Bridging between Mouse and Human Enhancer-Promoter Long-Range Interactions in Neural Stem Cells, to Understand Enhancer Function in Neurodevelopmental Disease

OVERVIEW OF THE SUPPLEMENTARY MATERIAL

Genome Browsers tracks with human syntenic enhancer-promoter Long Range Interactions:

UCSC Genome Browser

The hmsLRI are available as a remote track hub for UCSC Genome Browser You can browse them at:
http://genome.ucsc.edu/cgi-bin/hgHubConnect?redirect=manual&source=genome.ucsc.edu
Under the section "My Hubs" you can insert the following URL and add the Hub:
https://raw.githubusercontent.com/ctglab/hmsLRI_paper/main/UCSC_Genome_Browser_hub/hubDirectory/hub.txt

WashU Epigenome Browser

hmsLRI tracks for WashU Epigenome Browser are currently available as a local hub, you can download the "hub_config" folder from our supplementary files and browse the tracks at:
http://epigenomegateway.wustl.edu/browser/ selecting hg19 -> Tracks -> Local Tracks -> Add Local Hub and choose the hub_config folder to browse it

Supplementary Tables

Table S1

List of mouse enhancer-promoter LRI and their corresponding syntenic hmsLRI and hmsLRI-E
The "Active" and "Poised" sheets list long-range interactions involving epigenetic enhancers carrying H3K27Ac (active) and H3K4me1 (poised), as determined in Bertolini et al. (2019), and the corresponding syntenic regions in human (present paper). The Legend sheet inside the Table reports the meaning of all column headings.

Table S2

List of hmsLRI-E overlapping GWAS-derived sequence variants associated with schizophrenia, bipolar disorder and intelligence
Three different sheets report the analysis for scizophrenia (SCZ), bipolar disorder (bipolar), and intelligence.

Table S3

List of hmsLRI and hmsLRI-E showing copy number variation (CNV) in the datasets of NDD-associated CNV by Zarrei et al. (2019) and Coe et al. (2014).
The Coe Active, Coe Poised, Zarrei Active, Zarrei Poised sheets list hmsLRI and hmsLRI-E, involving Active and Poised enhancers respectively

Table S4

Mouse long-range interactions (in blue) connecting active or poised enhancers with promoters of genes involved in eye development (Williamson and FitzPatrick 2014), present in the wTR1, wTR2, wTR3 interactions datasets in (Bertolini et al. 2019), and their syntenic human equivalent (in orange). The last sheet, named "Unique", quotes the human enhancers removing possible duplicates originating from the presence of the corresponding mouse enhancer in more than one dataset (wTR1, wTR2, wTR3)

Table S5

Intragenic regions within eye-development genes carrying epigenetic enhancer marks that do not overlap with anchors (in blue) and their syntenic human equivalent determined with liftover (in orange). The last sheet, named "Unique", quotes the human enhancer intragenic regions, removing duplicates.