Bose, M. L. | bioRxiv Science

bioRxiv2026

Genetic demultiplexing and transcript start site identification from nanopore sequencing of 10x Genomics multiome libraries

Short-read Illumina sequencing of 10x Genomics single-nucleus multiome libraries captures only the 3 end of RNA transcripts, losing transcription start site (TSS) information. Here we demonstrate nanopore sequencing of 10x multiome libraries, which enables the profiling of full length transcripts. We show concordance with common short-read sequencing based workflows including successful genetic demultiplexing of nanopore data despite its higher error rate. We compare TSS identified using nanopore sequencing of multiome cDNA to those identified using a short-read 5 assay, and provide an optimized approach for the preprocessing of nanopore reads prior to TSS identification. We find that nanopore sequencing of multiome cDNA captures a median of 63% of the TSS detected by the 5 assay.

bioinformatics↗

bioRxiv2025

Massively parallel reporter assay reveals promoter-, position-, and strand-specific effects in transcription start sites

Massively parallel reporter assays (MPRA) are a high-throughput method of assessing the activity of candidate cis-regulatory sequences, and can be used to detect allelic differences at disease-associated variants. Previous MPRA studies have screened thousands of functional SNPs associated with various complex traits and conditions. Most MPRA libraries utilize a single plasmid configuration, a single minimal promoter to drive expression, and a single-strand orientation, which may fail to capture the context-dependent activity of disease-associated cis-regulatory elements. We interrogate the potential regulatory differences introduced by variable MPRA plasmid promoters and positions. We used an MPRA library to quantify the activity of 1,305 pancreatic islet-derived transcription start sites generated from CAP analysis of gene expression profiling. We cloned fragments upstream or downstream of a reporter gene along with either the human insulin (INS) promoter or a synthetic housekeeping promoter (SCP1). We used elastic net regression to predict position-specific fragment activity based on enrichment of transcription factor binding site motifs, and generalized linear models to predict position-specific fragment activity from tissue-specific chromatin state regulatory annotations. Our results support the use of MPRA strategies that account for context-dependent factors when assaying candidate regulatory elements in pursuit of understanding complex genetic diseases.

genomics↗