Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling

Ewing, Adam D.; Smits, Nathan; Sánchez‐Luque, Francisco J.; Faivre, J; Brennan, Paul M.; Richardson, Sandra R.; Cheetham, Seth W.; Faulkner, Geoffrey J.

doi:10.1016/j.molcel.2020.10.024

Cited by 143 publications

(142 citation statements)

References 97 publications

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“…Our analysis provides direct evidence that changes in epigenetic modification are actually occurring concordantly. This odds ratio-based analysis would also be useful for analyzing data from long-read DNA methylation sequencing [ 81 ].…”

Section: Discussionmentioning

confidence: 99%

Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells

et al. 2021

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Background TET enzymes mediate DNA demethylation by oxidizing 5-methylcytosine (5mC) in DNA to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Since these oxidized methylcytosines (oxi-mCs) are not recognized by the maintenance methyltransferase DNMT1, DNA demethylation can occur through “passive,” replication-dependent dilution when cells divide. A distinct, replication-independent (“active”) mechanism of DNA demethylation involves excision of 5fC and 5caC by the DNA repair enzyme thymine DNA glycosylase (TDG), followed by base excision repair. Results Here by analyzing inducible gene-disrupted mice, we show that DNA demethylation during primary T cell differentiation occurs mainly through passive replication-dependent dilution of all three oxi-mCs, with only a negligible contribution from TDG. In addition, by pyridine borane sequencing (PB-seq), a simple recently developed method that directly maps 5fC/5caC at single-base resolution, we detect the accumulation of 5fC/5caC in TDG-deleted T cells. We also quantify the occurrence of concordant demethylation within and near enhancer regions in the Il4 locus. In an independent system that does not involve cell division, macrophages treated with liposaccharide accumulate 5hmC at enhancers and show altered gene expression without DNA demethylation; loss of TET enzymes disrupts gene expression, but loss of TDG has no effect. We also observe that mice with long-term (1 year) deletion of Tdg are healthy and show normal survival and hematopoiesis. Conclusions We have quantified the relative contributions of TET and TDG to cell differentiation and DNA demethylation at representative loci in proliferating T cells. We find that TET enzymes regulate T cell differentiation and DNA demethylation primarily through passive dilution of oxi-mCs. In contrast, while we observe a low level of active, replication-independent DNA demethylation mediated by TDG, this process does not appear to be essential for immune cell activation or differentiation.

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Section: Discussionmentioning

confidence: 99%

Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells

et al. 2021

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“…Furthermore, whilst similar approaches are appropriate for RNA-seq data (36)(37)(38), where the signal is expected to be evenly distributed along each element, protein binding profiles are often localised and therefore difficult to detect using strategies that rely on uniquely mapped reads. Longread solutions to mapping the epigenetic status of TEs are so far largely limited to DNA methylation profiling, which can be performed on unfragmented DNA (39). In contrast, generation of histone modification or transcription factor binding profiles traditionally require chromatin fragmentation (~300bp) in order to achieve the desired resolution.…”

Section: Introductionmentioning

confidence: 99%

Locus-specific chromatin profiling of evolutionarily young transposable elements

Taylor

Lowe

Philippe

et al. 2021

Preprint

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Despite a vast expansion in the availability of epigenomic data, our knowledge of the chromatin landscape at interspersed repeats remains highly limited by difficulties in mapping short-read sequencing data to these regions. In particular, little is known about the locus-specific regulation of evolutionarily young transposable elements (TEs), which have been implicated in genome stability, gene regulation and innate immunity in a variety of developmental and disease contexts. Here we propose an approach for generating locus-specific protein-DNA binding profiles at interspersed repeats, which leverages information on the spatial proximity between repetitive and non-repetitive genomic regions. We demonstrate that the combination of HiChIP and a newly developed mapping tool (PAtChER) yields accurate protein enrichment profiles at individual repetitive loci. Using this approach, we reveal previously unappreciated variation in the epigenetic profiles of young TE loci in mouse and human cells. Insights gained using our method will be invaluable for dissecting the molecular determinants of TE regulation and their impact on the genome.

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“…The k -mer-based method presented here does not explicitly distinguish presence/absence-type polymorphisms from SNV polymorphisms in the non-LTR portion of HERV-K. K -mer signals due to individual substitutions, as would begin to accumulate after integration of a full length HERV-K provirus at a given locus, may also be detected. In total we document the nature of the HERV-K polymorphisms explaining over 20 of the loci reported here, yet many loci remain to be validated; increasing use of long-read sequencing should enable this soon [ 50 ].…”

Section: Discussionmentioning

confidence: 99%

Virus-derived variation in diverse human genomes

2021

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Acquisition of genetic material from viruses by their hosts can generate inter-host structural genome variation. We developed computational tools enabling us to study virus-derived structural variants (SVs) in population-scale whole genome sequencing (WGS) datasets and applied them to 3,332 humans. Although SVs had already been cataloged in these subjects, we found previously-overlooked virus-derived SVs. We detected non-germline SVs derived from squirrel monkey retrovirus (SMRV), human immunodeficiency virus 1 (HIV-1), and human T lymphotropic virus (HTLV-1); these variants are attributable to infection of the sequenced lymphoblastoid cell lines (LCLs) or their progenitor cells and may impact gene expression results and the biosafety of experiments using these cells. In addition, we detected new heritable SVs derived from human herpesvirus 6 (HHV-6) and human endogenous retrovirus-K (HERV-K). We report the first solo-direct repeat (DR) HHV-6 likely to reflect DR rearrangement of a known full-length endogenous HHV-6. We used linkage disequilibrium between single nucleotide variants (SNVs) and variants in reads that align to HERV-K, which often cannot be mapped uniquely using conventional short-read sequencing analysis methods, to locate previously-unknown polymorphic HERV-K loci. Some of these loci are tightly linked to trait-associated SNVs, some are in complex genome regions inaccessible by prior methods, and some contain novel HERV-K haplotypes likely derived from gene conversion from an unknown source or introgression. These tools and results broaden our perspective on the coevolution between viruses and humans, including ongoing virus-to-human gene transfer contributing to genetic variation between humans.

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Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling

Cited by 143 publications

References 97 publications

Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells

Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells

Locus-specific chromatin profiling of evolutionarily young transposable elements

Virus-derived variation in diverse human genomes

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