Transcript variant expression is the combination of transcriptional and post-transcriptional regulation. The regulatory environment at promotor regions is studied by short reads, but these do not reveal the contiguous promoter methylation landscape, which could be captured by LRS. Moreover, methods for integration of multi-omics long reads data do not exist. Our objectives are: 

• Develop a wet-lab protocol for long reads ATAC-seq and Nascent-seq using Nanopore. Apply to H1 human cell line.
• Develop an analysis pipeline to process lrATAC-seq data to identify chromatin accessibility and methylation.
• Integrate H1 lr-ATAC-seq and Nascent-seq data with LRGASP lrRNA-seq to infer transcript-specific regulatory patterns.
• Implement methods in the SQANTI and tappAS software tools.