Circular and Micro RNAs from Arabidopsis thaliana Flowers Are Simultaneously Isolated from AGO-IP Libraries
Abstract
:1. Introduction
2. Results
2.1. Identification of circRNAs in AGO-IP Libraries
2.2. circRNAs with miRNA Binding Sites
2.3. The circRNAs Harbor Reverse Complementary Sequences of miRNAs which Targeted mRNAs Present in AGO-IP Libraries
2.4. circRNAs Validation by RT-PCR and Sequencing
3. Discussion
4. Materials and Methods
4.1. mRNAseq and Small RNAs Libraries
4.2. circRNAs Identification in mRNAseq Libraries from AGO-IP
4.3. Analysis of Target mRNAs and miRNAs Counts in AGO-IP and Control Libraries
4.4. Plant Material and Growth Condition
4.5. RNA Extraction, RNase R Treatment and cDNA Synthesis
4.6. Primers Design
4.7. circRNAs and Parental mRNAs Amplification and Sequencing
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Identification Method | CircExplorer2 | FindCirc | TestRealign | |||
---|---|---|---|---|---|---|
Segemehl | Star | Tophat | - | - | ||
CircExplorer2 | Segemehl | 86 | 9 | 12 | 10 | 26 |
Star | - | 15 | 7 | 3 | 3 | |
Tophat | - | - | 23 | 7 | 7 | |
FindCirc | - | - | - | 1422 | 198 | |
TestRealign | - | - | - | - | 27,812 |
Library | Gene_ID | Circ_ID | Parental Gene Function | Origin | Exons | Length (nt) *** | Methods |
---|---|---|---|---|---|---|---|
DDH-IP | At1g02560 | circ_At1g02560 | Nuclear encoded CLP protease 5 | exonic | 2 | 123 | 5 |
DDH-IP | At1g12080 ** | circ_At1g12080 | Vacuolar calcium-binding protein-related | exonic * | 1 | 95 | 4 |
DDH-IP | At1g31810 | circ_At1g31810 | Formin Homology 14 | exonic | 1 | 50 | 3 |
DDH-IP | At1g52360 | circ_At1g52360 | Coatomer beta subunit | intronic | 1 | 224 | 3 |
DDH-IP | At2g02410 | circ_At2g02410 | K06962—uncharacterized protein (K06962) | exonic | 1 | 71 | 4 |
DDH-IP | At2g35940 ** | circ_At2g35940 | BEL1-like homeodomain 1 | exonic | 1 | 930 | 4 |
DDH-IP | At2g42170 ** | circ_At2g42170 | Actin family protein | exonic | 4 | 1063 | 5 |
DDH-IP | At5g16880 | circ_At5g16880 | Target of Myb protein 1 | exonic * | 1 | 49 | 4 |
DDH-IP | At5g56950 | circ_At5g56950 | NAP-1 Nucleosome assembly protein | intronic * | 1 | 118 | 4 |
DAH-IP | At3g01800 | circ_At3g01800 | Ribosome recycling factor | exonic | 1 | 68 | 4 |
DAH-IP | At3g13990 ** | circ_At3g13990 | Kinase-related protein (DUF1296) | exonic | 3 | 349 | 3 |
DAH-IP | At5g27720 ** | circ_At5g27720 | Small nuclear ribonucleoprotein family protein | exonic | 4 | 321 | 5 |
circRNA | circRNA Read Counts *** | miRNA | miRNA Read Counts | Inhibiton By | |||
---|---|---|---|---|---|---|---|
AGO-IP | Total RNA | AGO1-DDH | AGO1-DAH | Empty Vector | |||
circ_At1g12080 ** | 175 | 13 | miR4221-5p * | 265 | 171 | 7 | Cleavage |
miR838-3p * | 226 | 59 | 41 | Translation | |||
- | - | - | miR397a-5p * | 1014 | 520 | 29 | Translation |
- | - | - | miR5654-3p | 2 | 0 | 0 | Cleavage |
circ_At2g35940 | 8 | 0 | miR8182-5p * | 2 | 9 | 0 | Translation |
- | - | - | miR830-3p * | 29 | 13 | 0 | Cleavage |
- | - | - | miR833a-5p * | 50 | 35 | 17 | Translation |
- | - | - | miR8174-3p | - | - | - | Cleavage |
circ_At2g42170 | 8 | 0 | miR831-3p * | 81 | 11 | 3 | Translation |
- | - | - | miR838-3p * | 226 | 59 | 41 | Cleavage |
- | - | - | miR4239-5p * | 17 | 7 | 0 | Translation |
circ_At3g13990 ** | 17 | 0 | miR5637-5p | - | - | - | Cleavage |
- | - | - | miR780.2-3p | - | - | - | Cleavage |
circ_At5g27720 | 17 | 0 | miR838-3p * | 226 | 59 | 41 | Cleavage |
Target_Access | miRNA | Expectation | Inhibition By | Lenght | Target Counts * | Function | |
---|---|---|---|---|---|---|---|
AgoIP | Input | ||||||
At2g38080.1 | miR397a-5p | 1 | Cleavage | 2021 | 58 | 21 | Laccase/Diphenol oxidase |
At5g60020.1 | 1 | Cleavage | 2049 | 33 | 18 | Laccase 17 | |
At3g06040.1 | 3 | Cleavage | 864 | 29 | 14 | Ribosomal protein L12 | |
At3g06470.1 | 3 | Cleavage | 1092 | 75 | 4 | GNS1/SUR4 membrane protein | |
At3g54170.1 | miR4221-5p | 2.5 | Cleavage | 1262 | 22 | 10 | FKBP12 interacting protein 37 |
At4g13070.1 | 2.5 | Cleavage | 1775 | 8 | 2 | RNA-binding CRS1 | |
At5g60040.1 | 2.5 | Cleavage | 4582 | 62 | 22 | Nuclear RNA polymerase C1 | |
At1g13350.1 | 3 | Cleavage | 2454 | 142 | 24 | Protein kinase | |
At1g77660.1 | 3 | Cleavage | 1765 | 22 | 12 | H3K4-specific methyltransferase | |
At2g33240.1 | 3 | Cleavage | 5313 | 36 | 12 | Myosin XI D | |
At3g02170.1 | 3 | Cleavage | 3300 | 319 | 155 | Longifolia2 | |
At4g14510.1 | 3 | Cleavage | 2940 | 57 | 22 | CRM family member 3B | |
At1g31650.1 | 3 | Translation | 2255 | 164 | 28 | RHO guanyl- exchange factor 14 | |
At2g38610.1 | 3 | Translation | 1452 | 56 | 26 | RNA-binding KH protein | |
At2g35160.1 | miR8182-5p | 3 | Cleavage | 2798 | 20 | 9 | SU(VAR)3-9 homolog 5 |
At4g22580.1 | 3 | Cleavage | 1628 | 39 | 10 | Exostosin family protein | |
At1g23400.1 | 3 | Cleavage | 1822 | 81 | 24 | RNA-binding CRS1 | |
At1g49880.1 | miR831-3p | 2.5 | Translation | 803 | 50 | 2 | FAD-linked sulfhydryl oxidase |
At3g46060.1 | 3 | Translation | 1132 | 75 | 41 | RAS-related protein RABE1C | |
At2g36890.1 | miR833a-5p | 2.5 | Cleavage | 971 | 6 | 1 | Myb-like DNA-binding domain |
At3g12380.1 | miR838-3p | 2.5 | Cleavage | 2323 | 33 | 16 | Actin-related protein 5 |
At1g21740.1 | 3 | Cleavage | 2862 | 63 | 22 | Protein of unknown function | |
At1g64180.1 | 3 | Cleavage | 2072 | 13 | 3 | Intracellular transport protein | |
At1g70470.1 | 3 | Cleavage | 765 | 17 | 4 | No annotated domains | |
At4g01080.1 | 3 | Cleavage | 1583 | 98 | 33 | Trichome-birefringence like 26 | |
At5g09460.1 | 3 | Cleavage | 2546 | 124 | 41 | Transcription Factor SAC51 | |
At5g09461.1 | 3 | Cleavage | 2546 | 124 | 41 | Conserved peptide upstream ORF | |
At5g20110.1 | 3 | Cleavage | 778 | 28 | 2 | Dynein light chain type 1 | |
At5g46030.1 | 2 | Translation | 732 | 26 | 12 | Elongation factor Elf1 like | |
At2g44430.1 | 2.5 | Translation | 2196 | 98 | 19 | DNA-binding protein | |
At5g22640.1 | 2.5 | Translation | 2814 | 247 | 115 | MORN repeat-containing protein | |
At5g40340.1 | 2.5 | Translation | 3096 | 624 | 75 | Tudor/PWWP/MBT protein | |
At5g56210.1 | 2.5 | Translation | 2004 | 22 | 5 | WPP domain interacting protein 2 | |
At5g62390.1 | 2.5 | Translation | 1859 | 349 | 152 | BCL-2-associated athanogene 7 | |
At5g17910.1 | 3 | Translation | 4532 | 178 | 77 | No annotated domains | |
At5g41960.1 | 3 | Translation | 874 | 9 | 4 | No annotated domains | |
At5g57790.1 | 3 | Translation | 1407 | 29 | 12 | No annotated domains |
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Frydrych Capelari, É.; da Fonseca, G.C.; Guzman, F.; Margis, R. Circular and Micro RNAs from Arabidopsis thaliana Flowers Are Simultaneously Isolated from AGO-IP Libraries. Plants 2019, 8, 302. https://0-doi-org.brum.beds.ac.uk/10.3390/plants8090302
Frydrych Capelari É, da Fonseca GC, Guzman F, Margis R. Circular and Micro RNAs from Arabidopsis thaliana Flowers Are Simultaneously Isolated from AGO-IP Libraries. Plants. 2019; 8(9):302. https://0-doi-org.brum.beds.ac.uk/10.3390/plants8090302
Chicago/Turabian StyleFrydrych Capelari, Érika, Guilherme Cordenonsi da Fonseca, Frank Guzman, and Rogerio Margis. 2019. "Circular and Micro RNAs from Arabidopsis thaliana Flowers Are Simultaneously Isolated from AGO-IP Libraries" Plants 8, no. 9: 302. https://0-doi-org.brum.beds.ac.uk/10.3390/plants8090302