A SINE-VNTR-Alu in the LRIG2 Promoter Is Associated with Gene Expression at the Locus
Abstract
:1. Introduction
2. Results
2.1. SVA_LRIG2 Genotypes Were PCR Validated or Imputed for 288 Individuals
2.2. Increased Allele Dosage of SVA_LRIG2 Is Non-Significantly Associated with Reduced Transcription from the LRIG2 Locus
2.3. Increased Allele Dosage of SVA_LRIG2 Is Associated with Increased Methylation of the Nearest 450K Methylation Probe, cg23932873
2.4. Increased Methylation of cg23932873 Is Weakly Correlated with Decreased Expression of LRIG2
3. Discussion
4. Materials and Methods
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
NABEC | North American Brain Expression Consortium |
SVA | SINE-VNTR-Alu |
RIP | Retrotransposon insertion polymorphism |
LTR | Long terminal repeat |
Hg38 | Human genome assembly GRCh38 |
VNTR | Variable number tandem repeat |
SINE | Short interspersed nuclear element |
SNP | Single-nucleotide polymorphism |
CTCF | CCCTC-binding factor |
CTCFL | CTCF like |
LRIG2 | Leucine-rich repeats and immunoglobulin-like domains 2 |
dbRIP | Database of RIPs in humans |
dbGaP | Database of Genotypes and Phenotypes |
WGS | Whole-genome sequencing |
TPM | Transcripts per kilobase million |
mQTL | Methylation quantitative trait loci |
SE | Standard error |
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SVA_LRIG2 Genotype | Validated Counts | Imputed Counts | Total Counts |
---|---|---|---|
−/− | 14 | 35 | 49 |
+/− | 43 | 111 | 154 |
+/+ | 39 | 46 | 85 |
Total | 96 | 192 | 288 |
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Hall, A.; Moore, A.K.; Hernandez, D.G.; Billingsley, K.J.; Bubb, V.J.; Quinn, J.P.; NABEC (North American Brain Expression Consortium). A SINE-VNTR-Alu in the LRIG2 Promoter Is Associated with Gene Expression at the Locus. Int. J. Mol. Sci. 2020, 21, 8486. https://doi.org/10.3390/ijms21228486
Hall A, Moore AK, Hernandez DG, Billingsley KJ, Bubb VJ, Quinn JP, NABEC (North American Brain Expression Consortium). A SINE-VNTR-Alu in the LRIG2 Promoter Is Associated with Gene Expression at the Locus. International Journal of Molecular Sciences. 2020; 21(22):8486. https://doi.org/10.3390/ijms21228486
Chicago/Turabian StyleHall, Ashley, Anni K. Moore, Dena G. Hernandez, Kimberley J. Billingsley, Vivien J. Bubb, John P. Quinn, and NABEC (North American Brain Expression Consortium). 2020. "A SINE-VNTR-Alu in the LRIG2 Promoter Is Associated with Gene Expression at the Locus" International Journal of Molecular Sciences 21, no. 22: 8486. https://doi.org/10.3390/ijms21228486