RT Journal Article
SR Electronic
T1 Measuring Transcription Factor Binding and Gene Expression using Barcoded Self-Reporting Transposon Calling Cards and Transcriptomes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.04.15.439516
DO 10.1101/2021.04.15.439516
A1 Matthew Lalli
A1 Fengping Dong
A1 Xuhua Chen
A1 Jeffrey Milbrandt
A1 Joseph Dougherty
A1 Robi Mitra
YR 2021
UL http://biorxiv.org/content/early/2021/04/15/2021.04.15.439516.abstract
AB Calling cards technology using self-reporting transposons enables the identification of DNA-protein interactions through RNA sequencing. By introducing a DNA barcode into the calling card itself, we have drastically reduced the cost and labor requirements of calling card experiments in bulk populations of cells. An additional barcode incorporation during reverse transcription enables simultaneous transcriptome measurement in a facile and affordable protocol. We demonstrate that barcoded self-reporting transposons recover in vitro binding sites for four basic helix-loop-helix transcription factors with important roles in cell fate specification: ASCL1, MYOD1, NEUROD2, and NGN1. Further, simultaneous calling cards and transcriptional profiling during transcription factor overexpression identified both binding sites and gene expression changes for two of these factors. RNA-based identification of transcription factor binding sites and gene expression through barcoded self-reporting transposon calling cards and transcriptomes is a novel and powerful method to infer gene regulatory networks in a population of cells.Competing Interest StatementThe authors have declared no competing interest.