Identification and Functional Characterization of Alternative Transcripts of LncRNA HNF1A-AS1 and Their Impacts on Cell Growth, Differentiation, Liver Diseases, and in Response to Drug Induction
Abstract
:1. Introduction
2. Results
2.1. Identification of HNF1A-AS1 Alternative Transcripts in Human Livers and Cultured Cells
2.2. Design of Real-Time Quantitative PCR (RT-qPCR) Primers for Quantification of the Identified Transcripts
2.3. Expression Patterns of HNF1A-AS1 Transcripts during Stages of Hepatocyte Differentiation from Human Embryonic Stem Cells (hESC)
2.4. Expression Patterns of the Identified HNF1A-AS1 Transcripts during HepaRG Cell Growth and Differentiation
2.5. Expression Patterns of HNF1A-AS1 Transcripts during Rifampicin Treatment
2.6. Expression Patterns of the Identified HNF1A-AS1 Transcripts in Different Liver Disease Conditions
3. Discussion
4. Materials and Methods
4.1. Human Liver Samples Collection
4.2. Differentiation of hESC to Hepatocytes In Vitro
4.3. RNA Extraction and Reverse Transcription
4.4. Primer Design for PCR and Quantitative RT-qPCR
4.5. PCR
4.6. Gel Electrophoresis
4.7. Purification of PCR Products and Sanger Sequence
4.8. RT-qPCR
4.9. Data Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Transcript ID * | Name | Length (bp) | Exon Number |
---|---|---|---|
ENST00000619441.1 | HNF1A-AS1-205 | 343 | 2 |
ENST00000647473.1 | HNF1A-AS1-207 | 1144 | 5 |
ENST00000701967.1 | HNF1A-AS1-209 | 357 | 2 |
ENST00000701238.1 | HNF1A-AS1-208 | 582 | 2 |
ENST00000646404.1 | HNF1A-AS1-206 | 557 | 3 |
ENST00000537361.1 | HNF1A-AS1-203 | 659 | 2 |
ENST00000539163.1 | HNF1A-AS1-204 | 2455 | 1 |
ENST00000433033.3 | HNF1A-AS1-201 | 718 | 4 |
ENST00000535301.2 | HNF1A-AS1-202 | 546 | 2 |
Transcript | Primer (Forward) 5′–3′ | Primer (Reverse) 5′–3′ | Amplicon Size (bp) |
---|---|---|---|
HNF1A-AS1-205 | AGGAAGCACTTTGACCTCTG * | CCTACCCCACAGAGTCTGAT | 300 |
HNF1A-AS1-207 | ATCCCACCAAAGGGGGCT | TCACAGAAAAGAATCTGTTC | 731 |
HNF1A-AS1-209 | ATACAGGAAAGGGGAGCAGC ** | TCCACATCAGGTCCCATG *** | 220 |
HNF1A-AS1-208 | AGGAAGCACTTTGACCTCTG * | TCCACATCAGGTCCCATG *** | 280 |
HNF1A-AS1-206 | ATACAGGAAAGGGGAGCAGC ** | TCCACATCAGGTCCCATG *** | 387 |
HNF1A-AS1-203 | AGGAAGCACTTTGACCTCTG * | TGTTACAAGGTTCAGGGCTC | 477 |
HNF1A-AS1-204 | AGTTCCCTCCATCTAACATTCA | TTGTCTGGACTGAAGGACAA | 321 |
HNF1A-AS1-201 | GCCTGTGGCCATACAGGA | GACAGGAGCAAAACTGCT | 501 |
HNF1A-AS1-202 | AGGAAGCACTTTGACCTCTG * | ACAGAAGGAGACCCTGTC | 298 |
Transcript | Primer (Forward) 5′–3′ | Primer (Reverse) 5′–3′ | Amplicon Size (bp) |
---|---|---|---|
HNF1A-AS1-205N | ATGCTGTTTGGGCTGGTC | TGGGATTGGGTTCCTTTG | 138 |
HNF1A-AS1-205 | CACTCAGCCAGGATGAGG | TTTCCCTACCCCACAGAG | 207 |
HNF1A-AS1-208 | AGGAAGCACTTTGACCTCTG | TCCACATCAGGTCCCATG | 280 |
HNF1A-AS1-203N | TAAACACTAGCCAACACCC | AGCAGCAGCTTGACAAAT | 104 |
HNF1A-AS1-203 | ACTCAGCCAGCTGCTCCCTCTA | GCTGTGGGTGGCAGAAGAGGAC | 109 |
HNF1A-AS1-204 | AGTTCCCTCCATCTAACATTCA | TTGTCTGGACTGAAGGACAA | 321 |
CYP3A4 | GATTGACTCTCAGAATTCAAAAGAAACTGA | GGTGAGTGGCCAGTTCATACATAATG | 148 |
β-actin | GGACTTCGAGCAAGAGATGG | AGCACTGTGTTGGCGTACAG | 234 |
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Jin, J.; Nguyen, L.T.G.; Wassef, A.; Sadek, R.; Schmitt, T.M.; Guo, G.L.; Rasmussen, T.P.; Zhong, X.-b. Identification and Functional Characterization of Alternative Transcripts of LncRNA HNF1A-AS1 and Their Impacts on Cell Growth, Differentiation, Liver Diseases, and in Response to Drug Induction. Non-Coding RNA 2024, 10, 28. https://doi.org/10.3390/ncrna10020028
Jin J, Nguyen LTG, Wassef A, Sadek R, Schmitt TM, Guo GL, Rasmussen TP, Zhong X-b. Identification and Functional Characterization of Alternative Transcripts of LncRNA HNF1A-AS1 and Their Impacts on Cell Growth, Differentiation, Liver Diseases, and in Response to Drug Induction. Non-Coding RNA. 2024; 10(2):28. https://doi.org/10.3390/ncrna10020028
Chicago/Turabian StyleJin, Jing, Le Tra Giang Nguyen, Andrew Wassef, Ragui Sadek, Timothy M. Schmitt, Grace L. Guo, Theodore P. Rasmussen, and Xiao-bo Zhong. 2024. "Identification and Functional Characterization of Alternative Transcripts of LncRNA HNF1A-AS1 and Their Impacts on Cell Growth, Differentiation, Liver Diseases, and in Response to Drug Induction" Non-Coding RNA 10, no. 2: 28. https://doi.org/10.3390/ncrna10020028