UC.183, UC.110, and UC.84 Ultra-Conserved RNAs Are Mutually Exclusive with miR-221 and Are Engaged in the Cell Cycle Circuitry in Breast Cancer Cell Lines
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Mining of miRNA and T-UCRs Expression Profiles
2.2. Cultures, Cell Cycle Synchronization, Silencing, and Drug Treatments
2.3. Quantitative RT-PCRs
2.4. Statistical Analysis
3. Results and Discussion
3.1. Identification of T-UCRs Alternatively Expressed with miR-221
3.2. Analysis of T-UCRs Involvement in the Cell Cycle of BC Cells
3.3. Downstream Effectors of T-UCR Inhibition
3.4. Modulation of T-UCR Levels by Anticancer Drugs
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
ncRNA | non-coding RNA |
miRNA | microRNA |
T-UCR | transcribed ultra-conserved region |
UCR | ultra-conserved region |
lncRNA | long non-coding RNA |
BC | breast cancer |
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Bait | OSU Chip Definition | ncRNA | Genomic Strand | MIC (Strength) | MAS (Non Monotonicity) | Pearson Correlation (r) | Type of Correlation |
---|---|---|---|---|---|---|---|
miR-221 | MATURE | hsa-miR-222 | + | 0.42 | 0.03 | 0.70 | direct |
miR-221 | ULTRACONS | uc.84 | − | 0.32 | 0.03 | −0.55 | inverse |
miR-221 | MATURE | hsa-miR-634 | + | 0.28 | 0.01 | −0.52 | inverse |
miR-221 | ULTRACONS | uc.340 | + | 0.26 | 0.04 | −0.49 | inverse |
miR-221 | ULTRACONS | uc.478 | − | 0.26 | 0.01 | −0.49 | inverse |
miR-221 | ULTRACONS | uc.167 | + | 0.25 | 0.02 | −0.50 | inverse |
miR-221 | MATURE | hsa-miR-497 | + | 0.25 | 0.02 | −0.43 | inverse |
miR-221 | MATURE | hsa-miR-26b | + | 0.24 | 0.04 | 0.43 | direct |
miR-221 | MATURE | hsa-miR-26a | + | 0.24 | 0.06 | 0.40 | direct |
miR-221 | ULTRACONS | uc.110 | − | 0.24 | 0.04 | −0.45 | inverse |
miR-221 | MATURE | hsa-miR-602 | + | 0.24 | 0.04 | −0.45 | inverse |
miR-221 | ULTRACONS | uc.31 | + | 0.24 | 0.02 | −0.43 | inverse |
miR-221 | MATURE | hsa-miR-320 | + | 0.23 | 0.01 | 0.45 | direct |
miR-221 | ULTRACONS | uc.10 | − | 0.23 | 0.01 | −0.47 | inverse |
miR-221 | ULTRACONS | uc.48 | − | 0.23 | 0.02 | −0.48 | inverse |
miR-221 | ULTRACONS | uc.78 | + | 0.23 | 0.01 | −0.44 | inverse |
miR-221 | MATURE | hsa-miR-361-5p | + | 0.23 | 0.02 | 0.45 | direct |
miR-221 | ULTRACONS | uc.183 | + | 0.22 | 0.04 | −0.43 | inverse |
miR-221 | ULTRACONS | uc.96 | + | 0.22 | 0.03 | −0.41 | inverse |
miR-221 | ULTRACONS | uc.309 | − | 0.21 | 0.01 | −0.47 | inverse |
miR-221 | MATURE | hsa-miR-30a | + | 0.20 | 0.02 | 0.43 | direct |
miR-221 | ULTRACONS | uc.177 | − | 0.20 | 0.01 | −0.43 | inverse |
T-UCR | Strand | Chromosome Coordinates (hg19) | Chromosome Coordinates (hg38) | Length (nt) | Type | Annotations |
---|---|---|---|---|---|---|
uc.84 | − | chr2:157194706-157194914 | chr2:156338194-156338402 | 209 | exonic/ intronic | AK128708/intron of NR4A2; possible coding exon (42 amino acids starting with MET)—no known homology—Immediate-early response gene of the steroid-thyroid hormone-retinoid receptor superfamily [36] |
uc.340 | + | chr12:54090832-54091090 | chr12:53697048-53697306 | 259 | intergenic | partially overlaps with TCONS_00020432 lincRNA |
uc.478 | − | chrX:122599457-122599708 | chrX:123465606-123465857 | 252 | exonic | antisense of GRIA3 |
uc.167 | + | chr5:88179624-88179824 | chr5:88883807-88884007 | 201 | intronic | antisense of MEF2C |
uc.110 | − | chr2:237071382-237071624 | chr2:236162738-236162980 | 243 | intergenic | enhancer and overlaps with the transmap of GBX2, an embryonal transcription factor [37] |
uc.31 | + | chr1:88928018-88928270 | chr1:88462335-88462587 | 253 | intergenic | BC045705 upstream of TCONS_00001016/TCONS_00001015 |
uc.10 | − | chr1:10965574-10965848 | chr1:10905517-10905791 | 275 | intergenic | none |
uc.48 | − | chr2:20478333-20478630 | chr2:20278572-20278869 | 298 | exonic | overlaps with sense PUM2 |
uc.78 | + | chr2:145188354-145188601 | chr2:144430787-144431034 | 248 | intronic | antisense of ZEB2 |
uc.183 | + | chr5:171384520-171384755 | chr5:171957516-171957751 | 236 | exonic | antisense of FBXW11 [38,39,40,41] |
uc.96 | + | chr2:172820674-172820934 | chr2:171964152-171964412 | 261 | intronic | intron of HAT1—possible novel exon-homology to a non-human HAT [42,43,44,45] |
uc.309 | − | chr10:103267031-103267298 | chr10:101507274-101507541 | 268 | intronic | antisense of BTRC |
uc.177 | − | chr5:170417629-170417885 | chr5:170990625-170990881 | 257 | intronic | antisense of RANBP17 |
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Corrà, F.; Crudele, F.; Baldassari, F.; Bianchi, N.; Galasso, M.; Minotti, L.; Agnoletto, C.; Di Leva, G.; Brugnoli, F.; Reali, E.; et al. UC.183, UC.110, and UC.84 Ultra-Conserved RNAs Are Mutually Exclusive with miR-221 and Are Engaged in the Cell Cycle Circuitry in Breast Cancer Cell Lines. Genes 2021, 12, 1978. https://doi.org/10.3390/genes12121978
Corrà F, Crudele F, Baldassari F, Bianchi N, Galasso M, Minotti L, Agnoletto C, Di Leva G, Brugnoli F, Reali E, et al. UC.183, UC.110, and UC.84 Ultra-Conserved RNAs Are Mutually Exclusive with miR-221 and Are Engaged in the Cell Cycle Circuitry in Breast Cancer Cell Lines. Genes. 2021; 12(12):1978. https://doi.org/10.3390/genes12121978
Chicago/Turabian StyleCorrà, Fabio, Francesca Crudele, Federica Baldassari, Nicoletta Bianchi, Marco Galasso, Linda Minotti, Chiara Agnoletto, Gianpiero Di Leva, Federica Brugnoli, Eva Reali, and et al. 2021. "UC.183, UC.110, and UC.84 Ultra-Conserved RNAs Are Mutually Exclusive with miR-221 and Are Engaged in the Cell Cycle Circuitry in Breast Cancer Cell Lines" Genes 12, no. 12: 1978. https://doi.org/10.3390/genes12121978