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21 results on '"Payer, Lindsay M."'

11. Additional file 1 of Polymorphic mobile element insertions contribute to gene expression and alternative splicing in human tissues

Author

Xiaolong Cao, Yeting Zhang, Payer, Lindsay M., Lords, Hannah, Steranka, Jared P., Burns, Kathleen H., and Xing, Jinchuan

Abstract

Additional file 1: Figure S1. Overview of high confidence pMEIs in GTEx individuals. Figure S2. Enrichment of pMEIs around Transcription Starting Sites (TSSs) of genes. Figure S3. Agreement of the effect direction between a pair of tissues for eQTLs (lower-left) and sQTLs (upper-right).

Published
2020
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13. Figure S1 from Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells

Author

McKerrow, Wilson, Zuojian Tang, Steranka, Jared P., Payer, Lindsay M., Boeke, Jef D., Keefe, David, Fenyö, David, Burns, Kathleen H., and Chunhong Liu

Abstract

Single cell sorting by FACS. Suspension cells were labelled with PI. SSC-width and height, FSC-width and height, and PI were used to gate a subset of live single cell population, and to make sure that only live single cells were sorted.

Published
2019
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16. Aluinsertion variants alter mRNA splicing

Author

Payer, Lindsay M, primary, Steranka, Jared P, additional, Ardeljan, Daniel, additional, Walker, JaNiece, additional, Fitzgerald, Kathryn C, additional, Calabresi, Peter A, additional, Cooper, Thomas A, additional, and Burns, Kathleen H, additional

Published
2018
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19. Aluinsertion variants alter gene transcript levels

Author

Payer, Lindsay M., Steranka, Jared P., Kryatova, Maria S., Grillo, Giacomo, Lupien, Mathieu, Rocha, Pedro P., and Burns, Kathleen H.

Abstract

Aluare high copy number interspersed repeats that have accumulated near genes during primate and human evolution. They are a pervasive source of structural variation in modern humans. Impacts that Aluinsertions may have on gene expression are not well understood, although some have been associated with expression quantitative trait loci (eQTLs). Here, we directly test regulatory effects of polymorphic Aluinsertions in isolation of other variants on the same haplotype. To screen insertion variants for those with such effects, we used ectopic luciferase reporter assays and evaluated 110 Aluinsertion variants, including more than 40 with a potential role in disease risk. We observed a continuum of effects with significant outliers that up- or down-regulate luciferase activity. Using a series of reporter constructs, which included genomic context surrounding the Alu, we can distinguish between instances in which the Aludisrupts another regulator and those in which the Aluintroduces new regulatory sequence. We next focused on three polymorphic Aluloci associated with breast cancer that display significant effects in the reporter assay. We used CRISPR to modify the endogenous sequences, establishing cell lines varying in the Alugenotype. Our findings indicate that Alugenotype can alter expression of genes implicated in cancer risk, including PTHLH, RANBP9, and MYC. These data show that commonly occurring polymorphic Aluelements can alter transcript levels and potentially contribute to disease risk.

Published
2021
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21. Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells.

Author

McKerrow W, Tang Z, Steranka JP, Payer LM, Boeke JD, Keefe D, Fenyö D, Burns KH, and Liu C

Subjects
Cell Line, Humans, Sequence Analysis, DNA, Single-Cell Analysis, DNA Transposable Elements genetics, Long Interspersed Nucleotide Elements genetics, Mutagenesis, Insertional
Abstract

Long interspersed element-1 (LINE-1, L1) sequences, which comprise about 17% of human genome, are the product of one of the most active types of mobile DNAs in modern humans. LINE-1 insertion alleles can cause inherited and de novo genetic diseases, and LINE-1-encoded proteins are highly expressed in some cancers. Genome-wide LINE-1 mapping in single cells could be useful for defining somatic and germline retrotransposition rates, and for enabling studies to characterize tumour heterogeneity, relate insertions to transcriptional and epigenetic effects at the cellular level, or describe cellular phylogenies in development. Our laboratories have reported a genome-wide LINE-1 insertion site mapping method for bulk DNA, named transposon insertion profiling by sequencing (TIPseq). There have been significant barriers applying LINE-1 mapping to single cells, owing to the chimeric artefacts and features of repetitive sequences. Here, we optimize a modified TIPseq protocol and show its utility for LINE-1 mapping in single lymphoblastoid cells. Results from single-cell TIPseq experiments compare well to known LINE-1 insertions found by whole-genome sequencing and TIPseq on bulk DNA. Among the several approaches we tested, whole-genome amplification by multiple displacement amplification followed by restriction enzyme digestion, vectorette ligation and LINE-1-targeted PCR had the best assay performance. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.

Published
2020
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