Convergent evolution of cluster-wide Hox gene regulation in Bilateria

This repository contains the supplementary data and the custom code used in the publication cited below. How to use and cite these files and code All files and code are made publicly available and can be used for further research and other applications. However, if you use these resources in your work, we kindly ask you to cite our original publication. Vertebrate-like Hox gene regulation in Spiralia.Billie E. Davies#, Francisco M. Martín-Zamora#, Tom Frankish, Elise Parey, Nancy Ellis, Noura Maziak, Kero Guynes, Grygoriy Zolotarov, Yi-Jyun Luo, Ferdinand Marletaz, Juan M. Vaquerizas, Arnau Sebé-Pedrós, Nicolae Radu Zabet, Paul J. Hurd, José M. Martín-Durán. (# contributed equally) Author contact José M. Martín-Durán (chema.martin<at>qmul.ac.uk) (senior author, corresponding author) Billie E. Davies (b.e.davies<at>qmul.ac.uk) (co-first author) Francisco M. Martín-Zamora (fmartinzamora<at>altoslabs.com) (co-first author) Lab website: https://www.martinduranlab.com Index of data files contents 01. Chromatin conformation data (.mcool/.hic files): multiresolution Micro-C contact map files for O. fusiformis (early and late larval stages and adults), C. teleta (early larval and adult stages) and D. gyrociliatus (female adult). Name coding: OL = O. fusiformis early larva; OCL = O. fusiformis late larva; OA = O. fusiformis adult; CL = C. teleta early larva; CA = C. teleta adult; DG = D. gyrociliatus female adult. 02. Updated assemblies for C. teleta and D. gyrociliatus (.fasta and .gff3 files): Micro-C-based scaffolded genome assemblies and lifted over annotations for C. teleta and D. gyrociliatus. These are the assemblies and annotations used in downstream analyses. Ctel_chrom_microc_unmasked_v200624.fa: C. teleta updated assembly. Ctel_chrom_microc_v200624_genes.gff3: C. teleta annotation. Dgyr_assembly_microC_100924.fa: D. gyrociliatus updated assembly. Dgyr_microC_100924_genes.gff3: D. gyrociliatus annotation. 03. Annotations of compartments, TADs, and chromatin loops (.bed files): For compartments, we include both compartment annotation and eigenvalues. For TADs and loops, we include consensus and stage-specific calls. Species and stage code: OL = O. fusiformis early larva; OCL = O. fusiformis late larva; OA = O. fusiformis adult; CL = C. teleta early larva; CA = C. teleta adult; DG = D. gyrociliatus female adult. 04. ATAC-seq consensus data (.bed files): Consensus peak sets used to characterise compartments and TADs, and perform de novo motif discovery in boundaries and anchors. Ofus_allstages_MACS3bed_IDR_merged.bed (O. fusiformis) Ctel_allstages_MACS3bed_IDR_merged.bed (C. teleta) Dgyr_adult_ATAC_IDR.narrowPeak (D. gyrociliatus) 05. Homer de novo motif discovery: Outputs of de novo and known motif discovery in the ATAC-seq peaks overlapping consensus TAD boundaries and loop anchors (plus and minus one bin) in O. fusiformis, C. teleta, and D. gyrociliatus. Ofus_TB_Consensus_ATAC_pm1bin_bedIDR: O. fusiformis TAD boundaries. Ofus_LB_Consensus_ATAC_pm1bin_bedIDR: O. fusiformis loop anchors. Ctel_TB_Consensus_ATAC_pm1bin_bedIDR: C. teleta TAD boundaries. Ctel_LB_Consensus_ATAC_pm1bin_bedIDR: C. teleta loop anchors. Dgyr_TB_Consensus_ATAC_pm1bin: D. gyrociliatus TAD boundaries. 06. PhastCons data: Age/phylostratum of TAD boundaries, loop anchors, equivalent background sequences, and coding exons (for C. teleta only). Name coding: Ofus = O. fusiformis; Ctel = C. teleta; TAB = TAD boundary. 07. Motif transfer data: motif assignment for O. fusiformis, C. teleta and D. gyrociliatus based on protein sequence similarity with H. sapiens and Drosophila melanogaster, using JASPAR v2 IDs. Name coding: Owefus = O. fusiformis; Ctel = C. teleta; Dimgyr = D. gyrociliatus. 08. CUT&Tag bigwigs (.bw files): Coverage files for H3K4me3, H3K27me3, H3K4me1, and H3K27ac across blastula, gastrula, early larva (mitraria), and late larva (competent) of O. fusiformis. Naming convention: {number_id}-{stage}_replicate{replicate_number}_{hPTM}.bw (e.g., 01-blastula_replicate1_H3K4me3.bw). 09. CUT&Tag peaks (.bed files): Cross-stage consensus peak sets for H3K4me3, H3K27me3, H3K4me1, and H3K27ac in O. fusiformis. There are two types of peak sets, before and after Tn5 bias removal. Naming convention: Pre-removal: {number_id}-{hPTM}_DiffBind_consensus_peak_set.bed (e.g., 01-H3K4me3_DiffBind_consensus_peak_set.bed); Post-removal: {number_id}-{hPTM}_DiffBind_consensus_peak_set_no_Tn5_bias.bed (e.g., 05-H3K4me3_DiffBind_consensus_peak_set_no_Tn5_bias.bed). 10. CUT&Tag dynamics (.bed 6+4 files): Stage-specific IDR peak sets for Owenia H3K4me3, H3K27me3, H3K4me1, and H3K27ac across blastula, gastrula, early larva (mitraria), and late larva (competent) of O. fusiformis. There are two types of peak sets, before and after Tn5 bias removal. Naming convention: Pre-removal: {number_id}-{stage}_{hPTM}_IDR_peak_set.narrowPeak (e.g., 09-blastula_H3K4me3_IDR_peak_set.narrowPeak); Post-removal: {number_id}-{stage}_{hPTM}_IDR_peak_set_no_Tn5_bias.narrowPeak (e.g., 25-blastula-H3K4me3_IDR-peak_set_no_Tn5_bias.narrowPeak). 11. CUT&Tag chromatin states (.bed files): ChromHMM-predicted Chromatin states for blastula, gastrula, early larva (mitraria), and late larva (competent) of O. fusiformis. Naming convention: {number_id}-{stage}_ChromHMM_12_states_segments.bed 12. Chromatin conformation data (.hic files): multiresolution Hi-C contact map files for five spiralian species: chaeto.matrix.final.allres.hic: chaetognath Paraspadella gotoi. Lanat_merge_res.hic: brachiopod Lingula anatina. Lcine_merge_res.hic: polyplachophoran Lepidochitona cinerea. Llong_merge_res.hic: nemertean Lineus longissimus. Paust_merge_res.hic: phoronid Phoronis australis. 13. Code: scripts used in this project.