Research Project 11

Long reads multiomics methods to understand isoform regulatory biology

About the Project

Institute for Integrative Systems Biology (CSIC-UV)


Valencia, Spain

Ana Conesa

Main Supervisor

Universitat de València

PhD enrolment

Yearly salary

33.337,80 € (Gross)

Research Objectives

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.

Envisioned Secondments

  • ITT (Nicassio/Leornardi): Develop lrATAC-seq assay.
  • Nanopore (Aino Javelin): Develop lrATAC-seq assay.
  • UCSC (Angela Brooks): Learn FLAIR to pre-process Nanopore data.

About the Main Supervisor and Host Group

Ana Conesa

Institute for Integrative Systems Biology,

We are interested in understanding functional aspects of gene expression by combining a wide variety of high-throughput molecular techniques, including transcriptomics, epigenomics, proteomics, metabolomics, metagenomics and single-cell data, both for model and non-model species. Our lab develops statistical methods and user-friendly software tools to analyze these multi-omics data. Our most current interest is the application of long reads sequencing technologies for transcriptome analysis, the integration of multi-omics data to understand isoform regulatory biology, and the combination of environmental sequencing data to investigate the function of Microbial Dark Matter.