(A) All IAPLTR1 elements larger than 300 bps and the first 150bps of IAPEz-ints flanked by IAPLTR1 or IAPLTRs were clustered by sequence using PhyML with default settings. Major sequence variants …
Bases present in less than 10 % of IAPLTR elements were trimmed from the alignment. Sequences were clustered using PhyML with default settings. Each base is visualized by a different color: thymine …
Bases present in less than 10 % of IAPLTR elements were trimmed from the alignment. CpG dinucleotides are highlighted in light gray.
Consensus sequence of the IAPLTR1 clades at the region of increased ZFP989/Gm21082 binding. Arrows indicate locations of indels between clades. Previously identified Gm21082 binding motif from Wolf …
Each point refers to the percentage of IAPLTR1 proximal to a constitutively expressed gene at a given value. Distances were sampled every 2500bps.
Presence or absence of a IAP was determined using structural variants identified from the Sanger mouse genome project. If the entire IAP was found to be missing from the other mouse assembly, the …
(A) Percent of ERV LTRs elements that are variably methylated for a given TE subfamily and average maximum CpG score of the TE subfamily. The size of each dot is determined by the number of VM-loci …
(A) Aggregate plots of Cfp1 signal at variably methylated and other IAPLTRs. Heatmaps of Cfp1 signal at (B) VM-IAPLTRs and (C) all other IAPLTR1 and IAPLTR2 elements (2819 elements). Reads were …
(A) Observed over expected H3K4me3 signal at variably methylated and non-variably methylated IAPLTRs. Expected H3K4me3 signal determined using average H3K4me3 signal at 50 randomly selected loci …
P-values obtained from MEME.
(A) Observed over expected distribution of VM-TE elements in humans stratified by the evolutionary age of the TE. Expected distribution was determined using a random sampling of the hg38 genome the …
(A) UCSC genome browser screenshot of an LTR12C element which is hypomethylated in Tc1 mice and shows novel CFP1 recruitment in Tc1 mice. (B) CpG methylation of TE CpG islands (CGIs) and other TEs …
TEs were separated by CpG density and their capability of being silenced by a KZFP element shared between mouse and humans. Largely, these silenced repeat CGIs were found at Alu elements.
(A) Genome screenshot of an IAPLTR2 element with novel H3K4me3 enrichment in Trim28 haploinsufficient mice. (B) Breakdown of loci with novel H3K4me3 in Trim28 haploinsufficient mice. Age of each TE …
Evolutionary age was obtained from Dfam (Hubley et al., 2016).
Loci with high CpG density and loss of KZFP binding have the potential to recruit ZF-CxxC proteins to protect these TEs from being silenced. However, elements with high CpG density but strong KZFP …
Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
---|---|---|---|---|
Strain, strain background (Mus musculus) | Trim29+/D9 | Blewitt et al., 2005 | (RRID:MGI:3821610) | Haploinsufficient for Trim28 |
Strain, strain background (Mus musculus) | B6129S-Tc(HSA21)1TybEmcf/J | The Jackson Laboratory | Stock No: 010801 (JAX)(RRID:IMSR_JAX:010801) | 2 Mb of a freely segregating human fragment of Chr21 |
Antibody | Rabbit Polyclonal anti-CFP1 antibody | Millipore | ABE211(RRID:AB_10806210) | CUT&RUN(1:50 dilution) |
Antibody | Rabbit polyclonal anti-H3K4me3Antibody | Abcam | ab8580(RRID:AB_306649) | ChIP-seq(2 µg antibody per25 µg chromatin) |
Annotation of IAP clades.