Doucet, A. J. | bioRxiv Science

bioRxiv2023

Resolving the heterogeneity of L1 DNA methylation reveals the epigenetic and transcriptional interplay between L1s and their integration sites.

Long interspersed element-1 (L1) retrotransposons play important roles in human disease and evolution. Their global activity is repressed by DNA methylation, but studying the regulation of individual copies has been difficult. Here, we combine short- and long-read sequencing to resolve the DNA methylation profiles of these repeated sequences in a panel of normal and cancer cells genome-wide at single-locus resolution. We unveil key principles underpinning L1 methylation heterogeneity among cell-types, families and integration sites. First, intronic L1 methylation is intimately associated with gene transcription. Conversely, L1s can influence the methylation status of the upstream region over short distances (300 bp). This phenomenon is accompanied by the binding of specific transcription factors, which drive the expression of L1 and chimeric transcripts. Finally, L1 hypomethylation alone is generally insufficient to trigger L1 expression due to redundant silencing pathways. Our results illuminate the epigenetic and transcriptional interplay between retrotransposons and their host genome. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/522582v3_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@c78bbcorg.highwire.dtl.DTLVardef@a7112dorg.highwire.dtl.DTLVardef@58abf2org.highwire.dtl.DTLVardef@180d055_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIBs-ATLAS-seq profiles L1 position and methylation genome-wide C_LIO_LIL1 has a frequent but short-range (300 bp) influence on the DNA methylation status of the upstream sequence C_LIO_LIHypomethylated L1s are bound by tissue-specific transcription factors which drive L1 and chimeric transcripts synthesis C_LIO_LIL1 hypomethylation alone is insufficient to enable its transcription at most loci C_LI

genomics↗

bioRxiv2020

Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long non-coding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3 end of LINE-1_Cfs (i.e., LINE-1_Cf 3-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation. SignificanceAdvancements in long-read DNA sequencing technologies provide more comprehensive views of genomes. We used long-read sequences to assemble a Great Dane dog genome that provides several improvements over the existing reference derived from a Boxer dog. Assembly comparisons revealed that gaps in the Boxer assembly often occur at the beginning of protein-coding genes and have a high-GC content, which likely reflects limitations of previous technologies in resolving GC-rich sequences. Dimorphic LINE-1 and SINEC retrotransposon sequences represent the predominant differences between the Great Dane and Boxer assemblies. Proof-of-principle experiments demonstrated that expression of a canine LINE-1 could promote the retrotransposition of itself and a SINEC_Cf consensus sequence in cultured human cells. Thus, ongoing retrotransposon activity may contribute to canine genetic diversity.

genomics↗