Final Report Summary - CPIP (Chromosome Packing in Plants)
CPiP is a 2-year Marie Curie Fellowship funded by EC FP7. CPiP aimed to advance our understanding of the spatial organization of plant genomes by 1) generating and analyzing a high-resolution Hi-C map of Arabidopsis thaliana; 2) comparing Hi-C maps of A. thaliana accessions; 3) comparing Hi-C maps of several Cruciferous species closely related to A. thaliana; and 4) studying the dynamics of A. thaliana chromatin packing under temperature stress.
An optimized Hi-C protocol was developed including both wet lab and computational aspects. This enabled the generation of an A. thaliana Hi-C map with unprecedented resolution. The new insights from its detailed analysis were published in a top international genomics journal. As a substantial extension of this first high-resolution map, the A. thaliana Hi-C data have been further analyzed at sub-kb resolution with a newly developed computational strategy, from which features of local chromatin interactions, such as gene clustering and gene looping, have been systematically identified. In parallel, a new ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag Sequencing) method has been developed, which enabled highly efficient enrichment of Hi-C reads from selected genomic regions. By integrating these newly developed methods, it could be concluded that: 1) A. thaliana local chromatin packing differs from the patterns seen in animals. At a genomic level, Topologically Associating Domains (TADs), which are prominent in animals, are not an obvious structural feature of A. thaliana genome packing. 2) There are many regions that stand out because they have much higher intra-chromosomal interaction rates than neighboring regions. These regions are enriched with the repressive histone mark H3K27me3, suggesting that this epigenetic modification plays a role in organizing higher-order chromatin interaction in plants. 3) Over 1,000 insulator-like elements have been identified, which strongly correlate with highly transcribed genes. 4) At the individual gene-body level, a large number of genes, including some showing very low or no transcriptional activity, were found to adopt a looping structure, in which the Transcription Start Site (TSS) interacts with the 3’ region of the same gene.
As planned, various Hi-C libraries have been produced from A. thaliana accessions Ler-0 and Ws-2, and the closely related Cruciferous species A. lyrata and C. rubella. In addition, a technical improvement has been made to efficiently generate hybrid plants between A. thaliana and A. lyrata. From the comparative Hi-C analysis of this hybrid plant, large-scale spatial rearrangements of telomeres and KEE (KNOT ENGAGED ELEMENT) regions have been identified.
The optimized Hi-C work pipeline has been applied to other projects in the group to address challenges in assembling genome scaffolds (Poecilia reticulata and Capsella orientalis), and studying chromatin packing in other plant species (Oryza sativa). Knowledge transfer has been implemented through seminar talks and publication after peer-review. Furthermore, results obtained from in CPiP have led to collaborating projects with several research groups in Europe.
An optimized Hi-C protocol was developed including both wet lab and computational aspects. This enabled the generation of an A. thaliana Hi-C map with unprecedented resolution. The new insights from its detailed analysis were published in a top international genomics journal. As a substantial extension of this first high-resolution map, the A. thaliana Hi-C data have been further analyzed at sub-kb resolution with a newly developed computational strategy, from which features of local chromatin interactions, such as gene clustering and gene looping, have been systematically identified. In parallel, a new ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag Sequencing) method has been developed, which enabled highly efficient enrichment of Hi-C reads from selected genomic regions. By integrating these newly developed methods, it could be concluded that: 1) A. thaliana local chromatin packing differs from the patterns seen in animals. At a genomic level, Topologically Associating Domains (TADs), which are prominent in animals, are not an obvious structural feature of A. thaliana genome packing. 2) There are many regions that stand out because they have much higher intra-chromosomal interaction rates than neighboring regions. These regions are enriched with the repressive histone mark H3K27me3, suggesting that this epigenetic modification plays a role in organizing higher-order chromatin interaction in plants. 3) Over 1,000 insulator-like elements have been identified, which strongly correlate with highly transcribed genes. 4) At the individual gene-body level, a large number of genes, including some showing very low or no transcriptional activity, were found to adopt a looping structure, in which the Transcription Start Site (TSS) interacts with the 3’ region of the same gene.
As planned, various Hi-C libraries have been produced from A. thaliana accessions Ler-0 and Ws-2, and the closely related Cruciferous species A. lyrata and C. rubella. In addition, a technical improvement has been made to efficiently generate hybrid plants between A. thaliana and A. lyrata. From the comparative Hi-C analysis of this hybrid plant, large-scale spatial rearrangements of telomeres and KEE (KNOT ENGAGED ELEMENT) regions have been identified.
The optimized Hi-C work pipeline has been applied to other projects in the group to address challenges in assembling genome scaffolds (Poecilia reticulata and Capsella orientalis), and studying chromatin packing in other plant species (Oryza sativa). Knowledge transfer has been implemented through seminar talks and publication after peer-review. Furthermore, results obtained from in CPiP have led to collaborating projects with several research groups in Europe.