Todd-eLife-2019

Repository for scripts used in the bioinformatic analyses of the following publication:

Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells

Christopher D Todd, Özgen Deniz, Darren Taylor, Miguel R Branco

eLife 2019;8:e44344 doi: 10.7554/eLife.44344

Abstract:

Transposable elements (TEs) are thought to have helped establish gene regulatory networks. Both the embryonic and extraembryonic lineages of the early mouse embryo have seemingly co-opted TEs as enhancers, but there is little evidence that they play significant roles in gene regulation. Here we tested a set of long terminal repeat TE families for roles as enhancers in mouse embryonic and trophoblast stem cells. Epigenomic and transcriptomic data suggested that a large number of TEs helped to establish tissue-specific gene expression programmes. Genetic editing of individual TEs confirmed a subset of these regulatory relationships. However, a wider survey via CRISPR interference of RLTR13D6 elements in embryonic stem cells revealed that only a minority play significant roles in gene regulation. Our results suggest that a subset of TEs are important for gene regulation in early mouse development, and highlight the importance of functional experiments when evaluating gene regulatory roles of TEs.

Notes: A few abbreviations used throughout these scripts are

REDE (RetroElement Derived Enhancer - referred to as "TE+ Enhancers" in publication)

NEDE (Non-RetroElement Derived Enhancer - referred to as "TE- Enhancers" in publication)

ROI (Regions of Interest)

Scripts used in order:

1.Annotation/plotting of ChIP-seq, DNase-seq & ATAC-seq signals

Rscript ~/todd/Homer_analysis/Homer_annotate_peaks.R Rscript ~/todd/Homer_analysis/Plot_complexheatmaps.R Rscript ~/todd/Homer_analysis/annotate_trend_lookups.R

2.Plotting of DNase/ATAC-seq accessibility in various tissues

Rscript ~/todd/DHS/download_ENCODE_DHS.R Rscript ~/todd/DHS/DNase_across_ENCODE.R Rscript ~/todd/DHS/DNase_preimplantation.R

3.Motif analysis

Rscript ~/todd/Motif_analysis/Clustal_and_Motif_analysis.R Rscript ~/todd/Motif_analysis/Plot_Motif_percentage.R Rscript ~/todd/Motif_analysis/Motif_combination_analysis.R Rscript ~/todd/Motif_analysis/Motif_analysis_of_FIREWACh.R

4.Analysis of Methylation levels

Rscript ~/todd/Methylation_analysis/TE_methylation_analysis.R

5.Pairing Genes with TEs using HiC

Rscript ~/todd/PCHiC/Bait_lookup_files.R Rscript ~/todd/PCHiC/Gothic_lookup_files.R Rscript ~/todd/PCHiC/Pairing_Gothic_Data_to_Expression.R

6.Analysis of Gene expression

Rscript ~/todd/Expression_analysis/Plotting_ESC_TSC_gene_expression.R Rscript ~/todd/Expression_analysis/download_ENCODE_RNA.R Rscript ~/todd/Expression_analysis/Multi_tissue_expression_Gingeras_data.R Rscript ~/todd/Expression_analysis/ESC_differentiation.R Rscript ~/todd/Expression_analysis/TSC_differentiation.R

7.Guide design for CRISPRi

Rscript ~/todd/CRISPRi/Guide_design/Step1_Repeat_bed_coord_to_fasta.R Rscript ~/todd/CRISPRi/Guide_design/Step2_Get_All_potential_CRISPR_guides.R Rscript ~/todd/CRISPRi/Guide_design/Step3_Prep_CasOFF_input.R ~/Cas_OFFinder/cas-offinder cas_off_input.txt G cas_off_output.txt Rscript ~/todd/CRISPRi/Guide_design/Step5_CasOFF_Analysis_revised.R Rscript ~/todd/CRISPRi/Guide_design/Step6_pick_guides.R

8.Spatial analysis of TEs

Rscript ~/todd/Define_enhancers/Compartment_analysis.R

9.Analysis of CRISPRi results

Rscript ~/todd/CRISPRi/RLTR13D6_lookup_files.R Rscript ~/todd/CRISPRi/RLTR13D6_DESeq.R Rscript ~/todd/CRISPRi/CRISPRi_analysis.R