Research Project 11

Long reads multiomics methods to understand isoform regulatory biology

About the Project

Institute for Integrative Systems Biology (CSIC-UV)

Valencia, Spain

Tian-Yuan Liu

Early Stage Researcher

Ana Conesa

Main Supervisor

Universitat de València

PhD enrolment

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.

Early Stage Researcher

Tian-Yuan Liu

Institute for Integrative Systems Biology,

I earned my Bachelor’s degree in Bioengineering from Huazhong Agricultural University (HZAU), China, in 2020. During this period, I participated in an Undergraduate Program at the University of Florida, USA, which I successfully completed in June 2020.

My research journey began at the National Key Laboratory of Crop Genetic Improvement, HZAU, where I worked on gene transformation in rice seeds. At the University of Florida’s Cancer/Genetics Research Complex, I contributed to several projects, including the development of MirCure, a computational tool for miRNA annotations; a genome-wide transcriptional analysis for COVID-19 disease map genes; and the development of PaintOmics 4 for pathway analysis of multi-omics data.

The innovative approach and interdisciplinary nature of LongTREC caught my attention. Its emphasis on cutting-edge research and collaboration among renowned institutions promised an environment where I could further hone my skills and contribute meaningfully.

As a Doctoral Candidate in LongTREC, my primary goal is to integrate my background in Bioengineering with advanced computational methodologies to pioneer solutions for current long-read multi-comics challenges. I aim to contribute to the academic community and foster collaborations that translate research into real-world applications.

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.