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2019 Droso haplo (Finished)

Develop a pipeline for haplotyped RNASeq DNASeq Hi-C data


The work in progress is available here:


Porteur du projet

Francesconi Mirko


Francesconi Mirko

Laurent Modolo

Problématique biologique

Spatial chromatin organization plays an important role in gene expression regulation and diseases. Yet surprisingly no study has systematically explored how natural genetic variation affects chromatin conformation and how this impacts on gene expression. We will leverage millions of natural genetic variants in Drosophila melanogaster to address these fundamental questions.


Both cis variants (i.e. variants that alter binding sites for proteins that mediates chromatin contacts) and trans variants (i.e. variants that alters expression or aminoacid sequence of proteins that mediates chromatin contacts) have the potential to contribute to variation in chromatin conformation.

What is the relative contribution of cis and trans variants on chromatin conformation and on gene expression?


To address these questions we have collected Hi-C and RNA-seq data from both parents and their corresponding F1 hybrids between two highly genetically diverse inbred lines of Drosophila melanogaster from the Drosophila synthetic population resource. Samples were collected at early embryonic stage. Genomic sequences of the parental lines are publicly available. Comparing data from parental lines to haplotype specific data obtained from F1 hybrids from reciprocal crosses will also allow us to estimate both genetic effects and parent-of-origin epigenetic effects on chromatin conformation and gene expression.


La date du début du projet. 2019-11-26
La date d’obtention des données. 2019-1-1
La date d’obtention de l’intégralité des données. 2019-1-1
La date souhaitée de fin du projet. 2020-3-26


The mission for the bioinformatician is to assist the team in putting in place and finishing to develop a pipeline (which is already partially developed) to:

A- Call the genetic variants between the two haplotypes.

B- Construct the haplotype specific references.

C- Map the Hi-C and RNA-seq data onto the custom reference sequences and assign reads to either haplotypes

D- Estimate haplotype specific gene expression and chromatin contacts.