1
|
Li CZ, Liu YH, Pan D, Xia MH, Zhang Q, Li YC, Yuan GR, Wang JJ, Dou W. Genome-wide analysis of Panonychus citri microRNAs with a focus on potential insecticidal activity of 4 microRNAs to eggs and nymphs. INSECT SCIENCE 2024; 31:354-370. [PMID: 37641867 DOI: 10.1111/1744-7917.13265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/26/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023]
Abstract
Panonychus citri McGregor (Acari: Tetranychidae), a destructive citrus pest, causes considerable annual economic losses due to its short lifespan and rapid resistance development. MicroRNA (miRNA)-induced RNA interference is a promising approach for pest control because of endogenous regulation of pest growth and development. To search for miRNAs with potential insecticidal activity in P. citri, genome-wide analysis of miRNAs at different developmental stages was conducted, resulting in the identification of 136 miRNAs, including 73 known and 63 novel miRNAs. A total of 17 isomiRNAs and 12 duplicated miRNAs were characterized. MiR-1 and miR-252-5p were identified as reference miRNAs for P. citri and Tetranychus urticae. Based on differential expression analysis, treatments with miR-let-7a and miR-315 mimics and the miR-let-7a antagomir significantly reduced the egg hatch rate and resulted in abnormal egg development. Overexpression or downregulation of miR-34-5p and miR-305-5p through feeding significantly decreased the adult eclosion rate and caused molting defects. The 4 miRNAs, miR-let-7a, miR-315, miR-34-5p, and miR-305-5p, had important regulatory functions and insecticidal properties in egg hatching and adult eclosion. In general, these data advance our understanding of miRNAs in mite biology, which can assist future studies on insect-specific miRNA-based green pest control technology.
Collapse
Affiliation(s)
- Chuan-Zhen Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yu-Hang Liu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Deng Pan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Meng-Hao Xia
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Qiang Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yu-Chuang Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Guo-Rui Yuan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Wei Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, China
| |
Collapse
|
2
|
Wang Y, Tang X, Lu J. Convergent and divergent evolution of microRNA-mediated regulation in metazoans. Biol Rev Camb Philos Soc 2024; 99:525-545. [PMID: 37987240 DOI: 10.1111/brv.13033] [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: 08/22/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
The evolution of microRNAs (miRNAs) has been studied extensively to understand their roles in gene regulation and evolutionary processes. This review focuses on how miRNA-mediated regulation has evolved in bilaterian animals, highlighting both convergent and divergent evolution. Since animals and plants display significant differences in miRNA biogenesis and target recognition, the 'independent origin' hypothesis proposes that miRNA pathways in these groups independently evolved from the RNA interference (RNAi) pathway, leading to modern miRNA repertoires through convergent evolution. However, recent evidence raises the alternative possibility that the miRNA pathway might have already existed in the last common ancestor of eukaryotes, and that the differences in miRNA pathway and miRNA repertoires among animal and plant lineages arise from lineage-specific innovations and losses of miRNA pathways, miRNA acquisition, and loss of miRNAs after eukaryotic divergence. The repertoire of miRNAs has considerably expanded during bilaterian evolution, primarily through de novo creation and duplication processes, generating new miRNAs. Although ancient functionally established miRNAs are rarely lost, many newly emerged miRNAs are transient and lineage specific, following a birth-death evolutionary pattern aligning with the 'out-of-the-testis' and 'transcriptional control' hypotheses. Our focus then shifts to the convergent molecular evolution of miRNAs. We summarize how miRNA clustering and seed mimicry contribute to this phenomenon, and we review how miRNAs from different sources converge to degrade maternal messenger RNAs (mRNAs) during animal development. Additionally, we describe how miRNAs evolve across species due to changes in sequence, seed shifting, arm switching, and spatiotemporal expression patterns, which can result in variations in target sites among orthologous miRNAs across distant strains or species. We also provide a summary of the current understanding regarding how the target sites of orthologous miRNAs can vary across strains or distantly related species. Although many paralogous miRNAs retain their seed or mature sequences after duplication, alterations can occur in the seed or mature sequences or expression patterns of paralogous miRNAs, leading to functional diversification. We discuss our current understanding of the functional divergence between duplicated miRNAs, and illustrate how the functional diversification of duplicated miRNAs impacts target site evolution. By investigating these topics, we aim to enhance our current understanding of the functions and evolutionary dynamics of miRNAs. Additionally, we shed light on the existing challenges in miRNA evolutionary studies, particularly the complexity of deciphering the role of miRNA-mediated regulatory network evolution in shaping gene expression divergence and phenotypic differences among species.
Collapse
Affiliation(s)
- Yirong Wang
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| |
Collapse
|
3
|
Cadonic IG, Heath JW, Dixon B, Craig PM. Diploid and triploid Chinook salmon (Oncorhynchus tshawytscha) have altered microRNA responses in immune tissues after infection with Vibrio anguillarum. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 48:101121. [PMID: 37634278 DOI: 10.1016/j.cbd.2023.101121] [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: 05/12/2023] [Revised: 08/04/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023]
Abstract
Production of sterile fishes through artificial retention of a third set of chromosomes (triploidy) is a sustainable alternative for aquaculture since it reduces escapee pressure on wild populations. However, these fishes have reduced survival in stressful conditions and in response to infection. In this study, the impact of Vibrio anguillarum infection on diploid and triploid Chinook salmon (Oncorhynchus tshawytscha) was investigated to identify if there was any significant immune regulation by microRNAs (miRNA). Small RNAs from hindgut, head kidney, and spleen were sequenced to determine if miRNA transcript abundance was altered due to ploidy and infection in nine-month old full-sibling diploids and triploids. All three tissues had differentially expressed miRNA prior to infection, indicating subtle changes in epigenetic regulation due to increased ploidy. Additionally, miRNA were altered by infection, but there was only a difference in spleen miRNA expression between diploids and triploids at three days of infection. Furthermore, one miRNA (ssa-miR-2188-3p) was confirmed as having an altered response to infection in triploids compared to diploids, implicating potential immune dysregulation due to increased ploidy. The miRNAs identified in this study are predicted to target immune pathways, providing evidence for their importance in regulating responses to pathogens. This study is the first to investigate how increased ploidy alters miRNA expression in response to infection. Additionally, it provides evidence for epigenetic dysregulation in triploid fishes, which may contribute to their poor performance in response to stress.
Collapse
Affiliation(s)
- Ivan G Cadonic
- Dept. of Biology, University of Waterloo, Waterloo, ON, Canada. https://twitter.com/@IvanCadonic
| | - John W Heath
- Yellow Island Aquaculture Limited, Heriot Bay, BC. Canada
| | - Brian Dixon
- Dept. of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Paul M Craig
- Dept. of Biology, University of Waterloo, Waterloo, ON, Canada.
| |
Collapse
|
4
|
Chi X, Wang Z, Wang Y, Liu Z, Wang H, Xu B. Cross-Kingdom Regulation of Plant-Derived miRNAs in Modulating Insect Development. Int J Mol Sci 2023; 24:ijms24097978. [PMID: 37175684 PMCID: PMC10178792 DOI: 10.3390/ijms24097978] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
MicroRNAs (miRNAs), a class of non-coding small RNAs, are crucial regulatory factors in plants and animals at the post-transcriptional level. These tiny molecules suppress gene expression by complementary oligonucleotide binding to sites in the target messenger. Recently, the discovery of plant-derived miRNAs with cross-kingdom abilities to regulate gene expression in insects has promoted exciting discussion, although some controversies exist regarding the modulation of insect development by plant-derived miRNAs. Here, we review current knowledge about the mechanisms of miRNA biogenesis, the roles of miRNAs in coevolution between insects and plants, the regulation of insect development by plant-derived miRNAs, the cross-kingdom transport mechanisms of plant-derived miRNAs, and cross-kingdom regulation. In addition, the controversy regarding the modulation of insect development by plant-derived miRNAs also was discussed. Our review provides new insights for understanding complex plant-insect interactions and discovering new strategies for pest management and even crop genetic improvement.
Collapse
Affiliation(s)
- Xuepeng Chi
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271002, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China
| | - Zhe Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271002, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China
| | - Ying Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271002, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China
| | - Zhenguo Liu
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271002, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China
| | - Hongfang Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271002, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China
| | - Baohua Xu
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271002, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China
| |
Collapse
|
5
|
Bhatti JS, Khullar N, Vijayvergiya R, Navik U, Bhatti GK, Reddy PH. Mitochondrial miRNA as epigenomic signatures: Visualizing aging-associated heart diseases through a new lens. Ageing Res Rev 2023; 86:101882. [PMID: 36780957 DOI: 10.1016/j.arr.2023.101882] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 02/05/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
Aging bears many hard knocks, but heart disorders earn a particular allusion, being the most widespread. Cardiovascular diseases (CVDs) are becoming the biggest concern to mankind due to sundry health conditions directly or indirectly related to heart-linked abnormalities. Scientists know that mitochondria play a critical role in the pathophysiology of cardiac diseases. Both environment and genetics play an essential role in modulating and controlling mitochondrial functions. Even a minor abnormality may prove detrimental to heart function. Advanced age combined with an unhealthy lifestyle can cause most cardiomyocytes to be replaced by fibrotic tissue which upsets the conducting system and leads to arrhythmias. An aging heart encounters far more heart-associated comorbidities than a young heart. Many state-of-the-art technologies and procedures are already being used to prevent and treat heart attacks worldwide. However, it remains a mystery when this heart bomb would explode because it lacks an alarm. This calls for a novel and effective strategy for timely diagnosis and a sure-fire treatment. This review article provides a comprehensive overture of prospective potentials of mitochondrial miRNAs that predict complicated and interconnected pathways concerning heart ailments and signature compilations of relevant miRNAs as biomarkers to plot the role of miRNAs in epigenomics. This article suggests that analysis of DNA methylation patterns in age-associated heart diseases may determine age-impelled biomarkers of heart disease.
Collapse
Affiliation(s)
- Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India.
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab, India.
| | - Rajesh Vijayvergiya
- Department of Cardiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
| | - Umashanker Navik
- Department of Pharmacology, Central University of Punjab, Bathinda, India.
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India.
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Departments of Neurology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Nutritional Sciences Department, College of Human Sciences, Texas Tech University, Lubbock, TX 79409, USA.
| |
Collapse
|
6
|
Martínez Sosa F, Pilot M. Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review. Genes (Basel) 2023; 14:416. [PMID: 36833343 PMCID: PMC9957108 DOI: 10.3390/genes14020416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.
Collapse
Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, 80-680 Gdańsk, Poland
- Faculty of Biology, University of Gdańsk, 80-308 Gdańsk, Poland
| |
Collapse
|
7
|
Ste-Croix DT, Bélanger RR, Mimee B. Characterization of microRNAs in the cyst nematode Heterodera glycines identifies possible candidates involved in cross-kingdom interactions with its host Glycine max. RNA Biol 2023; 20:614-628. [PMID: 37599428 PMCID: PMC10443972 DOI: 10.1080/15476286.2023.2244790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 08/22/2023] Open
Abstract
The soybean cyst nematode (SCN - Heterodera glycines) is one of the most damaging pests to the cultivated soybean worldwide. Using a wide array of stylet-secreted effector proteins, this nematode can restructure its host cells into a complex and highly active feeding structure called the syncytium. Tight regulation of these proteins is thought to be essential to the successful formation of this syncytium. To date, multiple mechanisms have been proposed to regulate the expression of these proteins including through post-transcriptional regulation. MicroRNAs (miRNAs) are a class of small, roughly 22-nucleotide-long, non-coding RNA shown to regulate gene expression through its interaction with the 3' untranslated region of genes. These same small RNAs have also been hypothesized to be able to cross over kingdom barriers and regulate genes in other species in a process called cross-kingdom interactions. In this study, we characterized the miRNome of the SCN via sequencing of small-RNAs isolated from whole nematodes and exosomes representing all developmental stages. We identified 121 miRNA loci encoding 96 distinct miRNA families including multiple lineage- and species-specific candidates. Using a combination of plant- and animal-specific miRNA target predictors, we generated a unique repertoire of miRNA:mRNA interacting partners in the nematode and its host plant leading to the identification of a set of nine probable cross-kingdom miRNA candidates.
Collapse
Affiliation(s)
- Dave T. Ste-Croix
- Saint-Jean-Sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-Sur-Richelieu, Canada
- Département de Phytologie, Université Laval, Québec, Canada
| | - Richard R. Bélanger
- Département de Phytologie, Université Laval, Québec, Canada
- Centre de Recherche et d’Innovation sur les Végétaux (CRIV), Université Laval, Québec, Canada
| | - Benjamin Mimee
- Saint-Jean-Sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-Sur-Richelieu, Canada
| |
Collapse
|
8
|
Kitai H, Kato N, Ogami K, Komatsu S, Watanabe Y, Yoshino S, Koshi E, Tsubota S, Funahashi Y, Maeda T, Furuhashi K, Ishimoto T, Kosugi T, Maruyama S, Kadomatsu K, Suzuki HI. Systematic characterization of seed overlap microRNA cotargeting associated with lupus pathogenesis. BMC Biol 2022; 20:248. [PMID: 36357926 PMCID: PMC9650897 DOI: 10.1186/s12915-022-01447-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 10/21/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Combinatorial gene regulation by multiple microRNAs (miRNAs) is widespread and closely spaced target sites often act cooperatively to achieve stronger repression ("neighborhood" miRNA cotargeting). While miRNA cotarget sites are suggested to be more conserved and implicated in developmental control, the pathological significance of miRNA cotargeting remains elusive. RESULTS Here, we report the pathogenic impacts of combinatorial miRNA regulation on inflammation in systemic lupus erythematosus (SLE). In the SLE mouse model, we identified the downregulation of two miRNAs, miR-128 and miR-148a, by TLR7 stimulation in plasmacytoid dendritic cells. Functional analyses using human cell lines demonstrated that miR-128 and miR-148a additively target KLF4 via extensively overlapping target sites ("seed overlap" miRNA cotargeting) and suppress the inflammatory responses. At the transcriptome level, "seed overlap" miRNA cotargeting increases susceptibility to downregulation by two miRNAs, consistent with additive but not cooperative recruitment of two miRNAs. Systematic characterization further revealed that extensive "seed overlap" is a prevalent feature among broadly conserved miRNAs. Highly conserved target sites of broadly conserved miRNAs are largely divided into two classes-those conserved among eutherian mammals and from human to Coelacanth, and the latter, including KLF4-cotargeting sites, has a stronger association with both "seed overlap" and "neighborhood" miRNA cotargeting. Furthermore, a deeply conserved miRNA target class has a higher probability of haplo-insufficient genes. CONCLUSIONS Our study collectively suggests the complexity of distinct modes of miRNA cotargeting and the importance of their perturbations in human diseases.
Collapse
Affiliation(s)
- Hiroki Kitai
- Department of Nephrology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
| | - Noritoshi Kato
- Department of Nephrology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
| | - Koichi Ogami
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
| | - Shintaro Komatsu
- Department of Nephrology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
| | - Yu Watanabe
- Department of Nephrology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
| | - Seiko Yoshino
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
| | - Eri Koshi
- Department of Nephrology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
| | - Shoma Tsubota
- Department of Biochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
| | - Yoshio Funahashi
- Department of Nephrology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
- Present Address: Yoshio Funahashi, Department of Anesthesiology and Perioperative Medicine, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239 USA
| | - Takahiro Maeda
- Department of General Medicine, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki, Nagasaki 852-8501 Japan
| | - Kazuhiro Furuhashi
- Department of Nephrology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
| | - Takuji Ishimoto
- Department of Nephrology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
- Present Address: Takuji Ishimoto, Department of Nephrology and Rheumatology, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi 480-1195 Japan
| | - Tomoki Kosugi
- Department of Nephrology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
| | - Shoichi Maruyama
- Department of Nephrology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
| | - Kenji Kadomatsu
- Department of Biochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601 Japan
| | - Hiroshi I. Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550 Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601 Japan
| |
Collapse
|
9
|
Mármol-Sánchez E, Luigi-Sierra MG, Castelló A, Guan D, Quintanilla R, Tonda R, Amills M. Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes. Genet Sel Evol 2021; 53:43. [PMID: 33947333 PMCID: PMC8097994 DOI: 10.1186/s12711-021-00632-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 04/15/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Mature microRNAs (miRNAs) play an important role in repressing the expression of a wide range of mRNAs. The presence of polymorphic sites in miRNA genes and their corresponding 3'UTR binding sites can disrupt canonical conserved miRNA-mRNA pairings, and thus modify gene expression patterns. However, to date such polymorphic sites in miRNA genes and their association with gene expression phenotypes and complex traits are poorly characterized in pigs. RESULTS By analyzing whole-genome sequences from 120 pigs and wild boars from Europe and Asia, we identified 285 single nucleotide polymorphisms (SNPs) that map to miRNA loci, and 109,724 SNPs that are located in predicted 7mer-m8 miRNA binding sites within porcine 3'UTR. In porcine miRNA genes, SNP density is reduced compared with their flanking non-miRNA regions. By sequencing the genomes of five Duroc boars, we identified 12 miRNA SNPs that were subsequently genotyped in their offspring (N = 345, Lipgen population). Association analyses of miRNA SNPs with 38 lipid-related traits and hepatic and muscle microarray expression phenotypes recorded in the Lipgen population were performed. The most relevant detected association was between the genotype of the rs319154814 (G/A) SNP located in the apical loop of the ssc-miR-326 hairpin precursor and PPP1CC mRNA levels in the liver (q-value = 0.058). This result was subsequently confirmed by qPCR (P-value = 0.027). The rs319154814 (G/A) genotype was also associated with several fatty acid composition traits. CONCLUSIONS Our findings show a reduced variability of porcine miRNA genes, which is consistent with strong purifying selection, particularly in the seed region that plays a critical role in miRNA binding. Although it is generally assumed that SNPs mapping to the seed region are those with the most pronounced consequences on mRNA expression, we show that a SNP mapping to the apical region of ssc-miR-326 is significantly associated with hepatic mRNA levels of the PPP1CC gene, one of its predicted targets. Although experimental confirmation of such an interaction is reported in humans but not in pigs, this result highlights the need to further investigate the functional effects of miRNA polymorphisms that are located outside the seed region on gene expression in pigs.
Collapse
Affiliation(s)
- Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - María Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Anna Castelló
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Spain
| | - Raul Tonda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. .,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| |
Collapse
|
10
|
Dexheimer PJ, Cochella L. MicroRNAs: From Mechanism to Organism. Front Cell Dev Biol 2020; 8:409. [PMID: 32582699 PMCID: PMC7283388 DOI: 10.3389/fcell.2020.00409] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are short, regulatory RNAs that act as post-transcriptional repressors of gene expression in diverse biological contexts. The emergence of small RNA-mediated gene silencing preceded the onset of multicellularity and was followed by a drastic expansion of the miRNA repertoire in conjunction with the evolution of complexity in the plant and animal kingdoms. Along this process, miRNAs became an essential feature of animal development, as no higher metazoan lineage tolerated loss of miRNAs or their associated protein machinery. In fact, ablation of the miRNA biogenesis machinery or the effector silencing factors results in severe embryogenesis defects in every animal studied. In this review, we summarize recent mechanistic insight into miRNA biogenesis and function, while emphasizing features that have enabled multicellular organisms to harness the potential of this broad class of repressors. We first discuss how different mechanisms of regulation of miRNA biogenesis are used, not only to generate spatio-temporal specificity of miRNA production within an animal, but also to achieve the necessary levels and dynamics of expression. We then explore how evolution of the mechanism for small RNA-mediated repression resulted in a diversity of silencing complexes that cause different molecular effects on their targets. Multicellular organisms have taken advantage of this variability in the outcome of miRNA-mediated repression, with differential use in particular cell types or even distinct subcellular compartments. Finally, we present an overview of how the animal miRNA repertoire has evolved and diversified, emphasizing the emergence of miRNA families and the biological implications of miRNA sequence diversification. Overall, focusing on selected animal models and through the lens of evolution, we highlight canonical mechanisms in miRNA biology and their variations, providing updated insight that will ultimately help us understand the contribution of miRNAs to the development and physiology of multicellular organisms.
Collapse
Affiliation(s)
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| |
Collapse
|
11
|
Simkin A, Geissler R, McIntyre ABR, Grimson A. Evolutionary dynamics of microRNA target sites across vertebrate evolution. PLoS Genet 2020; 16:e1008285. [PMID: 32012152 PMCID: PMC7018135 DOI: 10.1371/journal.pgen.1008285] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 02/13/2020] [Accepted: 01/02/2020] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) control the abundance of the majority of the vertebrate transcriptome. The recognition sequences, or target sites, for bilaterian miRNAs are found predominantly in the 3' untranslated regions (3'UTRs) of mRNAs, and are amongst the most highly conserved motifs within 3'UTRs. However, little is known regarding the evolutionary pressures that lead to loss and gain of such target sites. Here, we quantify the selective pressures that act upon miRNA target sites. Notably, selective pressure extends beyond deeply conserved binding sites to those that have undergone recent substitutions. Our approach reveals that even amongst ancient animal miRNAs, which exert the strongest selective pressures on 3'UTR sequences, there are striking differences in patterns of target site evolution between miRNAs. Considering only ancient animal miRNAs, we find three distinct miRNA groups, each exhibiting characteristic rates of target site gain and loss during mammalian evolution. The first group both loses and gains sites rarely. The second group shows selection only against site loss, with site gains occurring at a neutral rate, whereas the third loses and gains sites at neutral or above expected rates. Furthermore, mutations that alter the strength of existing target sites are disfavored. Applying our approach to individual transcripts reveals variation in the distribution of selective pressure across the transcriptome and between miRNAs, ranging from strong selection acting on a small subset of targets of some miRNAs, to weak selection on many targets for other miRNAs. miR-20 and miR-30, and many other miRNAs, exhibit broad, deeply conserved targeting, while several other comparably ancient miRNAs show a lack of selective constraint, and a small number, including mir-146, exhibit evidence of rapidly evolving target sites. Our approach adds valuable perspective on the evolution of miRNAs and their targets, and can also be applied to characterize other 3'UTR regulatory motifs.
Collapse
Affiliation(s)
- Alfred Simkin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- Department of Biology, Elon University, Elon, North Carolina, United States of America
| | - Rene Geissler
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Alexa B. R. McIntyre
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| |
Collapse
|
12
|
Huang Y, Xiong J, Brown PB, Sun X. Discovery of MicroRNAs from Batrachuperus yenyuanensis Using Deep Sequencing and Prediction of Their Targets. BIOCHEMISTRY (MOSCOW) 2019; 84:380-389. [PMID: 31228929 DOI: 10.1134/s0006297919040059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs), a family of ∼22-nucleotide non-coding single-stranded RNA molecules, are considered as key post-transcriptional regulators of gene expression that regulate various biological processes in living organism. Many miRNAs have been identified in animals; however, few have been reported in Hynobiidae species. The present study is aimed to identify a full repertoire of miRNAs in Batrachuperus yenyuanensis (Yenyuan stream salamander), which would significantly increase our knowledge of miRNAs in amphibians. A small RNA library was constructed from B. yenyuanensis and sequenced using deep sequencing. As a result, 1,717,751 clean reads were obtained, representing 356 known and 80 novel miRNAs. Additionally, expression levels of eight randomly selected miRNAs in B. yenyuanensis were confirmed using the stem-loop quantitative real-time reverse transcription PCR. In addition, 13,972 targets were predicted for these identified miRNAs, although the physiological functions of many of these targets remain unknown. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested that the predicted targets are involved in a variety of physiological regulatory functions in B. yenyuanensis. These results provide useful information for further research on the miRNAs involved in the growth and development of B. yenyuanensis, as well as adaptation of this species to its high-altitude habitats.
Collapse
Affiliation(s)
- Y Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023, China.
| | - J Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023, China.
| | - P B Brown
- Purdue University, Department of Forestry and Natural Resources, West Lafayette, IN 47907, USA
| | - X Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023, China
| |
Collapse
|
13
|
Vaschetto LM, Ortiz N. The Role of Sequence Duplication in Transcriptional Regulation and Genome Evolution. Curr Genomics 2019; 20:405-408. [PMID: 32476997 PMCID: PMC7235390 DOI: 10.2174/1389202920666190320140721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 01/22/2019] [Accepted: 01/24/2019] [Indexed: 12/26/2022] Open
Abstract
Sequence duplication is nowadays recognized as an important mechanism that underlies the evolution of eukaryote genomes, being indeed one of the most powerful strategies for the generation of adaptive diversity by modulating transcriptional activity. The evolutionary novelties simultaneously associated with sequence duplication and differential gene expression can be collectively referred to as duplication-mediated transcriptional regulation. In the last years, evidence has emerged supporting the idea that sequence duplication and functionalization represent important evolutionary strategies acting at the genome level, and both coding and non-coding sequences have been found to be targets of such events. Moreover, it has been proposed that deleterious effects of sequence duplication might be potentially silenced by endogenous cell machinery (i.e., RNA interference, epigenetic repressive marks, etc). Along these lines, our aim is to highlight the role of sequence duplication on transcriptional activity and the importance of both in genome evolution.
Collapse
Affiliation(s)
- Luis M Vaschetto
- Instituto de Diversidad y Ecología Animal, Consejo Nacional de Investigaciones Científicas y Técnicas (IDEA, CONICET), Av. Vélez Sarsfield 299, X5000JJC Córdoba, Argentina.,Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, (FCEFyN, UNC), Av. Vélez Sarsfield 299, X5000JJC Córdoba, Argentina
| | - Natalia Ortiz
- Instituto de Diversidad y Ecología Animal, Consejo Nacional de Investigaciones Científicas y Técnicas (IDEA, CONICET), Av. Vélez Sarsfield 299, X5000JJC Córdoba, Argentina.,Cátedra de Genética de Poblaciones y Evolución, Facultad de Ciencias Exactas, Físicas y Naturales, UNC, Córdoba, Argentina
| |
Collapse
|