This repository contains the code used in the study:
"Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness"
Laverré et al. 2022, Genome Research — PMC8805723
This project explores the evolutionary conservation of regulatory landscapes and their impact on gene expression robustness. The analyses include:
- PCHi-C Data Processing: Mapping and filtering of Promoter Capture Hi-C (PCHi-C) raw data from human and mouse to identify promoter-enhancer interactions.
- Public Enhancer Annotation: Integration of publicly available enhancer datasets to characterize contacted regulatory elements.
- Simulated Chromatin Landscapes: All results are compared to a simulated chromatin contact landscape that preserves the observed distribution of contact distances and frequencies.
- Sequence Composition: Assessment of genomic features such as GC content, gene density, and repeat elements to understand their influence on regulatory landscape structure.
- Landscape Features: Analysis of key characteristics of regulatory landscapes including contact frequency, genomic distance between elements, and the number of contacts per gene.
- Sequence Alignment Across Species: Multi-species alignment of contacted regions to assess sequence conservation across 10 vertebrate genomes.
- Sequence and Synteny Conservation: Evaluation of both sequence similarity and syntenic context conservation to understand evolutionary stability of regulatory contacts.
- Chromatin Contact Conservation: Comparative analysis of promoter-enhancer interactions between human and mouse to identify conserved chromatin contacts.
- Gene Expression Quantification: Quantification and comparison of gene expression levels and patterns across species using RNA-seq data.
- Regulatory–Expression Correlation: Investigation of the relationship between regulatory landscape conservation and gene expression divergence.
If you use this code, please cite:
Laverré A, Tannier E, Necsulea A. Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness. Genome Res. 2022 Feb;32(2):280–296. doi:10.1101/gr.275901.121