1
|
Ta H, Nonomura KI. Profiling of 24-nt phasiRNAs in Rice Anther by Massively Parallel Sequencing and Stem-Loop Reverse Transcription PCR. Methods Mol Biol 2025; 2869:135-146. [PMID: 39499474 DOI: 10.1007/978-1-0716-4204-7_14] [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] [Indexed: 11/07/2024]
Abstract
Small RNAs are highly abundant and play important roles in plant reproduction. Profiling of small RNAs in reproductive tissues is a critical step in understanding their biology. Here, we describe a protocol for small RNA profiling in rice anthers, with a focus on an abundantly expressed but little-understood reproductive small RNA class named 24-nucleotide phased secondary small interfering RNAs (24-nt phasiRNAs). The protocol details small RNA library preparation steps for high-throughput sequencing, with a subsequent bioinformatic analysis framework. A low-throughput stem-loop reverse transcription PCR protocol for quick semi-quantification of small RNAs is also included as a complementary approach. The collective protocol, although focused on 24-nt phasiRNAs, should be amenable to other small RNA classes in various plant reproductive tissues.
Collapse
Affiliation(s)
- Huong Ta
- Plant Cytogenetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Ken-Ichi Nonomura
- Plant Cytogenetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.
- Genetics Course, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan.
| |
Collapse
|
2
|
Hernandez NP, Rawls A, Chen J, Zhang X, Wang Y, Gao X, Parisien M, Karaky M, Meloto CB, Montagna F, Dang H, Pan Y, Zhao Y, McLean S, Linnstaedt S, Diatchenko L, Nackley AG. miR-374 family is a key regulator of chronic primary pain onset. Pain Rep 2024; 9:e1199. [PMID: 39430682 PMCID: PMC11487220 DOI: 10.1097/pr9.0000000000001199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/01/2024] [Accepted: 07/12/2024] [Indexed: 10/22/2024] Open
Abstract
Introduction Chronic primary pain conditions (CPPCs) are linked to catecholamine activation of peripheral adrenergic receptors. Yet, catecholamine-dependent epigenetic mechanisms, such as microRNA (miRNA) regulation of mRNA transcripts, remain largely unknown. Objectives We sought to identify RNA species correlated with case status in 3 pain cohorts, to validate RNAs found to be dysregulated in a mouse model of CPPC onset, and to directly test the role of adrenergic receptors in miRNA regulation. Furthermore, we tested antinociceptive effects of miR-374 overexpression. Methods We used RNA-seq and quantitative reverse transcription polymerase chain reaction to measure RNA expression in 3 pain cohorts. Next, we validated identified RNAs with quantitative reverse transcription polymerase chain reaction in a mouse model of CPPC onset, measuring expression in plasma, peripheral (adipose, muscle, dorsal root ganglia [DRG]), and central (spinal cord) tissues. Then, we stimulated adrenergic receptors in primary adipocyte and DRG cultures to directly test regulation of microRNAs by adrenergic signaling. Furthermore, we used in vitro calcium imaging to measure the antinociceptive effects of miR-374 overexpression. Results We found that one miRNA family, miR-374, was downregulated in the plasma of individuals with temporomandibular disorder, fibromyalgia syndrome, or widespread pain following a motor vehicle collision. miR-374 was also downregulated in plasma, white adipose tissue, and spinal cord from mice with multisite mechanical sensitivity. miR-374 downregulation in plasma and spinal cord was female specific. Norepinephrine stimulation of primary adipocytes, but not DRG, led to decreased miR-374 expression. Furthermore, we identified tissue-specific and sex-specific changes in the expression of predicted miR-374 mRNA targets, including known (HIF1A, NUMB, TGFBR2) and new (ATXN7, CRK-II) pain targets. Finally, we demonstrated that miR-374 overexpression in DRG neurons reduced capsaicin-induced nociceptor activity. Conclusions Downregulation of miR-374 occurs between adrenergic receptor activation and mechanical hypersensitivity, and its adipocyte source implicates adipose signaling in nociception. Further study of miR-374 may inform therapeutic strategies for the millions worldwide who experience CPPCs.
Collapse
Affiliation(s)
- Nathaniel P. Hernandez
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
- Department of Anesthesiology, Center for Translational Pain Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Ashleigh Rawls
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Jiegen Chen
- Department of Anesthesiology, Center for Translational Pain Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Xin Zhang
- Department of Anesthesiology, Center for Translational Pain Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Yaomin Wang
- Department of Anesthesiology, Center for Translational Pain Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Xianglong Gao
- Department of Anesthesiology, Center for Translational Pain Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Marc Parisien
- Alan Edwards Centre for Research on Pain, Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC, Canada
| | - Mohamad Karaky
- Alan Edwards Centre for Research on Pain, Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC, Canada
| | - Carolina Beraldo Meloto
- Alan Edwards Centre for Research on Pain, Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC, Canada
| | - Francesca Montagna
- Alan Edwards Centre for Research on Pain, Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC, Canada
| | - Hong Dang
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yue Pan
- Department of Anesthesiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ying Zhao
- Department of Anesthesiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel McLean
- Department of Anesthesiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah Linnstaedt
- Department of Anesthesiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Luda Diatchenko
- Alan Edwards Centre for Research on Pain, Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC, Canada
| | - Andrea G. Nackley
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
- Department of Anesthesiology, Center for Translational Pain Medicine, Duke University School of Medicine, Durham, NC, USA
| |
Collapse
|
3
|
Pal AK, Gandhivel VHS, Nambiar AB, Shivaprasad PV. Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler. Nat Commun 2024; 15:7807. [PMID: 39242590 PMCID: PMC11379814 DOI: 10.1038/s41467-024-52239-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 08/29/2024] [Indexed: 09/09/2024] Open
Abstract
Genomic imprinting is observed in endosperm, a placenta-like seed tissue, where transposable elements (TEs) and repeat-derived small RNAs (sRNAs) mediate epigenetic changes in plants. In imprinting, uniparental gene expression arises due to parent-specific epigenetic marks on one allele but not on the other. The importance of sRNAs and their regulation in endosperm development or in imprinting is poorly understood in crops. Here we show that a previously uncharacterized CLASSY (CLSY)-family chromatin remodeler named OsCLSY3 is essential for rice endosperm development and imprinting, acting as an upstream player in the sRNA pathway. Comparative transcriptome and genetic analysis indicated its endosperm-preferred expression and its likely paternal imprinted nature. These important features are modulated by RNA-directed DNA methylation (RdDM) of tandemly arranged TEs in its promoter. Upon perturbation of OsCLSY3 in transgenic lines, we observe defects in endosperm development and a loss of around 70% of all sRNAs. Interestingly, well-conserved endosperm-specific sRNAs (siren) that are vital for reproductive fitness in angiosperms are also dependent on OsCLSY3. We observed that many imprinted genes and seed development-associated genes are under the control of OsCLSY3. These results support an essential role of OsCLSY3 in rice endosperm development and imprinting, and propose similar regulatory strategies involving CLSY3 homologs among other cereals.
Collapse
Affiliation(s)
- Avik Kumar Pal
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - Vivek Hari-Sundar Gandhivel
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - Amruta B Nambiar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India.
| |
Collapse
|
4
|
Berube B, Ernst E, Cahn J, Roche B, de Santis Alves C, Lynn J, Scheben A, Grimanelli D, Siepel A, Ross-Ibarra J, Kermicle J, Martienssen RA. Teosinte Pollen Drive guides maize diversification and domestication by RNAi. Nature 2024; 633:380-388. [PMID: 39112710 PMCID: PMC11390486 DOI: 10.1038/s41586-024-07788-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/04/2024] [Indexed: 08/17/2024]
Abstract
Selfish genetic elements contribute to hybrid incompatibility and bias or 'drive' their own transmission1,2. Chromosomal drive typically functions in asymmetric female meiosis, whereas gene drive is normally post-meiotic and typically found in males. Here, using single-molecule and single-pollen genome sequencing, we describe Teosinte Pollen Drive, an instance of gene drive in hybrids between maize (Zea mays ssp. mays) and teosinte mexicana (Z. mays ssp. mexicana) that depends on RNA interference (RNAi). 22-nucleotide small RNAs from a non-coding RNA hairpin in mexicana depend on Dicer-like 2 (Dcl2) and target Teosinte Drive Responder 1 (Tdr1), which encodes a lipase required for pollen viability. Dcl2, Tdr1 and the hairpin are in tight pseudolinkage on chromosome 5, but only when transmitted through the male. Introgression of mexicana into early cultivated maize is thought to have been critical to its geographical dispersal throughout the Americas3, and a tightly linked inversion in mexicana spans a major domestication sweep in modern maize4. A survey of maize traditional varieties and sympatric populations of teosinte mexicana reveals correlated patterns of admixture among unlinked genes required for RNAi on at least four chromosomes that are also subject to gene drive in pollen from synthetic hybrids. Teosinte Pollen Drive probably had a major role in maize domestication and diversification, and offers an explanation for the widespread abundance of 'self' small RNAs in the germ lines of plants and animals.
Collapse
Affiliation(s)
- Benjamin Berube
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Evan Ernst
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jonathan Cahn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Benjamin Roche
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Jason Lynn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, Center for Population Biology and Genome Center, University of California at Davis, Davis, CA, USA
| | - Jerry Kermicle
- Laboratory of Genetics, University of Wisconsin, Madison, WI, USA
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| |
Collapse
|
5
|
Kumar D, Venkadesan S, Prabha R, Begam S, Dutta B, Mishra DC, Chaturvedi KK, Jha GK, Solanke AU, Sevanthi AM. RiceMetaSys: Drought-miR, a one-stop solution for drought responsive miRNAs-mRNA module in rice. Database (Oxford) 2024; 2024:baae076. [PMID: 39167719 PMCID: PMC11338179 DOI: 10.1093/database/baae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/27/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024]
Abstract
MicroRNAs are key players involved in stress responses in plants and reports are available on the role of miRNAs in drought stress response in rice. This work reports the development of a database, RiceMetaSys: Drought-miR, based on the meta-analysis of publicly available sRNA datasets. From 28 drought stress-specific sRNA datasets, we identified 216 drought-responsive miRNAs (DRMs). The major features of the database include genotype-, tissue- and miRNA ID-specific search options and comparison of genotypes to identify common miRNAs. Co-localization of the DRMs with the known quantitative trait loci (QTLs), i.e., meta-QTL regions governing drought tolerance in rice pertaining to different drought adaptive traits, narrowed down this to 37 promising DRMs. To identify the high confidence target genes of DRMs under drought stress, degradome datasets and web resource on drought-responsive genes (RiceMetaSys: DRG) were used. Out of the 216 unique DRMs, only 193 had targets with high stringent parameters. Out of the 1081 target genes identified by Degradome datasets, 730 showed differential expression under drought stress in at least one accession. To retrieve complete information on the target genes, the database has been linked with RiceMetaSys: DRG. Further, we updated the RiceMetaSys: DRGv1 developed earlier with the addition of DRGs identified from RNA-seq datasets from five rice genotypes. We also identified 759 putative novel miRNAs and their target genes employing stringent criteria. Novel miRNA search has all the search options of known miRNAs and additionally, it gives information on their in silico validation features. Simple sequence repeat markers for both the miRNAs and their target genes have also been designed and made available in the database. Network analysis of the target genes identified 60 hub genes which primarily act through abscisic acid pathway and jasmonic acid pathway. Co-localization of the hub genes with the meta-QTL regions governing drought tolerance narrowed down this to 16 most promising DRGs. Database URL: http://14.139.229.201/RiceMetaSys_miRNA Updated database of RiceMetaSys URL: http://14.139.229.201/RiceMetaSysA/Drought/.
Collapse
Affiliation(s)
- Deepesh Kumar
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
- The Graduate School, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | | | - Ratna Prabha
- AKMU, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | - Shbana Begam
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Bipratip Dutta
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
- The Graduate School, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | - Dwijesh C Mishra
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - K K Chaturvedi
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Girish Kumar Jha
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Amolkumar U Solanke
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | | |
Collapse
|
6
|
Vega JM, Podio M, Orjuela J, Siena LA, Pessino SC, Combes MC, Mariac C, Albertini E, Pupilli F, Ortiz JPA, Leblanc O. Chromosome-scale genome assembly and annotation of Paspalum notatum Flüggé var. saurae. Sci Data 2024; 11:891. [PMID: 39152143 PMCID: PMC11329641 DOI: 10.1038/s41597-024-03731-0] [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: 02/19/2024] [Accepted: 08/02/2024] [Indexed: 08/19/2024] Open
Abstract
Paspalum notatum Flüggé is an economically important subtropical fodder grass that is widely used in the Americas. Here, we report a new chromosome-scale genome assembly and annotation of a diploid biotype collected in the center of origin of the species. Using Oxford Nanopore long reads, we generated a 557.81 Mb genome assembly (N50 = 56.1 Mb) with high gene completeness (BUSCO = 98.73%). Genome annotation identified 320 Mb (57.86%) of repetitive elements and 45,074 gene models, of which 36,079 have a high level of confidence. Further characterisation included the identification of 59 miRNA precursors together with their putative targets. The present work provides a comprehensive genomic resource for P. notatum improvement and a reference frame for functional and evolutionary research within the genus.
Collapse
Grants
- PUE 22920160100043CO Consejo Nacional de Investigaciones Científicas y Técnicas (National Scientific and Technical Research Council)
- PIP 11220200101680CO Consejo Nacional de Investigaciones Científicas y Técnicas (National Scientific and Technical Research Council)
- PICT 2019 3414 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- PICT 2019-02153 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- PICT-2017-1956 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- PIP 80020190300021UR Universidad Nacional de Rosario (National University of Rosario)
- 101007438 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)
- 872417 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)
- PRIN 2022Z4HLLJ Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- P2022KFJB5 Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
Collapse
Affiliation(s)
- Juan Manuel Vega
- Laboratorio de Biología Molecular, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR) CONICET-UNR, Facultad de Ciencias Agrarias, Campo Experimental Villarino, Universidad Nacional de Rosario, Zavalla (S2125ZAA), Santa Fe, Argentina
| | - Maricel Podio
- Laboratorio de Biología Molecular, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR) CONICET-UNR, Facultad de Ciencias Agrarias, Campo Experimental Villarino, Universidad Nacional de Rosario, Zavalla (S2125ZAA), Santa Fe, Argentina
| | - Julie Orjuela
- DIADE, Univ. Montpellier, CIRAD, IRD, Montpellier, France
| | - Lorena A Siena
- Laboratorio de Biología Molecular, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR) CONICET-UNR, Facultad de Ciencias Agrarias, Campo Experimental Villarino, Universidad Nacional de Rosario, Zavalla (S2125ZAA), Santa Fe, Argentina
| | - Silvina C Pessino
- Laboratorio de Biología Molecular, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR) CONICET-UNR, Facultad de Ciencias Agrarias, Campo Experimental Villarino, Universidad Nacional de Rosario, Zavalla (S2125ZAA), Santa Fe, Argentina
| | | | - Cedric Mariac
- DIADE, Univ. Montpellier, CIRAD, IRD, Montpellier, France
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06121, Perugia, Italy
| | - Fulvio Pupilli
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR), 06128, Perugia, Italy
| | - Juan Pablo A Ortiz
- Laboratorio de Biología Molecular, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR) CONICET-UNR, Facultad de Ciencias Agrarias, Campo Experimental Villarino, Universidad Nacional de Rosario, Zavalla (S2125ZAA), Santa Fe, Argentina.
| | | |
Collapse
|
7
|
Díez-Sainz E, Milagro FI, Aranaz P, Riezu-Boj JI, Lorente-Cebrián S. MicroRNAs from edible plants reach the human gastrointestinal tract and may act as potential regulators of gene expression. J Physiol Biochem 2024; 80:655-670. [PMID: 38662188 PMCID: PMC11502557 DOI: 10.1007/s13105-024-01023-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
Abstract
MicroRNAs (miRNAs) are small single-stranded non-coding RNA molecules that regulate gene expression at the post-transcriptional level. A cross-kingdom regulatory function has been unveiled for plant miRNAs (xenomiRs), which could shape inter-species interactions of plants with other organisms (bacteria and humans) and thus, be key functional molecules of plant-based food in mammals. However, discrepancies regarding the stability and bioavailability of dietary plant miRNAs on the host cast in doubt whether these molecules could have a significant impact on human physiology. The aim of the present study was to identify miRNAs in edible plants and determine their bioavailability on humans after an acute intake of plant-based products. It was found that plant food, including fruits, vegetables and greens, nuts, legumes, and cereals, contains a wide range of miRNAs. XenomiRs miR156e, miR159 and miR162 were detected in great abundance in edible plants and were present among many plant foods, and thus, they were selected as candidates to analyse their bioavailability in humans. These plant miRNAs resisted cooking processes (heat-treatments) and their relative presence increased in faeces after and acute intake of plant-based foods, although they were not detected in serum. Bioinformatic analysis revealed that these miRNAs could potentially target human and bacterial genes involved in processes such as cell signalling and metabolism. In conclusion, edible plants contain miRNAs, such as miR156e, miR159 and miR162, that could resist degradation during cooking and digestion and reach the distal segments of the gastrointestinal tract. Nevertheless, strategies should be developed to improve their absorption to potentially reach host tissues and organs and modulate human physiology.
Collapse
Affiliation(s)
- Ester Díez-Sainz
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008, Pamplona, Spain
| | - Fermín I Milagro
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008, Pamplona, Spain.
- Navarra Institute for Health Research (IdiSNA), 31008, Pamplona, Spain.
- Centro de Investigación Biomédica en Red Fisiopatología de La Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - Paula Aranaz
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008, Pamplona, Spain
| | - José I Riezu-Boj
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008, Pamplona, Spain
| | - Silvia Lorente-Cebrián
- Department of Pharmacology, Physiology and Legal and Forensic Medicine, Faculty of Health and Sport Science, University of Zaragoza, 50009, Saragossa, Spain
- Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza-CITA, 50013, Saragossa, Spain
- Aragón Health Research Institute (IIS-Aragon), 50009, Saragossa, Spain
| |
Collapse
|
8
|
Sun Y, Yang X, Wu R, Lv S, Li Y, Jia H, Yang Y, Li B, Chen W, Allan AC, Jiang G, Shi YN, Chen K. DNA methylation controlling abscisic acid catabolism responds to light to mediate strawberry fruit ripening. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1718-1734. [PMID: 38896078 DOI: 10.1111/jipb.13681] [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: 01/30/2024] [Accepted: 05/02/2024] [Indexed: 06/21/2024]
Abstract
Phytohormones, epigenetic regulation and environmental factors regulate fruit ripening but their interplay during strawberry fruit ripening remains to be determined. In this study, bagged strawberry fruit exhibited delayed ripening compared with fruit grown in normal light, correlating with reduced abscisic acid (ABA) accumulation. Transcription of the key ABA catabolism gene, ABA 8'-hydroxylase FaCYP707A4, was induced in bagged fruit. With light exclusion whole genome DNA methylation levels were up-regulated, corresponding to a delayed ripening process, while DNA methylation levels in the promoter of FaCYP707A4 were suppressed, correlating with increases in transcript and decreased ABA content. Experiments indicated FaCRY1, a blue light receptor repressed in bagged fruit and FaAGO4, a key protein involved in RNA-directed DNA methylation, could bind to the promoter of FaCYP707A4. The interaction between FaCRY1 and FaAGO4, and an increased enrichment of FaAGO4 directed to the FaCYP707A4 promoter in fruit grown under light suggests FaCRY1 may influence FaAGO4 to modulate the DNA methylation status of the FaCYP707A4 promoter. Furthermore, transient overexpression of FaCRY1, or an increase in FaCRY1 transcription by blue light treatment, increases the methylation level of the FaCYP707A4 promoter, while transient RNA interference of FaCRY1 displayed opposite phenotypes. These findings reveal a mechanism by which DNA methylation influences ABA catabolism, and participates in light-mediated strawberry ripening.
Collapse
Affiliation(s)
- Yunfan Sun
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Xiaofang Yang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Rongrong Wu
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Shouzheng Lv
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Yunduan Li
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Haoran Jia
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Yuying Yang
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Baijun Li
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Wenbo Chen
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Andrew C Allan
- New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Guihua Jiang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yan-Na Shi
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Kunsong Chen
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| |
Collapse
|
9
|
de Oliveira AC, Bovolenta LA, Figueiredo L, Ribeiro ADO, Pereira BJA, de Almeida TRA, Campos VF, Patton JG, Pinhal D. MicroRNA Transcriptomes Reveal Prevalence of Rare and Species-Specific Arm Switching Events During Zebrafish Ontogenesis. Evol Bioinform Online 2024; 20:11769343241263230. [PMID: 39055772 PMCID: PMC11271096 DOI: 10.1177/11769343241263230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/04/2024] [Indexed: 07/27/2024] Open
Abstract
In metazoans, microRNAs (miRNAs) are essential regulators of gene expression, affecting critical cellular processes from differentiation and proliferation, to homeostasis. During miRNA biogenesis, the miRNA strand that loads onto the RNA-induced Silencing Complex (RISC) can vary, leading to changes in gene targeting and modulation of biological pathways. To investigate the impact of these "arm switching" events on gene regulation, we analyzed a diverse range of tissues and developmental stages in zebrafish by comparing 5p and 3p arms accumulation dynamics between embryonic developmental stages, adult tissues, and sexes. We also compared variable arm usage patterns observed in zebrafish to other vertebrates including arm switching data from fish, birds, and mammals. Our comprehensive analysis revealed that variable arm usage events predominantly take place during embryonic development. It is also noteworthy that isomiR occurrence correlates to changes in arm selection evidencing an important role of microRNA distinct isoforms in reinforcing and modifying gene regulation by promoting dynamics switches on miRNA 5p and 3p arms accumulation. Our results shed new light on the emergence and coordination of gene expression regulation and pave the way for future investigations in this field.
Collapse
Affiliation(s)
- Arthur Casulli de Oliveira
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University-UNESP, Botucatu, São Paulo, Brazil
| | - Luiz Augusto Bovolenta
- Department of Structural and Functional Biology, Institute of Biosciences of Botucatu, São Paulo State University-UNESP, Botucatu, São Paulo, Brazil
| | - Lucas Figueiredo
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University-UNESP, Botucatu, São Paulo, Brazil
| | - Amanda De Oliveira Ribeiro
- Department of Structural and Functional Biology, Institute of Biosciences of Botucatu, São Paulo State University-UNESP, Botucatu, São Paulo, Brazil
| | - Beatriz Jacinto Alves Pereira
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University-UNESP, Botucatu, São Paulo, Brazil
| | - Talita Roberto Aleixo de Almeida
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University-UNESP, Botucatu, São Paulo, Brazil
| | - Vinicius Farias Campos
- Laboratory of Structural Genomics, Postgraduate Program in Biotechnology, Center for Technological Development, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville TN, USA
| | - Danillo Pinhal
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University-UNESP, Botucatu, São Paulo, Brazil
| |
Collapse
|
10
|
Edelbroek B, Kjellin J, Jerlström-Hultqvist J, Koskiniemi S, Söderbom F. Chromosome-level genome assembly and annotation of the social amoeba Dictyostelium firmibasis. Sci Data 2024; 11:678. [PMID: 38909042 PMCID: PMC11193728 DOI: 10.1038/s41597-024-03513-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024] Open
Abstract
Dicytostelium firmibasis is a member of Dictyostelia, a group of social amoebae that upon starvation display aggregative multicellularity where the amoebae transition from uni- to multicellular life. The D. firmibasis genome assembly that is currently available is of limited use due to its low contiguity, large number of undetermined bases, and lack of annotations. Here we used Nanopore long read sequencing, complemented with Illumina sequencing, and developmental transcriptomics as well as small RNA-sequencing, to present a new, fully annotated, chromosome-level D. firmibasis genome assembly. The new assembly contains no undetermined bases, and consists mainly of six large contigs representing the chromosomes, as well as a complete mitochondrial genome. This new genome assembly will be a valuable tool, allowing comprehensive comparison to Dictyostelium discoideum, the dictyostelid genetically tractable model. Further, the new genome will be important for studies of evolutionary processes governing the transition from unicellular to multicellular organisms and will aid in the sequencing and annotation of other dictyostelids genomes, many of which are currently of poor quality.
Collapse
Affiliation(s)
- Bart Edelbroek
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden.
| | - Jonas Kjellin
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Jon Jerlström-Hultqvist
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden.
| |
Collapse
|
11
|
Wu X, Chen S, Lin F, Muhammad F, Xu H, Wu L. Comparative and functional analysis unveils the contribution of photoperiod to DNA methylation, sRNA accumulation, and gene expression variations in short-day and long-day grasses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1955-1971. [PMID: 38491864 DOI: 10.1111/tpj.16721] [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: 12/28/2023] [Revised: 02/01/2024] [Accepted: 03/06/2024] [Indexed: 03/18/2024]
Abstract
Photoperiod employs complicated networks to regulate various developmental processes in plants, including flowering transition. However, the specific mechanisms by which photoperiod affects epigenetic modifications and gene expression variations in plants remain elusive. In this study, we conducted a comprehensive analysis of DNA methylation, small RNA (sRNA) accumulation, and gene expressions under different daylengths in facultative long-day (LD) grass Brachypodium distachyon and short-day (SD) grass rice. Our results showed that while overall DNA methylation levels were minimally affected by different photoperiods, CHH methylation levels were repressed under their favorable light conditions, particularly in rice. We identified numerous differentially methylated regions (DMRs) that were influenced by photoperiod in both plant species. Apart from differential sRNA clusters, we observed alterations in the expression of key components of the RNA-directed DNA methylation pathway, DNA methyltransferases, and demethylases, which may contribute to the identified photoperiod-influenced CHH DMRs. Furthermore, we identified many differentially expressed genes in response to different daylengths, some of which were associated with the DMRs. Notably, we discovered a photoperiod-responsive gene MYB11 in the transcriptome of B. distachyon, and further demonstrated its role as a flowering inhibitor by repressing FT1 transcription. Together, our comparative and functional analysis sheds light on the effects of daylength on DNA methylation, sRNA accumulation, and gene expression variations in LD and SD plants, thereby facilitating better designing breeding programs aimed at developing high-yield crops that can adapt to local growing seasons.
Collapse
Affiliation(s)
- Xia Wu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Siyi Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Feng Lin
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Institute, Zhejiang University, Sanya, Hainan, 572000, China
| | - Fahad Muhammad
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Haiming Xu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Liang Wu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Institute, Zhejiang University, Sanya, Hainan, 572000, China
| |
Collapse
|
12
|
Cherubino Ribeiro TH, Baldrich P, de Oliveira RR, Fernandes-Brum CN, Mathioni SM, de Sousa Cardoso TC, de Souza Gomes M, do Amaral LR, Pimenta de Oliveira KK, Dos Reis GL, Meyers BC, Chalfun-Junior A. The floral development of the allotetraploid Coffea arabica L. correlates with a small RNA dynamic reprogramming. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1848-1863. [PMID: 38488203 DOI: 10.1111/tpj.16713] [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: 09/13/2023] [Revised: 12/05/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Noncoding and coding RNAs are key regulators of plant growth, development, and stress responses. To investigate the types of transcripts accumulated during the vegetative to reproductive transition and floral development in the Coffea arabica L., we sequenced small RNA libraries from eight developmental stages, up to anthesis. We combined these data with messenger RNA and PARE sequencing of two important development stages that marks the transition of an apparent latent to a rapid growth stage. In addition, we took advantage of multiple in silico tools to characterize genomic loci producing small RNAs such as phasiRNAs, miRNAs, and tRFs. Our differential and co-expression analysis showed that some types of small RNAs such as tRNAs, snoRNAs, snRNAs, and phasiRNAs preferentially accumulate in a stage-specific manner. Members of the miR482/miR2118 superfamily and their 21-nucleotide phasiRNAs originating from resistance genes show a robust co-expression pattern that is maintained across all the evaluated developmental stages. Finally, the majority of miRNAs accumulate in a family stage-specific manner, related to modulated hormonal responses and transcription factor expression.
Collapse
Affiliation(s)
- Thales Henrique Cherubino Ribeiro
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
| | | | - Raphael Ricon de Oliveira
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
| | - Christiane Noronha Fernandes-Brum
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
| | | | - Thaís Cunha de Sousa Cardoso
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, Lavras, 38700-128, MG, Brazil
| | - Matheus de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, Lavras, 38700-128, MG, Brazil
| | - Laurence Rodrigues do Amaral
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, Lavras, 38700-128, MG, Brazil
| | - Kellen Kauanne Pimenta de Oliveira
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
| | - Gabriel Lasmar Dos Reis
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
| | - Blake C Meyers
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
- Division of Plant Sciences and Technology, University of Missouri-Columbia, Columbia, MI, 65211, USA
| | - Antonio Chalfun-Junior
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
| |
Collapse
|
13
|
Takei T, Tsukada M, Tamura K, Hara-Nishimura I, Fukao Y, Kurihara Y, Matsui M, Saze H, Tsuzuki M, Watanabe Y, Hamada T. ARGONAUTE1-binding Tudor domain proteins function in small interfering RNA production for RNA-directed DNA methylation. PLANT PHYSIOLOGY 2024; 195:1333-1346. [PMID: 38446745 DOI: 10.1093/plphys/kiae135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 03/08/2024]
Abstract
Transposable elements (TEs) contribute to plant evolution, development, and adaptation to environmental changes, but the regulatory mechanisms are largely unknown. RNA-directed DNA methylation (RdDM) is 1 TE regulatory mechanism in plants. Here, we identified that novel ARGONAUTE 1 (AGO1)-binding Tudor domain proteins Precocious dissociation of sisters C/E (PDS5C/E) are involved in 24-nt siRNA production to establish RdDM on TEs in Arabidopsis thaliana. PDS5 family proteins are subunits of the eukaryote-conserved cohesin complex. However, the double mutant lacking angiosperm-specific subfamily PDS5C and PDS5E (pds5c/e) exhibited different developmental phenotypes and transcriptome compared with those of the double mutant lacking eukaryote-conserved subfamily PDS5A and PDS5B (pds5a/b), suggesting that the angiosperm-specific PDS5C/E subfamily has a unique function in angiosperm plants. Proteome and imaging analyses revealed that PDS5C/E interact with AGO1. The pds5c/e double mutant had defects in 24-nt siRNA accumulation and CHH DNA methylation on TEs. In addition, some lncRNAs that accumulated in the pds5c/e mutant were targeted by AGO1-loading 21-nt miRNAs and 21-nt siRNAs. These results indicate that PDS5C/E and AGO1 participate in 24-nt siRNA production for RdDM in the cytoplasm. These findings indicate that angiosperm plants evolved a new regulator, the PDS5C/E subfamily, to control the increase in TEs during angiosperm evolution.
Collapse
Affiliation(s)
- Takahito Takei
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Department of Bioscience, Faculty of Life Science, Okayama University of Science, Okayama 700-0005, Japan
| | - Michio Tsukada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Kentaro Tamura
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | | | - Yoichiro Fukao
- Graduate School of Life Science, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Yukio Kurihara
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Minami Matsui
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Nanobioscience, Department of Life and Environmental System Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Hidetoshi Saze
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Masayuki Tsuzuki
- Faculty of Agriculture and Marine Science, Kochi University, Kochi 783-8502, Japan
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Takahiro Hamada
- Department of Bioscience, Faculty of Life Science, Okayama University of Science, Okayama 700-0005, Japan
| |
Collapse
|
14
|
Ressel S, Kumar S, Bermúdez-Barrientos JR, Gordon K, Lane J, Wu J, Abreu-Goodger C, Schwarze J, Buck A. RNA-RNA interactions between respiratory syncytial virus and miR-26 and miR-27 are associated with regulation of cell cycle and antiviral immunity. Nucleic Acids Res 2024; 52:4872-4888. [PMID: 38412296 PMCID: PMC11109944 DOI: 10.1093/nar/gkae116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 02/01/2024] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
microRNAs (miRNAs) regulate nearly all physiological processes but our understanding of exactly how they function remains incomplete, particularly in the context of viral infections. Here, we adapt a biochemical method (CLEAR-CLIP) and analysis pipeline to identify targets of miRNAs in lung cells infected with Respiratory syncytial virus (RSV). We show that RSV binds directly to miR-26 and miR-27 through seed pairing and demonstrate that these miRNAs target distinct gene networks associated with cell cycle and metabolism (miR-27) and antiviral immunity (miR-26). Many of the targets are de-repressed upon infection and we show that the miR-27 targets most sensitive to miRNA inhibition are those associated with cell cycle. Finally, we demonstrate that high confidence chimeras map to long noncoding RNAs (lncRNAs) and pseudogenes in transcriptional regulatory regions. We validate that a proportion of miR-27 and Argonaute 2 (AGO2) is nuclear and identify a long non-coding RNA (lncRNA) as a miR-27 target that is linked to transcriptional regulation of nearby genes. This work expands the target networks of miR-26 and miR-27 to include direct interactions with RSV and lncRNAs and implicate these miRNAs in regulation of key genes that impact the viral life cycle associated with cell cycle, metabolism, and antiviral immunity.
Collapse
Affiliation(s)
- Sarah Ressel
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sujai Kumar
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | | | - Katrina Gordon
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Julia Lane
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Jin Wu
- Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Cei Abreu-Goodger
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Jürgen Schwarze
- Child Life and Health, Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Amy H Buck
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| |
Collapse
|
15
|
Zhan J, Bélanger S, Lewis S, Teng C, McGregor M, Beric A, Schon MA, Nodine MD, Meyers BC. Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function. Proc Natl Acad Sci U S A 2024; 121:e2402285121. [PMID: 38739785 PMCID: PMC11127045 DOI: 10.1073/pnas.2402285121] [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: 02/04/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024] Open
Abstract
Reproductive phasiRNAs (phased, small interfering RNAs) are broadly present in angiosperms and play crucial roles in sustaining male fertility. While the premeiotic 21-nt (nucleotides) phasiRNAs and meiotic 24-nt phasiRNA pathways have been extensively studied in maize (Zea mays) and rice (Oryza sativa), a third putative category of reproductive phasiRNAs-named premeiotic 24-nt phasiRNAs-have recently been reported in barley (Hordeum vulgare) and wheat (Triticum aestivum). To determine whether premeiotic 24-nt phasiRNAs are also present in maize and related species and begin to characterize their biogenesis and function, we performed a comparative transcriptome and degradome analysis of premeiotic and meiotic anthers from five maize inbred lines and three teosinte species/subspecies. Our data indicate that a substantial subset of the 24-nt phasiRNA loci in maize and teosinte are already highly expressed at the premeiotic phase. The premeiotic 24-nt phasiRNAs are similar to meiotic 24-nt phasiRNAs in genomic origin and dependence on DCL5 (Dicer-like 5) for biogenesis, however, premeiotic 24-nt phasiRNAs are unique in that they are likely i) not triggered by microRNAs, ii) not loaded by AGO18 proteins, and iii) not capable of mediating PHAS precursor cleavage. In addition, we also observed a group of premeiotic 24-nt phasiRNAs in rice using previously published data. Together, our results indicate that the premeiotic 24-nt phasiRNAs constitute a unique class of reproductive phasiRNAs and are present more broadly in the grass family (Poaceae) than previously known.
Collapse
Affiliation(s)
- Junpeng Zhan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan430070, China
- Hubei Hongshan Laboratory, Wuhan430070, China
- Donald Danforth Plant Science Center, St. Louis, MO63132
| | - Sébastien Bélanger
- Donald Danforth Plant Science Center, St. Louis, MO63132
- The James Hutton Institute, Dundee, ScotlandDD2 5DA, United Kingdom
| | - Scott Lewis
- Donald Danforth Plant Science Center, St. Louis, MO63132
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO63130
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, MO63132
- Genome Center, University of California, Davis, CA95616
- Department of Plant Sciences, University of California, Davis, CA95616
| | | | - Aleksandra Beric
- Donald Danforth Plant Science Center, St. Louis, MO63132
- Division of Plant Science and Technology, University of Missouri, Columbia, MO65211
| | - Michael A. Schon
- Laboratory of Molecular Biology, Wageningen University, Wageningen6708 PB, the Netherlands
| | - Michael D. Nodine
- Laboratory of Molecular Biology, Wageningen University, Wageningen6708 PB, the Netherlands
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, St. Louis, MO63132
- Genome Center, University of California, Davis, CA95616
- Department of Plant Sciences, University of California, Davis, CA95616
- Division of Plant Science and Technology, University of Missouri, Columbia, MO65211
| |
Collapse
|
16
|
Gravot A, Liégard B, Quadrana L, Veillet F, Aigu Y, Bargain T, Bénéjam J, Lariagon C, Lemoine J, Colot V, Manzanares-Dauleux MJ, Jubault M. Two adjacent NLR genes conferring quantitative resistance to clubroot disease in Arabidopsis are regulated by a stably inherited epiallelic variation. PLANT COMMUNICATIONS 2024; 5:100824. [PMID: 38268192 PMCID: PMC11121752 DOI: 10.1016/j.xplc.2024.100824] [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: 09/05/2023] [Revised: 12/21/2023] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Clubroot caused by the protist Plasmodiophora brassicae is a major disease affecting cultivated Brassicaceae. Using a combination of quantitative trait locus (QTL) fine mapping, CRISPR-Cas9 validation, and extensive analyses of DNA sequence and methylation patterns, we revealed that the two adjacent neighboring NLR (nucleotide-binding and leucine-rich repeat) genes AT5G47260 and AT5G47280 cooperate in controlling broad-spectrum quantitative partial resistance to the root pathogen P. brassicae in Arabidopsis and that they are epigenetically regulated. The variation in DNA methylation is not associated with any nucleotide variation or any transposable element presence/absence variants and is stably inherited. Variations in DNA methylation at the Pb-At5.2 QTL are widespread across Arabidopsis accessions and correlate negatively with variations in expression of the two genes. Our study demonstrates that natural, stable, and transgenerationally inherited epigenetic variations can play an important role in shaping resistance to plant pathogens by modulating the expression of immune receptors.
Collapse
Affiliation(s)
- Antoine Gravot
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | - Benjamin Liégard
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | - Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), 75005 Paris, France
| | - Florian Veillet
- IGEPP INRAE, Institut Agro, Université de Rennes, 29260 Ploudaniel, France
| | - Yoann Aigu
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | - Tristan Bargain
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | - Juliette Bénéjam
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | | | - Jocelyne Lemoine
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), 75005 Paris, France
| | | | - Mélanie Jubault
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France.
| |
Collapse
|
17
|
Sun MS, Jia Y, Chen XY, Chen JS, Guo Y, Fu FF, Xue LJ. Regulatory microRNAs and phasiRNAs of paclitaxel biosynthesis in Taxus chinensis. FRONTIERS IN PLANT SCIENCE 2024; 15:1403060. [PMID: 38779066 PMCID: PMC11109412 DOI: 10.3389/fpls.2024.1403060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024]
Abstract
Paclitaxel (trade name Taxol) is a rare diterpenoid with anticancer activity isolated from Taxus. At present, paclitaxel is mainly produced by the semi-synthetic method using extract of Taxus tissues as raw materials. The studies of regulatory mechanisms in paclitaxel biosynthesis would promote the production of paclitaxel through tissue/cell culture approaches. Here, we systematically identified 990 transcription factors (TFs), 460 microRNAs (miRNAs), and 160 phased small interfering RNAs (phasiRNAs) in Taxus chinensis to explore their interactions and potential roles in regulation of paclitaxel synthesis. The expression levels of enzyme genes in cone and root were higher than those in leaf and bark. Nearly all enzyme genes in the paclitaxel synthesis pathway were significantly up-regulated after jasmonate treatment, except for GGPPS and CoA Ligase. The expression level of enzyme genes located in the latter steps of the synthesis pathway was significantly higher in female barks than in male. Regulatory TFs were inferred through co-expression network analysis, resulting in the identification of TFs from diverse families including MYB and AP2. Genes with ADP binding and copper ion binding functions were overrepresented in targets of miRNA genes. The miRNA targets were mainly enriched with genes in plant hormone signal transduction, mRNA surveillance pathway, cell cycle and DNA replication. Genes in oxidoreductase activity, protein-disulfide reductase activity were enriched in targets of phasiRNAs. Regulatory networks were further constructed including components of enzyme genes, TFs, miRNAs, and phasiRNAs. The hierarchical regulation of paclitaxel production by miRNAs and phasiRNAs indicates a robust regulation at post-transcriptional level. Our study on transcriptional and posttranscriptional regulation of paclitaxel synthesis provides clues for enhancing paclitaxel production using synthetic biology technology.
Collapse
Affiliation(s)
| | | | | | | | | | - Fang-Fang Fu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Nanjing Forestry University, Nanjing, China
| | - Liang-Jiao Xue
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Nanjing Forestry University, Nanjing, China
| |
Collapse
|
18
|
Edelbroek B, Kjellin J, Biryukova I, Liao Z, Lundberg T, Noegel A, Eichinger L, Friedländer M, Söderbom F. Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity. Nucleic Acids Res 2024; 52:3121-3136. [PMID: 38375870 PMCID: PMC11014262 DOI: 10.1093/nar/gkae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/21/2024] Open
Abstract
MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in both plants and animals. They are thought to have evolved convergently in these lineages and hypothesized to have played a role in the evolution of multicellularity. In line with this hypothesis, miRNAs have so far only been described in few unicellular eukaryotes. Here, we investigate the presence and evolution of miRNAs in Amoebozoa, focusing on species belonging to Acanthamoeba, Physarum and dictyostelid taxonomic groups, representing a range of unicellular and multicellular lifestyles. miRNAs that adhere to both the stringent plant and animal miRNA criteria were identified in all examined amoebae, expanding the total number of protists harbouring miRNAs from 7 to 15. We found conserved miRNAs between closely related species, but the majority of species feature only unique miRNAs. This shows rapid gain and/or loss of miRNAs in Amoebozoa, further illustrated by a detailed comparison between two evolutionary closely related dictyostelids. Additionally, loss of miRNAs in the Dictyostelium discoideum drnB mutant did not seem to affect multicellular development and, hence, demonstrates that the presence of miRNAs does not appear to be a strict requirement for the transition from uni- to multicellular life.
Collapse
Affiliation(s)
- Bart Edelbroek
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| | - Jonas Kjellin
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| | - Inna Biryukova
- Science for Life Laboratory, The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Zhen Liao
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| | - Torgny Lundberg
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| | - Angelika A Noegel
- Centre for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Ludwig Eichinger
- Centre for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Marc R Friedländer
- Science for Life Laboratory, The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| |
Collapse
|
19
|
Enriquez-Felix EE, Pérez-Salazar C, Rico-Ruiz JG, Calheiros de Carvalho A, Cruz-Morales P, Villalobos-Escobedo JM, Herrera-Estrella A. Argonaute and Dicer are essential for communication between Trichoderma atroviride and fungal hosts during mycoparasitism. Microbiol Spectr 2024; 12:e0316523. [PMID: 38441469 PMCID: PMC10986496 DOI: 10.1128/spectrum.03165-23] [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: 08/23/2023] [Accepted: 02/17/2024] [Indexed: 04/06/2024] Open
Abstract
Trichoderma species are known for their mycoparasitic activity against phytopathogenic fungi that cause significant economic losses in agriculture. During mycoparasitism, Trichoderma spp. recognize molecules produced by the host fungus and release secondary metabolites and hydrolytic enzymes to kill and degrade the host's cell wall. Here, we explored the participation of the Trichoderma atroviride RNAi machinery in the interaction with six phytopathogenic fungi of economic importance. We determined that both Argonaute-3 and Dicer-2 play an essential role during mycoparasitism. Using an RNA-Seq approach, we identified that perception, detox, and cell wall degradation depend on the T. atroviride-RNAi when interacting with Alternaria alternata, Rhizoctonia solani AG2, and R. solani AG5. Furthermore, we constructed a gene co-expression network that provides evidence of two gene modules regulated by RNAi, which play crucial roles in essential processes during mycoparasitism. In addition, based on small RNA-seq, we conclude that siRNAs regulate amino acid and carbon metabolism and communication during the Trichoderma-host interaction. Interestingly, our data suggest that siRNAs might regulate allorecognition (het) and transport genes in a cross-species manner. Thus, these results reveal a fine-tuned regulation in T. atroviride dependent on siRNAs that is essential during the biocontrol of phytopathogenic fungi, showing a greater complexity of this process than previously established.IMPORTANCEThere is an increasing need for plant disease control without chemical pesticides to avoid environmental pollution and resistance, and the health risks associated with the application of pesticides are increasing. Employing Trichoderma species in agriculture to control fungal diseases is an alternative plant protection strategy that overcomes these issues without utilizing chemical fungicides. Therefore, understanding the biocontrol mechanisms used by Trichoderma species to antagonize other fungi is critical. Although there has been extensive research about the mechanisms involved in the mycoparasitic capability of Trichoderma species, there are still unsolved questions related to how Trichoderma regulates recognition, attack, and defense mechanisms during interaction with a fungal host. In this work, we report that the Argonaute and Dicer components of the RNAi machinery and the small RNAs they process are essential for gene regulation during mycoparasitism by Trichoderma atroviride.
Collapse
Affiliation(s)
- Eli Efrain Enriquez-Felix
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
| | - Camilo Pérez-Salazar
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
| | - José Guillermo Rico-Ruiz
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
| | | | - Pablo Cruz-Morales
- Novo Nordisk Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- The LatAmBio Initiative, Irapuato, Guanajuato, Mexico
| | - José Manuel Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
- The LatAmBio Initiative, Irapuato, Guanajuato, Mexico
- Plant and Microbial Biology Department, University of California, Berkeley, Carlifornia, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, Carlifornia, USA
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
- The LatAmBio Initiative, Irapuato, Guanajuato, Mexico
| |
Collapse
|
20
|
Zhan J, Bélanger S, Lewis S, Teng C, McGregor M, Beric A, Schon MA, Nodine MD, Meyers BC. Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587306. [PMID: 38617318 PMCID: PMC11014486 DOI: 10.1101/2024.03.29.587306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Reproductive phasiRNAs are broadly present in angiosperms and play crucial roles in sustaining male fertility. While the premeiotic 21-nt phasiRNAs and meiotic 24-nt phasiRNA pathways have been extensively studied in maize (Zea mays) and rice (Oryza sativa), a third putative category of reproductive phasiRNAs-named premeiotic 24-nt phasiRNAs-have recently been reported in barley (Hordeum vulgare) and wheat (Triticum aestivum). To determine whether premeiotic 24-nt phasiRNAs are also present in maize and related species and begin to characterize their biogenesis and function, we performed a comparative transcriptome and degradome analysis of premeiotic and meiotic anthers from five maize inbred lines and three teosinte species/subspecies. Our data indicate that a substantial subset of the 24-nt phasiRNA loci in maize and teosinte are already highly expressed at premeiotic phase. The premeiotic 24-nt phasiRNAs are similar to meiotic 24-nt phasiRNAs in genomic origin and dependence on DCL5 for biogenesis, however, premeiotic 24-nt phasiRNAs are unique in that they are likely (i) not triggered by microRNAs, (ii) not loaded by AGO18 proteins, and (iii) not capable of mediating cis-cleavage. In addition, we also observed a group of premeiotic 24-nt phasiRNAs in rice using previously published data. Together, our results indicate that the premeiotic 24-nt phasiRNAs constitute a unique class of reproductive phasiRNAs and are present more broadly in the grass family (Poaceae) than previously known.
Collapse
Affiliation(s)
- Junpeng Zhan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Sébastien Bélanger
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- The James Hutton Institute, Dundee, Scotland DD2 5DA, UK
| | - Scott Lewis
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63130, USA
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | | | - Aleksandra Beric
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Michael A. Schon
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708 PB, the Netherlands
| | - Michael D. Nodine
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708 PB, the Netherlands
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| |
Collapse
|
21
|
Li G, Chen C, Chen P, Meyers BC, Xia R. sRNAminer: A multifunctional toolkit for next-generation sequencing small RNA data mining in plants. Sci Bull (Beijing) 2024; 69:784-791. [PMID: 38246798 DOI: 10.1016/j.scib.2023.12.049] [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: 10/13/2023] [Revised: 11/25/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024]
Abstract
Small RNAs (sRNAs), found extensively in plants, play an essential role in plant growth and development. Although various sRNA analysis tools have been developed for plants, the use of most of them depends on programming and command-line environments, which is a challenge for many wet-lab biologists. Furthermore, current sRNA analysis tools mostly focus on the analysis of certain type of sRNAs and are resource-intensive, normally demanding an immense amount of time and effort to learn the use of numerous tools or scripts and assemble them into a workable pipeline to get the final results. Here, we present sRNAminer, a powerful stand-alone toolkit with a user-friendly interface that integrates all common functions for the analysis of three major types of plant sRNAs: microRNAs (miRNAs), phased small interfering RNAs (phasiRNAs), and heterochromatic siRNAs (hc-siRNAs). We constructed a curated or "golden" set of MIRNA and PHAS loci, which was used to assess the performance of sRNAminer in comparison to other existing tools. The results showed that sRNAminer outperformed these tools in multiple aspects, highlighting its functionality. In addition, to enable an efficient evaluation of sRNA annotation results, we developed Integrative Genomics Viewer (IGV)-sRNA, a modified genome browser optimized from IGV and we incorporated it as a functional module in sRNAminer. IGV-sRNA can display a wealth of sRNA-specific features, enabling a more comprehensive understanding of sRNA data. sRNAminer and IGV-sRNA are both platform-independent software that can be run under all operating systems. They are now freely available at https://github.com/kli28/sRNAminer and https://gitee.com/CJchen/IGV-sRNA.
Collapse
Affiliation(s)
- Guanliang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510640, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510640, China
| | - Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510640, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510640, China.
| | - Peike Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510640, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510640, China
| | - Blake C Meyers
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA; Division of Plant Science and Technology, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510640, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510640, China.
| |
Collapse
|
22
|
Dew-Budd KJ, Chow HT, Kendall T, David BC, Rozelle JA, Mosher RA, Beilstein MA. Mating system is associated with seed phenotypes upon loss of RNA-directed DNA methylation in Brassicaceae. PLANT PHYSIOLOGY 2024; 194:2136-2148. [PMID: 37987565 DOI: 10.1093/plphys/kiad622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/03/2023] [Accepted: 10/23/2023] [Indexed: 11/22/2023]
Abstract
In plants, de novo DNA methylation is guided by 24-nt short interfering (si)RNAs in a process called RNA-directed DNA methylation (RdDM). Primarily targeted at transposons, RdDM causes transcriptional silencing and can indirectly influence expression of neighboring genes. During reproduction, a small number of siRNA loci are dramatically upregulated in the maternally derived seed coat, suggesting that RdDM might have a special function during reproduction. However, the developmental consequence of RdDM has been difficult to dissect because disruption of RdDM does not result in overt phenotypes in Arabidopsis (Arabidopsis thaliana), where the pathway has been most thoroughly studied. In contrast, Brassica rapa mutants lacking RdDM have a severe seed production defect, which is determined by the maternal sporophytic genotype. To explore the factors that underlie the different phenotypes of these species, we produced RdDM mutations in 3 additional members of the Brassicaceae family: Camelina sativa, Capsella rubella, and Capsella grandiflora. Among these 3 species, only mutations in the obligate outcrosser, C. grandiflora, displayed a seed production defect similar to Brassica rapa mutants, suggesting that mating system is a key determinant for reproductive phenotypes in RdDM mutants.
Collapse
Affiliation(s)
- Kelly J Dew-Budd
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Hiu Tung Chow
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Timmy Kendall
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Brandon C David
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - James A Rozelle
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Rebecca A Mosher
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Mark A Beilstein
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| |
Collapse
|
23
|
Čermák V, Kašpar T, Fischer L. SPT6L, a newly discovered ancestral component of the plant RNA-directed DNA methylation pathway. FRONTIERS IN PLANT SCIENCE 2024; 15:1372880. [PMID: 38576781 PMCID: PMC10991848 DOI: 10.3389/fpls.2024.1372880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/20/2024] [Indexed: 04/06/2024]
Abstract
RNA-directed DNA methylation (RdDM) is driven by small RNAs (sRNAs) complementary to the nascent transcript of RNA polymerase V (Pol V). sRNAs associated with ARGONAUTE (AGO) proteins are tethered to Pol V mainly by the AGO-hook domain of its subunit NRPE1. We found, by in silico analyses, that Pol V strongly colocalizes on chromatin with another AGO-hook protein, SPT6-like (SPT6L), which is a known essential transcription elongation factor of Pol II. Our phylogenetic analysis revealed that SPT6L acquired its AGO-binding capacity already in the most basal streptophyte algae, even before the emergence of Pol V, suggesting that SPT6L might be a driving force behind the RdDM evolution. Since its emergence, SPT6L with the AGO-hook represents the only conserved SPT6 homolog in Viridiplantae, implying that the same protein is involved in both Pol II and Pol V complexes. To better understand the role of SPT6L in the Pol V complex, we characterized genomic loci where these two colocalize and uncovered that DNA methylation there is more dynamic, driven by higher levels of sRNAs often from non-canonical RdDM pathways and more dependent on chromatin modifying and remodeling proteins like MORC. Pol V loci with SPT6L are highly depleted in helitrons but enriched in gene promoters for which locally and temporally precise methylation is necessary. In view of these results, we discuss potential roles of multiple AGO-hook domains present in the Pol V complex and speculate that SPT6L mediates de novo methylation of naïve loci by interconnecting Pol II and Pol V activities.
Collapse
Affiliation(s)
- Vojtěch Čermák
- Laboratory of Plant Cell Biology and Biotechnology, Faculty of Science, Department of Experimental Plant Biology, Charles University, Prague, Czechia
| | | | | |
Collapse
|
24
|
Zhang Y, Huang J, Xie F, Huang Q, Jiao H, Cheng W. Identification of plant microRNAs using convolutional neural network. FRONTIERS IN PLANT SCIENCE 2024; 15:1330854. [PMID: 38567128 PMCID: PMC10985208 DOI: 10.3389/fpls.2024.1330854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/22/2024] [Indexed: 04/04/2024]
Abstract
MicroRNAs (miRNAs) are of significance in tuning and buffering gene expression. Despite abundant analysis tools that have been developed in the last two decades, plant miRNA identification from next-generation sequencing (NGS) data remains challenging. Here, we show that we can train a convolutional neural network to accurately identify plant miRNAs from NGS data. Based on our methods, we also present a user-friendly pure Java-based software package called Small RNA-related Intelligent and Convenient Analysis Tools (SRICATs). SRICATs encompasses all the necessary steps for plant miRNA analysis. Our results indicate that SRICATs outperforms currently popular software tools on the test data from five plant species. For non-commercial users, SRICATs is freely available at https://sourceforge.net/projects/sricats.
Collapse
|
25
|
Gu C, Pei MS, Guo ZH, Wu L, Qi KJ, Wang XP, Liu H, Liu Z, Lang Z, Zhang S. Multi-omics provide insights into the regulation of DNA methylation in pear fruit metabolism. Genome Biol 2024; 25:70. [PMID: 38486226 PMCID: PMC10938805 DOI: 10.1186/s13059-024-03200-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 02/19/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Extensive research has been conducted on fruit development in crops, but the metabolic regulatory networks underlying perennial fruit trees remain poorly understood. To address this knowledge gap, we conduct a comprehensive analysis of the metabolome, proteome, transcriptome, DNA methylome, and small RNAome profiles of pear fruit flesh at 11 developing stages, spanning from fruitlet to ripening. Here, we systematically investigate the metabolic landscape and regulatory network involved. RESULTS We generate an association database consisting of 439 metabolites and 14,399 genes to elucidate the gene regulatory network of pear flesh metabolism. Interestingly, we detect increased DNA methylation in the promoters of most genes within the database during pear flesh development. Application of a DNA methylation inhibitor to the developing fruit represses chlorophyll degradation in the pericarp and promotes xanthophyll, β-carotene, and abscisic acid (ABA) accumulation in the flesh. We find the gradual increase in ABA production during pear flesh development is correlated with the expression of several carotenoid pathway genes and multiple transcription factors. Of these transcription factors, the zinc finger protein PbZFP1 is identified as a positive mediator of ABA biosynthesis in pear flesh. Most ABA pathway genes and transcription factors are modified by DNA methylation in the promoters, although some are induced by the DNA methylation inhibitor. These results suggest that DNA methylation inhibits ABA accumulation, which may delay fruit ripening. CONCLUSION Our findings provide insights into epigenetic regulation of metabolic regulatory networks during pear flesh development, particularly with regard to DNA methylation.
Collapse
Affiliation(s)
- Chao Gu
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mao-Song Pei
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-Hua Guo
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lei Wu
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kai-Jie Qi
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xue-Ping Wang
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong Liu
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Zhaobo Lang
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Shaoling Zhang
- Jiangsu Engineering Research Center for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
26
|
Zayakin P. sRNAflow: A Tool for the Analysis of Small RNA-Seq Data. Noncoding RNA 2024; 10:6. [PMID: 38250806 PMCID: PMC10801628 DOI: 10.3390/ncrna10010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/29/2023] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
The analysis of small RNA sequencing data across a range of biofluids is a significant research area, given the diversity of RNA types that hold potential diagnostic, prognostic, and predictive value. The intricate task of segregating the complex mixture of small RNAs from both human and other species, including bacteria, fungi, and viruses, poses one of the most formidable challenges in the analysis of small RNA sequencing data, currently lacking satisfactory solutions. This study introduces sRNAflow, a user-friendly bioinformatic tool with a web interface designed for the analysis of small RNAs obtained from biological fluids. Tailored to the unique requirements of such samples, the proposed pipeline addresses various challenges, including filtering potential RNAs from reagents and environment, classifying small RNA types, managing small RNA annotation overlap, conducting differential expression assays, analysing isomiRs, and presenting an approach to identify the sources of small RNAs within samples. sRNAflow also encompasses an alternative alignment-free analysis of RNA-seq data, featuring clustering and initial RNA source identification using BLAST. This comprehensive approach facilitates meaningful comparisons of results between different analytical methods.
Collapse
Affiliation(s)
- Pawel Zayakin
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia;
- European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| |
Collapse
|
27
|
Kesidou D, Bennett M, Monteiro JP, McCracken IR, Klimi E, Rodor J, Condie A, Cowan S, Caporali A, Wit JBM, Mountford JC, Brittan M, Beqqali A, Baker AH. Extracellular vesicles from differentiated stem cells contain novel proangiogenic miRNAs and induce angiogenic responses at low doses. Mol Ther 2024; 32:185-203. [PMID: 38096818 PMCID: PMC10787168 DOI: 10.1016/j.ymthe.2023.11.023] [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: 05/16/2023] [Revised: 10/10/2023] [Accepted: 11/22/2023] [Indexed: 01/06/2024] Open
Abstract
Extracellular vesicles (EVs) released from healthy endothelial cells (ECs) have shown potential for promoting angiogenesis, but their therapeutic efficacy remains poorly understood. We have previously shown that transplantation of a human embryonic stem cell-derived endothelial cell product (hESC-ECP), promotes new vessel formation in acute ischemic disease in mice, likely via paracrine mechanism(s). Here, we demonstrated that EVs from hESC-ECPs (hESC-eEVs) significantly increased EC tube formation and wound closure in vitro at ultralow doses, whereas higher doses were ineffective. More important, EVs isolated from the mesodermal stage of the differentiation (hESC-mEVs) had no effect. Small RNA sequencing revealed that hESC-eEVs have a unique transcriptomic profile and are enriched in known proangiogenic microRNAs (miRNAs, miRs). Moreover, an in silico analysis identified three novel hESC-eEV-miRNAs with potential proangiogenic function. Differential expression analysis suggested that two of those, miR-4496 and miR-4691-5p, are highly enriched in hESC-eEVs. Overexpression of miR-4496 or miR-4691-5p resulted in increased EC tube formation and wound closure in vitro, validating the novel proangiogenic function of these miRNAs. In summary, we demonstrated that hESC-eEVs are potent inducers of EC angiogenic response at ultralow doses and contain a unique EV-associated miRNA repertoire, including miR-4496 and miR-4691-5p, with novel proangiogenic function.
Collapse
Affiliation(s)
- Despoina Kesidou
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Matthew Bennett
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - João P Monteiro
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK; Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian R McCracken
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK; Institute of Developmental and Regenerative Medicine, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX3 7TY, UK
| | - Eftychia Klimi
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Julie Rodor
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Alison Condie
- Scottish National Blood Transfusion Service, Edinburgh EH14 4BE, UK
| | - Scott Cowan
- Scottish National Blood Transfusion Service, Edinburgh EH14 4BE, UK
| | - Andrea Caporali
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Jan B M Wit
- Mirabilis Therapeutics BV, Maastricht, the Netherlands
| | | | - Mairi Brittan
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Abdelaziz Beqqali
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK.
| | - Andrew H Baker
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK; CARIM Institute, University of Maastricht, Maastricht 6229HX, the Netherlands.
| |
Collapse
|
28
|
Felgines L, Rymen B, Martins LM, Xu G, Matteoli C, Himber C, Zhou M, Eis J, Coruh C, Böhrer M, Kuhn L, Chicher J, Pandey V, Hammann P, Wohlschlegel J, Waltz F, Law JA, Blevins T. CLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.26.573199. [PMID: 38234754 PMCID: PMC10793415 DOI: 10.1101/2023.12.26.573199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Eukaryotes must balance the need for gene transcription by RNA polymerase II (Pol II) against the danger of mutations caused by transposable element (TE) proliferation. In plants, these gene expression and TE silencing activities are divided between different RNA polymerases. Specifically, RNA polymerase IV (Pol IV), which evolved from Pol II, transcribes TEs to generate small interfering RNAs (siRNAs) that guide DNA methylation and block TE transcription by Pol II. While the Pol IV complex is recruited to TEs via SNF2-like CLASSY (CLSY) proteins, how Pol IV partners with the CLSYs remains unknown. Here we identified a conserved CYC-YPMF motif that is specific to Pol IV and is positioned on the complex exterior. Furthermore, we found that this motif is essential for the co-purification of all four CLSYs with Pol IV, but that only one CLSY is present in any given Pol IV complex. These findings support a "one CLSY per Pol IV" model where the CYC-YPMF motif acts as a CLSY-docking site. Indeed, mutations in and around this motif phenocopy pol iv null mutants. Together, these findings provide structural and functional insights into a critical protein feature that distinguishes Pol IV from other RNA polymerases, allowing it to promote genome stability by targeting TEs for silencing.
Collapse
|
29
|
Díez-Sainz E, Lorente-Cebrián S, Aranaz P, Amri EZ, Riezu-Boj JI, Milagro FI. miR482f and miR482c-5p from edible plant-derived foods inhibit the expression of pro-inflammatory genes in human THP-1 macrophages. Front Nutr 2023; 10:1287312. [PMID: 38099184 PMCID: PMC10719859 DOI: 10.3389/fnut.2023.1287312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/06/2023] [Indexed: 12/17/2023] Open
Abstract
Background Edible plants can exert anti-inflammatory activities in humans, being potentially useful in the treatment of inflammatory diseases. Plant-derived microRNAs have emerged as cross-kingdom gene expression regulators and could act as bioactive molecules involved in the beneficial effects of some edible plants. We investigated the role of edible plant-derived microRNAs in the modulation of pro-inflammatory human genes. Methods MicroRNAs from plant-derived foods were identified by next-generation sequencing. MicroRNAs with inflammatory putative targets were selected, after performing in silico analyses. The expression of candidate plant-derived miRNAs was analyzed by qPCR in edible plant-derived foods and their effects were evaluated in THP-1 monocytes differentiated to macrophages. The bioavailability of candidate plant miRNAs in humans was evaluated in feces and serum samples by qPCR. Results miR482f and miR482c-5p are present in several edible plant-derived foods, such as fruits, vegetables, and cooked legumes and cereals, and fats and oils. Transfections with miR482f and miR482c-5p mimics decreased the gene expression of CLEC7A and NFAM1, and TRL6, respectively, in human THP-1 monocytes differentiated to macrophages, which had an impact on gene expression profile of inflammatory biomarkers. Both microRNAs (miR482f and miR482c-5p) resisted degradation during digestion and were detected in human feces, although not in serum. Conclusion Our findings suggest that miR482f and miR482c-5p can promote an anti-inflammatory gene expression profile in human macrophages in vitro and their bioavailability in humans can be achieved through diet, but eventually restricted at the gut level.
Collapse
Affiliation(s)
- Ester Díez-Sainz
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
| | - Silvia Lorente-Cebrián
- Department of Pharmacology, Physiology and Legal and Forensic Medicine, Faculty of Health and Sport Science, University of Zaragoza, Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza-CITA, Zaragoza, Spain
- Aragón Health Research Institute (IIS-Aragon), Zaragoza, Spain
| | - Paula Aranaz
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | | | - José I. Riezu-Boj
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - Fermín I. Milagro
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
30
|
Ma X, Nie Z, Huang H, Yan C, Li S, Hu Z, Wang Y, Yin H. Small RNA profiling reveals that an ovule-specific microRNA, cja-miR5179, targets a B-class MADS-box gene in Camellia japonica. ANNALS OF BOTANY 2023; 132:1007-1020. [PMID: 37831901 PMCID: PMC10808017 DOI: 10.1093/aob/mcad155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND AND AIMS The functional specialization of microRNA and its target genes is often an important factor in the establishment of spatiotemporal patterns of gene expression that are essential to plant development and growth. In different plant lineages, understanding the functional conservation and divergence of microRNAs remains to be explored. METHODS To identify small regulatory RNAs underlying floral patterning, we performed a tissue-specific profiling of small RNAs in various floral organs from single and double flower varieties (flowers characterized by multiple layers of petals) in Camellia japonica. We identified cja-miR5179, which belongs to a deeply conserved microRNA family that is conserved between angiosperms and basal plants but frequently lost in eudicots. We characterized the molecular function of cja-miR5179 and its target - a B-function MADS-box gene - through gene expression analysis and transient expression assays. KEY RESULTS We showed that cja-miR5179 is exclusively expressed in ovule tissues at the early stage of floral development. We found that cja-miR5179 targets the coding sequences of a DEFICIENS-like B-class gene (CjDEF) mRNA, which is located in the K motif of the MADS-box domain; and the target sites of miR5179/MADS-box were consistent in Camellia and orchids. Furthermore, through a petal transient-expression assay, we showed that the BASIC PENTACYSTEINE proteins bind to the GA-rich motifs in the cja-miR5179 promoter region and suppresses its expression. CONCLUSIONS We propose that the regulation between miR5179 and a B-class MADS-box gene in C. japonica has a deep evolutionary origin before the separation of monocots and dicots. During floral development of C. japonica, cja-miR5179 is specifically expressed in the ovule, which may be required for the inhibition of CjDEF function. This work highlights the evolutionary conservation as well as functional divergence of small RNAs in floral development.
Collapse
Affiliation(s)
- Xianjin Ma
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Ziyan Nie
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Hu Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Chao Yan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- Experimental Center for Subtropical Forestry, Chinese Academy of Forestry, Fenyi, Jiangxi 336600, China
| | - Sijia Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Zhikang Hu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Yupeng Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| |
Collapse
|
31
|
Guo Y, Qi Y, Feng Y, Yang Y, Xue L, El-Kassaby YA, Wang G, Fu F. Inferring the Regulatory Network of miRNAs on Terpene Trilactone Biosynthesis Affected by Environmental Conditions. Int J Mol Sci 2023; 24:17002. [PMID: 38069325 PMCID: PMC10707241 DOI: 10.3390/ijms242317002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
As a medicinal tree species, ginkgo (Ginkgo biloba L.) and terpene trilactones (TTLs) extracted from its leaves are the main pharmacologic activity constituents and important economic indicators of its value. The accumulation of TTLs is known to be affected by environmental stress, while the regulatory mechanism of environmental response mediated by microRNAs (miRNAs) at the post-transcriptional levels remains unclear. Here, we focused on grafted ginkgo grown in northwestern, southwestern, and eastern-central China and integrally analyzed RNA-seq and small RNA-seq high-throughput sequencing data as well as metabolomics data from leaf samples of ginkgo clones grown in natural environments. The content of bilobalide was highest among detected TTLs, and there was more than a twofold variation in the accumulation of bilobalide between growth conditions. Meanwhile, transcriptome analysis found significant differences in the expression of 19 TTL-related genes among ginkgo leaves from different environments. Small RNA sequencing and analysis showed that 62 of the 521 miRNAs identified were differentially expressed among different samples, especially the expression of miRN50, miR169h/i, and miR169e was susceptible to environmental changes. Further, we found that transcription factors (ERF, MYB, C3H, HD-ZIP, HSF, and NAC) and miRNAs (miR319e/f, miRN2, miRN54, miR157, miR185, and miRN188) could activate or inhibit the expression of TTL-related genes to participate in the regulation of terpene trilactones biosynthesis in ginkgo leaves by weighted gene co-regulatory network analysis. Our findings provide new insights into the understanding of the regulatory mechanism of TTL biosynthesis but also lay the foundation for ginkgo leaves' medicinal value improvement under global change.
Collapse
Affiliation(s)
- Ying Guo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Yongli Qi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Yangfan Feng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Yuting Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Liangjiao Xue
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
| | - Guibin Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Fangfang Fu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| |
Collapse
|
32
|
Xie Y, Ying S, Li Z, Zhang Y, Zhu J, Zhang J, Wang M, Diao H, Wang H, Zhang Y, Ye L, Zhuang Y, Zhao F, Teng W, Zhang W, Tong Y, Cho J, Dong Z, Xue Y, Zhang Y. Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat. Nat Commun 2023; 14:7465. [PMID: 37978184 PMCID: PMC10656477 DOI: 10.1038/s41467-023-42771-9] [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: 02/07/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023] Open
Abstract
Transposable elements (TEs) comprise ~85% of the common wheat genome, which are highly diverse among subgenomes, possibly contribute to polyploid plasticity, but the causality is only assumed. Here, by integrating data from gene expression cap analysis and epigenome profiling via hidden Markov model in common wheat, we detect a large proportion of enhancer-like elements (ELEs) derived from TEs producing nascent noncoding transcripts, namely ELE-RNAs, which are well indicative of the regulatory activity of ELEs. Quantifying ELE-RNA transcriptome across typical developmental stages reveals that TE-initiated ELE-RNAs are mainly from RLG_famc7.3 specifically expanded in subgenome A. Acquisition of spike-specific transcription factor binding likely confers spike-specific expression of RLG_famc7.3-initiated ELE-RNAs. Knockdown of RLG_famc7.3-initiated ELE-RNAs resulted in global downregulation of spike-specific genes and abnormal spike development. These findings link TE expansion to regulatory specificity and polyploid developmental plasticity, highlighting the functional impact of TE-driven regulatory innovation on polyploid evolution.
Collapse
Affiliation(s)
- Yilin Xie
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Songbei Ying
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Zijuan Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu'e Zhang
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiafu Zhu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Jinyu Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Meiyue Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Huishan Diao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Haoyu Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- Henan University, School of Life Science, Kaifeng, Henan, 457000, China
| | - Yuyun Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Luhuan Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yili Zhuang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Wan Teng
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Yiping Tong
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jungnam Cho
- Department of Biosciences, Durham University, Durham, DH1 3LE, United Kingdom.
| | - Zhicheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
| | - Yongbiao Xue
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Centre for Bioinformation, Beijing, 100101, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| |
Collapse
|
33
|
Berube B, Ernst E, Cahn J, Roche B, de Santis Alves C, Lynn J, Scheben A, Siepel A, Ross-Ibarra J, Kermicle J, Martienssen R. Teosinte Pollen Drive guides maize diversification and domestication by RNAi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548689. [PMID: 37503269 PMCID: PMC10370002 DOI: 10.1101/2023.07.12.548689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Meiotic drivers subvert Mendelian expectations by manipulating reproductive development to bias their own transmission. Chromosomal drive typically functions in asymmetric female meiosis, while gene drive is normally postmeiotic and typically found in males. Using single molecule and single-pollen genome sequencing, we describe Teosinte Pollen Drive, an instance of gene drive in hybrids between maize (Zea mays ssp. mays) and teosinte mexicana (Zea mays ssp. mexicana), that depends on RNA interference (RNAi). 22nt small RNAs from a non-coding RNA hairpin in mexicana depend on Dicer-Like 2 (Dcl2) and target Teosinte Drive Responder 1 (Tdr1), which encodes a lipase required for pollen viability. Dcl2, Tdr1, and the hairpin are in tight pseudolinkage on chromosome 5, but only when transmitted through the male. Introgression of mexicana into early cultivated maize is thought to have been critical to its geographical dispersal throughout the Americas, and a tightly linked inversion in mexicana spans a major domestication sweep in modern maize. A survey of maize landraces and sympatric populations of teosinte mexicana reveals correlated patterns of admixture among unlinked genes required for RNAi on at least 4 chromosomes that are also subject to gene drive in pollen from synthetic hybrids. Teosinte Pollen Drive likely played a major role in maize domestication and diversification, and offers an explanation for the widespread abundance of "self" small RNAs in the germlines of plants and animals.
Collapse
Affiliation(s)
- Benjamin Berube
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724
| | - Evan Ernst
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724
| | - Jonathan Cahn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724
| | - Benjamin Roche
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724
| | | | - Jason Lynn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724
| | - Jeffrey Ross-Ibarra
- Dept. of Evolution & Ecology, Center for Population Biology and Genome Center, University of California, Davis CA
| | - Jerry Kermicle
- Laboratory of Genetics, University of Wisconsin, Madison WI
| | - Rob Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724
| |
Collapse
|
34
|
Meijer A, Atighi MR, Demeestere K, De Meyer T, Vandepoele K, Kyndt T. Dicer-like 3a mediates intergenerational resistance against root-knot nematodes in rice via hormone responses. PLANT PHYSIOLOGY 2023; 193:2071-2085. [PMID: 37052181 DOI: 10.1093/plphys/kiad215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
In a continuously changing and challenging environment, passing down the memory of encountered stress factors to offspring could provide an evolutionary advantage. In this study, we demonstrate the existence of "intergenerational acquired resistance" in the progeny of rice (Oryza sativa) plants attacked by the belowground parasitic nematode Meloidogyne graminicola. Transcriptome analyses revealed that genes involved in defense pathways are generally downregulated in progeny of nematode-infected plants under uninfected conditions but show a stronger induction upon nematode infection. This phenomenon was termed "spring loading" and depends on initial downregulation by the 24-nucleotide (nt) siRNA biogenesis gene dicer-like 3a (dcl3a) involved in the RNA-directed DNA methylation pathway. Knockdown of dcl3a led to increased nematode susceptibility and abolished intergenerational acquired resistance, as well as jasmonic acid/ethylene spring loading in the offspring of infected plants. The importance of ethylene signaling in intergenerational resistance was confirmed by experiments on a knockdown line of ethylene insensitive 2 (ein2b), which lacks intergenerational acquired resistance. Taken together, these data indicate a role for DCL3a in regulating plant defense pathways during both within-generation and intergenerational resistance against nematodes in rice.
Collapse
Affiliation(s)
- Anikó Meijer
- Department of Biotechnology, Ghent University, Ghent 9000, Belgium
| | - Mohammad Reza Atighi
- Department of Biotechnology, Ghent University, Ghent 9000, Belgium
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, PO Box 14115-336 Tehran, Iran
| | - Kristof Demeestere
- Department of Green Chemistry and Technology, Research group EnVOC, Ghent University, Ghent 9000, Belgium
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent 9000, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent 9052, Belgium
| | - Tina Kyndt
- Department of Biotechnology, Ghent University, Ghent 9000, Belgium
| |
Collapse
|
35
|
Regmi R, Newman TE, Khentry Y, Kamphuis LG, Derbyshire MC. Genome-wide identification of Sclerotinia sclerotiorum small RNAs and their endogenous targets. BMC Genomics 2023; 24:582. [PMID: 37784009 PMCID: PMC10544508 DOI: 10.1186/s12864-023-09686-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Several phytopathogens produce small non-coding RNAs of approximately 18-30 nucleotides (nt) which post-transcriptionally regulate gene expression. Commonly called small RNAs (sRNAs), these small molecules were also reported to be present in the necrotrophic pathogen Sclerotinia sclerotiorum. S. sclerotiorum causes diseases in more than 400 plant species, including the important oilseed crop Brassica napus. sRNAs can further be classified as microRNAs (miRNAs) and short interfering RNAs (siRNAs). Certain miRNAs can activate loci that produce further sRNAs; these secondary sRNA-producing loci are called 'phased siRNA' (PHAS) loci and have only been described in plants. To date, very few studies have characterized sRNAs and their endogenous targets in S. sclerotiorum. RESULTS We used Illumina sequencing to characterize sRNAs from fungal mycelial mats of S. sclerotiorum spread over B. napus leaves. In total, eight sRNA libraries were prepared from in vitro, 12 h post-inoculation (HPI), and 24 HPI mycelial mat samples. Cluster analysis identified 354 abundant sRNA clusters with reads of more than 100 Reads Per Million (RPM). Differential expression analysis revealed upregulation of 34 and 57 loci at 12 and 24 HPI, respectively, in comparison to in vitro samples. Among these, 25 loci were commonly upregulated. Altogether, 343 endogenous targets were identified from the major RNAs of 25 loci. Almost 88% of these targets were annotated as repeat element genes, while the remaining targets were non-repeat element genes. Fungal degradome reads confirmed cleavage of two transposable elements by one upregulated sRNA. Altogether, 24 milRNA loci were predicted with both mature and milRNA* (star) sequences; these are both criteria associated previously with experimentally verified miRNAs. Degradome sequencing data confirmed the cleavage of 14 targets. These targets were related to repeat element genes, phosphate acetyltransferases, RNA-binding factor, and exchange factor. A PHAS gene prediction tool identified 26 possible phased interfering loci with 147 phasiRNAs from the S. sclerotiorum genome, suggesting this pathogen might produce sRNAs that function similarly to miRNAs in higher eukaryotes. CONCLUSIONS Our results provide new insights into sRNA populations and add a new resource for the study of sRNAs in S. sclerotiorum.
Collapse
Affiliation(s)
- Roshan Regmi
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Floreat, WA, 6014, Australia
- Present address: Microbiome for One Systems Health, CSIRO, Urrbrae, South Australia, Australia
| | - Toby E Newman
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Yuphin Khentry
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Floreat, WA, 6014, Australia
| | - Mark C Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
| |
Collapse
|
36
|
Noureddine Y, da Rocha M, An J, Médina C, Mejias J, Mulet K, Quentin M, Abad P, Zouine M, Favery B, Jaubert-Possamai S. AUXIN RESPONSIVE FACTOR8 regulates development of the feeding site induced by root-knot nematodes in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5752-5766. [PMID: 37310189 DOI: 10.1093/jxb/erad208] [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: 11/23/2022] [Accepted: 06/12/2023] [Indexed: 06/14/2023]
Abstract
Root-knot nematodes (RKN) from the genus Meloidogyne induce the dedifferentiation of root vascular cells into giant multinucleate feeding cells. These feeding cells result from an extensive reprogramming of gene expression, and auxin is known to be a key player in their development. However, little is known about how the auxin signal is transmitted during giant cell development. Integrative analyses combining transcriptome and small non-coding RNA datasets with the specific sequencing of cleaved transcripts identified genes targeted by miRNAs in tomato (Solanum lycopersicum) galls. The two auxin-responsive transcription factors ARF8A and ARF8B, and their miRNA167 regulators, were identified as robust gene-miRNA pair candidates to be involved in the tomato response to M. incognita. Spatiotemporal expression analysis using promoter-β-glucuronidase (GUS) fusions showed the up-regulation of ARF8A and ARF8B in RKN-induced feeding cells and surrounding cells. The generation and phenotyping of CRISPR (clustered regularly interspaced palindromic repeats) mutants demonstrated the role of ARF8A and ARF8B in giant cell development and allowed the characterization of their downstream regulated genes.
Collapse
Affiliation(s)
- Yara Noureddine
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Martine da Rocha
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Jing An
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France
| | - Clémence Médina
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Joffrey Mejias
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Karine Mulet
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Michaël Quentin
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Pierre Abad
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Mohamed Zouine
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France
| | - Bruno Favery
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
- International Research Organization for Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | | |
Collapse
|
37
|
Zayakin P, Sadovska L, Eglītis K, Romanchikova N, Radoviča-Spalviņa I, Endzeliņš E, Liepniece-Karele I, Eglītis J, Linē A. Extracellular Vesicles-A Source of RNA Biomarkers for the Detection of Breast Cancer in Liquid Biopsies. Cancers (Basel) 2023; 15:4329. [PMID: 37686605 PMCID: PMC10487078 DOI: 10.3390/cancers15174329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Over the past decade, extracellular vesicles (EVs) have emerged as a promising source of cancer-derived RNAs for liquid biopsies. However, blood contains a pool of heterogeneous EVs released by a variety of cell types, making the identification of cancer RNA biomarkers challenging. Here, we performed deep sequencing of plasma EV RNA cargo in 32 patients with locally advanced breast cancer (BC) at diagnosis and 7 days after breast surgery and in 30 cancer-free healthy controls (HCs). To identify BC-derived RNA biomarkers, we searched for RNAs that had higher levels in BC EVs at the time of diagnosis compared with HCs and decreased after surgery. Data analysis showed that the fractions of miRNAs, snRNAs, snoRNAs, and tRFs were increased, but the fraction of lncRNAs was decreased in BC EVs as compared to HCs. BC-derived biomarker candidates were identified across various RNA biotypes. Considered individually, they had very high specificity but moderate sensitivity for the detection of BC, whereas a biomarker model composed of eight RNAs: SNORD3H, SNORD1C, SNORA74D, miR-224-5p, piR-32949, lnc-IFT-122-2, lnc-C9orf50-4, and lnc-FAM122C-3 was able to distinguish BC from HC EVs with an AUC of 0.902 (95% CI = 0.872-0.931, p = 3.4 × 10-9) in leave-one-out cross-validation. Furthermore, a number of RNA biomarkers were correlated with the ER and HER2 expression and additional biomarker models were created to predict hormone receptor and HER2 status. Overall, this study demonstrated that the RNA composition of plasma EVs is altered in BC patients and that they contain cancer-derived RNA biomarkers that can be used for BC detection and monitoring using liquid biopsies.
Collapse
Affiliation(s)
- Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| | - Lilite Sadovska
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| | - Kristaps Eglītis
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, LV-1038 Riga, Latvia; (K.E.)
| | - Nadezhda Romanchikova
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| | | | - Edgars Endzeliņš
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| | | | - Jānis Eglītis
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, LV-1038 Riga, Latvia; (K.E.)
| | - Aija Linē
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| |
Collapse
|
38
|
Colicchio JM, Amstutz CL, Garcia N, Prabhu KN, Cairns TM, Akman M, Gottilla T, Gollery T, Stricklin SL, Bayer TS. A tool for rapid, automated characterization of population epigenomics in plants. Sci Rep 2023; 13:12915. [PMID: 37591855 PMCID: PMC10435466 DOI: 10.1038/s41598-023-38356-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/06/2023] [Indexed: 08/19/2023] Open
Abstract
Epigenetic variation in plant populations is an important factor in determining phenotype and adaptation to the environment. However, while advances have been made in the molecular and computational methods to analyze the methylation status of a given sample of DNA, tools to profile and compare the methylomes of multiple individual plants or groups of plants at high resolution and low cost are lacking. Here, we describe a computational approach and R package (sounDMR) that leverages the benefits of long read nanopore sequencing to enable robust identification of differential methylation from complex experimental designs, as well as assess the variability within treatment groups and identify individual plants of interest. We demonstrate the utility of this approach by profiling a population of Arabidopsis thaliana exposed to a demethylating agent and identify genomic regions of high epigenetic variability between individuals. Given the low cost of nanopore sequencing devices and the ease of sample preparation, these results show that high resolution epigenetic profiling of plant populations can be made more broadly accessible in plant breeding and biotechnology.
Collapse
Affiliation(s)
| | | | | | | | | | - Melis Akman
- Sound Agriculture Company, Emeryville, CA, USA
| | | | | | | | | |
Collapse
|
39
|
Mann CWG, Sawyer A, Gardiner DM, Mitter N, Carroll BJ, Eamens AL. RNA-Based Control of Fungal Pathogens in Plants. Int J Mol Sci 2023; 24:12391. [PMID: 37569766 PMCID: PMC10418863 DOI: 10.3390/ijms241512391] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Our duty to conserve global natural ecosystems is increasingly in conflict with our need to feed an expanding population. The use of conventional pesticides not only damages the environment and vulnerable biodiversity but can also still fail to prevent crop losses of 20-40% due to pests and pathogens. There is a growing call for more ecologically sustainable pathogen control measures. RNA-based biopesticides offer an eco-friendly alternative to the use of conventional fungicides for crop protection. The genetic modification (GM) of crops remains controversial in many countries, though expression of transgenes inducing pathogen-specific RNA interference (RNAi) has been proven effective against many agronomically important fungal pathogens. The topical application of pathogen-specific RNAi-inducing sprays is a more responsive, GM-free approach to conventional RNAi transgene-based crop protection. The specific targeting of essential pathogen genes, the development of RNAi-nanoparticle carrier spray formulations, and the possible structural modifications to the RNA molecules themselves are crucial to the success of this novel technology. Here, we outline the current understanding of gene silencing pathways in plants and fungi and summarize the pioneering and recent work exploring RNA-based biopesticides for crop protection against fungal pathogens, with a focus on spray-induced gene silencing (SIGS). Further, we discuss factors that could affect the success of RNA-based control strategies, including RNA uptake, stability, amplification, and movement within and between the plant host and pathogen, as well as the cost and design of RNA pesticides.
Collapse
Affiliation(s)
- Christopher W. G. Mann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.W.G.M.); (A.S.); (B.J.C.)
| | - Anne Sawyer
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.W.G.M.); (A.S.); (B.J.C.)
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (D.M.G.); (N.M.)
| | - Donald M. Gardiner
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (D.M.G.); (N.M.)
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (D.M.G.); (N.M.)
| | - Bernard J. Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.W.G.M.); (A.S.); (B.J.C.)
| | - Andrew L. Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| |
Collapse
|
40
|
Li Y, Shi Y, Li Y, Lu J, Sun Y, Zhang Y, Chen W, Yang X, Grierson D, Lang Z, Jiang G, Chen K. DNA methylation mediated by RdDM pathway and demethylation affects furanone accumulation through regulation of QUINONE OXIDOREDUCTASE in strawberry. HORTICULTURE RESEARCH 2023; 10:uhad131. [PMID: 37560014 PMCID: PMC10407599 DOI: 10.1093/hr/uhad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/19/2023] [Indexed: 08/11/2023]
Abstract
Recently, increasing evidence suggests that DNA methylation plays a crucial role in fruit ripening. However, the role of DNA methylation in regulating specific traits, such as flavor, remains unclear. Here, we report a role of DNA methylation in affecting furanone biosynthesis in strawberry. Strawberry quinone oxidoreductase (FaQR) is a key enzyme in furanone biosynthesis. There are four FaQR homologs in strawberry cultivar 'Yuexin', and one of them, FaQR3, contributes ~50% of FaQR transcripts, indicating a major role of FaQR3 in furanone biosynthesis. Through characterization of levels of DNA methylation and FaQR3 transcript and furanone contents during fruit ripening and after the application of DNA methylation inhibitor, we found that the DNA methylation level of the FaQR3 promoter was negatively correlated with FaQR3 expression and furanone accumulation, suggesting that DNA methylation may be involved in furanone biosynthesis through adjusting FaQR3 expression, and responded to different temperatures consistently. In addition, transient expression of a gene in the RNA-directed DNA methylation (RdDM) pathway, FaAGO4, and enrichment analysis of the 24-nucleotide siRNAs suggested that DNA methylation in the FaQR3 promoter is mediated by the RdDM pathway. Transient RNA interference (RNAi) of FaDML indicated that the demethylation pathway may be involved in regulating furanone accumulation. These findings provide new insights into the role of DNA methylation and demethylation in affecting flavor quality in strawberry during fruit ripening.
Collapse
Affiliation(s)
- Yunduan Li
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yanna Shi
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yichen Li
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Jiao Lu
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yunfan Sun
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yuanyuan Zhang
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Wenbo Chen
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Xiaofang Yang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Donald Grierson
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Zhaobo Lang
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guihua Jiang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Kunsong Chen
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| |
Collapse
|
41
|
Signor S, Vedanayagam J, Kim BY, Wierzbicki F, Kofler R, Lai EC. Rapid evolutionary diversification of the flamenco locus across simulans clade Drosophila species. PLoS Genet 2023; 19:e1010914. [PMID: 37643184 PMCID: PMC10495008 DOI: 10.1371/journal.pgen.1010914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 09/11/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Suppression of transposable elements (TEs) is paramount to maintain genomic integrity and organismal fitness. In D. melanogaster, the flamenco locus is a master suppressor of TEs, preventing the mobilization of certain endogenous retrovirus-like TEs from somatic ovarian support cells to the germline. It is transcribed by Pol II as a long (100s of kb), single-stranded, primary transcript, and metabolized into ~24-32 nt Piwi-interacting RNAs (piRNAs) that target active TEs via antisense complementarity. flamenco is thought to operate as a trap, owing to its high content of recent horizontally transferred TEs that are enriched in antisense orientation. Using newly-generated long read genome data, which is critical for accurate assembly of repetitive sequences, we find that flamenco has undergone radical transformations in sequence content and even copy number across simulans clade Drosophilid species. Drosophila simulans flamenco has duplicated and diverged, and neither copy exhibits synteny with D. melanogaster beyond the core promoter. Moreover, flamenco organization is highly variable across D. simulans individuals. Next, we find that D. simulans and D. mauritiana flamenco display signatures of a dual-stranded cluster, with ping-pong signals in the testis and/or embryo. This is accompanied by increased copy numbers of germline TEs, consistent with these regions operating as functional dual-stranded clusters. Overall, the physical and functional diversity of flamenco orthologs is testament to the extremely dynamic consequences of TE arms races on genome organization, not only amongst highly related species, but even amongst individuals.
Collapse
Affiliation(s)
- Sarah Signor
- Biological Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Jeffrey Vedanayagam
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
- Department of Neuroscience, Developmental and Regenerative Biology, University of Texas at San Antonio, Texas, United States of America
| | - Bernard Y. Kim
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Filip Wierzbicki
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Eric C. Lai
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
| |
Collapse
|
42
|
Bakirbas A, Castro-Rodriguez R, Walker EL. The Small RNA Component of Arabidopsis thaliana Phloem Sap and Its Response to Iron Deficiency. PLANTS (BASEL, SWITZERLAND) 2023; 12:2782. [PMID: 37570935 PMCID: PMC10421156 DOI: 10.3390/plants12152782] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 08/13/2023]
Abstract
In order to discover sRNA that might function during iron deficiency stress, RNA was prepared from phloem exudates of Arabidopsis thaliana, and used for RNA-seq. Bioanalyzer results indicate that abundant RNA from phloem is small in size-less than 200 nt. Moreover, typical rRNA bands were not observed. Sequencing of eight independent phloem RNA samples indicated that tRNA-derived fragments, specifically 5' tRFs and 5' tRNA halves, are highly abundant in phloem sap, comprising about 46% of all reads. In addition, a set of miRNAs that are present in phloem sap was defined, and several miRNAs and sRNAs were identified that are differentially expressed during iron deficiency.
Collapse
Affiliation(s)
- Ahmet Bakirbas
- Biology Department and Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA;
| | | | - Elsbeth L. Walker
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
| |
Collapse
|
43
|
Payne D, Li Y, Govindan G, Kumar A, Thomas J, Addo-Quaye CA, Pereira A, Sunkar R. High Daytime Temperature Responsive MicroRNA Profiles in Developing Grains of Rice Varieties with Contrasting Chalkiness. Int J Mol Sci 2023; 24:11631. [PMID: 37511395 PMCID: PMC10380806 DOI: 10.3390/ijms241411631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
High temperature impairs starch biosynthesis in developing rice grains and thereby increases chalkiness, affecting the grain quality. Genome encoded microRNAs (miRNAs) fine-tune target transcript abundances in a spatio-temporal specific manner, and this mode of gene regulation is critical for a myriad of developmental processes as well as stress responses. However, the role of miRNAs in maintaining rice grain quality/chalkiness during high daytime temperature (HDT) stress is relatively unknown. To uncover the role of miRNAs in this process, we used five contrasting rice genotypes (low chalky lines Cyp, Ben, and KB and high chalky lines LaGrue and NB) and compared the miRNA profiles in the R6 stage caryopsis samples from plants subjected to prolonged HDT (from the onset of fertilization through R6 stage of caryopsis development). Our small RNA analysis has identified approximately 744 miRNAs that can be grouped into 291 families. Of these, 186 miRNAs belonging to 103 families are differentially regulated under HDT. Only two miRNAs, Osa-miR444f and Osa-miR1866-5p, were upregulated in all genotypes, implying that the regulations greatly varied between the genotypes. Furthermore, not even a single miRNA was commonly up/down regulated specifically in the three tolerant genotypes. However, three miRNAs (Osa-miR1866-3p, Osa-miR5150-3p and canH-miR9774a,b-3p) were commonly upregulated and onemiRNA (Osa-miR393b-5p) was commonly downregulated specifically in the sensitive genotypes (LaGrue and NB). These observations suggest that few similarities exist within the low chalky or high chalky genotypes, possibly due to high genetic variation. Among the five genotypes used, Cypress and LaGrue are genetically closely related, but exhibit contrasting chalkiness under HDT, and thus, a comparison between them is most relevant. This comparison revealed a general tendency for Cypress to display miRNA regulations that could decrease chalkiness under HDT compared with LaGrue. This study suggests that miRNAs could play an important role in maintaining grain quality in HDT-stressed rice.
Collapse
Affiliation(s)
- David Payne
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Yongfang Li
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ganesan Govindan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Anuj Kumar
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Julie Thomas
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Charles A Addo-Quaye
- Department of Computer Science and Cybersecurity, Metropolitan State University, Saint Paul, MN 55106, USA
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| |
Collapse
|
44
|
Liu ZW, Liu J, Liu F, Zhong X. Depositing centromere repeats induces heritable intragenic heterochromatin establishment and spreading in Arabidopsis. Nucleic Acids Res 2023; 51:6039-6054. [PMID: 37094065 PMCID: PMC10325890 DOI: 10.1093/nar/gkad306] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 04/10/2023] [Accepted: 04/19/2023] [Indexed: 04/26/2023] Open
Abstract
Stable transmission of non-DNA-sequence-based epigenetic information contributes to heritable phenotypic variants and thus to biological diversity. While studies on spontaneous natural epigenome variants have revealed an association of epialleles with a wide range of biological traits in both plants and animals, the function, transmission mechanism, and stability of an epiallele over generations in a locus-specific manner remain poorly investigated. Here, we invented a DNA sequence deposition strategy to generate a locus-specific epiallele by depositing CEN180 satellite repeats into a euchromatic target locus in Arabidopsis. Using CRISPR/Cas9-mediated knock-in system, we demonstrated that depositing CEN180 repeats can induce heterochromatin nucleation accompanied by DNA methylation, H3K9me2, and changes in the nucleosome occupancy at the insertion sites. Interestingly, both DNA methylation and H3K9me2 are restricted within the depositing sites and depletion of an H3K9me2 demethylase IBM1 enables the outward heterochromatin propagation into the neighboring regions, leading to inheritable target gene silencing to persist for at least five generations. Together, these results demonstrate the promise of employing a cis-engineering system for the creation of stable and site-specific epialleles and provide important insights into functional epigenome studies and locus-specific transgenerational epigenetic inheritance.
Collapse
Affiliation(s)
- Zhang-Wei Liu
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
- Wisconsin Institute for Discovery & Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jie Liu
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
- Wisconsin Institute for Discovery & Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Xuehua Zhong
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
- Wisconsin Institute for Discovery & Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
45
|
Rego N, Libisch MG, Rovira C, Tosar JP, Robello C. Comparative microRNA profiling of Trypanosoma cruzi infected human cells. Front Cell Infect Microbiol 2023; 13:1187375. [PMID: 37424776 PMCID: PMC10322668 DOI: 10.3389/fcimb.2023.1187375] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction Trypanosoma cruzi, the causative agent of Chagas disease, can infect almost any nucleated cell in the mammalian host. Although previous studies have described the transcriptomic changes that occur in host cells during parasite infection, the understanding of the role of post-transcriptional regulation in this process is limited. MicroRNAs, a class of short non-coding RNAs, are key players in regulating gene expression at the post-transcriptional level, and their involvement in the host-T. cruzi interplay is a growing area of research. However, to our knowledge, there are no comparative studies on the microRNA changes that occur in different cell types in response to T. cruzi infection. Methods and results Here we investigated microRNA changes in epithelial cells, cardiomyocytes and macrophages infected with T. cruzi for 24 hours, using small RNA sequencing followed by careful bioinformatics analysis. We show that, although microRNAs are highly cell type-specific, a signature of three microRNAs -miR-146a, miR-708 and miR-1246, emerges as consistently responsive to T. cruzi infection across representative human cell types. T. cruzi lacks canonical microRNA-induced silencing mechanisms and we confirm that it does not produce any small RNA that mimics known host microRNAs. We found that macrophages show a broad response to parasite infection, while microRNA changes in epithelial and cardiomyocytes are modest. Complementary data indicated that cardiomyocyte response may be greater at early time points of infection. Conclusions Our findings emphasize the significance of considering microRNA changes at the cellular level and complement previous studies conducted at higher organizational levels, such as heart samples. While miR-146a has been previously implicated in T. cruzi infection, similarly to its involvement in many other immunological responses, miR-1246 and miR-708 are demonstrated here for the first time. Given their expression in multiple cell types, we anticipate our work as a starting point for future investigations into their role in the post-transcriptional regulation of T. cruzi infected cells and their potential as biomarkers for Chagas disease.
Collapse
Affiliation(s)
- Natalia Rego
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - María Gabriela Libisch
- Laboratorio de Interacciones Hospedero Patógeno/UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Carlos Rovira
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden
| | - Juan Pablo Tosar
- Laboratorio de Genómica Funcional, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Unidad de Bioquímica Analítica, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Carlos Robello
- Laboratorio de Interacciones Hospedero Patógeno/UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| |
Collapse
|
46
|
Manley BF, Lotharukpong JS, Barrera-Redondo J, Llewellyn T, Yildirir G, Sperschneider J, Corradi N, Paszkowski U, Miska EA, Dallaire A. A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis. G3 (BETHESDA, MD.) 2023; 13:jkad077. [PMID: 36999556 PMCID: PMC10234402 DOI: 10.1093/g3journal/jkad077] [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: 12/15/2022] [Accepted: 03/17/2023] [Indexed: 06/02/2023]
Abstract
The root systems of most plant species are aided by the soil-foraging capacities of symbiotic arbuscular mycorrhizal (AM) fungi of the Glomeromycotina subphylum. Despite recent advances in our knowledge of the ecology and molecular biology of this mutualistic symbiosis, our understanding of the AM fungi genome biology is just emerging. Presented here is a close to T2T genome assembly of the model AM fungus Rhizophagus irregularis DAOM197198, achieved through Nanopore long-read DNA sequencing and Hi-C data. This haploid genome assembly of R. irregularis, alongside short- and long-read RNA-Sequencing data, was used to produce a comprehensive annotation catalog of gene models, repetitive elements, small RNA loci, and DNA cytosine methylome. A phylostratigraphic gene age inference framework revealed that the birth of genes associated with nutrient transporter activity and transmembrane ion transport systems predates the emergence of Glomeromycotina. While nutrient cycling in AM fungi relies on genes that existed in ancestor lineages, a burst of Glomeromycotina-restricted genetic innovation is also detected. Analysis of the chromosomal distribution of genetic and epigenetic features highlights evolutionarily young genomic regions that produce abundant small RNAs, suggesting active RNA-based monitoring of genetic sequences surrounding recently evolved genes. This chromosome-scale view of the genome of an AM fungus genome reveals previously unexplored sources of genomic novelty in an organism evolving under an obligate symbiotic life cycle.
Collapse
Affiliation(s)
- Bethan F Manley
- SPUN|Society for the Protection of Underground Networks, 3500 South DuPont Highway, Suite EI-101, Dover, DE 19901, USA
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Jaruwatana S Lotharukpong
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, Tübingen 72076, Germany
| | - Josué Barrera-Redondo
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, Tübingen 72076, Germany
| | - Theo Llewellyn
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond TW9 3DS, UK
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Gokalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, ON, Canada K1N 6N5
| | - Jana Sperschneider
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, Canada K1N 6N5
| | - Uta Paszkowski
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge CB3 0LE, UK
| | - Eric A Miska
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Alexandra Dallaire
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond TW9 3DS, UK
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| |
Collapse
|
47
|
Natali L, Luna Pizarro G, Moyano S, de la Cruz-Thea B, Musso J, Rópolo AS, Eichner N, Meister G, Musri MM, Feliziani C, Touz MC. The Exosome-like Vesicles of Giardia Assemblages A, B, and E Are Involved in the Delivering of Distinct Small RNA from Parasite to Parasite. Int J Mol Sci 2023; 24:ijms24119559. [PMID: 37298511 DOI: 10.3390/ijms24119559] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/27/2023] [Accepted: 04/03/2023] [Indexed: 06/12/2023] Open
Abstract
The genetically related assemblages of the intestinal protozoa parasite Giardia lamblia are morphologically indistinguishable and are often derived from specific hosts. The Giardia assemblages are separated by large genetic distances, which might account for their relevant biological and pathogenic differences. In this work, we analyzed the RNAs cargo released into exosomal-like vesicles (ElVs) by the assemblages A and B, which differentially infect humans, and the assemblage E, which infects hoofed animals. The RNA sequencing analysis revealed that the ElVs of each assemblage contained distinct small RNA (sRNA) biotypes, suggesting a preference for specific packaging in each assemblage. These sRNAs were classified into three categories, ribosomal-small RNAs (rsRNAs), messenger-small RNAs (msRNAs), and transfer-small RNAs (tsRNAs), which may play a regulatory role in parasite communication and contribute to host-specificity and pathogenesis. Uptake experiments showed, for the first time, that ElVs were successfully internalized by the parasite trophozoites. Furthermore, we observed that the sRNAs contained inside these ElVs were first located below the plasma membrane but then distributed along the cytoplasm. Overall, the study provides new insights into the molecular mechanisms underlying the host-specificity and pathogenesis of G. lamblia and highlights the potential role of sRNAs in parasite communication and regulation.
Collapse
Affiliation(s)
- Lautaro Natali
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Gabriel Luna Pizarro
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Sofía Moyano
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Benjamin de la Cruz-Thea
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Juliana Musso
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Andrea S Rópolo
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Norbert Eichner
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Melina M Musri
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Constanza Feliziani
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - María C Touz
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| |
Collapse
|
48
|
Singh A, AT V, Gupta K, Sharma S, Kumar S. Long non-coding RNA and microRNA landscape of two major domesticated cotton species. Comput Struct Biotechnol J 2023; 21:3032-3044. [PMID: 37266406 PMCID: PMC10229759 DOI: 10.1016/j.csbj.2023.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/03/2023] Open
Abstract
Allotetraploid cotton plants Gossypium hirsutum and Gossypium barbadense have been widely cultivated for their natural, renewable textile fibres. Even though ncRNAs in domesticated cotton species have been extensively studied, systematic identification and annotation of lncRNAs and miRNAs expressed in various tissues and developmental stages under various biological contexts are limited. This influences the comprehension of their functions and future research on these cotton species. Here, we report high confidence lncRNAs and miRNA collection from G. hirsutum accession and G. barbadense accession using large-scale RNA-seq and small RNA-seq datasets incorporated into a user-friendly database, CoNCRAtlas. This database provides a wide range and depth of lncRNA and miRNA annotation based on the systematic integration of extensive annotations such as expression patterns derived from transcriptome data analysis in thousands of samples, as well as multi-omics annotations. We assume this comprehensive resource will accelerate evolutionary and functional studies in ncRNAs and inform future breeding programs for cotton improvement. CoNCRAtlas is accessible at http://www.nipgr.ac.in/CoNCRAtlas/.
Collapse
Affiliation(s)
- Ajeet Singh
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
- Postdoctoral Associate, Ophthalmology, Baylor College of Medicine, Houston, TX, USA
| | - Vivek AT
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Kanika Gupta
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Shruti Sharma
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Shailesh Kumar
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| |
Collapse
|
49
|
Hari Sundar G V, Swetha C, Basu D, Pachamuthu K, Raju S, Chakraborty T, Mosher RA, Shivaprasad PV. Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains. Genome Res 2023; 33:715-728. [PMID: 37277199 PMCID: PMC10317121 DOI: 10.1101/gr.277353.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/16/2023] [Indexed: 06/07/2023]
Abstract
Across eukaryotes, gene regulation is manifested via chromatin states roughly distinguished as heterochromatin and euchromatin. The establishment, maintenance, and modulation of the chromatin states is mediated using several factors including chromatin modifiers. However, factors that avoid the intrusion of silencing signals into protein-coding genes are poorly understood. Here we show that a plant specific paralog of RNA polymerase (Pol) II, named Pol IV, is involved in avoidance of facultative heterochromatic marks in protein-coding genes, in addition to its well-established functions in silencing repeats and transposons. In its absence, H3K27 trimethylation (me3) mark intruded the protein-coding genes, more profoundly in genes embedded with repeats. In a subset of genes, spurious transcriptional activity resulted in small(s) RNA production, leading to post-transcriptional gene silencing. We show that such effects are significantly pronounced in rice, a plant with a larger genome with distributed heterochromatin compared with Arabidopsis Our results indicate the division of labor among plant-specific polymerases, not just in establishing effective silencing via sRNAs and DNA methylation but also in influencing chromatin boundaries.
Collapse
Affiliation(s)
- Vivek Hari Sundar G
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
| | - Chenna Swetha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
| | - Debjani Basu
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
| | - Kannan Pachamuthu
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
| | - Steffi Raju
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
| | - Tania Chakraborty
- School of Plant Sciences, The University of Arizona, Tucson, Arizona 85721, USA
| | - Rebecca A Mosher
- School of Plant Sciences, The University of Arizona, Tucson, Arizona 85721, USA
| | - P V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India;
| |
Collapse
|
50
|
Wajnberg G, Allain EP, Roy JW, Srivastava S, Saucier D, Morin P, Marrero A, O’Connell C, Ghosh A, Lewis SM, Ouellette RJ, Crapoulet N. Application of annotation-agnostic RNA sequencing data analysis tools for biomarker discovery in liquid biopsy. FRONTIERS IN BIOINFORMATICS 2023; 3:1127661. [PMID: 37252342 PMCID: PMC10213969 DOI: 10.3389/fbinf.2023.1127661] [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: 12/19/2022] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
RNA sequencing analysis is an important field in the study of extracellular vesicles (EVs), as these particles contain a variety of RNA species that may have diagnostic, prognostic and predictive value. Many of the bioinformatics tools currently used to analyze EV cargo rely on third-party annotations. Recently, analysis of unannotated expressed RNAs has become of interest, since these may provide complementary information to traditional annotated biomarkers or may help refine biological signatures used in machine learning by including unknown regions. Here we perform a comparative analysis of annotation-free and classical read-summarization tools for the analysis of RNA sequencing data generated for EVs isolated from persons with amyotrophic lateral sclerosis (ALS) and healthy donors. Differential expression analysis and digital-droplet PCR validation of unannotated RNAs also confirmed their existence and demonstrates the usefulness of including such potential biomarkers in transcriptome analysis. We show that find-then-annotate methods perform similarly to standard tools for the analysis of known features, and can also identify unannotated expressed RNAs, two of which were validated as overexpressed in ALS samples. We demonstrate that these tools can therefore be used for a stand-alone analysis or easily integrated into current workflows and may be useful for re-analysis as annotations can be integrated post hoc.
Collapse
Affiliation(s)
| | - Eric P. Allain
- Atlantic Cancer Research Institute, Moncton, NB, Canada
- Department of Clinical Genetics, Vitalité Health Network, Dr. Georges-L.-Dumont University Hospital Centre, Moncton, NB, Canada
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Jeremy W. Roy
- Atlantic Cancer Research Institute, Moncton, NB, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | | | - Daniel Saucier
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
| | - Pier Morin
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
| | - Alier Marrero
- Dr. Georges-L.-Dumont University Hospital Centre, Moncton, NB, Canada
| | | | - Anirban Ghosh
- Atlantic Cancer Research Institute, Moncton, NB, Canada
| | - Stephen M. Lewis
- Atlantic Cancer Research Institute, Moncton, NB, Canada
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Rodney J. Ouellette
- Atlantic Cancer Research Institute, Moncton, NB, Canada
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
- Dr. Georges-L.-Dumont University Hospital Centre, Moncton, NB, Canada
| | | |
Collapse
|