1
|
Xiao H, Ma C, Peng R, Xie M. Insights into the role of non-coding RNAs in the development of insecticide resistance in insects. Front Genet 2024; 15:1429411. [PMID: 39036703 PMCID: PMC11257933 DOI: 10.3389/fgene.2024.1429411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 06/10/2024] [Indexed: 07/23/2024] Open
Abstract
Pest control heavily relies on chemical pesticides has been going on for decades. However, the indiscriminate use of chemical pesticides often results in the development of resistance in pests. Almost all pests have developed some degree of resistance to pesticides. Research showed that the mechanisms of insecticide resistance in insects encompass metabolic resistance, behavioral resistance, penetration resistance and target-site resistance. Research on the these mechanisms has been mainly focused on the cis-regulatory or trans-regulatory for the insecticide resistance-related genes, with less attention paid to non-coding RNAs (ncRNAs), such as microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). There has been increased studies focus on understanding how these ncRNAs are involved in post-transcriptional regulation of insecticide resistance-related genes. Besides, the formatted endogenous RNA (ceRNA) regulatory networks (lncRNA/circRNA-miRNA-mRNA) has been identified as a key player in governing insect resistance formation. This review delves into the functions and underlying mechanisms of miRNA, lncRNA, and circRNA in regulating insect resistance. ncRNAs orchestrate insect resistance by modulating the expression of detoxification enzyme genes, insecticide target genes, as well as receptor genes, effectively regulating both target-site, metabolic and penetration resistance in insects. It also explores the regulatory mechanisms of ceRNA networks in the development of resistance. By enhancing our understanding of the mechanisms of ncRNAs in insecticide resistance, it will not only provide valuable insights into the new mechanisms of insecticide resistance but also help to enrich new directions in ncRNAs gene regulation research.
Collapse
Affiliation(s)
- Huamei Xiao
- Key Laboratory of Crop Growth and Development Regulation of Jiangxi Province, College of Life Sciences and Resource Environment, Yichun University, Yichun, China
| | | | | | | |
Collapse
|
2
|
Hussain MS, Agrawal M, Shaikh NK, Saraswat N, Bahl G, Maqbool Bhat M, Khurana N, Bisht AS, Tufail M, Kumar R. Beyond the Genome: Deciphering the Role of MALAT1 in Breast Cancer Progression. Curr Genomics 2024; 25:343-357. [PMID: 39323624 PMCID: PMC11420562 DOI: 10.2174/0113892029305656240503045154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 09/27/2024] Open
Abstract
The MALAT1, a huge non-coding RNA, recently came to light as a multifaceted regulator in the intricate landscape of breast cancer (BC) progression. This review explores the multifaceted functions and molecular interactions of MALAT1, shedding light on its profound implications for understanding BC pathogenesis and advancing therapeutic strategies. The article commences by acknowledging the global impact of BC and the pressing need for insights into its molecular underpinnings. It is stated that the core lncRNA MALAT1 has a range of roles in both healthy and diseased cell functions. The core of this review unravels MALAT1's multifaceted role in BC progression, elucidating its participation in critical processes like resistance, invasion, relocation, and proliferating cells to therapy. It explores the intricate mechanisms through which MALAT1 modulates gene expression, interacts with other molecules, and influences signalling pathways. Furthermore, the paper emphasizes MALAT1's clinical significance as a possible prognostic and diagnostic biomarker. Concluding on a forward-looking note, the review highlights the broader implications of MALAT1 in BC biology, such as its connections to therapy resistance and metastasis. It underscores the significance of deeper investigations into these intricate molecular interactions to pave the way for precision medicine approaches. This review highlights the pivotal role of MALAT1 in BC progression by deciphering its multifaceted functions beyond the genome, offering profound insights into its implications for disease understanding and the potential for targeted therapeutic interventions.
Collapse
Affiliation(s)
- Md Sadique Hussain
- School of Pharmaceutical Sciences, Jaipur National University, Jaipur, Rajasthan (302017), India
| | - Mohit Agrawal
- Department of Pharmacology, School of Medical & Allied Sciences, K.R. Mangalam University, Gurugram 122103, India
| | - Nusratbanu K Shaikh
- Department of Quality Assurance, Smt. N. M. Padalia Pharmacy College, Ahmedabad, 382210, Gujarat, India
| | - Nikita Saraswat
- School of Pharmaceutical Sciences, Jaipur National University, Jaipur, Rajasthan (302017), India
| | - Gurusha Bahl
- School of Pharmaceutical Sciences, Jaipur National University, Jaipur, Rajasthan (302017), India
| | - Mudasir Maqbool Bhat
- Department of Pharmaceutical Sciences, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Navneet Khurana
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Ajay Singh Bisht
- School of Pharmaceutical Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun, Uttarakhand (248001), India
| | - Muhammad Tufail
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital, Central South University, Changsha, China
| | - Rajesh Kumar
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| |
Collapse
|
3
|
Geens B, Goossens S, Li J, Van de Peer Y, Vanden Broeck J. Untangling the gordian knot: The intertwining interactions between developmental hormone signaling and epigenetic mechanisms in insects. Mol Cell Endocrinol 2024; 585:112178. [PMID: 38342134 DOI: 10.1016/j.mce.2024.112178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Hormones control developmental and physiological processes, often by regulating the expression of multiple genes simultaneously or sequentially. Crosstalk between hormones and epigenetics is pivotal to dynamically coordinate this process. Hormonal signals can guide the addition and removal of epigenetic marks, steering gene expression. Conversely, DNA methylation, histone modifications and non-coding RNAs can modulate regional chromatin structure and accessibility and regulate the expression of numerous (hormone-related) genes. Here, we provide a review of the interplay between the classical insect hormones, ecdysteroids and juvenile hormones, and epigenetics. We summarize the mode-of-action and roles of these hormones in post-embryonic development, and provide a general overview of epigenetic mechanisms. We then highlight recent advances on the interactions between these hormonal pathways and epigenetics, and their involvement in development. Furthermore, we give an overview of several 'omics techniques employed in the field. Finally, we discuss which questions remain unanswered and possible avenues for future research.
Collapse
Affiliation(s)
- Bart Geens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Stijn Goossens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Jia Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| |
Collapse
|
4
|
Zhang S, Wang R, Zhu X, Zhang L, Liu X, Sun L. Characteristics and expression of lncRNA and transposable elements in Drosophila aneuploidy. iScience 2023; 26:108494. [PMID: 38125016 PMCID: PMC10730892 DOI: 10.1016/j.isci.2023.108494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/28/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Aneuploidy can globally affect the expression of the whole genome, which is detrimental to organisms. Dosage-sensitive regulators usually have multiple intermolecular interactions, and changes in their stoichiometry are responsible for the dysregulation of the regulatory network. Currently, studies on noncoding genes in aneuploidy are relatively rare. We studied the characteristics and expression profiles of long noncoding RNAs (lncRNAs) and transposable elements (TEs) in aneuploid Drosophila. It is found that lncRNAs and TEs are affected by genomic imbalance and appear to be more sensitive to an inverse dosage effect than mRNAs. Several dosage-sensitive lncRNAs and TEs were detected for their expression patterns during embryogenesis, and their biological functions in the ovary and testes were investigated using tissue-specific RNAi. This study advances our understanding of the noncoding sequences in imbalanced genomes and provides a novel perspective for the study of aneuploidy-related human diseases such as cancer.
Collapse
Affiliation(s)
- Shuai Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ruixue Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xilin Zhu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ludan Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xinyu Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China
| |
Collapse
|
5
|
Qian J, Jiang M, Ding Z, Gu D, Bai H, Cai M, Yao D. Role of Long Non-coding RNA in Nerve Regeneration. Int J Neurosci 2023:1-14. [PMID: 37937941 DOI: 10.1080/00207454.2023.2280446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
Nerve injury can be caused by a variety of factors. It often takes a long time to repair a nerve injury and severe nerve injury is even difficult to heal. Therefore, increasing attention has focused on nerve injury and repair. Long non-coding RNA (lncRNA) is a newly discovered non-coding RNA with a wide range of biological activities. Numerous studies have shown that a variety of lncRNAs undergo changes in expression after nerve injury, indicating that lncRNAs may be involved in various biological processes of nerve repair and regeneration. Herein, we summarize the biological roles of lncRNAs in neurons, glial cells and other cells during nerve injury and regeneration, which will help lncRNAs to be better applied in nerve injury and regeneration in the future.
Collapse
Affiliation(s)
- Jiaxi Qian
- School of Life Sciences, Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, P.R. China
| | - Maorong Jiang
- School of Life Sciences, Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, P.R. China
| | - Zihan Ding
- School of Life Sciences, Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, P.R. China
| | - Dandan Gu
- School of Life Sciences, Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, P.R. China
| | - Huiyuan Bai
- School of Life Sciences, Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, P.R. China
| | - Min Cai
- Medical School of Nantong University, Nantong, P.R. China
| | - Dengbing Yao
- School of Life Sciences, Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, P.R. China
| |
Collapse
|
6
|
Fan X, Gao X, Zang H, Guo S, Jing X, Zhang Y, Liu X, Zou P, Chen M, Huang Z, Chen D, Guo R. Diverse Regulatory Manners and Potential Roles of lncRNAs in the Developmental Process of Asian Honey Bee ( Apis cerana) Larval Guts. Int J Mol Sci 2023; 24:15399. [PMID: 37895079 PMCID: PMC10607868 DOI: 10.3390/ijms242015399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are crucial modulators in a variety of biological processes, such as gene expression, development, and immune defense. However, little is known about the function of lncRNAs in the development of Asian honey bee (Apis cerana) larval guts. Here, on the basis of our previously obtained deep-sequencing data from the 4-, 5-, and 6-day-old larval guts of A. cerana workers (Ac4, Ac5, and Ac6 groups), an in-depth transcriptome-wide investigation was conducted to decipher the expression pattern, regulatory manners, and potential roles of lncRNAs during the developmental process of A. cerana worker larval guts, followed by the verification of the relative expression of differentially expressed lncRNAs (DElncRNAs) and the targeting relationships within a competing endogenous RNA (ceRNA) axis. In the Ac4 vs. Ac5 and Ac5 vs. Ac6 comparison groups, 527 and 498 DElncRNAs were identified, respectively, which is suggestive of the dynamic expression of lncRNAs during the developmental process of larval guts. A cis-acting analysis showed that 330 and 393 neighboring genes of the aforementioned DElncRNAs were respectively involved in 29 and 32 functional terms, such as cellular processes and metabolic processes; these neighboring genes were also respectively engaged in 246 and 246 pathways such as the Hedgehog signaling pathway and the Wnt signaling pathway. Additionally, it was found that 79 and 76 DElncRNAs as potential antisense lncRNAs may, respectively, interact with 72 and 60 sense-strand mRNAs. An investigation of competing endogenous RNA (ceRNA) networks suggested that 75 (155) DElncRNAs in the Ac4 vs. Ac5 (Ac5 vs. Ac6) comparison group could target 7 (5) DEmiRNAs and further bind to 334 (248) DEmRNAs, which can be annotated to 33 (29) functional terms and 186 (210) pathways, including 12 (16) cellular- and humoral-immune pathways (lysosome pathway, necroptosis, MAPK signaling pathway, etc.) and 11 (10) development-associated signaling pathways (Wnt, Hippo, AMPK, etc.). The RT-qPCR detection of five randomly selected DElncRNAs confirmed the reliability of the used sequencing data. Moreover, the results of a dual-luciferase reporter assay were indicative of the binding relationship between MSTRG.11294.1 and miR-6001-y and between miR-6001-y and ncbi_107992440. These results demonstrate that DElncRNAs are likely to modulate the developmental process of larval guts via the regulation of the source genes' transcription, interaction with mRNAs, and ceRNA networks. Our findings not only yield new insights into the developmental mechanism underlying A. cerana larval guts, but also provide a candidate ceRNA axis for further functional dissection.
Collapse
Affiliation(s)
- Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Xuze Gao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - He Zang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Sijia Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Xin Jing
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Yiqiong Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Xiaoyu Liu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Peiyuan Zou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Mengjun Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Zhijian Huang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| |
Collapse
|
7
|
Meng LW, Yuan GR, Chen ML, Zheng LS, Dou W, Peng Y, Bai WJ, Li ZY, Vontas J, Wang JJ. Cuticular competing endogenous RNAs regulate insecticide penetration and resistance in a major agricultural pest. BMC Biol 2023; 21:187. [PMID: 37667263 PMCID: PMC10478477 DOI: 10.1186/s12915-023-01694-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND The continuously developing pesticide resistance is a great threat to agriculture and human health. Understanding the mechanisms of insecticide resistance is a key step in dealing with the phenomenon. Insect cuticle is recently documented to delay xenobiotic penetration which breaks the previous stereotype that cuticle is useless in insecticide resistance, while the underlying mechanism remains scarce. RESULTS Here, we find the integument contributes over 40.0% to insecticide resistance via different insecticide delivery strategies in oriental fruit fly. A negative relationship exists between cuticle thickening and insecticide penetration in resistant/susceptible, also in field strains of oriental fruit fly which is a reason for integument-mediated resistance. Our investigations uncover a regulator of insecticide penetration that miR-994 mimic treatment causes cuticle thinning and increases susceptibility to malathion, whereas miR-994 inhibitor results in opposite phenotypes. The target of miR-994 is a most abundant cuticle protein (CPCFC) in resistant/susceptible integument expression profile, which possesses capability of chitin-binding and influences the cuticle thickness-mediated insecticide penetration. Our analyses find an upstream transcriptional regulatory signal of miR-994 cascade, long noncoding RNA (lnc19419), that indirectly upregulates CPCFC in cuticle of the resistant strain by sponging miR-994. Thus, we elucidate the mechanism of cuticular competing endogenous RNAs for regulating insecticide penetration and demonstrate it also exists in field strain of oriental fruit fly. CONCLUSIONS We unveil a regulatory axis of lnc19419 ~ miR-994 ~ CPCFC on the cuticle thickness that leads to insecticide penetration resistance. These findings indicate that competing endogenous RNAs regulate insecticide resistance by modulating the cuticle thickness and provide insight into the resistance mechanism in insects.
Collapse
Affiliation(s)
- Li-Wei Meng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guo-Rui Yuan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Meng-Ling Chen
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China
| | - Li-Sha Zheng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China
| | - Wei Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yu Peng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China
| | - Wen-Jie Bai
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China
| | - Zhen-Yu Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China
| | - John Vontas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Greece
- Pesticide Science Laboratory, Department of Crop Science, Agricultural University of Athens, Athens, 11855, Greece
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China.
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
8
|
MacPherson RA, Shankar V, Anholt RRH, Mackay TFC. Genetic and genomic analyses of Drosophila melanogaster models of chromatin modification disorders. Genetics 2023; 224:iyad061. [PMID: 37036413 PMCID: PMC10411607 DOI: 10.1093/genetics/iyad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/10/2022] [Accepted: 03/30/2023] [Indexed: 04/11/2023] Open
Abstract
Switch/sucrose nonfermentable (SWI/SNF)-related intellectual disability disorders (SSRIDDs) and Cornelia de Lange syndrome are rare syndromic neurodevelopmental disorders with overlapping clinical phenotypes. SSRIDDs are associated with the BAF (Brahma-Related Gene-1 associated factor) complex, whereas CdLS is a disorder of chromatin modification associated with the cohesin complex. Here, we used RNA interference in Drosophila melanogaster to reduce the expression of six genes (brm, osa, Snr1, SMC1, SMC3, vtd) orthologous to human genes associated with SSRIDDs and CdLS. These fly models exhibit changes in sleep, activity, startle behavior (a proxy for sensorimotor integration), and brain morphology. Whole genome RNA sequencing identified 9,657 differentially expressed genes (FDR < 0.05), 156 of which are differentially expressed in both sexes in SSRIDD- and CdLS-specific analyses, including Bap60, which is orthologous to SMARCD1, an SSRIDD-associated BAF component. k-means clustering reveals genes co-regulated within and across SSRIDD and CdLS fly models. RNAi-mediated reduction of expression of six genes co-regulated with focal genes brm, osa, and/or Snr1 recapitulated changes in the behavior of the focal genes. Based on the assumption that fundamental biological processes are evolutionarily conserved, Drosophila models can be used to understand underlying molecular effects of variants in chromatin-modification pathways and may aid in the discovery of drugs that ameliorate deleterious phenotypic effects.
Collapse
Affiliation(s)
- Rebecca A MacPherson
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Vijay Shankar
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Robert R H Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Trudy F C Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| |
Collapse
|
9
|
Delbare SYN, Jain AM, Clark AG, Wolfner MF. Transcriptional programs are activated and microRNAs are repressed within minutes after mating in the Drosophila melanogaster female reproductive tract. BMC Genomics 2023; 24:356. [PMID: 37370014 PMCID: PMC10294459 DOI: 10.1186/s12864-023-09397-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND The female reproductive tract is exposed directly to the male's ejaculate, making it a hotspot for mating-induced responses. In Drosophila melanogaster, changes in the reproductive tract are essential to optimize fertility. Many changes occur within minutes after mating, but such early timepoints are absent from published RNA-seq studies. We measured transcript abundances using RNA-seq and microRNA-seq of reproductive tracts of unmated and mated females collected at 10-15 min post-mating. We further investigated whether early transcriptome changes in the female reproductive tract are influenced by inhibiting BMPs in secondary cells, a condition that depletes exosomes from the male's ejaculate. RESULTS We identified 327 differentially expressed genes. These were mostly upregulated post-mating and have roles in tissue morphogenesis, wound healing, and metabolism. Differentially abundant microRNAs were mostly downregulated post-mating. We identified 130 predicted targets of these microRNAs among the differentially expressed genes. We saw no detectable effect of BMP inhibition in secondary cells on transcript levels in the female reproductive tract. CONCLUSIONS Our results indicate that mating induces early changes in the female reproductive tract primarily through upregulation of target genes, rather than repression. The upregulation of certain target genes might be mediated by the mating-induced downregulation of microRNAs. Male-derived exosomes and other BMP-dependent products were not uniquely essential for this process. Differentially expressed genes and microRNAs provide candidates that can be further examined for their participation in the earliest alterations of the reproductive tract microenvironment.
Collapse
Affiliation(s)
- Sofie Y N Delbare
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA.
| | - Asha M Jain
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew G Clark
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Mariana F Wolfner
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA
| |
Collapse
|
10
|
MacPherson RA, Shankar V, Anholt RRH, Mackay TFC. Genetic and Genomic Analyses of Drosophila melanogaster Models of Chromatin Modification Disorders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.534923. [PMID: 37034595 PMCID: PMC10081333 DOI: 10.1101/2023.03.30.534923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Switch/Sucrose Non-Fermentable (SWI/SNF)-related intellectual disability disorders (SSRIDDs) and Cornelia de Lange syndrome are rare syndromic neurodevelopmental disorders with overlapping clinical phenotypes. SSRIDDs are associated with the BAF (Brahma-Related Gene-1 Associated Factor) complex, whereas CdLS is a disorder of chromatin modification associated with the cohesin complex. Here, we used RNA interference in Drosophila melanogaster to reduce expression of six genes (brm, osa, Snr1, SMC1, SMC3, vtd) orthologous to human genes associated with SSRIDDs and CdLS. These fly models exhibit changes in sleep, activity, startle behavior (a proxy for sensorimotor integration) and brain morphology. Whole genome RNA sequencing identified 9,657 differentially expressed genes (FDR < 0.05), 156 of which are differentially expressed in both sexes in SSRIDD- and CdLS-specific analyses, including Bap60, which is orthologous to SMARCD1, a SSRIDD-associated BAF component, k-means clustering reveals genes co-regulated within and across SSRIDD and CdLS fly models. RNAi-mediated reduction of expression of six genes co-regulated with focal genes brm, osa, and/or Snr1 recapitulated changes in behavior of the focal genes. Based on the assumption that fundamental biological processes are evolutionarily conserved, Drosophila models can be used to understand underlying molecular effects of variants in chromatin-modification pathways and may aid in discovery of drugs that ameliorate deleterious phenotypic effects.
Collapse
Affiliation(s)
- Rebecca A. MacPherson
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Vijay Shankar
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Robert R. H. Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Trudy F. C. Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| |
Collapse
|
11
|
Recent Advances and Future Potential of Long Non-Coding RNAs in Insects. Int J Mol Sci 2023; 24:ijms24032605. [PMID: 36768922 PMCID: PMC9917219 DOI: 10.3390/ijms24032605] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
Over the last decade, long non-coding RNAs (lncRNAs) have witnessed a steep rise in interest amongst the scientific community. Because of their functional significance in several biological processes, i.e., alternative splicing, epigenetics, cell cycle, dosage compensation, and gene expression regulation, lncRNAs have transformed our understanding of RNA's regulatory potential. However, most knowledge concerning lncRNAs comes from mammals, and our understanding of the potential role of lncRNAs amongst insects remains unclear. Technological advances such as RNA-seq have enabled entomologists to profile several hundred lncRNAs in insect species, although few are functionally studied. This article will review experimentally validated lncRNAs from different insects and the lncRNAs identified via bioinformatic tools. Lastly, we will discuss the existing research challenges and the future of lncRNAs in insects.
Collapse
|
12
|
Noncoding RNA Regulation of Hormonal and Metabolic Systems in the Fruit Fly Drosophila. Metabolites 2023; 13:metabo13020152. [PMID: 36837772 PMCID: PMC9967906 DOI: 10.3390/metabo13020152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023] Open
Abstract
The importance of RNAs is commonly recognised thanks to protein-coding RNAs, whereas non-coding RNAs (ncRNAs) were conventionally regarded as 'junk'. In the last decade, ncRNAs' significance and roles are becoming noticeable in various biological activities, including those in hormonal and metabolic regulation. Among the ncRNAs: microRNA (miRNA) is a small RNA transcript with ~20 nucleotides in length; long non-coding RNA (lncRNA) is an RNA transcript with >200 nucleotides; and circular RNA (circRNA) is derived from back-splicing of pre-mRNA. These ncRNAs can regulate gene expression levels at epigenetic, transcriptional, and post-transcriptional levels through various mechanisms in insects. A better understanding of these crucial regulators is essential to both basic and applied entomology. In this review, we intend to summarise and discuss the current understanding and knowledge of miRNA, lncRNA, and circRNA in the best-studied insect model, the fruit fly Drosophila.
Collapse
|
13
|
Fedorova S, Dorogova NV, Karagodin DA, Oshchepkov DY, Brusentsov II, Klimova NV, Baricheva EM. The complex role of transcription factor GAGA in germline death during Drosophila spermatogenesis: transcriptomic and bioinformatic analyses. PeerJ 2023; 11:e14063. [PMID: 36643636 PMCID: PMC9835689 DOI: 10.7717/peerj.14063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 08/26/2022] [Indexed: 01/11/2023] Open
Abstract
The GAGA protein (also known as GAF) is a transcription factor encoded by the Trl gene in D. melanogaster. GAGA is involved in the regulation of transcription of many genes at all stages of fly development and life. Recently, we investigated the participation of GAGA in spermatogenesis and discovered that Trl mutants experience massive degradation of germline cells in the testes. Trl underexpression induces autophagic death of spermatocytes, thereby leading to reduced testis size. Here, we aimed to determine the role of the transcription factor GAGA in the regulation of ectopic germline cell death. We investigated how Trl underexpression affects gene expression in the testes. We identified 15,993 genes in three biological replicates of our RNA-seq analysis and compared transcript levels between hypomorphic Trl R85/Trl 362 and Oregon testes. A total of 2,437 differentially expressed genes were found, including 1,686 upregulated and 751 downregulated genes. At the transcriptional level, we detected the development of cellular stress in the Trl-mutant testes: downregulation of the genes normally expressed in the testes (indicating slowed or abrogated spermatocyte differentiation) and increased expression of metabolic and proteolysis-related genes, including stress response long noncoding RNAs. Nonetheless, in the Flybase Gene Ontology lists of genes related to cell death, autophagy, or stress, there was no enrichment with GAGA-binding sites. Furthermore, we did not identify any specific GAGA-dependent cell death pathway that could regulate spermatocyte death. Thus, our data suggest that GAGA deficiency in male germline cells leads to an imbalance of metabolic processes, impaired mitochondrial function, and cell death due to cellular stress.
Collapse
Affiliation(s)
- Svetlana Fedorova
- Department of Cell Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
| | - Natalya V. Dorogova
- Department of Cell Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
| | - Dmitriy A. Karagodin
- Department of Cell Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
| | - Dmitry Yu Oshchepkov
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
| | - Ilya I. Brusentsov
- Department of Cell Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
| | - Natalya V. Klimova
- Department of Molecular Genetics, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
| | - Elina M. Baricheva
- Department of Cell Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
| |
Collapse
|
14
|
Huang S, Jing D, Xu L, Luo G, Hu Y, Wu T, Hu Y, Li F, He K, Qin W, Sun Y, Liu H. Genome-wide identification and functional analysis of long non-coding RNAs in Chilo suppressalis reveal their potential roles in chlorantraniliprole resistance. Front Physiol 2023; 13:1091232. [PMID: 36699669 PMCID: PMC9868556 DOI: 10.3389/fphys.2022.1091232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Long non-coding RNAs, referred to as lncRNAs, perform essential functions in some biological processes, including reproduction, metamorphosis, and other critical life functions. Yet, lncRNAs are poorly understood in pesticide resistance, and no reports to date have characterized which lncRNAs are associated with chlorantraniliprole resistance in Chilo suppressalis. Here, RNA-seq was performed on two strains of C. suppressalis exposed to chlorantraniliprole: one is a susceptible strain (S), and the other is a resistant strain (R). In total, 3,470 lncRNAs were identified from 40,573 merged transcripts in six libraries, including 1,879 lincRNAs, 245 intronic lncRNAs, 853 sense lncRNAs, and 493 antisense lncRNAs. Moreover, differential expression analysis revealed 297 and 335 lncRNAs upregulated in S and R strains, respectively. Differentially expressed (DE) lncRNAs are usually assumed to be involved in the chlorantraniliprole resistance in C. suppressalis. As potential targets, adjacent protein-coding genes (within <1000 kb range upstream or downstream of DE lncRNAs), especially detoxification enzyme genes (cytochrome P450s, carboxyl/cholinesterases/esterases, and ATP-binding cassette transporter), were analyzed. Furthermore, the strand-specific RT-PCR was conducted to confirm the transcript orientation of randomly selected 20 DE lincRNAs, and qRT-PCR was carried out to verify the expression status of 8 out of them. MSTRG.25315.3, MSTRG.25315.6, and MSTRG.7482.1 were upregulated in the R strain. Lastly, RNA interference and bioassay analyses indicated overexpressed lincRNA MSTRG.7482.1 was involved in chlorantraniliprole resistance. In conclusion, we represent, for the first time, the genome-wide identification of chlorantraniliprole-resistance-related lncRNAs in C. suppressalis. It elaborates the views underlying the mechanism conferring chlorantraniliprole resistance in lncRNAs.
Collapse
Affiliation(s)
- Shuijin Huang
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Dong Jing
- Institute of Insect Sciences/Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lu Xu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Guanghua Luo
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Yanyue Hu
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Ting Wu
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Yao Hu
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang City, China
| | - Fei Li
- Institute of Insect Sciences/Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Kang He
- Institute of Insect Sciences/Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wenjing Qin
- Institute of Soil Fertilizer and Environmental Resource, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Yang Sun
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, China,*Correspondence: Yang Sun, ; Hui Liu,
| | - Hui Liu
- Institute of Red Soil and Germplasm Resources in Jiangxi, Nanchang, China,*Correspondence: Yang Sun, ; Hui Liu,
| |
Collapse
|
15
|
Singh AK. Hsrω and Other lncRNAs in Neuronal Functions and Disorders in Drosophila. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010017. [PMID: 36675966 PMCID: PMC9865238 DOI: 10.3390/life13010017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/27/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Long noncoding RNAs (lncRNAs) have a crucial role in epigenetic, transcriptional and posttranscriptional regulation of gene expression. Many of these regulatory lncRNAs, such as MALAT1, NEAT1, HOTAIR, etc., are associated with different neurodegenerative diseases in humans. The lncRNAs produced by the hsrω gene are known to modulate neurotoxicity in polyQ and amyotrophic lateral sclerosis disease models of Drosophila. Elevated expression of hsrω lncRNAs exaggerates, while their genetic depletion through hsrω-RNAi or in an hsrω-null mutant background suppresses, the disease pathogenicity. This review discusses the possible mechanistic details and implications of the functions of hsrω lncRNAs in the modulation of neurodegenerative diseases.
Collapse
Affiliation(s)
- Anand Kumar Singh
- Interdisciplinary School of Life Sciences, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| |
Collapse
|
16
|
Zafar J, Huang J, Xu X, Jin F. Analysis of Long Non-Coding RNA-Mediated Regulatory Networks of Plutella xylostella in Response to Metarhizium anisopliae Infection. INSECTS 2022; 13:916. [PMID: 36292864 PMCID: PMC9604237 DOI: 10.3390/insects13100916] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) represent a diverse class of RNAs that are structurally similar to messenger RNAs (mRNAs) but do not encode proteins. Growing evidence suggests that in response to biotic and abiotic stresses, the lncRNAs play crucial regulatory roles in plants and animals. However, the potential role of lncRNAs during fungal infection has yet to be characterized in Plutella xylostella, a devastating pest of cruciferous crops. In the current study, we performed a strand-specific RNA sequencing of Metarhizium anisopliae-infected (Px36hT, Px72hT) and uninfected (Px36hCK, Px72hCK) P. xylostella fat body tissues. Comprehensive bioinformatic analysis revealed a total of 5665 and 4941 lncRNAs at 36 and 72-h post-infection (hpi), including 563 (Px36hT), 532 (Px72hT) known and 5102 (Px36hT), 4409 (Px72hT) novel lncRNA transcripts. These lncRNAs shared structural similarities with their counterparts in other species, including shorter exon and intron length, fewer exon numbers, and a lower expression profile than mRNAs. LncRNAs regulate the expression of neighboring protein-coding genes by acting in a cis and trans manner. Functional annotation and pathway analysis of cis-acting lncRNAs revealed their role in several immune-related genes, including Toll, serpin, transferrin, βGRP etc. Furthermore, we identified multiple lncRNAs acting as microRNA (miRNA) precursors. These miRNAs can potentially regulate the expression of mRNAs involved in immunity and development, suggesting a crucial lncRNA-miRNA-mRNA complex. Our findings will provide a genetic resource for future functional studies of lncRNAs involved in P. xylostella immune responses to M. anisopliae infection and shed light on understanding insect host-pathogen interactions.
Collapse
Affiliation(s)
| | | | - Xiaoxia Xu
- Correspondence: (X.X.); (F.J.); Tel.: +86-135-6047-8369 (F.J.)
| | - Fengliang Jin
- Correspondence: (X.X.); (F.J.); Tel.: +86-135-6047-8369 (F.J.)
| |
Collapse
|
17
|
Shao TL, Ting RT, Lee MC. Identification of Lsd1-interacting non-coding RNAs as regulators of fly oogenesis. Cell Rep 2022; 40:111294. [PMID: 36044841 DOI: 10.1016/j.celrep.2022.111294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 06/03/2022] [Accepted: 08/10/2022] [Indexed: 11/03/2022] Open
Abstract
Lysine-specific demethylase 1 (Lsd1) plays a key role in balancing cell proliferation and differentiation. Lsd1 has been recently reported to associate with specific long noncoding RNAs (lncRNAs) to account for oncogenic gene expression in cancer cells. However, how lncRNA-Lsd1 interplay affects cell-specific differentiation remains elusive in vivo. Here, through Lsd1 specific RNA immunopecipitation sequencing (RIP-seq) experiments, we identify three long hairpin RNAs as Lsd1-interacting non-coding RNAs (LINRs) from fly ovaries. Knocking out LINR-1 and LINR-2 affects fly egg production, while each of the LINR deletion mutant females produce eggs with reduced hatch rate, indicating important functions of LINRs in supporting oogenesis. At the cellular level, LINR-2 regulates the differentiation of germline stem cells and follicle progenitors likely though modulating the expression and function of Lsd1 in vivo. Our identification of ovarian LINRs presents a physiological example of dynamic lncRNA-Lsd1 interplay that regulates stem cell/progenitor differentiation.
Collapse
Affiliation(s)
- Tzu-Ling Shao
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ruei-Teng Ting
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ming-Chia Lee
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| |
Collapse
|
18
|
Zhang L, Zhang S, Wang R, Sun L. Genome-Wide Identification of Long Noncoding RNA and Their Potential Interactors in ISWI Mutants. Int J Mol Sci 2022; 23:ijms23116247. [PMID: 35682924 PMCID: PMC9181106 DOI: 10.3390/ijms23116247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 11/17/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been identified as key regulators of gene expression and participate in many vital physiological processes. Chromatin remodeling, being an important epigenetic modification, has been identified in many biological activities as well. However, the regulatory mechanism of lncRNA in chromatin remodeling remains unclear. In order to characterize the genome-wide lncRNA expression and their potential interacting factors during this process in Drosophila, we investigated the expression pattern of lncRNAs and mRNAs based on the transcriptome analyses and found significant differences between lncRNAs and mRNAs. Then, we performed TSA-FISH experiments of candidate lncRNAs and their potential interactors that have different functions in Drosophila embryos to determine their expression pattern. In addition, we also analyzed the expression of transposable elements (TEs) and their interactors to explore their expression in ISWI mutants. Our results provide a new perspective for understanding the possible regulatory mechanism of lncRNAs and TEs as well as their targets in chromatin remodeling.
Collapse
|
19
|
Zhou H, Wu S, Liu L, Li R, Jin P, Li S. Drosophila Relish Activating lncRNA-CR33942 Transcription Facilitates Antimicrobial Peptide Expression in Imd Innate Immune Response. Front Immunol 2022; 13:905899. [PMID: 35720331 PMCID: PMC9201911 DOI: 10.3389/fimmu.2022.905899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/02/2022] [Indexed: 12/29/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are an emerging class of regulators that play crucial roles in regulating the strength and duration of innate immunity. However, little is known about the regulation of Drosophila innate immunity-related lncRNAs. In this study, we first revealed that overexpression of lncRNA-CR33942 could strengthen the expression of the Imd pathway antimicrobial peptide (AMP) genes Diptericin (Dpt) and Attacin-A (AttA) after infection, and vice versa. Secondly, RNA-seq analysis of lncRNA-CR33942-overexpressing flies post Gram-negative bacteria infection confirmed that lncRNA-CR33942 positively regulated the Drosophila immune deficiency (Imd) pathway. Mechanistically, we found that lncRNA-CR33942 interacts and enhances the binding of NF-κB transcription factor Relish to Dpt and AttA promoters, thereby facilitating Dpt and AttA expression. Relish could also directly promote lncRNA-CR33942 transcription by binding to its promoter. Finally, rescue experiments and dynamic expression profiling post-infection demonstrated the vital role of the Relish/lncRNA-CR33942/AMP regulatory axis in enhancing Imd pathway and maintaining immune homeostasis. Our study elucidates novel mechanistic insights into the role of lncRNA-CR33942 in activating Drosophila Imd pathway and the complex regulatory interaction during the innate immune response of animals.
Collapse
Affiliation(s)
- Hongjian Zhou
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Shanshan Wu
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Li Liu
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Ruimin Li
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Shengjie Li
- Jiangsu Provincial Key Construction Laboratory of Special Biomass Byproduct Resource Utilization, School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| |
Collapse
|
20
|
Zhou H, Li S, Pan W, Wu S, Ma F, Jin P. Interaction of lncRNA-CR33942 with Dif/Dorsal Facilitates Antimicrobial Peptide Transcriptions and Enhances Drosophila Toll Immune Responses. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1978-1988. [PMID: 35379744 DOI: 10.4049/jimmunol.2100658] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 02/02/2022] [Indexed: 01/08/2023]
Abstract
The Drosophila Toll signaling pathway mainly responds to Gram-positive (G+) bacteria or fungal infection, which is highly conserved with mammalian TLR signaling pathway. Although many positive and negative regulators involved in the immune response of the Toll pathway have been identified in Drosophila, the roles of long noncoding RNAs (lncRNAs) in Drosophila Toll immune responses are poorly understood to date. In this study, our results demonstrate that lncRNA-CR33942 is mainly expressed in the nucleus and upregulated after Micrococcus luteus infection. Especially, lncRNA-CR33942 not only modulates differential expressions of multiple antimicrobial peptide genes but also affects the Drosophila survival rate during response to G+ bacterial infection based on the transiently overexpressing and the knockdown lncRNA-CR33942 assays in vivo. Mechanically, lncRNA-CR33942 interacts with the NF-κB transcription factors Dorsal-related immunity factor/Dorsal to promote the transcriptions of antimicrobial peptides drosomycin and metchnikowin, thus enhancing Drosophila Toll immune responses. Taken together, this study identifies lncRNA-CR33942 as a positive regulator of Drosophila innate immune response to G+ bacterial infection to facilitate Toll signaling via interacting with Dorsal-related immunity factor/Dorsal. It would be helpful to reveal the roles of lncRNAs in Toll immune response in Drosophila and provide insights into animal innate immunity.
Collapse
Affiliation(s)
- Hongjian Zhou
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and
| | - Shengjie Li
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and.,Jiangsu Provincial Key Construction Laboratory of Special Biomass Byproduct Resource Utilization, School of Food Science, Nanjing Xiaozhuang University, Nanjing, People's Republic of China
| | - Wanwan Pan
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and
| | - Shanshan Wu
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and
| |
Collapse
|
21
|
Abd El Halim HM, Ali A. Long noncoding RNAs: Emerging players regulating innate immune memory in the red flour beetle. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 127:104304. [PMID: 34756931 DOI: 10.1016/j.dci.2021.104304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/03/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
A variety of strategies have been evolved to eradicate invading microbes. Phagocytes have developed in vertebrates and invertebrates to confer a non-specific immune response to pathogens. Besides, vertebrates have evolved lymphocytes to develop memory cells that can quickly respond upon the next exposure to the same pathogen. Although lymphocytes are absent in invertebrates, historical evidence, dating back to the 1920s, indicated the presence of immune memory in invertebrates. However, the concept of long-lasting non-specific defense predominated until recent evidence has been introduced in the first decade of the 21st century. Although more evidence has been introduced later, the molecular mechanism underlying the innate immune memory is largely undefined in invertebrates. Long noncoding RNAs (lncRNAs) have demonstrated a role in regulating various biological processes, including immune response. In this review, we will explore the potential role of lncRNAs in developing innate immune memory in the red flour beetle (Tribolium castaneum).
Collapse
Affiliation(s)
| | - Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742-231, USA; Department of Zoology, Faculty of Science, Benha University, Benha, 13518, Egypt.
| |
Collapse
|
22
|
Camilleri-Robles C, Amador R, Klein CC, Guigó R, Corominas M, Ruiz-Romero M. Genomic and functional conservation of lncRNAs: lessons from flies. Mamm Genome 2022; 33:328-342. [PMID: 35098341 PMCID: PMC9114055 DOI: 10.1007/s00335-021-09939-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/09/2021] [Indexed: 12/18/2022]
Abstract
Over the last decade, the increasing interest in long non-coding RNAs (lncRNAs) has led to the discovery of these transcripts in multiple organisms. LncRNAs tend to be specifically, and often lowly, expressed in certain tissues, cell types and biological contexts. Although lncRNAs participate in the regulation of a wide variety of biological processes, including development and disease, most of their functions and mechanisms of action remain unknown. Poor conservation of the DNA sequences encoding for these transcripts makes the identification of lncRNAs orthologues among different species very challenging, especially between evolutionarily distant species such as flies and humans or mice. However, the functions of lncRNAs are unexpectedly preserved among different species supporting the idea that conservation occurs beyond DNA sequences and reinforcing the potential of characterising lncRNAs in animal models. In this review, we describe the features and roles of lncRNAs in the fruit fly Drosophila melanogaster, focusing on genomic and functional comparisons with human and mouse lncRNAs. We also discuss the current state of advances and limitations in the study of lncRNA conservation and future perspectives.
Collapse
|
23
|
Zhang Y, Wang X, Cheng XK, Zong YY, He RQ, Chen G, Qin YJ. Clinical significance and effect of lncRNA BBOX1-AS1 on the proliferation and migration of lung squamous cell carcinoma. Oncol Lett 2021; 23:17. [PMID: 34820016 PMCID: PMC8607367 DOI: 10.3892/ol.2021.13135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/19/2021] [Indexed: 12/25/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have a role in the occurrence and development of lung squamous cell carcinoma (LUSC). lncRNA γ-butyrobetaine hydroxylase 1 (BBOX1)-antisense 1 (AS1) may contribute to disease development. However, there are no studies on the role of BBOX1-AS1 in LUSC to date. In the present study, an in-house gene microarray analysis was performed to detect the differentially expressed lncRNAs and mRNAs between three pairs of LUSC and normal lung tissues. Only one lncRNA, BBOX1-AS1, was differentially expressed in the in-house microarray and The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and ArrayExpress databases. Reverse transcription-quantitative PCR (RT-qPCR) was then performed and the original RNA-sequencing data from the TCGA, GEO and ArrayExpress datasets were used to determine the expression and clinical value of BBOX1-AS1 in LUSC. In addition, a Cell Counting Kit-8 assay, cell cycle analysis and scratch assay were performed to explore whether BBOX1-AS1 expression affected the proliferation and migration of LUSC cells in vitro. The results of the RT-qPCR analysis and data obtained from the TCGA database, GEO datasets, in-house gene microarray and standard mean deviation analysis all supported the upregulated expression level of BBOX1-AS1 in LUSC. Furthermore, silencing of BBOX1-AS1 inhibited the proliferation and migration of LUSC cells according to in vitro assays. In addition, the cells were arrested in S-phase after knockdown of BBOX1-AS1. In conclusion, the expression level of BBOX1-AS1 was upregulated in LUSC tissues. BBOX1-AS1 may exert an oncogenic effect on LUSC by regulating various biological functions. However, additional functional experiments should be performed to verify the exact mechanism.
Collapse
Affiliation(s)
- Yu Zhang
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250000, P.R. China
| | - Xiao Wang
- Department of Orthopedics, Shandong Second Provincial General Hospital, Shandong Provincial ENT Hospital, Jinan, Shandong 250000, P.R. China
| | - Xian-Kui Cheng
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250000, P.R. China
| | - Yuan-Yuan Zong
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250000, P.R. China
| | - Rong-Quan He
- Department of Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Ye-Jun Qin
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250000, P.R. China
| |
Collapse
|
24
|
Zhou H, Li S, Wu S, Jin P, Ma F. LncRNA-CR11538 Decoys Dif/Dorsal to Reduce Antimicrobial Peptide Products for Restoring Drosophila Toll Immunity Homeostasis. Int J Mol Sci 2021; 22:ijms221810117. [PMID: 34576280 PMCID: PMC8468853 DOI: 10.3390/ijms221810117] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/12/2021] [Accepted: 09/17/2021] [Indexed: 11/29/2022] Open
Abstract
Avoiding excessive or insufficient immune responses and maintaining homeostasis are critical for animal survival. Although many positive or negative modulators involved in immune responses have been identified, little has been reported to date concerning whether the long non-coding RNA (lncRNA) can regulate Drosophila immunity response. In this study, we firstly discover that the overexpression of lncRNA-CR11538 can inhibit the expressions of antimicrobial peptides Drosomycin (Drs) and Metchnikowin (Mtk) in vivo, thereby suppressing the Toll signaling pathway. Secondly, our results demonstrate that lncRNA-CR11538 can interact with transcription factors Dif/Dorsal in the nucleus based on both subcellular localization and RIP analyses. Thirdly, our findings reveal that lncRNA-CR11538 can decoy Dif/Dorsal away from the promoters of Drs and Mtk to repress their transcriptions by ChIP-qPCR and dual luciferase report experiments. Fourthly, the dynamic expression changes of Drs, Dif, Dorsal and lncRNA-CR11538 in wild-type flies (w1118) at different time points after M. luteus stimulation disclose that lncRNA-CR11538 can help Drosophila restore immune homeostasis in the later period of immune response. Overall, our study reveals a novel mechanism by which lncRNA-CR11538 serves as a Dif/Dorsal decoy to downregulate antimicrobial peptide expressions for restoring Drosophila Toll immunity homeostasis, and provides a new insight into further studying the complex regulatory mechanism of animal innate immunity.
Collapse
Affiliation(s)
- Hongjian Zhou
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China; (H.Z.); (S.L.); (S.W.); (F.M.)
| | - Shengjie Li
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China; (H.Z.); (S.L.); (S.W.); (F.M.)
- Jiangsu Provincial Key Construction Laboratory of Special Biomass Byproduct Resource Utilization, School of Food Science, Nanjing Xiaozhuang University, Nanjing 211171, China
| | - Shanshan Wu
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China; (H.Z.); (S.L.); (S.W.); (F.M.)
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China; (H.Z.); (S.L.); (S.W.); (F.M.)
- Correspondence: ; Tel.: +86-25-85891050
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China; (H.Z.); (S.L.); (S.W.); (F.M.)
| |
Collapse
|
25
|
Murgas L, Contreras-Riquelme S, Martínez-Hernandez JE, Villaman C, Santibáñez R, Martin AJM. Automated generation of context-specific gene regulatory networks with a weighted approach in Drosophila melanogaster. Interface Focus 2021; 11:20200076. [PMID: 34123358 PMCID: PMC8193463 DOI: 10.1098/rsfs.2020.0076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2021] [Indexed: 01/22/2023] Open
Abstract
The regulation of gene expression is a key factor in the development and maintenance of life in all organisms. Even so, little is known at whole genome scale for most genes and contexts. We propose a method, Tool for Weighted Epigenomic Networks in Drosophila melanogaster (Fly T-WEoN), to generate context-specific gene regulatory networks starting from a reference network that contains all known gene regulations in the fly. Unlikely regulations are removed by applying a series of knowledge-based filters. Each of these filters is implemented as an independent module that considers a type of experimental evidence, including DNA methylation, chromatin accessibility, histone modifications and gene expression. Fly T-WEoN is based on heuristic rules that reflect current knowledge on gene regulation in D. melanogaster obtained from the literature. Experimental data files can be generated with several standard procedures and used solely when and if available. Fly T-WEoN is available as a Cytoscape application that permits integration with other tools and facilitates downstream network analysis. In this work, we first demonstrate the reliability of our method to then provide a relevant application case of our tool: early development of D. melanogaster. Fly T-WEoN together with its step-by-step guide is available at https://weon.readthedocs.io.
Collapse
Affiliation(s)
- Leandro Murgas
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.,Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
| | - Sebastian Contreras-Riquelme
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.,Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370146, Chile
| | - J Eduardo Martínez-Hernandez
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.,Centro de Modelamiento Molecular, Biofísica y Bioinformática-CM2B2, Facultad de Ciencias Químicas y Farmaceuticas, Universidad de Chile, Santiago 8380492, Chile.,Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
| | - Camilo Villaman
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.,Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
| | - Rodrigo Santibáñez
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| | - Alberto J M Martin
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| |
Collapse
|
26
|
Qiao H, Wang J, Wang Y, Yang J, Wei B, Li M, Wang B, Li X, Cao Y, Tian L, Li D, Yao L, Kan Y. Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori. BMC Genomics 2021; 22:374. [PMID: 34022797 PMCID: PMC8140452 DOI: 10.1186/s12864-021-07692-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/06/2021] [Indexed: 12/13/2022] Open
Abstract
Background 20-hydroxyecdysone (20E) plays important roles in insect molting and metamorphosis. 20E-induced autophagy has been detected during the larval–pupal transition in different insects. In Bombyx mori, autophagy is induced by 20E in the larval fat body. Long non-coding RNAs (lncRNAs) function in various biological processes in many organisms, including insects. Many lncRNAs have been reported to be potential for autophagy occurrence in mammals, but it has not been investigated in insects. Results RNA libraries from the fat body of B. mori dissected at 2 and 6 h post-injection with 20E were constructed and sequenced, and comprehensive analysis of lncRNAs and mRNAs was performed. A total of 1035 lncRNAs were identified, including 905 lincRNAs and 130 antisense lncRNAs. Compared with mRNAs, lncRNAs had longer transcript length and fewer exons. 132 lncRNAs were found differentially expressed at 2 h post injection, compared with 64 lncRNAs at 6 h post injection. Thirty differentially expressed lncRNAs were common at 2 and 6 h post-injection, and were hypothesized to be associated with the 20E response. Target gene analysis predicted 6493 lncRNA-mRNA cis pairs and 42,797 lncRNA-mRNA trans pairs. The expression profiles of LNC_000560 were highly consistent with its potential target genes, Atg4B, and RNAi of LNC_000560 significantly decreased the expression of LNC_000560 and Atg4B. These results indicated that LNC_000560 was potentially involved in the 20E-induced autophagy of the fat body by regulating Atg4B. Conclusions This study provides the genome-wide identification and functional characterization of lncRNAs associated with 20E-induced autophagy in the fat body of B. mori. LNC_000560 and its potential target gene were identified to be related to 20-regulated autophagy in B. mori. These results will be helpful for further studying the regulatory mechanisms of lncRNAs in autophagy and other biological processes in this insect model. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07692-1.
Collapse
Affiliation(s)
- Huili Qiao
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Jingya Wang
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China.,School of Life Science, Zhengzhou University, 450001, Zhengzhou, Henan, China
| | - Yuanzhuo Wang
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Juanjuan Yang
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Bofan Wei
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Miaomiao Li
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China.,School of Life Science, Zhengzhou University, 450001, Zhengzhou, Henan, China
| | - Bo Wang
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Xiaozhe Li
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Yang Cao
- State Key Laboratory of Silkworm Genome Biology / Biological Science Research Center, Southwest University, 400716, Chongqing, China.,Guangdong Laboratory for Lingnan Modern Agriculture/Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642, Guangzhou, Guangdong, China
| | - Ling Tian
- Guangdong Laboratory for Lingnan Modern Agriculture/Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642, Guangzhou, Guangdong, China
| | - Dandan Li
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Lunguang Yao
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Yunchao Kan
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China.
| |
Collapse
|
27
|
LncRNA: A Potential Research Direction in Intestinal Barrier Function. Dig Dis Sci 2021; 66:1400-1408. [PMID: 32591966 DOI: 10.1007/s10620-020-06417-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 06/14/2020] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides and play important roles in a variety of diseases. LncRNAs are involved in many biologic processes including cell differentiation, development, and apoptosis. The intestinal barrier is considered one of the most important protective barriers in humans. Severe damage or dysfunction of the intestinal barrier may be associated with the occurrence and development of many diseases, such as inflammatory bowel disease and ulcerative colitis. LncRNAs have been found to be associated with intestinal barrier function in some studies, which are at an early stage. In this review, we introduce the roles of LncRNAs in the intestinal barrier and investigate the possibility of lncRNAs as a research field in the intestinal barrier.
Collapse
|
28
|
Meng LW, Yuan GR, Chen ML, Dou W, Jing TX, Zheng LS, Peng ML, Bai WJ, Wang JJ. Genome-wide identification of long non-coding RNAs (lncRNAs) associated with malathion resistance in Bactrocera dorsalis. PEST MANAGEMENT SCIENCE 2021; 77:2292-2301. [PMID: 33423365 DOI: 10.1002/ps.6256] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/09/2020] [Accepted: 01/10/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play important roles in the regulation of biological processes and have been identified in many species including insects. However, the association between lncRNAs and pesticide resistance in insect species such as Bactrocera dorsalis is unknown. RESULTS RNA-seq was performed on malathion resistant (MR1) and susceptible (MS) strains of B. dorsalis and a total of 6171 lncRNAs transcripts were identified. These included 3728 lincRNAs, 653 antisense lncRNAs, 1402 intronic lncRNAs, and 388 sense lncRNAs. A total of 40 and 52 upregulated lncRNAs were found in females and males of the MR1 strain compared to 54 and 49 in the same sexes of the MS strain, respectively. Twenty-seven of these lncRNAs showed the same trend of expression in both females and males in the MR1 strain, in which 15 lncRNAs were upregulated and 12 were downregulated. RT-qPCR results indicated that the differentially expressed lncRNAs were associated with malathion resistance. The lnc15010.10 and lnc3774.2 were highly expressed in the cuticle of the MR1 strain, indicating that these two lncRNAs may be related to malathion resistance. RNAi of lnc3774.2 and a bioassay showed that malathion resistance was possibly influenced by changes in the B. dorsalis cuticle. CONCLUSION LncRNAs of B. dorsalis potentially related to the malathion resistance were identified. Two lncRNAs appear to influence malathion resistance via modulating the structure, or components, of the cuticle. © 2021 Society of Chemical Industry.
Collapse
Affiliation(s)
- Li-Wei Meng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Guo-Rui Yuan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Meng-Ling Chen
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Wei Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Tian-Xing Jing
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Li-Sha Zheng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Meng-Lan Peng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Wen-Jie Bai
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| |
Collapse
|
29
|
Choudhary C, Sharma S, Meghwanshi KK, Patel S, Mehta P, Shukla N, Do DN, Rajpurohit S, Suravajhala P, Shukla JN. Long Non-Coding RNAs in Insects. Animals (Basel) 2021; 11:1118. [PMID: 33919662 PMCID: PMC8069800 DOI: 10.3390/ani11041118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 12/27/2022] Open
Abstract
Only a small subset of all the transcribed RNAs are used as a template for protein translation, whereas RNA molecules that are not translated play a very important role as regulatory non-coding RNAs (ncRNAs). Besides traditionally known RNAs (ribosomal and transfer RNAs), ncRNAs also include small non-coding RNAs (sncRNAs) and long non-coding RNAs (lncRNAs). The lncRNAs, which were initially thought to be junk, have gained a great deal attention because of their regulatory roles in diverse biological processes in animals and plants. Insects are the most abundant and diverse group of animals on this planet. Recent studies have demonstrated the role of lncRNAs in almost all aspects of insect development, reproduction, and genetic plasticity. In this review, we describe the function and molecular mechanisms of the mode of action of different insect lncRNAs discovered up to date.
Collapse
Affiliation(s)
- Chhavi Choudhary
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer 305801, India; (C.C.); (K.K.M.)
| | - Shivasmi Sharma
- Department of Biotechnology, Amity University Jaipur, Jaipur 303002, India; (S.S.); (S.P.)
| | - Keshav Kumar Meghwanshi
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer 305801, India; (C.C.); (K.K.M.)
| | - Smit Patel
- Department of Biotechnology, Amity University Jaipur, Jaipur 303002, India; (S.S.); (S.P.)
| | - Prachi Mehta
- Division of Biological & Life Sciences, School of Arts and Sciences, Ahmedabad University, Gujarat 380009, India; (P.M.); (S.R.)
| | - Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, India;
| | - Duy Ngoc Do
- Institute of Research and Development, Duy Tan University, Danang 550000, Vietnam;
| | - Subhash Rajpurohit
- Division of Biological & Life Sciences, School of Arts and Sciences, Ahmedabad University, Gujarat 380009, India; (P.M.); (S.R.)
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, India;
- Bioclues.org, Vivekananda Nagar, Kukatpally, Hyderabad, Telangana 500072, India
| | - Jayendra Nath Shukla
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer 305801, India; (C.C.); (K.K.M.)
| |
Collapse
|
30
|
Millet-Boureima C, He S, Le TBU, Gamberi C. Modeling Neoplastic Growth in Renal Cell Carcinoma and Polycystic Kidney Disease. Int J Mol Sci 2021; 22:3918. [PMID: 33920158 PMCID: PMC8070407 DOI: 10.3390/ijms22083918] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022] Open
Abstract
Renal cell carcinoma (RCC) and autosomal dominant polycystic kidney disease (ADPKD) share several characteristics, including neoplastic cell growth, kidney cysts, and limited therapeutics. As well, both exhibit impaired vasculature and compensatory VEGF activation of angiogenesis. The PI3K/AKT/mTOR and Ras/Raf/ERK pathways play important roles in regulating cystic and tumor cell proliferation and growth. Both RCC and ADPKD result in hypoxia, where HIF-α signaling is activated in response to oxygen deprivation. Primary cilia and altered cell metabolism may play a role in disease progression. Non-coding RNAs may regulate RCC carcinogenesis and ADPKD through their varied effects. Drosophila exhibits remarkable conservation of the pathways involved in RCC and ADPKD. Here, we review the progress towards understanding disease mechanisms, partially overlapping cellular and molecular dysfunctions in RCC and ADPKD and reflect on the potential for the agile Drosophila genetic model to accelerate discovery science, address unresolved mechanistic aspects of these diseases, and perform rapid pharmacological screens.
Collapse
Affiliation(s)
- Cassandra Millet-Boureima
- Department of Biology, Concordia University, Montreal, QC H4B 1R6, Canada; (C.M.-B.); (S.H.); (T.B.U.L.)
| | - Stephanie He
- Department of Biology, Concordia University, Montreal, QC H4B 1R6, Canada; (C.M.-B.); (S.H.); (T.B.U.L.)
| | - Thi Bich Uyen Le
- Department of Biology, Concordia University, Montreal, QC H4B 1R6, Canada; (C.M.-B.); (S.H.); (T.B.U.L.)
- Haematology-Oncology Research Group, National University Cancer Institute, Singapore 119228, Singapore
| | - Chiara Gamberi
- Department of Biology, Coastal Carolina University, Conway, SC 29528-6054, USA
| |
Collapse
|
31
|
Vitorino R, Guedes S, Amado F, Santos M, Akimitsu N. The role of micropeptides in biology. Cell Mol Life Sci 2021; 78:3285-3298. [PMID: 33507325 PMCID: PMC11073438 DOI: 10.1007/s00018-020-03740-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022]
Abstract
Micropeptides are small polypeptides coded by small open-reading frames. Progress in computational biology and the analyses of large-scale transcriptomes and proteomes have revealed that mammalian genomes produce a large number of transcripts encoding micropeptides. Many of these have been previously annotated as long noncoding RNAs. The role of micropeptides in cellular homeostasis maintenance has been demonstrated. This review discusses different types of micropeptides as well as methods to identify them, such as computational approaches, ribosome profiling, and mass spectrometry.
Collapse
Affiliation(s)
- Rui Vitorino
- Departamento de Cirurgia E Fisiologia, Faculdade de Medicina da Universidade Do Porto, UnIC, Porto, Portugal.
- Department of Medical Sciences, iBiMED, University of Aveiro, Aveiro, Portugal.
| | - Sofia Guedes
- Departamento de Química, LAQV-REQUIMTE, Universidade de Aveiro, Aveiro, Portugal
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Francisco Amado
- Departamento de Química, LAQV-REQUIMTE, Universidade de Aveiro, Aveiro, Portugal
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Manuel Santos
- Department of Medical Sciences, iBiMED, University of Aveiro, Aveiro, Portugal
| | | |
Collapse
|
32
|
Berger CA, Steinberg DK, Copley NJ, Tarrant AM. De novo transcriptome assembly of the Southern Ocean copepod Rhincalanus gigas sheds light on developmental changes in gene expression. Mar Genomics 2021; 58:100835. [PMID: 33526377 DOI: 10.1016/j.margen.2021.100835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/30/2020] [Accepted: 12/30/2020] [Indexed: 11/18/2022]
Abstract
Copepods are small crustaceans that dominate most zooplankton communities in terms of both abundance and biomass. In the polar oceans, a subset of large lipid-storing copepods occupy central positions in the food web because of their important role in linking phytoplankton and microzooplankton with higher trophic levels. In this paper, we generated a high-quality de novo transcriptome for Rhincalanus gigas, the largest-and among the most abundant-of the Southern Ocean copepods. We then conducted transcriptional profiling to characterize the developmental transition between late-stage juveniles and adult females. We found that juvenile R. gigas substantially upregulate lipid synthesis and glycolysis pathways relative to females, as part of a developmental gene expression program that also implicates processes such as muscle growth, chitin formation, and ion transport. This study provides the first transcriptional profile of a developmental transition within Rhincalanus gigas or any endemic Southern Ocean copepod, thereby extending our understanding of copepod molecular physiology.
Collapse
Affiliation(s)
- Cory A Berger
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States; MIT-WHOI Joint Program in Oceanography/Applied Ocean Science & Engineering, Cambridge and Woods Hole, MA, USA
| | - Deborah K Steinberg
- Virginia Institute of Marine Science, William & Mary, Gloucester Pt, VA 23062, United States
| | - Nancy J Copley
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Ann M Tarrant
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States.
| |
Collapse
|
33
|
Tsurumi A, Li WX. Aging mechanisms-A perspective mostly from Drosophila. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 1:e10026. [PMID: 36619249 PMCID: PMC9744567 DOI: 10.1002/ggn2.10026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 04/04/2020] [Accepted: 04/08/2020] [Indexed: 01/11/2023]
Abstract
A mechanistic understanding of the natural aging process, which is distinct from aging-related disease mechanisms, is essential for developing interventions to extend lifespan or healthspan. Here, we discuss current trends in aging research and address conceptual and experimental challenges in the field. We examine various molecular markers implicated in aging with an emphasis on the role of heterochromatin and epigenetic changes. Studies in model organisms have been advantageous in elucidating conserved genetic and epigenetic mechanisms and assessing interventions that affect aging. We highlight the use of Drosophila, which allows controlled studies for evaluating genetic and environmental contributors to aging conveniently. Finally, we propose the use of novel methodologies and future strategies using Drosophila in aging research.
Collapse
Affiliation(s)
- Amy Tsurumi
- Department of SurgeryMassachusetts General Hospital, and Harvard Medical SchoolBostonMassachusettsUSA
- Department of Microbiology and ImmunologyHarvard Medical SchoolBostonMassachusettsUSA
- Shriners Hospitals for Children‐Boston®BostonMassachusettsUSA
| | - Willis X. Li
- Department of MedicineUniversity of California at San DiegoLa JollaCaliforniaUSA
| |
Collapse
|
34
|
Pan C, Wang Y, Tao L, Zhang H, Deng Q, Yang Z, Chi Z, Yang Y. Single-molecule real-time sequencing of the full-length transcriptome of loquat under low-temperature stress. PLoS One 2020; 15:e0238942. [PMID: 32915882 PMCID: PMC7485763 DOI: 10.1371/journal.pone.0238942] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/26/2020] [Indexed: 01/01/2023] Open
Abstract
In this study, third-generation full-length (FL) transcriptome sequencing was performed of loquat using single-molecule real-time(SMRT) sequencing from the pooled cDNA of embryos of young loquat fruit under different low temperatures (three biological replicates for treatments of 1°C, -1°C, and -3°C, for 12 h or 24 h) and the control group(three biological replicates for treatments of room temperature), Illumina sequencing was used to correct FL transcriptome sequences. A total of 3 PacBio Iso-Seq libraries (1–2 kb, 2–3 kb and 3–6 kb) and 21 Illumina transcriptome libraries were constructed, a total of 13.41 Gb of clean reads were generated, which included 215,636 reads of insert (ROIs) and 121,654 FL, non-chimaric (FLNC) reads. Transcript clustering analysis of the FLNC reads revealed 76,586 consensus isoforms, and a total of 12,520 high-quality transcript sequences corrected with non-FL sequences were used for subsequent analysis. After the redundant reads were removed, 38,435 transcripts were obtained. A total of 27,905 coding DNA sequences (CDSs) were identified, and 407 long non-coding RNAs (lncRNAs) were ultimately predicted. Additionally, 24,832 simple sequence repeats (SSRs) were identified, and a total of 1,295 alternative splicing (AS) events were predicted. Furthermore, 37,993 transcripts were annotated in eight functional databases. This is the first study to perform SMRT sequencing of the FL transcriptome of loquat. The obtained transcriptomic data are conducive for further exploration of the mechanism of loquat freezing injury and thus serve as an important theoretical basis for generating new loquat material and for identifying new ways to improve loquat cold resistance.
Collapse
Affiliation(s)
- Cuiping Pan
- College of Horticulture, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Yongqing Wang
- College of Horticulture, Sichuan Agricultural University, Wenjiang, Sichuan, China
- * E-mail:
| | - Lian Tao
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Hui Zhang
- College of Horticulture, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Qunxian Deng
- College of Horticulture, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Zhiwu Yang
- College of Horticulture, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Zhuoheng Chi
- College of Horticulture, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Yunmiao Yang
- College of Horticulture, Sichuan Agricultural University, Wenjiang, Sichuan, China
| |
Collapse
|
35
|
Lecheta MC, Awde DN, O’Leary TS, Unfried LN, Jacobs NA, Whitlock MH, McCabe E, Powers B, Bora K, Waters JS, Axen HJ, Frietze S, Lockwood BL, Teets NM, Cahan SH. Integrating GWAS and Transcriptomics to Identify the Molecular Underpinnings of Thermal Stress Responses in Drosophila melanogaster. Front Genet 2020; 11:658. [PMID: 32655626 PMCID: PMC7324644 DOI: 10.3389/fgene.2020.00658] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/29/2020] [Indexed: 12/12/2022] Open
Abstract
Thermal tolerance of an organism depends on both the ability to dynamically adjust to a thermal stress and preparatory developmental processes that enhance thermal resistance. However, the extent to which standing genetic variation in thermal tolerance alleles influence dynamic stress responses vs. preparatory processes is unknown. Here, using the model species Drosophila melanogaster, we used a combination of Genome Wide Association mapping (GWAS) and transcriptomic profiling to characterize whether genes associated with thermal tolerance are primarily involved in dynamic stress responses or preparatory processes that influence physiological condition at the time of thermal stress. To test our hypotheses, we measured the critical thermal minimum (CTmin) and critical thermal maximum (CTmax) of 100 lines of the Drosophila Genetic Reference Panel (DGRP) and used GWAS to identify loci that explain variation in thermal limits. We observed greater variation in lower thermal limits, with CTmin ranging from 1.81 to 8.60°C, while CTmax ranged from 38.74 to 40.64°C. We identified 151 and 99 distinct genes associated with CTmin and CTmax, respectively, and there was strong support that these genes are involved in both dynamic responses to thermal stress and preparatory processes that increase thermal resistance. Many of the genes identified by GWAS were involved in the direct transcriptional response to thermal stress (72/151 for cold; 59/99 for heat), and overall GWAS candidates were more likely to be differentially expressed than other genes. Further, several GWAS candidates were regulatory genes that may participate in the regulation of stress responses, and gene ontologies related to development and morphogenesis were enriched, suggesting many of these genes influence thermal tolerance through effects on development and physiological status. Overall, our results suggest that thermal tolerance alleles can influence both dynamic plastic responses to thermal stress and preparatory processes that improve thermal resistance. These results also have utility for directly comparing GWAS and transcriptomic approaches for identifying candidate genes associated with thermal tolerance.
Collapse
Affiliation(s)
- Melise C. Lecheta
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - David N. Awde
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Thomas S. O’Leary
- Department of Biology, University of Vermont, Burlington, VT, United States
| | - Laura N. Unfried
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Nicholas A. Jacobs
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Miles H. Whitlock
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Eleanor McCabe
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Beck Powers
- Department of Biology, University of Vermont, Burlington, VT, United States
| | - Katie Bora
- Department of Biology, University of Vermont, Burlington, VT, United States
| | - James S. Waters
- Department of Biology, Providence College, Providence, RI, United States
| | - Heather J. Axen
- Department of Biology and Biomedical Sciences, Salve Regina College, Providence, RI, United States
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, United States
| | - Brent L. Lockwood
- Department of Biology, University of Vermont, Burlington, VT, United States
| | - Nicholas M. Teets
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Sara H. Cahan
- Department of Biology, University of Vermont, Burlington, VT, United States
| |
Collapse
|
36
|
Song J, Zhou S. Post-transcriptional regulation of insect metamorphosis and oogenesis. Cell Mol Life Sci 2020; 77:1893-1909. [PMID: 31724082 PMCID: PMC11105025 DOI: 10.1007/s00018-019-03361-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 10/18/2019] [Accepted: 10/30/2019] [Indexed: 12/17/2022]
Abstract
Metamorphic transformation from larvae to adults along with the high fecundity is key to insect success. Insect metamorphosis and reproduction are governed by two critical endocrines, juvenile hormone (JH), and 20-hydroxyecdysone (20E). Recent studies have established a crucial role of microRNA (miRNA) in insect metamorphosis and oogenesis. While miRNAs target genes involved in JH and 20E-signaling pathways, these two hormones reciprocally regulate miRNA expression, forming regulatory loops of miRNA with JH and 20E-signaling cascades. Insect metamorphosis and oogenesis rely on the coordination of hormones, cognate genes, and miRNAs for precise regulation. In addition, the alternative splicing of genes in JH and 20E-signaling pathways has distinct functions in insect metamorphosis and oogenesis. We, therefore, focus in this review on recent advances in post-transcriptional regulation, with the emphasis on the regulatory role of miRNA and alternative splicing, in insect metamorphosis and oogenesis. We will highlight important new findings of miRNA interactions with hormonal signaling and alternative splicing of JH receptor heterodimer gene Taiman.
Collapse
Affiliation(s)
- Jiasheng Song
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Shutang Zhou
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| |
Collapse
|