chromatin-evolution-analysis's Introduction

Chromatin evolution

This repository contains all the necessary code to reproduce the comparative proteomics & comparative genomics analyses of our manuscript A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution (Grau-Bové et al., Nature Ecology and Evolution 2022, free PDF available here).

The data and code are structured as follows:

Classification of canonical and variant histones: see results_histones_phylo folder. Classification of histone variants using phylogenetic and pairwise similarity approaches, and characterisation of N-terminal tails in archaea.

Evolutionary analysis of the chromatin enzymatic machinery and readers: see results_toolkit_phylo folder. Identification of orthologous groups in chromatin modification-related enzyme families from selected eukaryotic species, analyses of their prokaryotic homology, fusions with transposon-associated domains, and more. This folder also includes detailed instructions on how to get all the genomic data used in this study.

hPTM conservation: see results_PTMs folder. Includes consensus alignments and our database of histone post-translational modifications with homologous positions in each canonical histone. Here we analyse proteomics data from Proteome Discoverer to identify homologous PTMs.

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