Projects

This page contains GenPlay projects available for download. These projects illustrate the type of data analysis and visualization that can be done with GenPlay. There are two sections: the first one contains projects that were used as supporting data of published articles. The second section contains the projects created for the Tutorials page of this website.

How to start a project

You first need to download and install GenPlay from the Downloads page. Then, you need to download the project you want to launch. Once the download is finished, double click on the project file to start GenPlay and load the project. Loading a project might take a few minutes.

Projects from published work

Methylation

Mechanisms of Establishment and Functional Significance of DNA Demethylation during Erythroid Differentiation

Authors

Boris Bartholdy, Julien Lajugie, Zi Yan, Shouping Zhang, Rituparna Mukhopadhyay, John M Greally, Masako Suzuki and Eric E Bouhassira

Abstract

Erythroid differentiation is associated with global DNA demethylation, but a complete methylome was lacking in the erythroid lineage. We have generated allele-specific base resolution methylomes of primary basophilic erythroblasts (BasoE) and compared these to eight other cell types. We found that DNA demethylation during differentiation from Hematopoietic Stem/Progenitor Cells (HSPCs) to BasoE occurred predominantly in intergenic sequences and in inactive gene bodies causing the formation of Partially Methylated Domains (PMDs) in 74% of the BasoE methylome. We found that Differentially Methylated Regions (DMR) between HSPCs and BasoE occurred mostly in putative enhancer regions and were most often associated with GATA, EKLF and AP1 binding motifs. Surprisingly, promoters silent in both HSPCs and BasoE exhibited much more dramatic chromatin changes during differentiation than activated promoters. Unmethylated silent promoters were often associated with active chromatin states in Highly Methylated Domains (HMDs) but with Polycomb-repression in PMDs, indicating that silent promoters are generally regulated differently in HMDs and PMDs. We show that long PMDs replicate late but that short PMDs replicate early and therefore that the partial methylation of DNA after replication during erythroid expansion occurs throughout S phase of the cell cycle. We propose that baseline maintenance methylation following replication decreases during erythroid differentiation resulting in PMD formation and that the presence of HMDs in the BasoE methylome results from transcription-associated DNA methylation of gene bodies. We detected about 700 large allele-specific DMRs that were enriched in SNPs, suggesting that primary DNA sequence might be a determinant of DNA methylation levels within PMDs.

Article

http://www.bloodadvances.org/content/2/15/1833

GenPlay Project

Methyl_seq_paper_figure_1.gppf

3_2_3_3_AS_methylation_data.gppf

GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface

Authors

Julien Lajugie, Nicolas Fourel and Eric E Bouhassira

Abstract

The number of human genomes sequenced is growing exponentially. The vast majority of these genomes are assembled by comparison to a single reference sequence. This is problematic because of the large amount of genetic variations in human populations. Parallel analysis and visualization of the indels and structural variants present in multiple human genomes is complex because it requires the display of sequences that are unique to specific genomes and absent from the reference sequence. We describe here, GenPlay Multi-Genome, an application that can be used to visualize SNPs, indels and structural variants in multiple human genomes. GenPlay Multi-Genome is ideal for the comparison in a graphic interface of expression and epigenetic data obtained from multiple phased genomes. GenPlay Multi- Genome is also useful to analyze data that has been aligned to custom genomes rather than to a reference genome.

Article

http://bioinformatics.oxfordjournals.org/content/31/1/109.long

GenPlay Project

MG_Demo.zip

Note: Uncompress the zip file and double click on MG_demo.gppf to start GenPlay (make sure that GenPlay is installed on your system).

Allele-Specific Genome-Wide Profiling in Human Primary Erythroblasts Reveal Replication Program Organization

Authors

Rituparna Mukhopadhyay, Julien Lajugie, Nicolas Fourel, Ari Selzer, Michael Schizas, Boris Bartholdy, Jessica Mar, Chii Mei Lin, Melvenia M. Martin, Michael Ryan, Mirit I. Aladjem and Eric E. Bouhassira

Abstract

We have developed a new approach based on TimEX-seq to characterize allele-specific timing of DNA replication genome-wide in human primary basophilic erythroblasts. We show that the two chromosome homologs replicate at the same time in about 88% of the genome and that large structural variants are preferentially associated with asynchronously replications. We identified about 600 megabase-sized asynchronously replicated domains in two tested individuals. We show that the longest asynchronously replicated domains are enriched in imprinted genes suggesting that structural variants and parental imprinting are two causes of replication asynchrony in the human genome. Biased chromosome X inactivation in one of the two individuals tested was another source of detectable replication asynchrony. Analysis of high-resolution TimEX profiles revealed timing wrinkles, which are previously undetected, highly reproducible, variations of the timing of replication in the 100kb-range that exist within the well-characterized megabase-sized replication timing domains. We show that these wrinkles correspond to clusters of origins of replication that we detected using novel nascent strands DNA profiling methods. Analysis of the distribution of replication origins revealed dramatic differences in initiation of replication frequency during S phase and a strong association, in both synchronous and asynchronous regions, between origins of replication and three genomic features: G-quadruplexes, CpG Islands and transcription start sites. The frequency of initiation in asynchronous regions was similar in the two homologs. Asynchronous regions were richer in origins of replication than synchronous regions.

Article

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004319

GenPlay Project

Timing_and_NS_Profiles_2013.gppf

Readme.txt

Allele-Specific Analysis of DNA Replication Origins in Mammalian Cells

Authors

Bartholdy B, Mukhopadhyay R, Lajugie J, Aladjem MI, Bouhassira EE

Abstract

The mechanisms that control the location and timing of firing of replication origins are poorly understood. Using a novel functional genomic approach based on the analysis of SNPs and indels in phased human genomes, we observe that replication asynchrony is associated with small cumulative variations in the initiation efficiency of multiple origins between the chromosome homologues, rather than with the activation of dormant origins. Allele-specific measurements demonstrate that the presence of G-quadruplex-forming sequences does not correlate with the efficiency of initiation. Sequence analysis reveals that the origins are highly enriched in sequences with profoundly asymmetric G/C and A/T nucleotide distributions and are almost completely depleted of antiparallel triplex-forming sequences. We therefore propose that although G4-forming sequences are abundant in replication origins, an asymmetry in nucleotide distribution, which increases the propensity of origins to unwind and adopt non-B DNA structure, rather than the ability to form G4, is directly associated with origin activity.

Article

PubMed

GenPlay Project

AS_Analysis_of_replication_origins.gppf

Readme.txt

Identification of a BET Family Bromodomain/Casein Kinase II/TAF-Containing Complex as a Regulator of Mitotic Condensin Function

Authors

Hyun-Soo Kim, Rituparna Mukhopadhyay, Scott B. Rothbart, Andrea C. Silva, Vincent Vanoosthuyse, Ernest Radovani, Thomas Kislinger, Assen Roguev, Colm J. Ryan, Jiewei Xu, Harlizawati Jahari, Kevin G. Hardwick, Jack F. Greenblatt, Nevan J. Krogan, Jeffrey S. Fillingham, Brian D. Strahl, Eric E. Bouhassira, Winfried Edelmann, Michael-Christopher Keogh

Abstract

Condensin is a central regulator of mitotic genome structure with mutants showing poorly condensed chromosomes and profound segregation defects. Here, we identify NCT, a complex comprising the Nrc1 BET-family tandem bromodomain protein (SPAC631.02), casein kinase II (CKII), and several TAFs, as a regulator of condensin function. We show that NCT and condensin bind similar genomic regions but only briefly colocalize during the periods of chromosome condensation and decondensation. This pattern of NCT binding at the core centromere, the region of maximal condensin enrichment, tracks the abundance of acetylated histone H4, as regulated by the Hat1-Mis16 acetyltransferase complex and recognized by the first Nrc1 bromodomain. Strikingly, mutants in NCT or Hat1-Mis16 restore the formation of segregation-competent chromosomes in cells containing defective condensin. These results are consistent with a model where NCT targets CKII to chromatin in a cell-cycle-directed manner in order to modulate the activity of condensin during chromosome condensation and decondensation.

Article

http://www.cell.com/cell-reports/fulltext/S2211-1247(14)00063-1

GenPlay Project

Kim_CellRep_2014.gppf

Readme.txt

Projects from tutorials

ChIP-Seq Tutorial

Goal

The objective of the ChIP-Seq tutorial is to illustrate how GenPlay can be used to isolate peaks from the data generated from a ChIP-Seq experiment. Then, to generate a list of genes that have a peak in their promoter and finally to associate the score of the peak summit with each promoter.

Tutorial

ChIP-Seq Tutorial

Project File

ChIP-Seq_Tutorial.gppf

TimEX Tutorial

Goal

The TimEX tutorial illustrates how GenPlay can be used to show timing of replication profiles. The goal of the tutorial is to compute the correlation coefficient between the replication timing in human embryonic stem (ES) cells and in primary basophilic erythroblasts derived in culture from primary CD34 positive cells.

Tutorial

TimEX Tutorial

Project File

TimEX_Tutorial.gppf

Multi-Genome Tutorial

Goal

The multi-genome tutorial explains how to display data mapped on genome assembly GRCh37/Hg19 and GRCh38/Hg38 simultaneously.

Tutorial

GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial

Note: An older version of this tutorial is available for NCBI36/hg18 - GRCh37/hg19: Multi-Genome Tutorial

Project File

hg19-hg38_Multi-genome.zip

Note: To start the project you need to unpack the zip archive and to double click on the file called hg19-hg38_Multi-genome.gppf. Make sure that GenPlay is installed on your computer.

Note2: For the NCBI36/hg18 - GRCh37/hg19 version, click on the following link: GenPlayMG-Reference_Genome_Tutorial.zip. To start the project you need to unpack the zip archive and to double click on the file called GenPlay-MG – Reference genome tutorial.gppf. Make sure that GenPlay is installed on your computer.