and SKA2 orientations. EMSA and ChIP assays demonstrated that NF-Y binds to and directly transactivates the PRR11-SKA2 bidirectional promoter. SiRNA-mediated NF-Y depletion significantly downregulated PRR11 and SKA2 expression. Expression of both PRR11 and SKA2 was significantly upregulated in lung cancer. Expression of the two genes was highly correlated with each other and with NF-Y expression. Remarkably, high expression of both PRR11 and SKA2 was associated with poorer prognosis in lung cancer patients compared with high expression of one gene or low expression of both genes. Knockdown of PRR11 and/or SKA2 remarkably reduced cell proliferation, migration, and invasion in lung cancer cells. Thus, the PRR11-SKA2 bidirectional transcription unit, which is a novel direct target of NF-Y, is essential for the accelerated proliferation and motility of lung cancer cells and may represent a potential target in the diagnosis and/or treatment of human lung cancer.
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Affiliation(s)
- Yitao Wang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Chundong Zhang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Huali Weng
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Yi Li
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Wei Cai
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Mengyu Xie
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Yinjiang Long
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Qing Ai
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Zhu Liu
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Gang Du
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Sen Wang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Yulong Niu
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Fangzhou Song
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Toshinori Ozaki
- Laboratory of DNA Damage Signaling, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuohku, Chiba 260-8717, Japan
| | - Youquan Bu
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China.
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A 92-gene cancer classifier predicts the site of origin for neuroendocrine tumors. Mod Pathol 2014; 27:44-54. [PMID: 23846576 DOI: 10.1038/modpathol.2013.105] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 05/08/2013] [Accepted: 05/11/2013] [Indexed: 01/04/2023]
Abstract
A diagnosis of neuroendocrine carcinoma is often morphologically straight-forward; however, the tumor site of origin may remain elusive in a metastatic presentation. Neuroendocrine tumor subtyping has important implications for staging and patient management. In this study, the novel use and performance of a 92-gene molecular cancer classifier for determination of the site of tumor origin are described in a series of 75 neuroendocrine tumors (44 metastatic, 31 primary; gastrointestinal (n=12), pulmonary (n=22), Merkel cell (n=10), pancreatic (n=10), pheochromocytoma (n=10), and medullary thyroid carcinoma (n=11)). Formalin-fixed, paraffin-embedded samples passing multicenter pathologist adjudication were blinded and tested by a 92-gene molecular assay that predicts tumor type/subtype based upon relative quantitative PCR expression measurements for 87 tumor-related and 5 reference genes. The 92-gene assay demonstrated 99% (74/75; 95% confidence interval (CI) 0.93-0.99) accuracy for classification of neuroendocrine carcinomas and correctly subtyped the tumor site of origin in 95% (71/75; 95% CI 0.87-0.98) of cases. Analysis of gene expression subsignatures within the 92-gene assay panel showed 4 genes with promising discriminatory value for tumor typing and 15 genes for tumor subtyping. The 92-gene classifier demonstrated excellent accuracy for classifying and determining the site of origin in tumors with neuroendocrine differentiation. These results show promise for use of this test to aid in classifying neuroendocrine tumors of indeterminate primary site, particularly in the metastatic setting.
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Didych DA, Shamsutdinov MF, Smirnov NA, Akopov SB, Monastyrskaya GS, Uspenskaya NY, Nikolaev LG, Sverdlov ED. Human PSENEN and U2AF1L4 genes are concertedly regulated by a genuine bidirectional promoter. Gene 2012; 515:34-41. [PMID: 23246698 DOI: 10.1016/j.gene.2012.11.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 10/31/2012] [Accepted: 11/29/2012] [Indexed: 11/16/2022]
Abstract
Head-to-head genes with a short distance between their transcription start sites may constitute up to 10% of all genes in the genomes of various species. It was hypothesized that this intergenic space may represent bidirectional promoters which are able to initiate transcription of both genes, but the true bidirectionality was proved only for a few of them. We present experimental evidence that, according to several criteria, a 269 bp region located between the PSENEN and U2AF1L4 human genes is a genuine bidirectional promoter regulating a concerted divergent transcription of these genes. Concerted transcription of PSENEN and U2AF1L4 can be necessary for regulation of T-cell activity.
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Affiliation(s)
- D A Didych
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
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Abstract
Neuroblastoma is a pediatric tumor of the sympathetic nervous system. Amplification and overexpression of the MYCN proto-oncogene occurs in approximately 20% of neuroblastomas and is associated with advanced stage disease, rapid tumor progression, and poor prognosis. MYCN encodes the transcriptional regulator N-myc, which has been shown to both up- and downregulate many target genes involved in cell cycle, DNA damage, differentiation, and apoptosis in neuroblastoma. During the last years, it has become clear that N-myc also modulates the expression of several classes of noncoding RNAs, in particular microRNAs. MicroRNAs are the most widely studied noncoding RNA molecules in neuroblastoma. They function as negative regulators of gene expression at the posttranscriptional level in diverse cellular processes. Aberrant regulation of miRNA expression has been implicated in the pathogenesis of neuroblastoma. While the N-myc protein is established as an important regulator of several miRNAs involved in neuroblastoma tumorigenesis, tumor suppressor miRNAs have also been documented to repress MYCN expression and inhibit cell proliferation of MYCN-amplified neuroblastoma cells. It is now becoming increasingly evident that N-myc also regulates the expression of long noncoding RNAs such as T-UCRs and ncRAN. This review summarizes the current knowledge about the interplay between N-myc and noncoding RNAs in neuroblastoma and how this contributes to neuroblastoma tumorigenesis.
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Affiliation(s)
- Jochen Buechner
- Department of Pediatrics, University Hospital of North Norway, Tromsø, Norway
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Liu B, Chen J, Shen B. Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs. BMC SYSTEMS BIOLOGY 2011; 5 Suppl 1:S2. [PMID: 21689477 PMCID: PMC3121118 DOI: 10.1186/1752-0509-5-s1-s2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Background Bi-directional gene pairs have received considerable attention for their prevalence in vertebrate genomes. However, their biological relevance and exact regulatory mechanism remain less understood. To study the inner properties of this gene organization and the difference between bi- and uni-directional genes, we conducted a genome-wide investigation in terms of their sequence composition, functional association and regulatory motif discovery. Results We identified 1210 bi-directional gene pairs based on the GRCh37 assembly data, accounting for 11.6% of all the human genes owning RNAs. CpG islands were detected in 98.42% of bi-directional promoters and 61.07% of unidirectional promoters. Functional enrichment analysis in GO and GeneGO both revealed that bi-directional genes tend to be associated with housekeeping functions in metabolism pathways and nuclear processes, and 46.84% of the pair members are involved in the same biological function. By fold-enrichment analysis, we characterized 73 and 43 putative transcription factor binding sites(TFBS) that preferentially occur in bi-directional promoters from TRANSFAC and JASPAR database respectively. By text mining, some of them were verified by individual experiments and several novel binding motifs were also identified. Conclusions Bi-directional promoters feature a significant enrichment of CpG-islands as well as a high GC content. We provided insight into the function constraints of bi-directional genes and found that paired genes are biased toward functional similarities. We hypothesized that the functional association underlies the co-expression of bi-directional genes. Furthermore, we proposed a set of putative regulatory motifs in the bi-directional promoters for further experimental studies to investigate transcriptional regulation of bi-directional genes.
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Affiliation(s)
- Bingchuan Liu
- Center for Systems Biology, Soochow University, Suzhou, China
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29
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Huyen DV, Bany BM. Evidence for a conserved function of heart and neural crest derivatives expressed transcript 2 in mouse and human decidualization. Reproduction 2011; 142:353-68. [PMID: 21527398 DOI: 10.1530/rep-11-0060] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Previously, we showed that heart and neural crest derivatives expressed transcript 2 (Hand2) mRNA levels dramatically increase in mouse uterine endometrial stromal cells (ESCs) as they undergo decidualization in vivo. However, to date, little is known about the expression and function of this transcription factor in mouse or human uterus decidualization. Therefore, this study was conducted to provide a more detailed assessment of Hand2 gene expression and function in the mouse uterus during the peri-implantation period and also in mouse plus human ESCs during decidualization in vitro. The results show that Hand2 mRNA and protein levels increase in the mouse uterus during decidualization and this does not depend on the presence of a conceptus. Interestingly, Hand2 mRNA and protein are present in ESCs adjacent to the luminal epithelium in the uterus prior to the onset of implantation. We find that progesterone is likely a regulator of Hand2 expression during uterine sensitization of the mouse uterus. Finally, Hand2 expression increases in mouse and human fibroblast cells as they undergo decidualization in vitro. This expression is significantly increased in response to prostaglandin E(2). In particular, reduction of Hand2 expression in these cells using small hairpin RNA or small interfering RNA approaches results in the reduced extent of decidualization as shown by the reduced expression of a subset of decidualization markers. The results of this study support the hypothesis that Hand2 expression not only plays an important role in decidualization but may also play a role in obtaining proper progesterone-dependent uterine sensitization required for implantation to begin.
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Affiliation(s)
- D V Huyen
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901, USA
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Garcia SAB, Nagai MA. Transcriptional regulation of bidirectional gene pairs by 17-β-estradiol in MCF-7 breast cancer cells. Braz J Med Biol Res 2010; 44:112-22. [PMID: 21180879 DOI: 10.1590/s0100-879x2010007500149] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 12/08/2010] [Indexed: 11/22/2022] Open
Abstract
Using cDNA microarray analysis, we previously identified a set of differentially expressed genes in primary breast tumors based on the status of estrogen and progesterone receptors. In the present study, we performed an integrated computer-assisted and manual search of potential estrogen response element (ERE) binding sites in the promoter region of these genes to characterize their potential to be regulated by estrogen receptors (ER). Publicly available databases were used to annotate the position of these genes in the genome and to extract a 5'flanking region 2 kb upstream to 2 kb downstream of the transcription start site for transcription binding site analysis. The search for EREs and other binding sites was performed using several publicly available programs. Overall, approximately 40% of the genes analyzed were potentially able to be regulated by estrogen via ER. In addition, 17% of these genes are located very close to other genes organized in a head-to-head orientation with less than 1.0 kb between their transcript units, sharing a bidirectional promoter, and could be classified as bidirectional gene pairs. Using quantitative real-time PCR, we further investigated the effects of 17β-estradiol and antiestrogens on the expression of the bidirectional gene pairs in MCF-7 breast cancer cells. Our results showed that some of these gene pairs, such as TXNDC9/EIF5B, GALNS/TRAPPC2L, and SERINC1/PKIB, are modulated by 17β-estradiol via ER in MCF-7 breast cancer cells. Here, we also characterize the promoter region of potential ER-regulated genes and provide new information on the transcriptional regulation of bidirectional gene pairs.
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Affiliation(s)
- S A B Garcia
- Disciplina de Oncologia, Departamento de Radiologia, Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Arnaldo 455, São Paulo, SP, Brazil
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When needles look like hay: how to find tissue-specific enhancers in model organism genomes. Dev Biol 2010; 350:239-54. [PMID: 21130761 DOI: 10.1016/j.ydbio.2010.11.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 11/11/2010] [Accepted: 11/22/2010] [Indexed: 01/22/2023]
Abstract
A major prerequisite for the investigation of tissue-specific processes is the identification of cis-regulatory elements. No generally applicable technique is available to distinguish them from any other type of genomic non-coding sequence. Therefore, researchers often have to identify these elements by elaborate in vivo screens, testing individual regions until the right one is found. Here, based on many examples from the literature, we summarize how functional enhancers have been isolated from other elements in the genome and how they have been characterized in transgenic animals. Covering computational and experimental studies, we provide an overview of the global properties of cis-regulatory elements, like their specific interactions with promoters and target gene distances. We describe conserved non-coding elements (CNEs) and their internal structure, nucleotide composition, binding site clustering and overlap, with a special focus on developmental enhancers. Conflicting data and unresolved questions on the nature of these elements are highlighted. Our comprehensive overview of the experimental shortcuts that have been found in the different model organism communities and the new field of high-throughput assays should help during the preparation phase of a screen for enhancers. The review is accompanied by a list of general guidelines for such a project.
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Oh-Hashi K, Koga H, Ikeda S, Shimada K, Hirata Y, Kiuchi K. Role of an ER stress response element in regulating the bidirectional promoter of the mouse CRELD2 - ALG12 gene pair. BMC Genomics 2010; 11:664. [PMID: 21106106 PMCID: PMC3091781 DOI: 10.1186/1471-2164-11-664] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 11/25/2010] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Recently, we identified cysteine-rich with EGF-like domains 2 (CRELD2) as a novel endoplasmic reticulum (ER) stress-inducible gene and characterized its transcriptional regulation by ATF6 under ER stress conditions. Interestingly, the CRELD2 and asparagine-linked glycosylation 12 homolog (ALG12) genes are arranged as a bidirectional (head-to-head) gene pair and are separated by less than 400 bp. In this study, we characterized the transcriptional regulation of the mouse CRELD2 and ALG12 genes that is mediated by a common bidirectional promoter. RESULTS This short intergenic region contains an ER stress response element (ERSE) sequence and is well conserved among the human, rat and mouse genomes. Microarray analysis revealed that CRELD2 and ALG12 mRNAs were induced in Neuro2a cells by treatment with thapsigargin (Tg), an ER stress inducer, in a time-dependent manner. Other ER stress inducers, tunicamycin and brefeldin A, also increased the expression of these two mRNAs in Neuro2a cells. We then tested for the possible involvement of the ERSE motif and other regulatory sites of the intergenic region in the transcriptional regulation of the mouse CRELD2 and ALG12 genes by using variants of the bidirectional reporter construct. With regards to the promoter activities of the CRELD2-ALG12 gene pair, the entire intergenic region hardly responded to Tg, whereas the CRELD2 promoter constructs of the proximal region containing the ERSE motif showed a marked responsiveness to Tg. The same ERSE motif of ALG12 gene in the opposite direction was less responsive to Tg. The direction and the distance of this motif from each transcriptional start site, however, has no impact on the responsiveness of either gene to Tg treatment. Additionally, we found three putative sequences in the intergenic region that antagonize the ERSE-mediated transcriptional activation. CONCLUSIONS These results show that the mouse CRELD2 and ALG12 genes are arranged as a unique bidirectional gene pair and that they may be regulated by the combined interactions between ATF6 and multiple other transcriptional factors. Our studies provide new insights into the complex transcriptional regulation of bidirectional gene pairs under pathophysiological conditions.
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Affiliation(s)
- Kentaro Oh-Hashi
- Department of Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
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Dávila López M, Martínez Guerra JJ, Samuelsson T. Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes. PLoS One 2010; 5:e10654. [PMID: 20498846 PMCID: PMC2871058 DOI: 10.1371/journal.pone.0010654] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 04/26/2010] [Indexed: 01/03/2023] Open
Abstract
The order of genes in eukaryotes is not entirely random. Studies of gene order conservation are important to understand genome evolution and to reveal mechanisms why certain neighboring genes are more difficult to separate during evolution. Here, genome-wide gene order information was compiled for 64 species, representing a wide variety of eukaryotic phyla. This information is presented in a browser where gene order may be displayed and compared between species. Factors related to non-random gene order in eukaryotes were examined by considering pairs of neighboring genes. The evolutionary conservation of gene pairs was studied with respect to relative transcriptional direction, intergenic distance and functional relationship as inferred by gene ontology. The results show that among gene pairs that are conserved the divergently and co-directionally transcribed genes are much more common than those that are convergently transcribed. Furthermore, highly conserved pairs, in particular those of fungi, are characterized by a short intergenic distance. Finally, gene pairs of metazoa and fungi that are evolutionary conserved and that are divergently transcribed are much more likely to be related by function as compared to poorly conserved gene pairs. One example is the ribosomal protein gene pair L13/S16, which is unusual as it occurs both in fungi and alveolates. A specific functional relationship between these two proteins is also suggested by the fact that they are part of the same operon in both eubacteria and archaea. In conclusion, factors associated with non-random gene order in eukaryotes include relative gene orientation, intergenic distance and functional relationships. It seems likely that certain pairs of genes are conserved because the genes involved have a transcriptional and/or functional relationship. The results also indicate that studies of gene order conservation aid in identifying genes that are related in terms of transcriptional control.
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Affiliation(s)
- Marcela Dávila López
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Göteborg, Sweden
| | - Juan José Martínez Guerra
- Departmento de Química, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes, Mexico
| | - Tore Samuelsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Göteborg, Sweden
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