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Cingaram PR, Beckedorff F, Yue J, Liu F, Dos Santos HG, Shiekhattar R. Enhancing Transcriptome Mapping with Rapid PRO-seq Profiling of Nascent RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593182. [PMID: 38766081 PMCID: PMC11100740 DOI: 10.1101/2024.05.08.593182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Precision nuclear run-on (PRO) sequencing (PRO-seq) is a powerful technique for mapping polymerase active sites with nucleotide resolution and measuring newly synthesized transcripts at both promoters and enhancer elements. The current PRO-seq protocol is time-intensive, technically challenging, and requires a large amount of starting material. To overcome these limitations, we developed rapid PRO-seq (rPRO-seq) which utilizes pre-adenylated single-stranded DNAs (AppDNA), a dimer blocking oligonucleotide (DBO), on-bead 5' RNA end repair, and column-based purification. These modifications enabled efficient transcriptome mapping within a single day (∼12 hours) increasing ligation efficiency, abolished adapter dimers, and reduced sample loss and RNA degradation. We demonstrate the reproducibility of rPRO-seq in measuring polymerases at promoters, gene bodies, and enhancers as compared to original PRO-seq protocols. Additionally, rPRO-seq is scalable, allowing for transcriptome mapping with as little as 25,000 cells. We apply rPRO-seq to study the role of Integrator in mouse hematopoietic stem and progenitor cell (mHSPC) homeostasis, identifying Ints11 as an essential component of transcriptional regulation and RNA processing in mHSPC homeostasis. Overall, rPRO-seq represents a significant advance in the field of nascent transcript analyses and will be a valuable tool for generating patient-specific genome-wide transcription profiles with minimal sample requirements.
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Kang J, Chung A, Suresh S, Bonzi LC, Sourisse JM, Ramirez‐Calero S, Romeo D, Petit‐Marty N, Pegueroles C, Schunter C. Long non-coding RNAs mediate fish gene expression in response to ocean acidification. Evol Appl 2024; 17:e13655. [PMID: 38357358 PMCID: PMC10866067 DOI: 10.1111/eva.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
The majority of the transcribed genome does not have coding potential but these non-coding transcripts play crucial roles in transcriptional and post-transcriptional regulation of protein-coding genes. Regulation of gene expression is important in shaping an organism's response to environmental changes, ultimately impacting their survival and persistence as population or species face global change. However, the roles of long non-coding RNAs (lncRNAs), when confronted with environmental changes, remain largely unclear. To explore the potential role of lncRNAs in fish exposed to ocean acidification (OA), we analyzed publicly available brain RNA-seq data from a coral reef fish Acanthochromis polyacanthus. We annotated the lncRNAs in its genome and examined the expression changes of intergenic lncRNAs (lincRNAs) between A. polyacanthus samples from a natural CO2 seep and a nearby control site. We identified 4728 lncRNAs, including 3272 lincRNAs in this species. Remarkably, 93.03% of these lincRNAs were species-specific. Among the 125 highly expressed lincRNAs and 403 differentially expressed lincRNAs in response to elevated CO2, we observed that lincRNAs were either neighboring or potentially trans-regulating differentially expressed coding genes associated with pH regulation, neural signal transduction, and ion transport, which are known to be important in the response to OA in fish. In summary, lncRNAs may facilitate fish acclimation and mediate the responses of fish to OA by modulating the expression of crucial coding genes, which offers insight into the regulatory mechanisms underlying fish responses to environmental changes.
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Affiliation(s)
- Jingliang Kang
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Arthur Chung
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Sneha Suresh
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Lucrezia C. Bonzi
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Jade M. Sourisse
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Sandra Ramirez‐Calero
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Daniele Romeo
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Natalia Petit‐Marty
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Cinta Pegueroles
- Department of Genetics, Microbiology and Statistics, Institute for Research on Biodiversity (IRBio)University of BarcelonaBarcelonaSpain
| | - Celia Schunter
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
- State Key Laboratory of Marine Pollution and Department of ChemistryCity University of Hong KongHong Kong SARChina
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Zhang L, Ma X, Tong P, Zheng B, Zhu M, Peng B, Wang J, Liu Y. RNA-Seq analysis of long non-coding RNA in human intestinal epithelial cells infected by Shiga toxin-producing Escherichia coli. Cytokine 2024; 173:156421. [PMID: 37944420 DOI: 10.1016/j.cyto.2023.156421] [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: 08/14/2023] [Revised: 10/28/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND The Shiga toxin-producing Escherichia coli (STEC) infects animals and induces acute intestinal inflammation. Long non-coding RNAs (lncRNAs) are known to play crucial roles in modulating inflammation response. However, it is not clear whether lncRNAs are involved in STEC-induced inflammation. METHODS AND RESULTS To understand the association of lncRNAs with STEC infection, we used RNA-seq technology to analyze the profiles of lncRNAs in Mock-infected and STEC-infected human intestinal epithelial cells (HIECs). We detected a total of 702 lncRNAs differentially expressed by STEC infection. 583 differentially expressed lncRNAs acted as competitive microRNAs (miRNAs) binding elements in regulating the gene expression involved in TNF signaling pathway, IL-17 signaling pathway, PI3K-Akt signaling pathway, and apoptosis pathways. We analyzed 3 targeted genes, TRADD, TRAF1 and TGFB2, which were differentially regulated by mRNA-miRNA-lncRNA interaction network, potentially involved in the inflammatory and apoptotic response to STEC infection. Functional analysis of up/downstream genes associated with differentially expressed lncRNAs revealed their role in adheres junction and endocytosis. We also used the qRT-PCR technique to validate 8 randomly selected differentially expressed lncRNAs and mRNAs in STEC-infected HIECs. CONCLUSION Our results, for the first time, revealed differentially expressed lncRNAs induced by STEC infection of HIECs. The results will help investigate the molecular mechanisms for the inflammatory responses induced by STEC.
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Affiliation(s)
- Liuqing Zhang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Xuelian Ma
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Panpan Tong
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Baili Zheng
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Mingyue Zhu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Bin Peng
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Jinquan Wang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Yingyu Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China.
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Wu JL, Hu RY, Li NN, Tan J, Zhou CX, Han B, Xu SF. Integrative Analysis of lncRNA-mRNA Co-expression Provides Novel Insights Into the Regulation of Developmental Transitions in Female Varroa destructor. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.842704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Varroa destructor is a major pathogenic driver of the Western honeybee colony losses globally. Understanding the developmental regulation of V. destructor is critical to develop effective control measures. Development is a complex biological process regulated by numerous genes and long non-coding RNAs (lncRNAs); however, the underlying regulation of lncRNAs in the development of V. destructor remains unknown. In this study, we analyzed the RNA sequencing (RNA-Seq) data derived from the four stages of female V. destructor in the reproductive phase (i.e., egg, protonymph, deutonymph, and adult). The identified differentially expressed mRNAs and lncRNAs exhibited a stage-specific pattern during developmental transitions. Further functional enrichment established that fat digestion and absorption, ATP-binding cassette (ABC) transporters, mitogen-activated protein kinase (MAPK) signaling pathway, and ubiquitin-proteasome pathway play key roles in the maturation of female V. destructor. Moreover, the lncRNAs and mRNAs of some pivotal genes were significantly upregulated at the deutonymph stage, such as cuticle protein 65/6.4/63/38 and mucin 5AC, suggesting that deutonymph is the key stage of metamorphosis development and pathogen resistance acquisition for female V. destructor. Our study provides novel insights into a foundational understanding of V. destructor biology.
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Long Non-coding RNA ZFPM2-AS1: A Novel Biomarker in the Pathogenesis of Human Cancers. Mol Biotechnol 2022; 64:725-742. [DOI: 10.1007/s12033-021-00443-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/22/2021] [Indexed: 10/19/2022]
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Focus on the Mechanisms and Functions of Pyroptosis, Inflammasomes, and Inflammatory Caspases in Infectious Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2501279. [PMID: 35132346 PMCID: PMC8817853 DOI: 10.1155/2022/2501279] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/28/2021] [Indexed: 12/17/2022]
Abstract
Eukaryotic cells can initiate several distinct self-destruction mechanisms to display essential roles for the homeostasis maintenance, development, and survival of an organism. Pyroptosis, a key response mode in innate immunity, also referred to as caspase-1-dependent proinflammatory programmed necrotic cell death activated by human caspase-1/4/5, or mouse caspase-1/11, plays indispensable roles in response to cytoplasmic insults and immune defense against infectious diseases. These inflammatory caspases are employed by the host to eliminate pathogen infections such as bacteria, viruses, protozoans, and fungi. Gasdermin D requires to be cleaved and activated by these inflammatory caspases to trigger the pyroptosis process. Physiological rupture of cells results in the release of proinflammatory cytokines, the alarmins IL-1β and IL-18, symbolizing the inflammatory potential of pyroptosis. Moreover, long noncoding RNAs play direct or indirect roles in the upstream of the pyroptosis trigger pathway. Here, we review in detail recently acquired insights into the central roles of inflammatory caspases, inflammasomes, and pyroptosis, as well as the crosstalk between pyroptosis and long noncoding RNAs in mediating infection immunity and pathogen clearance.
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Effects of Long Noncoding RNA HOTAIR Targeting miR-138 on Inflammatory Response and Oxidative Stress in Rat Cardiomyocytes Induced by Hypoxia and Reoxygenation. DISEASE MARKERS 2022; 2021:4273274. [PMID: 34970356 PMCID: PMC8714338 DOI: 10.1155/2021/4273274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/12/2021] [Indexed: 11/19/2022]
Abstract
Objective To investigate the effects of HOX transcript antisense RNA (HOTAIR) and miR-138 on inflammatory response and oxidative stress (OS) induced by IRI in rat cardiomyocytes. Methods H9C2 cells were divided into the control group, H/R group, H/R+siRNA NC group, H/R+si-HOTAIR group, and H/R+si-HOTAIR+inhibitor group. Expression levels of HOTAIR, miR-138, and inflammatory factors were detected by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). The double luciferase reporter gene assay was used to detect the targeting relationship between HOTAIR and miR-138. Results Compared with the control group, the level of miR-138 and SOD in the H/R group was obviously reduced, while the expression levels of the HOTAIR, MDA, and NF-κB pathway were obviously increased. Compared with the H/R group, the level of miR-138 and SOD in the H/R+si-HOTAIR group was obviously increased, and the expression levels of the HOTAIR, MDA, and NF-κB pathway were obviously decreased. Compared with the H/R+si-HOTAIR group, the level of SOD in the H/R+si-HOTAIR+inhibitor group decreased; MDA content and the NF-κB pathway expression level increased. In the double luciferase reporter gene assay, compared with the HOTAIR wt+NC group, the luciferase activity of the HOTAIR wt+miR-138 mimic group was obviously decreased. Conclusions Silent HOTAIR can promote the expression of miR-138 and inhibit H/R-induced inflammatory response and OS by regulating the NF-κB pathway, thus protecting cardiomyocytes.
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Li YX, Liu T, Liang YW, Huang JJ, Huang JS, Liu XG, Cheng ZY, Lu SX, Li M, Huang L. Integrative analysis of long non-coding RNA and messenger RNA expression in toll-like receptor 4-primed mesenchymal stem cells of ankylosing spondylitis. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1563. [PMID: 34790769 PMCID: PMC8576702 DOI: 10.21037/atm-21-5020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/16/2021] [Indexed: 11/06/2022]
Abstract
Background The precise pathogenesis of ankylosing spondylitis (AS) is still largely unknown at present. Our previous study found that toll-like receptor 4 (TLR4) downregulated and performed immunoregulatory dysfunction in mesenchymal stem cells from AS patients (AS-MSCs). The aim of this study was to explore the expression profiles of long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) in TLR4-primed AS-MSCs, and to clarify the potential mechanisms. Methods The immunoregulatory effects of MSCs were determined after TLR4 activation. Next, the differentially-expressed (DE) lncRNAs and mRNAs between AS-MSCs and TLR4-primed AS-MSCs [stimulated by lipopolysaccharide (LPS)] were identified via high-throughput sequencing followed by quantitative real-time PCR (qRT-PCR) confirmation. Finally, bioinformatics analyses were performed to identify the critical biological functions, signaling pathways, and associated functional networks involved in the TLR4-primed immunoregulatory function of AS-MSCs. Results A total of 147 DE lncRNAs and 698 DE mRNAs were identified between TLR4-primed AS-MSCs and unstimulated AS-MSCs. Of these, 107 lncRNAs were upregulated and 40 were downregulated (fold change ≥2, P<0.05), while 504 mRNAs were upregulated and 194 were downregulated (fold change ≥2, P<0.05). Five lncRNAs and five mRNAs with the largest fold changes were respectively verified by qRT-PCR. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses demonstrated that the DE mRNAs and lncRNAs were highly associated with the inflammatory response, such as NOD-like receptor (NLR) signaling pathway, the TNF signaling pathway and the NF-κB signaling pathway. Cis-regulation prediction revealed eight novel lncRNAs, while trans-regulation prediction revealed 15 lncRNAs, respectively. Eight core pairs of lncRNA and target mRNA in the lncRNA-transcription factor (TF)-mRNA network were as follows: PACERR-PTGS2, LOC105378085-SOD2, LOC107986655-HIVEP2, MICB-DT-MICB, LOC105373925-SP140L, LOC107984251-IFIT5, LOC112268267-GBP2, and LOC101926887-IFIT3, respectively. Conclusions TLR4 activation in AS can enhance the immunoregulatory ability of MSCs. Eight core pairs of lncRNA and target mRNA were observed in TLR4-primed AS-MSCs, which could contribute to understanding the potential mechanism of AS-MSC immunoregulatory dysfunction.
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Affiliation(s)
- Yu-Xi Li
- Department of Orthopaedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ting Liu
- Department of Anaesthesia, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yu-Wei Liang
- Department of Orthopaedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jia-Jun Huang
- Department of Orthopaedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jun-Shen Huang
- Department of Orthopaedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiang-Ge Liu
- Department of Orthopaedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zi-Ying Cheng
- Department of Orthopaedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shi-Xin Lu
- Department of Orthopaedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ming Li
- Department of Orthopaedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lin Huang
- Department of Orthopaedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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Baruah PM, Krishnatreya DB, Bordoloi KS, Gill SS, Agarwala N. Genome wide identification and characterization of abiotic stress responsive lncRNAs in Capsicum annuum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:221-236. [PMID: 33706183 DOI: 10.1016/j.plaphy.2021.02.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/22/2021] [Indexed: 05/25/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a type of non-coding transcripts having length of more than 200 nucleotides lacking protein-coding ability. In the present study, 12807 lncRNAs were identified in Capsicum annuum tissues exposed to abiotic stress conditions viz. heat, cold, osmotic and salinity stress. Expression analysis of lncRNAs in different treatment conditions demonstrates their stress-specific expression. Thirty lncRNAs were found to act as precursors for 10 microRNAs (miRNAs) of C. annuum. Additionally, a total of 1807 lncRNAs were found to interact with 194 miRNAs which targeted 621 mRNAs of C. annuum. Among these, 344 lncRNAs were found to act as target mimics for 621 genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that out of those 621 gene sequences, 546 were tagged with GO terms, 105 Enzyme Code (EC) numbers were assigned to 246 genes and 223 genes are found to be involved in 63 biological pathways. In this report, we have highlighted the prospective role of lncRNAs in different abiotic stress conditions by interacting with miRNAs and regulating stress responsive transcription factors (TFs) such as DoF, WRKY, MYB, bZIP and ERF in C. annuum.
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Affiliation(s)
- Pooja Moni Baruah
- Department of Botany, Gauhati University, Jalukbari, Guwahati, Assam, 781014, India
| | | | | | - Sarvajeet Singh Gill
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124 001, India
| | - Niraj Agarwala
- Department of Botany, Gauhati University, Jalukbari, Guwahati, Assam, 781014, India.
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Montigny A, Tavormina P, Duboe C, San Clémente H, Aguilar M, Valenti P, Lauressergues D, Combier JP, Plaza S. Drosophila primary microRNA-8 encodes a microRNA-encoded peptide acting in parallel of miR-8. Genome Biol 2021; 22:118. [PMID: 33892772 PMCID: PMC8063413 DOI: 10.1186/s13059-021-02345-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 04/09/2021] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Recent genome-wide studies of many species reveal the existence of a myriad of RNAs differing in size, coding potential and function. Among these are the long non-coding RNAs, some of them producing functional small peptides via the translation of short ORFs. It now appears that any kind of RNA presumably has a potential to encode small peptides. Accordingly, our team recently discovered that plant primary transcripts of microRNAs (pri-miRs) produce small regulatory peptides (miPEPs) involved in auto-regulatory feedback loops enhancing their cognate microRNA expression which in turn controls plant development. Here we investigate whether this regulatory feedback loop is present in Drosophila melanogaster. RESULTS We perform a survey of ribosome profiling data and reveal that many pri-miRNAs exhibit ribosome translation marks. Focusing on miR-8, we show that pri-miR-8 can produce a miPEP-8. Functional assays performed in Drosophila reveal that miPEP-8 affects development when overexpressed or knocked down. Combining genetic and molecular approaches as well as genome-wide transcriptomic analyses, we show that miR-8 expression is independent of miPEP-8 activity and that miPEP-8 acts in parallel to miR-8 to regulate the expression of hundreds of genes. CONCLUSION Taken together, these results reveal that several Drosophila pri-miRs exhibit translation potential. Contrasting with the mechanism described in plants, these data shed light on the function of yet undescribed primary-microRNA-encoded peptides in Drosophila and their regulatory potential on genome expression.
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Affiliation(s)
- Audrey Montigny
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse 3, CNRS UMR5546, 31320, Auzeville-Tolosane, France
| | - Patrizia Tavormina
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse 3, CNRS UMR5546, 31320, Auzeville-Tolosane, France
| | - Carine Duboe
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse 3, CNRS UMR5546, 31320, Auzeville-Tolosane, France
| | - Hélène San Clémente
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse 3, CNRS UMR5546, 31320, Auzeville-Tolosane, France
| | - Marielle Aguilar
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse 3, CNRS UMR5546, 31320, Auzeville-Tolosane, France
| | - Philippe Valenti
- Laboratoire MCD, Centre de Biologie Intégrative, Université de Toulouse 3, CNRS UMR5077, Bat 4R4, 118 route de Narbonne, 31062, Toulouse, France
| | - Dominique Lauressergues
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse 3, CNRS UMR5546, 31320, Auzeville-Tolosane, France
| | - Jean-Philippe Combier
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse 3, CNRS UMR5546, 31320, Auzeville-Tolosane, France
| | - Serge Plaza
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse 3, CNRS UMR5546, 31320, Auzeville-Tolosane, France.
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Farley EJ, Eggleston H, Riehle MM. Filtering the Junk: Assigning Function to the Mosquito Non-Coding Genome. INSECTS 2021; 12:186. [PMID: 33671692 PMCID: PMC7926655 DOI: 10.3390/insects12020186] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/07/2021] [Accepted: 02/11/2021] [Indexed: 01/21/2023]
Abstract
The portion of the mosquito genome that does not code for proteins contains regulatory elements that likely underlie variation for important phenotypes including resistance and susceptibility to infection with arboviruses and Apicomplexan parasites. Filtering the non-coding genome to uncover these functional elements is an expanding area of research, though identification of non-coding regulatory elements is challenging due to the lack of an amino acid-like code for the non-coding genome and a lack of sequence conservation across species. This review focuses on three types of non-coding regulatory elements: (1) microRNAs (miRNAs), (2) long non-coding RNAs (lncRNAs), and (3) enhancers, and summarizes current advances in technical and analytical approaches for measurement of each of these elements on a genome-wide scale. The review also summarizes and highlights novel findings following application of these techniques in mosquito-borne disease research. Looking beyond the protein-coding genome is essential for understanding the complexities that underlie differential gene expression in response to arboviral or parasite infection in mosquito disease vectors. A comprehensive understanding of the regulation of gene and protein expression will inform transgenic and other vector control methods rooted in naturally segregating genetic variation.
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Affiliation(s)
| | | | - Michelle M. Riehle
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA; (E.J.F.); (H.E.)
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Henninger JE, Oksuz O, Shrinivas K, Sagi I, LeRoy G, Zheng MM, Andrews JO, Zamudio AV, Lazaris C, Hannett NM, Lee TI, Sharp PA, Cissé II, Chakraborty AK, Young RA. RNA-Mediated Feedback Control of Transcriptional Condensates. Cell 2021; 184:207-225.e24. [PMID: 33333019 PMCID: PMC8128340 DOI: 10.1016/j.cell.2020.11.030] [Citation(s) in RCA: 270] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/09/2020] [Accepted: 11/16/2020] [Indexed: 12/11/2022]
Abstract
Regulation of biological processes typically incorporates mechanisms that initiate and terminate the process and, where understood, these mechanisms often involve feedback control. Regulation of transcription is a fundamental cellular process where the mechanisms involved in initiation have been studied extensively, but those involved in arresting the process are poorly understood. Modeling of the potential roles of RNA in transcriptional control suggested a non-equilibrium feedback control mechanism where low levels of RNA promote condensates formed by electrostatic interactions whereas relatively high levels promote dissolution of these condensates. Evidence from in vitro and in vivo experiments support a model where RNAs produced during early steps in transcription initiation stimulate condensate formation, whereas the burst of RNAs produced during elongation stimulate condensate dissolution. We propose that transcriptional regulation incorporates a feedback mechanism whereby transcribed RNAs initially stimulate but then ultimately arrest the process.
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Affiliation(s)
| | - Ozgur Oksuz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Krishna Shrinivas
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; NSF-Simons Center for Mathematical & Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ido Sagi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Gary LeRoy
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Ming M Zheng
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - J Owen Andrews
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alicia V Zamudio
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Charalampos Lazaris
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nancy M Hannett
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Phillip A Sharp
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ibrahim I Cissé
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA 02139, USA.
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Feng B, Li S, Wang Q, Tang L, Huang F, Zhang Z, Mahboobe S, Shao C. lncRNA DMRT2-AS acts as a transcriptional regulator of dmrt2 involving in sex differentiation in the Chinese tongue sole (Cynoglossus semilaevis). Comp Biochem Physiol B Biochem Mol Biol 2020; 253:110542. [PMID: 33301875 DOI: 10.1016/j.cbpb.2020.110542] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/17/2022]
Abstract
Long non-coding RNAs (lncRNAs) contribute to various biological processes, including sexual development. As a member of the DMRT family, dmrt2 plays a very important role in sex determination and differentiation. In this study, we cloned and characterized the lncRNA DMRT2-AS (referred to as dmrt2 antisense) associated with dmrt2 from the gonads of the Chinese tongue sole (Cynoglossus semilaevis). The full-length cDNA of DMRT2-AS was 537 bp. Based on a sequence alignment, DMRT2-AS overlapped with dmrt2 in reverse on exon 4 and intron 3, with a region of overlap of 221 bp on exon 4. RT-qPCR showed that DMRT2-AS was highly expressed in the testis of Chinese tongue sole. In addition, the expression of DMRT2-AS increased continuously during male gonadal development. In vitro experiments and bioinformatics predictions showed that DMRT2-AS promoted the expression of dmrt2 at the transcriptional level. These results suggest that DMRT2-AS acts as a transcriptional regulator of dmrt2 and plays an important role in the gonadal differentiation of male.
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Affiliation(s)
- Bo Feng
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Shuo Li
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo University, Ningbo 315211, China
| | - Qian Wang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266003, China
| | - Lili Tang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266003, China
| | - Fei Huang
- Genosys, Inc., Shenzhen 518000, China
| | - Zhihua Zhang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Shahid Mahboobe
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266003, China.
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14
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Aznaourova M, Schmerer N, Schmeck B, Schulte LN. Disease-Causing Mutations and Rearrangements in Long Non-coding RNA Gene Loci. Front Genet 2020; 11:527484. [PMID: 33329688 PMCID: PMC7735109 DOI: 10.3389/fgene.2020.527484] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
The classic understanding of molecular disease-mechanisms is largely based on protein-centric models. During the past decade however, genetic studies have identified numerous disease-loci in the human genome that do not encode proteins. Such non-coding DNA variants increasingly gain attention in diagnostics and personalized medicine. Of particular interest are long non-coding RNA (lncRNA) genes, which generate transcripts longer than 200 nucleotides that are not translated into proteins. While most of the estimated ~20,000 lncRNAs currently remain of unknown function, a growing number of genetic studies link lncRNA gene aberrations with the development of human diseases, including diabetes, AIDS, inflammatory bowel disease, or cancer. This suggests that the protein-centric view of human diseases does not capture the full complexity of molecular patho-mechanisms, with important consequences for molecular diagnostics and therapy. This review illustrates well-documented lncRNA gene aberrations causatively linked to human diseases and discusses potential lessons for molecular disease models, diagnostics, and therapy.
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Affiliation(s)
- Marina Aznaourova
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Nils Schmerer
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Bernd Schmeck
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany.,Systems Biology Platform, German Center for Lung Research (DZL), Philipps University Marburg, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Leon N Schulte
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany.,Systems Biology Platform, German Center for Lung Research (DZL), Philipps University Marburg, Marburg, Germany
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15
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Barbieri E, Hill C, Quesnel-Vallières M, Zucco AJ, Barash Y, Gardini A. Rapid and Scalable Profiling of Nascent RNA with fastGRO. Cell Rep 2020; 33:108373. [PMID: 33176136 PMCID: PMC7702699 DOI: 10.1016/j.celrep.2020.108373] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 09/15/2020] [Accepted: 10/19/2020] [Indexed: 12/20/2022] Open
Abstract
Genome-wide profiling of nascent RNA has become a fundamental tool to study transcription regulation. Unlike steady-state RNA-sequencing (RNA-seq), nascent RNA profiling mirrors real-time activity of RNA polymerases and provides an accurate readout of transcriptome-wide variations. Some species of nuclear RNAs (i.e., large intergenic noncoding RNAs [lincRNAs] and eRNAs) have a short half-life and can only be accurately gauged by nascent RNA techniques. Furthermore, nascent RNA-seq detects post-cleavage RNA at termination sites and promoter-associated antisense RNAs, providing insights into RNA polymerase II (RNAPII) dynamics and processivity. Here, we present a run-on assay with 4-thio ribonucleotide (4-S-UTP) labeling, followed by reversible biotinylation and affinity purification via streptavidin. Our protocol allows streamlined sample preparation within less than 3 days. We named the technique fastGRO (fast Global Run-On). We show that fastGRO is highly reproducible and yields a more complete and extensive coverage of nascent RNA than comparable techniques can. Importantly, we demonstrate that fastGRO is scalable and can be performed with as few as 0.5 × 106 cells. Barbieri et al. developed fastGRO, a nascent RNA-sequencing technique based on nuclear run-on. Using a streamlined, under-3-days protocol, fastGRO tracks the activity of RNA polymerase for differential gene expression analysis, polymerase kinetic studies, and profiling of lowly expressed and unstable RNA species. A low-input fastGRO protocol profiles nascent RNA in as little as 0.5 × 106 cells.
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Affiliation(s)
- Elisa Barbieri
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Connor Hill
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Mathieu Quesnel-Vallières
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Avery J Zucco
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Alessandro Gardini
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA.
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16
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Chen D, Du Y, Fan X, Zhu Z, Jiang H, Wang J, Fan Y, Chen H, Zhou D, Xiong C, Zheng Y, Xu X, Luo Q, Guo R. Reconstruction and functional annotation of Ascosphaera apis full-length transcriptome utilizing PacBio long reads combined with Illumina short reads. J Invertebr Pathol 2020; 176:107475. [PMID: 32976816 DOI: 10.1016/j.jip.2020.107475] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 08/26/2020] [Accepted: 09/16/2020] [Indexed: 01/19/2023]
Abstract
Ascosphaera apis is a widespread fungal pathogen of honeybee larvae that results in chalkbrood disease, leading to heavy losses for the beekeeping industry in China and many other countries. This work was aimed at generating a full-length transcriptome of A. apis using PacBio single-molecule real-time (SMRT) sequencing. Here, more than 23.97 Gb of clean reads was generated from long-read sequencing of A. apis mycelia, including 464,043 circular consensus sequences (CCS) and 394,142 full-length non-chimeric (FLNC) reads. In total, we identified 174,095 high-confidence transcripts covering 5141 known genes with an average length of 2728 bp. We also discovered 2405 genic loci and 11,623 isoforms that have not been annotated yet within the current reference genome. Additionally, 16,049, 10,682, 4520 and 7253 of the discovered transcripts have annotations in the Non-redundant protein (Nr), Clusters of Eukaryotic Orthologous Groups (KOG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Moreover, 1205 long non-coding RNAs (lncRNAs) were identified, which have less exons, shorter exon and intron lengths, shorter transcript lengths, lower GC percent, lower expression levels, and fewer alternative splicing (AS) evens, compared with protein-coding transcripts. A total of 253 members from 17 transcription factor (TF) families were identified from our transcript datasets. Finally, the expression of A. apis isoforms was validated using a molecular approach. Overall, this is the first report of a full-length transcriptome of entomogenous fungi including A. apis. Our data offer a comprehensive set of reference transcripts and hence contributes to improving the genome annotation and transcriptomic study of A. apis.
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Affiliation(s)
- Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Yu Du
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Zhiwei Zhu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Haibin Jiang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Jie Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Yuanchan Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Huazhi Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Dingding Zhou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Cuiling Xiong
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Yanzhen Zheng
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Xijian Xu
- Jiangxi Province Institute of Apiculture, 330201 Nanchang, Jiangxi, China
| | - Qun Luo
- Jiangxi Province Institute of Apiculture, 330201 Nanchang, Jiangxi, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China; Engineering Research Center of Processing and Application of Bee Products of Ministry of Education, Fuzhou 350002, Fujian Province, China.
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17
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Huang Z, Liu J, Li L, Guo Y, Luo Q, Li J. Long non-coding RNA expression profiling of macrophage line RAW264.7 infected by Mycobacterium tuberculosis. Biotech Histochem 2020; 95:403-410. [PMID: 32077318 DOI: 10.1080/10520295.2019.1707874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been implicated in regulation of biological processes. The role of lncRNAs in macrophages in response to Mycobacterium tuberculosis infection has not been explored. We used high throughput lncRNA microarray analysis to detect differentially expressed lncRNAs and mRNAs in RAW264.7 macrophages with or without M. tuberculosis infection. Quantitative real-time PCR (qRT-PCR) was used to verify the microarray results. Bioinformatics analysis (GO and KEGG) were used to explore the function of significantly dysregulated genes. Microarray results indicated that 1,487 lncRNAs (791 up and 696 down) and 910 mRNAs (536 up and 374 down) were expressed differentially in RAW264.7 macrophages with M. tuberculosis infection compared to controls. GO and pathway analysis revealed that up-regulated mRNAs were involved in immune response, immune system process, system development or TNF signaling pathway, and antigen processing and presentation. To the contrary, down-regulated mRNAs participated in system development, regulation of biological processes and peroxisome proliferator-activated receptor (PPAR) signaling pathway. qRT-PCR results of 10 lncRNAs and mRNAs were consistent with the microarray data. M. tuberculosis infection of macrophages caused enhanced expression of lncRNA AK151345 in a time- and dose-dependent manner. We determined comprehensive expression profiles of differentially expressed lncRNAs in RAW264.7 macrophages infected by M. tuberculosis.
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Affiliation(s)
- Zikun Huang
- Department of Clinical Laboratory, the First Affiliated Hospital of Nanchang University , Nanchang 330006, China
| | - Jianing Liu
- 2014 grade of Queen Mary Department of Medical College of Nanchang University , Nanchang 330006, China
| | - Lu Li
- 2014 grade of Queen Mary Department of Medical College of Nanchang University , Nanchang 330006, China
| | - Yang Guo
- Department of Clinical Laboratory, the First Affiliated Hospital of Nanchang University , Nanchang 330006, China
| | - Qing Luo
- Department of Clinical Laboratory, the First Affiliated Hospital of Nanchang University , Nanchang 330006, China
| | - Junming Li
- Department of Clinical Laboratory, the First Affiliated Hospital of Nanchang University , Nanchang 330006, China
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18
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Trizzino M, Barbieri E, Petracovici A, Wu S, Welsh SA, Owens TA, Licciulli S, Zhang R, Gardini A. The Tumor Suppressor ARID1A Controls Global Transcription via Pausing of RNA Polymerase II. Cell Rep 2019; 23:3933-3945. [PMID: 29949775 DOI: 10.1016/j.celrep.2018.05.097] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/20/2018] [Accepted: 05/30/2018] [Indexed: 12/17/2022] Open
Abstract
AT-rich interactive domain-containing proteins 1A and 1B (ARID1A and ARID1B) are mutually exclusive subunits of the chromatin remodeler SWI/SNF. ARID1A is the most frequently mutated chromatin regulator across all cancers, and ovarian clear cell carcinoma (OCCC) carries the highest prevalence of ARID1A mutations (∼57%). Despite evidence implicating ARID1A in tumorigenesis, the mechanism remains elusive. Here, we demonstrate that ARID1A binds active regulatory elements in OCCC. Depletion of ARID1A represses RNA polymerase II (RNAPII) transcription but results in modest changes to accessibility. Specifically, pausing of RNAPII is severely impaired after loss of ARID1A. Compromised pausing results in transcriptional dysregulation of active genes, which is compensated by upregulation of ARID1B. However, a subset of ARID1A-dependent genes is not rescued by ARID1B, including many p53 and estrogen receptor (ESR1) targets. Our results provide insight into ARID1A-mediated tumorigenesis and unveil functions of SWI/SNF in modulating RNAPII dynamics.
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Affiliation(s)
- Marco Trizzino
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Elisa Barbieri
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Ana Petracovici
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Shuai Wu
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Sarah A Welsh
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Tori A Owens
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Silvia Licciulli
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Rugang Zhang
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Alessandro Gardini
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA.
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19
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Wang YM, Trinh MP, Zheng Y, Guo K, Jimenez LA, Zhong W. Analysis of circulating non-coding RNAs in a non-invasive and cost-effective manner. Trends Analyt Chem 2019; 117:242-262. [PMID: 32292220 PMCID: PMC7156030 DOI: 10.1016/j.trac.2019.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Non-coding RNAs (ncRNAs) participate in regulation of gene expression, and are highly relevant to pathological development. They are found to be stably present in diverse body fluids, including those in the circulatory system, which can be sampled non-invasively for clinical tests. Thus, circulating ncRNAs have great potential to be disease biomarkers. However, tremendous efforts are desired to discover and utilize ncRNAs as biomarkers in clinical diagnosis, calling for technological advancement in analysis of circulating ncRNAs in biospecimens. Hence, this review summarizes the recent developments in this area, highlighting the works devoted to cancer diagnosis and prognosis. Three main directions are focused: 1) Extraction and purification of ncRNAs from body fluids; 2) Quantification of the purified circulating ncRNAs; and 3) Microfluidic platforms for integration of both steps to enable point-of-care diagnostics. These technologies have laid a solid foundation to move forward the applications of circulating ncRNAs in disease diagnosis and cure.
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Affiliation(s)
- Yu-Min Wang
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
- Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry and Environment, South China Normal University, Guangzhou, Guangdong 510006, P. R. China
| | - Michael Patrick Trinh
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Yongzan Zheng
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Kaizhu Guo
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Luis A. Jimenez
- Program in Biomedical Sciences, University of California at Riverside, Riverside, California 92521, United States
| | - Wenwan Zhong
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
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20
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Xu H, Cao L, Sun B, Wei Y, Liang M. Transcriptomic Analysis of Potential "lncRNA-mRNA" Interactions in Liver of the Marine Teleost Cynoglossus semilaevis Fed Diets With Different DHA/EPA Ratios. Front Physiol 2019; 10:331. [PMID: 31001132 PMCID: PMC6454198 DOI: 10.3389/fphys.2019.00331] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 03/11/2019] [Indexed: 01/22/2023] Open
Abstract
Long non-coding RNAs (lncRNA) have emerged as important regulators of lipid metabolism and have been shown to play multifaceted roles in controlling transcriptional gene regulation, but very little relevant information has been available in fish, especially in non-model fish species. With a feeding trial on a typical marine teleost tongue sole C. semilaevis followed by transcriptomic analysis, the present study investigated the possible involvement of lncRNA in hepatic mRNA expression in response to different levels of dietary DHA and EPA, which are two most important fatty acids for marine fish. An 80-day feeding trial was conducted in a flow-through seawater system, and in this trial three experimental diets differing basically in DHA/EPA ratio, i.e., 0.61 (D/E-0.61), 1.46 (D/E-1.46), and 2.75 (D/E-2.75), were randomly assigned to 9 tanks of experimental fish. A total of 124.04 G high quality genome-wide clean data about coding and non-coding transcripts was obtained in the analysis of hepatic transcriptome. Compared to diet D/E-0.61, D/E-1.46 up-regulated expression of 178 lncRNAs and 2629 mRNAs, and down-regulated that of 47 lncRNAs and 3059 mRNAs, while D/E-2.75 resulted in much less change in gene expression. The co-expression and co-localization analysis of differentially expressed (DE) lncRNA and mRNA among dietary groups were then conducted. The co-expressed DE lncRNA and mRNA were primarily enriched in GO terms such as Metabolic process, Intracellular organelle, Catalytic activity, and Oxidoreductase activity, as well as in KEGG pathways such as Ribosome and Oxidative phosphorylation. Overlap of co-expression and co-localization analysis, i.e., lncRNA–mRNA matches “XR_523541.1–solute carrier family 16, member 5 (slc16a5)” and “LNC_000285–bromodomain adjacent to zinc finger domain 2A (baz2a),” were observed in all inter-group comparisons, indicating that they might crucially mediate the effects of dietary DHA and EPA on hepatic gene expression in tongue sole. In conclusion, this was the first time in marine teleost to investigate the possible lncRNA–mRNA interactions in response to dietary fatty acids. The results provided novel knowledge of lncRNAs in non-model marine teleost, and will serve as important resources for future studies that further investigate the roles of lncRNAs in lipid metabolism of marine teleost.
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Affiliation(s)
- Houguo Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lin Cao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Beijing Institute of Feed Control, Beijing, China
| | - Bo Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Yuliang Wei
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Mengqing Liang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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21
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Glastad KM, Hunt BG, Goodisman MAD. Epigenetics in Insects: Genome Regulation and the Generation of Phenotypic Diversity. ANNUAL REVIEW OF ENTOMOLOGY 2019; 64:185-203. [PMID: 30285490 DOI: 10.1146/annurev-ento-011118-111914] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Epigenetic inheritance is fundamentally important to cellular differentiation and developmental plasticity. In this review, we provide an introduction to the field of molecular epigenetics in insects. Epigenetic information is passed across cell divisions through the methylation of DNA, the modification of histone proteins, and the activity of noncoding RNAs. Much of our knowledge of insect epigenetics has been gleaned from a few model species. However, more studies of epigenetic information in traditionally nonmodel taxa will help advance our understanding of the developmental and evolutionary significance of epigenetic inheritance in insects. To this end, we also provide a brief overview of techniques for profiling and perturbing individual facets of the epigenome. Doing so in diverse cellular, developmental, and taxonomic contexts will collectively help shed new light on how genome regulation results in the generation of diversity in insect form and function.
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Affiliation(s)
- Karl M Glastad
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Griffin, Georgia 30223, USA;
| | - Michael A D Goodisman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
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22
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Dhanoa JK, Sethi RS, Verma R, Arora JS, Mukhopadhyay CS. Long non-coding RNA: its evolutionary relics and biological implications in mammals: a review. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2018; 60:25. [PMID: 30386629 PMCID: PMC6201556 DOI: 10.1186/s40781-018-0183-7] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/05/2018] [Indexed: 02/08/2023]
Abstract
The central dogma of gene expression propounds that DNA is transcribed to mRNA and finally gets translated into protein. Only 2–3% of the genomic DNA is transcribed to protein-coding mRNA. Interestingly, only a further minuscule part of genomic DNA encodes for long non-coding RNAs (lncRNAs) which are characteristically more than 200 nucleotides long and can be transcribed from both protein-coding (e.g. H19 and TUG1) as well as non-coding DNA by RNA polymerase II. The lncRNAs do not have open reading frames (with some exceptions), 3`-untranslated regions (3’-UTRs) and necessarily these RNAs lack any translation-termination regions, however, these can be spliced, capped and polyadenylated as mRNA molecules. The flexibility of lncRNAs confers them specific 3D-conformations that eventually enable the lncRNAs to interact with proteins, DNA or other RNA molecules via base pairing or by forming networks. The lncRNAs play a major role in gene regulation, cell differentiation, cancer cell invasion and metastasis and chromatin remodeling. Deregulation of lncRNA is also responsible for numerous diseases in mammals. Various studies have revealed their significance as biomarkers for prognosis and diagnosis of cancer. The aim of this review is to overview the salient features, evolution, biogenesis and biological importance of these molecules in the mammalian system.
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Affiliation(s)
- Jasdeep Kaur Dhanoa
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab India
| | - Ram Saran Sethi
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab India
| | - Ramneek Verma
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab India
| | - Jaspreet Singh Arora
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab India
| | - Chandra Sekhar Mukhopadhyay
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab India
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23
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Han D, Gao X, Wang M, Qiao Y, Xu Y, Yang J, Dong N, He J, Sun Q, Lv G, Xu C, Tao J, Ma N. Long noncoding RNA H19 indicates a poor prognosis of colorectal cancer and promotes tumor growth by recruiting and binding to eIF4A3. Oncotarget 2017; 7:22159-73. [PMID: 26989025 PMCID: PMC5008352 DOI: 10.18632/oncotarget.8063] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/23/2016] [Indexed: 02/06/2023] Open
Abstract
The overall biological role and clinical significance of long non-coding RNA H19 in colorectal cancer (CRC) remain largely unknown. Here, we firstly report that the lncRNA H19 recruits eIF4A3 and promotes the CRC cell proliferation. We observed higher expression of H19 was significantly correlated with tumor differentiation and advanced TNM stage in a cohort of 83 CRC patients. Multivariate analyses revealed that expression of H19 served as an independent predictor for overall survival and disease-free survival. Further experiments revealed that overexpression of H19 promoted the proliferation of CRC cells, while depletion of H19 inhibited cell viability and induced growth arrest. Moreover, expression profile data showed that H19 upregulated a series of cell-cycle genes. Using bioinformatics prediction and RNA immunoprecipitation assays, we identified eIF4A3 as an RNA-binding protein that binds to H19. We confirmed that combining eIF4A3 with H19 obstructed the recruitment of eIF4A3 to the cell-cycle gene mRNA. Our results suggest that H19, as a growth regulator, could serve as a candidate prognostic biomarker and target for new therapies in human CRC.
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Affiliation(s)
- Dong Han
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China.,Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Xu Gao
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China.,Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Meng Wang
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yu Qiao
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China.,Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Ya Xu
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Jing Yang
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Nazhen Dong
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Jun He
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Qian Sun
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Guixiang Lv
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Changqing Xu
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Ji Tao
- Department of Gastrointestinal Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, China
| | - Ning Ma
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China.,Heilongjiang Academy of Medical Sciences, Harbin, China
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24
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De Quattro C, Pè ME, Bertolini E. Long noncoding RNAs in the model species Brachypodium distachyon. Sci Rep 2017; 7:11252. [PMID: 28900227 PMCID: PMC5595811 DOI: 10.1038/s41598-017-11206-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023] Open
Abstract
Eukaryotic genomes are pervasively transcribed and only a small portion of the transcribed sequences belongs to protein coding genes. High-throughput sequencing technology contributed to consolidate this perspective, allowing the identification of numerous noncoding RNAs with key roles in biological processes. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nt with limited phylogenetic conservation, expressed at low levels and characterized by tissue/organ specific expression profiles. Although a large set of lncRNAs has been identified, the functional roles of lncRNAs are only beginning to be recognized and the molecular mechanism of lncRNA-mediated gene regulation remains largely unexplored, particularly in plants where their annotation and characterization are still incomplete. Using public and proprietary poly-(A)+ RNA-seq data as well as a collection of full length ESTs from several organs, developmental stages and stress conditions in three Brachypodium distachyon inbred lines, we describe the identification and the main features of thousands lncRNAs. Here we provide a genome-wide characterization of lncRNAs, highlighting their intraspecies conservation and describing their expression patterns among several organs/tissues and stress conditions. This work represents a fundamental resource to deepen our knowledge on long noncoding RNAs in C3 cereals, allowing the Brachypodium community to exploit these results in future research programs.
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Affiliation(s)
- Concetta De Quattro
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
| | - Edoardo Bertolini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA.
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25
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Yan G, Wang X, Yang M, Lu L, Zhou Q. Long non-coding RNA TUG1 promotes progression of oral squamous cell carcinoma through upregulating FMNL2 by sponging miR-219. Am J Cancer Res 2017; 7:1899-1912. [PMID: 28979812 PMCID: PMC5622224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 07/19/2017] [Indexed: 06/07/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a prevalent oral disease with a high morbidity and mortality rate. Several long non-coding RNAs (lncRNAs) were identified as important regulators of carcinogenesis. However, the pathogenic implications of TUG1 in OSCC are still unclear. In the present study, the expression of TUG1 was increased in OSCC cells. Knockdown of TUG1 inhibited cell proliferation, migration, and invasion, and induced cell cycle arrest at G0/G1 phase, whereas overexpression of TUG1 exerted the opposite effect on OSCC cells. A reciprocal repressive interaction between TUG1 and miR-219 was found, and miR-219 inhibition abolished the tumor-suppressive effect of TUG1 knockdown on cell growth and motility. Furthermore, bioinformatics analysis and luciferase reporter assay showed that FMNL2 was a direct target of miR-219. Restoration of FMNL2 abrogated the miR-219-induced inhibition of cell proliferation, cell cycle progression, migration, and invasion. Besides, overexpression of TUG1 promoted tumor growth and metastasis in vivo. Clinically, the expression of TUG1 and FMNL2 were increased, but miR-219 was decreased in primary tumors compared to non-tumor tissues. Both the upregulated TUG1, and FMNL2 and the downregulated miR-219 was associated with advanced stage of OSCC and poor overall survival. Notably, multivariate analyses confirmed that FMNL2 was an independent risk factor for OSCC. In conclusion, our data revealed that TUG1 confers oncogenic function in OSCC and TUG1/miR-219/FMNL2 axis may be a novel therapeutic strategy in this disease.
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Affiliation(s)
- Guangqi Yan
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University117 Nanjing North Street, Shenyang 110002, Liaoning, China
| | - Xue Wang
- Department of Orthodontics, Stomatology Hospital of Shenyang138 Zhongshan Road, Shenyang 110002, Liaoning, China
| | - Mingliang Yang
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University117 Nanjing North Street, Shenyang 110002, Liaoning, China
| | - Li Lu
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University117 Nanjing North Street, Shenyang 110002, Liaoning, China
| | - Qing Zhou
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University117 Nanjing North Street, Shenyang 110002, Liaoning, China
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Li M, Guan H. Noncoding RNAs Regulating NF-κB Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 927:317-36. [PMID: 27376741 DOI: 10.1007/978-981-10-1498-7_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As transcription factors that regulate expression of a variety of genes essential for diverse physiological and pathological processes, nuclear factor kappa B (NF-κB) family molecules play important roles in the development and progression of malignant tumor, and constitutive activation of NF-κB has been evidenced in various types of tumor tissues. Underlying its pathologic role, deregulated expression and/or transactivating activity of NF-κB usually involves multiple layers of molecular mechanisms. Noncoding RNAs, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are known to modulate expression and biological functions of regulatory proteins in a variety of cancer contexts. In this chapter, the regulatory role of miRNAs and lncRNAs in NF-κB signaling in malignant diseases will be discussed.
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Affiliation(s)
- Mengfeng Li
- Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, China.
| | - Hongyu Guan
- Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, China
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27
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Long Non-Coding RNAs Regulating Immunity in Insects. Noncoding RNA 2017; 3:ncrna3010014. [PMID: 29657286 PMCID: PMC5832008 DOI: 10.3390/ncrna3010014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 03/04/2017] [Accepted: 03/07/2017] [Indexed: 02/06/2023] Open
Abstract
Recent advances in modern technology have led to the understanding that not all genetic information is coded into protein and that the genomes of each and every organism including insects produce non-coding RNAs that can control different biological processes. Among RNAs identified in the last decade, long non-coding RNAs (lncRNAs) represent a repertoire of a hidden layer of internal signals that can regulate gene expression in physiological, pathological, and immunological processes. Evidence shows the importance of lncRNAs in the regulation of host–pathogen interactions. In this review, an attempt has been made to view the role of lncRNAs regulating immune responses in insects.
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28
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D'Ascenzo L, Leonarski F, Vicens Q, Auffinger P. Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops. RNA (NEW YORK, N.Y.) 2017; 23:259-269. [PMID: 27999116 PMCID: PMC5311481 DOI: 10.1261/rna.059097.116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/29/2016] [Indexed: 06/06/2023]
Abstract
When thinking about RNA three-dimensional structures, coming across GNRA and UNCG tetraloops is perceived as a boon since their folds have been extensively described. Nevertheless, analyzing loop conformations within RNA and RNP structures led us to uncover several instances of GNRA and UNCG loops that do not fold as expected. We noticed that when a GNRA does not assume its "natural" fold, it adopts the one we typically associate with a UNCG sequence. The same folding interconversion may occur for loops with UNCG sequences, for instance within tRNA anticodon loops. Hence, we show that some structured tetranucleotide sequences starting with G or U can adopt either of these folds. The underlying structural basis that defines these two fold types is the mutually exclusive stacking of a backbone oxygen on either the first (in GNRA) or the last nucleobase (in UNCG), generating an oxygen-π contact. We thereby propose to refrain from using sequences to distinguish between loop conformations. Instead, we suggest using descriptors such as U-turn (for "GNRA-type" folds) and a newly described Z-turn (for "UNCG-type" folds). Because tetraloops adopt for the largest part only two (inter)convertible turns, we are better able to interpret from a structural perspective loop interchangeability occurring in ribosomes and viral RNA. In this respect, we propose a general view on the inclination for a given sequence to adopt (or not) a specific fold. We also suggest how long-noncoding RNAs may adopt discrete but transient structures, which are therefore hard to predict.
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Affiliation(s)
- Luigi D'Ascenzo
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Filip Leonarski
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland
| | - Quentin Vicens
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Pascal Auffinger
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
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29
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Frigault JJ, Morin MD, Morin PJ. Differential expression and emerging functions of non-coding RNAs in cold adaptation. J Comp Physiol B 2016; 187:19-28. [PMID: 27866230 DOI: 10.1007/s00360-016-1049-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/07/2016] [Accepted: 10/26/2016] [Indexed: 01/16/2023]
Abstract
Several species undergo substantial physiological and biochemical changes to confront the harsh conditions associated with winter. Small mammalian hibernators and cold-hardy insects are examples of natural models of cold adaptation that have been amply explored. While the molecular picture associated with cold adaptation has started to become clearer in recent years, notably through the use of high-throughput experimental approaches, the underlying cold-associated functions attributed to several non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), remain to be better characterized. Nevertheless, key pioneering work has provided clues on the likely relevance of these molecules in cold adaptation. With an emphasis on mammalian hibernation and insect cold hardiness, this work first reviews various molecular changes documented so far in these processes. The cascades leading to miRNA and lncRNA production as well as the mechanisms of action of these non-coding RNAs are subsequently described. Finally, we present examples of differentially expressed non-coding RNAs in models of cold adaptation and elaborate on the potential significance of this modulation with respect to low-temperature adaptation.
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Affiliation(s)
- Jacques J Frigault
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, NB, E1A 3E9, Canada
| | - Mathieu D Morin
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, NB, E1A 3E9, Canada
| | - Pier Jr Morin
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, NB, E1A 3E9, Canada.
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30
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Li J, Lian Y, Yan C, Cai Z, Ding J, Ma Z, Peng P, Wang K. Long non-coding RNA FOXP4-AS1 is an unfavourable prognostic factor and regulates proliferation and apoptosis in colorectal cancer. Cell Prolif 2016; 50. [PMID: 27790757 DOI: 10.1111/cpr.12312] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/22/2016] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES Despite improvements in diagnosis and treatment, colorectal cancer (CRC) remains the third most common malignancy, and fourth-leading cause of cancer-related death worldwide, and has a particularly high incidence in Western countries. Recent studies have suggested that long non-coding RNAs (lncRNAs) compose a novel class of regulators of cancer biological processes, such as proliferation, apoptosis and metastasis. Here, we report that lncRNA FOXP4-AS1 acts as a functional oncogene in CRC pathogenesis. Moreover, we have attempted to investigate the effects of FOXP4-AS1 on tumour progression, both in vitro and in vivo. MATERIALS AND METHODS In this study, bioinformatic analyses and qPCR were performed to investigate FOXP4-AS1 expression in CRC tissue samples and CRC cell lines. We inhibited FOXP4-AS1 expression via FOXP4-AS1-specific siRNA transfection. Cell proliferation was assessed using cell viability and colony formation assays, as well as by flow cytometry and ethynyl deoxyuridine (Edu) analyses. Apoptosis was assessed using flow cytometry. Animal tumour xenografts were generated, and immunohistochemistry (IHC) was performed to evaluate effects of FOXP4-AS1 on CRC tumour growth in vivo. RESULTS We found that FOXP4-AS1 was up-regulated in CRC tissues and cell lines and that its overexpression positively correlated with advanced pathological stages and larger tumour size. Additionally, we found that FOXP4-AS1 knockdown inhibited cell proliferation and induced apoptosis. Furthermore, FOXP4-AS1 knockdown induced marked increase in number of cells in G0/G1 phase and reduction in number of cells in S phase, in DLD-1, HT-29 and HCT116 cell lines. Consistent with these findings, FOXP4-AS1 silencing inhibited tumour growth in vivo. CONCLUSION These findings suggest that FOXP4-AS1 plays a crucial role in CRC progression and may be a new biomarker in patients with CRC.
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Affiliation(s)
- Juan Li
- The Second Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yifan Lian
- The Second Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Changsheng Yan
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zeling Cai
- Department of General Surgery, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jie Ding
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhonghua Ma
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Peng Peng
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Keming Wang
- The Second Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
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31
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Zhu XT, Yuan JH, Zhu TT, Li YY, Cheng XY. Long noncoding RNA glypican 3 (GPC3) antisense transcript 1 promotes hepatocellular carcinoma progression via epigenetically activating GPC3. FEBS J 2016; 283:3739-3754. [DOI: 10.1111/febs.13839] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 07/16/2016] [Accepted: 08/26/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Xiao-ting Zhu
- Department of Anatomy, Histology and Embryology; Shanghai Jiao Tong University School of Medicine; China
| | - Ji-hang Yuan
- Department of Medical Genetics; Second Military Medical University; Shanghai China
| | - Teng-teng Zhu
- Department of Anatomy, Histology and Embryology; Shanghai Jiao Tong University School of Medicine; China
| | - Yang-yang Li
- Department of Anatomy, Histology and Embryology; Shanghai Jiao Tong University School of Medicine; China
| | - Xiao-yang Cheng
- Department of Anatomy, Histology and Embryology; Shanghai Jiao Tong University School of Medicine; China
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32
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Lin X, Han M, Cheng L, Chen J, Zhang Z, Shen T, Wang M, Wen B, Ni T, Han C. Expression dynamics, relationships, and transcriptional regulations of diverse transcripts in mouse spermatogenic cells. RNA Biol 2016; 13:1011-1024. [PMID: 27560004 DOI: 10.1080/15476286.2016.1218588] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Among all tissues of the metazoa, the transcritpome of testis displays the highest diversity and specificity. However, its composition and dynamics during spermatogenesis have not been fully understood. Here, we have identified 20,639 message RNAs (mRNAs), 7,168 long non-coding RNAs (lncRNAs) and 15,101 circular RNAs (circRNAs) in mouse spermatogenic cells, and found many of them were specifically expressed in testes. lncRNAs are significantly more testis-specific than mRNAs. At all stages, mRNAs are generally more abundant than lncRNAs, and linear transcripts are more abundant than circRNAs. We showed that the productions of circRNAs and piRNAs were highly regulated instead of random processes. Based on the results of a small-scale functional screening experiment using cultured mouse spermatogonial stem cells, many evolutionarily conserved lncRNAs are likely to play roles in spermatogenesis. Typical classes of transcription factor binding sites are enriched in the promoters of testis-specific m/lncRNA genes. Target genes of CREM and RFX2, 2 key TFs for spermatogenesis, were further validated by using ChIP-chip assays and RNA-seq on RFX2-knockout spermatogenic cells. Our results contribute to the current understanding of the transcriptomic complexity of spermatogenic cells and provide a valuable resource from which many candidate genes may be selected for further functional studies.
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Affiliation(s)
- Xiwen Lin
- a State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing , China
| | - Miao Han
- b State Key Laboratory of Genetic Engineering & Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai , China
| | - Lu Cheng
- c Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University , Shanghai , China
| | - Jian Chen
- a State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing , China.,d Graduate University of Chinese Academy of Sciences , Beijing , China
| | - Zhuqiang Zhang
- a State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing , China.,d Graduate University of Chinese Academy of Sciences , Beijing , China
| | - Ting Shen
- b State Key Laboratory of Genetic Engineering & Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai , China
| | - Min Wang
- a State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing , China
| | - Bo Wen
- b State Key Laboratory of Genetic Engineering & Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai , China.,c Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University , Shanghai , China
| | - Ting Ni
- b State Key Laboratory of Genetic Engineering & Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai , China
| | - Chunsheng Han
- a State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing , China
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33
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Li C, Zhou L, He J, Fang XQ, Zhu SW, Xiong MM. Increased long noncoding RNA SNHG20 predicts poor prognosis in colorectal cancer. BMC Cancer 2016; 16:655. [PMID: 27543107 PMCID: PMC4992210 DOI: 10.1186/s12885-016-2719-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 08/11/2016] [Indexed: 02/07/2023] Open
Abstract
Background Long noncoding RNAs (lncRNAs) have been suggested to be involved in the development and progression of malignancies. However, the investigation of small nucleolar RNA host gene 20 (SNHG20) on cancer progression remains unknown. The present study aims to explore the clinical significance of SNHG20 and its potential molecular mechanism in colorectal cancer (CRC). Methods Quantitative real-time PCR (qRT-PCR) was used to measure the SNHG20 expression in a total of 107 CRC tissues and CRC cell lines. Loss of function approach was employed to explore the biological roles of SNHG20 in vitro. Its potential molecular mechanism was further verified by western blotting and qRT-PCR. Results The results suggested that SNHG20 expression was significantly upregulated in CRC tissues compared to corresponding normal tissues from 107 CRC patients. High expression of SNHG20 was remarkably associated with advanced TNM stage in patients with CRC. Multivariate analyses unraveled that SNHG20 expression was an independent prognostic factor for overall survival in CRC patients. Further functional assays revealed that knockdown of SNHG20 suppressed cell proliferation, invasion and migration, and cell cycle progression in CRC cells. Moreover, SNHG20 regulated cell growth through modulation of a series of cell cycle-associated genes. Conclusions Our findings suggest that dysregulation of SNHG20 participates in CRC progression and may serve as a potential therapeutic target in CRC patients.
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Affiliation(s)
- Cong Li
- Department of Minimally Invasive Surgery, The People's Hospital of Chizhou, Chizhou, 247000, China
| | - Li Zhou
- Department of Minimally Invasive Surgery, The People's Hospital of Chizhou, Chizhou, 247000, China
| | - Jun He
- Department of Minimally Invasive Surgery, The People's Hospital of Chizhou, Chizhou, 247000, China
| | - Xue-Qing Fang
- Department of Minimally Invasive Surgery, The People's Hospital of Chizhou, Chizhou, 247000, China
| | - Shao-Wen Zhu
- Department of Minimally Invasive Surgery, The People's Hospital of Chizhou, Chizhou, 247000, China
| | - Mao-Ming Xiong
- Department of General Surgery, First Hospital Affiliated to Anhui Medical University, Hefei, 230022, China.
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Long noncoding RNAs in B-cell development and activation. Blood 2016; 128:e10-9. [PMID: 27381906 DOI: 10.1182/blood-2015-11-680843] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 06/28/2016] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are potentially important regulators of cell differentiation and development, but little is known about their roles in B lymphocytes. Using RNA-seq and de novo transcript assembly, we identified 4516 lncRNAs expressed in 11 stages of B-cell development and activation. Most of these lncRNAs have not been previously detected, even in the closely related T-cell lineage. Comparison with lncRNAs previously described in human B cells identified 185 mouse lncRNAs that have human orthologs. Using chromatin immunoprecipitation-seq, we classified 20% of the lncRNAs as either enhancer-associated (eRNA) or promoter-associated RNAs. We identified 126 eRNAs whose expression closely correlated with the nearest coding gene, thereby indicating the likely location of numerous enhancers active in the B-cell lineage. Furthermore, using this catalog of newly discovered lncRNAs, we show that PAX5, a transcription factor required to specify the B-cell lineage, bound to and regulated the expression of 109 lncRNAs in pro-B and mature B cells and 184 lncRNAs in acute lymphoblastic leukemia.
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35
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Jiang X, Lei R, Ning Q. Circulating long noncoding RNAs as novel biomarkers of human diseases. Biomark Med 2016; 10:757-69. [PMID: 27347748 DOI: 10.2217/bmm-2016-0039] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are a kind of noncoding RNAs which are longer than ˜200 nucleotides, lacking of protein-encoding capacity and are implicated in the pathogenesis of various diseases. Recently, it was demonstrated that lncRNAs could be released into the circulation and be stable in blood. Circulating lncRNAs have been reported to have potential in distinguishing patients from healthy individuals. Therefore, the detection of circulating lncRNAs may be valuable for improving the diagnosis and prognosis of various diseases. This review summarized the current understanding of circulating lncRNAs as novel biomarkers of various human diseases, such as cancer, cardiovascular diseases, nervous system diseases and other diseases, which highlighted the significance of circulating lncRNAs as novel diagnostic and prognostic biomarkers of human diseases.
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Affiliation(s)
- Xiaoying Jiang
- Department of Biochemistry & Molecular Biology, School of Medicine, Xi'an Jiaotong University, Xi'an, 710061 Shaanxi, China
| | - Ronghui Lei
- Department of Biochemistry & Molecular Biology, School of Medicine, Xi'an Jiaotong University, Xi'an, 710061 Shaanxi, China
| | - Qilan Ning
- Department of Biochemistry & Molecular Biology, School of Medicine, Xi'an Jiaotong University, Xi'an, 710061 Shaanxi, China
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Xie Z, Li J, Wang P, Li Y, Wu X, Wang S, Su H, Deng W, Liu Z, Cen S, Ouyang Y, Wu Y, Shen H. Differential Expression Profiles of Long Noncoding RNA and mRNA of Osteogenically Differentiated Mesenchymal Stem Cells in Ankylosing Spondylitis. J Rheumatol 2016; 43:1523-31. [PMID: 27182066 DOI: 10.3899/jrheum.151181] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2016] [Indexed: 02/07/2023]
Abstract
OBJECTIVE We previously demonstrated that mesenchymal stem cells (MSC) from patients with ankylosing spondylitis (AS; ASMSC) have a greater osteogenic differentiation capacity than MSC from healthy donors (HDMSC) and that this difference underlies the pathogenesis of pathological osteogenesis in AS. Here we compared expression levels of long noncoding RNA (lncRNA) and mRNA between osteogenically differentiated ASMSC and HDMSC and explored the precise mechanism underlying abnormal osteogenic differentiation in ASMSC. METHODS HDMSC and ASMSC were induced with osteogenic differentiation medium for 10 days. Microarray analyses were then performed to identify lncRNA and mRNA differentially expressed between HDMSC and ASMSC, which were then subjected to bioinformatics analysis and confirmed by quantitative real-time PCR (qRT-PCR) assays. In addition, coding-non-coding gene co-expression (CNC) networks were constructed to examine the relationships between the lncRNA and mRNA expression patterns. RESULTS A total of 520 lncRNA and 665 mRNA were differentially expressed in osteogenically differentiated ASMSC compared with HDMSC. Bioinformatics analysis revealed 64 signaling pathways with significant differences, including transforming growth factor-β signaling. qRT-PCR assays confirmed the reliability of the microarray data. The CNC network indicated that 4 differentially expressed lncRNA, including lnc-ZNF354A-1, lnc-LIN54-1, lnc-FRG2C-3, and lnc-USP50-2 may be involved in the abnormal osteogenic differentiation of ASMSC. CONCLUSION Our study characterized the differential lncRNA and mRNA expression profiles of osteogenically differentiated ASMSC and identified 4 lncRNA that may participate in the abnormal osteogenic differentiation of ASMSC. These results provide insight into the pathogenesis of pathological osteogenesis in AS.
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Affiliation(s)
- Zhongyu Xie
- From the Department of Orthopedics, and the Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, P.R. China.Z. Xie, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; J. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; P. Wang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; X. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Wang, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Su, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; W. Deng, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Z. Liu, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Cen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Ouyang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Shen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University
| | - Jinteng Li
- From the Department of Orthopedics, and the Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, P.R. China.Z. Xie, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; J. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; P. Wang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; X. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Wang, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Su, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; W. Deng, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Z. Liu, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Cen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Ouyang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Shen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University
| | - Peng Wang
- From the Department of Orthopedics, and the Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, P.R. China.Z. Xie, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; J. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; P. Wang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; X. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Wang, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Su, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; W. Deng, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Z. Liu, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Cen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Ouyang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Shen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University
| | - Yuxi Li
- From the Department of Orthopedics, and the Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, P.R. China.Z. Xie, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; J. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; P. Wang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; X. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Wang, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Su, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; W. Deng, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Z. Liu, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Cen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Ouyang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Shen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University
| | - Xiaohua Wu
- From the Department of Orthopedics, and the Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, P.R. China.Z. Xie, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; J. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; P. Wang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; X. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Wang, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Su, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; W. Deng, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Z. Liu, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Cen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Ouyang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Shen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University
| | - Shan Wang
- From the Department of Orthopedics, and the Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, P.R. China.Z. Xie, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; J. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; P. Wang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; X. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Wang, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Su, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; W. Deng, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Z. Liu, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Cen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Ouyang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Shen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University
| | - Hongjun Su
- From the Department of Orthopedics, and the Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, P.R. China.Z. Xie, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; J. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; P. Wang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; X. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Wang, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Su, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; W. Deng, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Z. Liu, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Cen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Ouyang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Shen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University
| | - Wen Deng
- From the Department of Orthopedics, and the Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, P.R. China.Z. Xie, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; J. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; P. Wang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; X. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Wang, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Su, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; W. Deng, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Z. Liu, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Cen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Ouyang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Shen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University
| | - Zhenhua Liu
- From the Department of Orthopedics, and the Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, P.R. China.Z. Xie, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; J. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; P. Wang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; X. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Wang, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Su, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; W. Deng, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Z. Liu, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Cen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Ouyang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Shen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University
| | - Shuizhong Cen
- From the Department of Orthopedics, and the Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, P.R. China.Z. Xie, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; J. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; P. Wang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; X. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Wang, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Su, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; W. Deng, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Z. Liu, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Cen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Ouyang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Shen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University
| | - Yi Ouyang
- From the Department of Orthopedics, and the Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, P.R. China.Z. Xie, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; J. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; P. Wang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; X. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Wang, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Su, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; W. Deng, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Z. Liu, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Cen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Ouyang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Shen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University
| | - Yanfeng Wu
- From the Department of Orthopedics, and the Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, P.R. China.Z. Xie, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; J. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; P. Wang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; X. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Wang, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Su, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; W. Deng, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Z. Liu, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Cen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Ouyang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Shen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University
| | - Huiyong Shen
- From the Department of Orthopedics, and the Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, P.R. China.Z. Xie, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; J. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; P. Wang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Li, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; X. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Wang, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Su, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; W. Deng, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Z. Liu, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; S. Cen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Ouyang, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Y. Wu, MD, Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; H. Shen, MD, Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University.
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Abstract
The role of genome architecture in transcription regulation has become the focus of an increasing number of studies over the past decade. Chromatin organization can have a significant impact on gene expression by promoting or restricting the physical proximity between regulatory DNA elements. Given that any change in chromatin state has the potential to alter DNA folding and the proximity between control elements, the spatial organization of chromatin is inherently linked to its molecular composition. In this review, we explore how modulators of chromatin state and organization might keep gene expression in check. We discuss recent findings and present some of the less well-studied aspects of spatial genome organization such as chromatin dynamics and regulation by non-coding RNAs.
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Davie JR, Xu W, Delcuve GP. Histone H3K4 trimethylation: dynamic interplay with pre-mRNA splicing. Biochem Cell Biol 2016; 94:1-11. [DOI: 10.1139/bcb-2015-0065] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Histone H3 lysine 4 trimethylation (H3K4me3) is often stated as a mark of transcriptionally active promoters. However, closer study of the positioning of H3K4me3 shows the mark locating primarily after the first exon at the 5′ splice site and overlapping with a CpG island in mammalian cells. There are several enzyme complexes that are involved in the placement of the H3K4me3 mark, including multiple protein complexes containing SETD1A, SETD1B, and MLL1 enzymes (writers). CXXC1, which is associated with SETD1A and SETD1B, target these enzymes to unmethylated CpG islands. Lysine demethylases (KDM5 family members, erasers) demethylate H3K4me3. The H3K4me3 mark is recognized by several proteins (readers), including lysine acetyltransferase complexes, chromatin remodelers, and RNA bound proteins involved in pre-mRNA splicing. Interestingly, attenuation of H3K4me3 impacts pre-mRNA splicing, and inhibition of pre-mRNA splicing attenuates H3K4me3.
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Affiliation(s)
- James R. Davie
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Wayne Xu
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Genevieve P. Delcuve
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
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Mellor J, Woloszczuk R, Howe FS. The Interleaved Genome. Trends Genet 2016; 32:57-71. [DOI: 10.1016/j.tig.2015.10.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 09/29/2015] [Accepted: 10/23/2015] [Indexed: 12/25/2022]
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Abstract
All living organisms sense and respond to harmful changes in their intracellular and extracellular environment through complex signaling pathways that lead to changes in gene expression and cellular function in order to maintain homeostasis. Long non-coding RNAs (lncRNAs), a large and heterogeneous group of functional RNAs, play important roles in cellular response to stressful conditions. lncRNAs constitute a significant fraction of the genes differentially expressed in response to diverse stressful stimuli and, once induced, contribute to the regulation of downstream cellular processes, including feedback regulation of key stress response proteins. While many lncRNAs seem to be induced in response to a specific stress, there is significant overlap between lncRNAs induced in response to different stressful stimuli. In addition to stress-induced RNAs, several constitutively expressed lncRNAs also exert a strong regulatory impact on the stress response. Although our understanding of the contribution of lncRNAs to the cellular stress response is still highly rudimentary, the existing data point to the presence of a complex network of lncRNAs, miRNAs, and proteins in regulation of the cellular response to stress.
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Affiliation(s)
- Saba Valadkhan
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
| | - Alberto Valencia-Hipólito
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
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41
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Abstract
Long non-coding RNAs (lncRNAs) are a class of RNA molecules that are changing how researchers view eukaryotic gene regulation. Once considered to be non-functional products of low-level aberrant transcription from non-coding regions of the genome, lncRNAs are now viewed as important epigenetic regulators and several lncRNAs have now been demonstrated to be critical players in the development and/or maintenance of cancer. Similarly, the emerging variety of interactions between lncRNAs and MYC, a well-known oncogenic transcription factor linked to most types of cancer, have caught the attention of many biomedical researchers. Investigations exploring the dynamic interactions between lncRNAs and MYC, referred to as the lncRNA-MYC network, have proven to be especially complex. Genome-wide studies have shown that MYC transcriptionally regulates many lncRNA genes. Conversely, recent reports identified lncRNAs that regulate MYC expression both at the transcriptional and post-transcriptional levels. These findings are of particular interest because they suggest roles of lncRNAs as regulators of MYC oncogenic functions and the possibility that targeting lncRNAs could represent a novel avenue to cancer treatment. Here, we briefly review the current understanding of how lncRNAs regulate chromatin structure and gene transcription, and then focus on the new developments in the emerging field exploring the lncRNA-MYC network in cancer.
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Affiliation(s)
- Michael J. Hamilton
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Matthew D. Young
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Silvia Sauer
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Ernest Martinez
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
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Long Noncoding RNAs in Digestive System Malignancies: A Novel Class of Cancer Biomarkers and Therapeutic Targets? Gastroenterol Res Pract 2015; 2015:319861. [PMID: 26064090 PMCID: PMC4429197 DOI: 10.1155/2015/319861] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 04/20/2015] [Indexed: 01/17/2023] Open
Abstract
High throughput methodologies have revealed the existence of an unexpectedly large number of long noncoding RNAs (lncRNAs). The unconventional role of lncRNAs in gene expression regulation and their broad implication in oncogenic and tumor suppressive pathways have introduced lncRNAs as novel biological tumor markers. The most prominent example of lncRNAs application in routine clinical practice is PCA3, a FDA-approved biomarker for prostate cancer. Regarding digestive system malignancies, the oncogenic HOTAIR is one of the most widely studied lncRNAs in the preclinical level and has already been identified as a potent prognostic marker for major malignancies of the gastrointestinal tract. Here, we provide an overview of recent findings regarding the emerging role of lncRNAs not only as key regulators of cancer initiation and progression in colon, stomach, pancreatic, liver, and esophageal cancers, but also as reliable tumor markers and therapeutic tools. lncRNAs can be easily, rapidly, and cost-effectively determined in tissues, serum, and gastric juice, making them highly versatile analytes. Taking also into consideration the largely unmet clinical need for early diagnosis and more accurate prognostic/predictive markers for gastrointestinal cancer patients, we comment upon the perspectives of lncRNAs as efficient molecular tools that could aid in the clinical management.
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Muñoz-Cánoves P, Di Croce L. Special issue: epigenetics: introduction. FEBS J 2015; 282:1569-70. [PMID: 25828932 DOI: 10.1111/febs.13281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 03/25/2015] [Indexed: 12/17/2022]
Abstract
Epigenetic studies focus on changes in genetic information that rely on histone modification, which complements information encoded by the DNA sequence. Research in this rapidly expanding field has greatly contributed to a better understanding of processes such as gene regulation, chromatin structure, and cell differentiation and disease. The most recent advances in this area are reviewed in the collection of papers included in this Special Issue.
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Affiliation(s)
- Pura Muñoz-Cánoves
- Department of Experimental and Health Sciences, Pompeu Fabra University, CIBER on Neurodegenerative Diseases, Barcelona, Spain; Institucio Catalana de Recerca i Estudis Avancçats, Barcelona, Spain.
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