Mouse retrotransposons: sequence structure, evolutionary age, genomic distribution and function

Kawase, Masaki; Ichiyanagi, Kenji

doi:10.1266/ggs.23-00221

Cited by 2 publications

(2 citation statements)

References 125 publications

(153 reference statements)

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“…In addition to 7 LINE subfamilies, 99 LTR subfamilies, 11 SINE subfamilies, and one subfamily of DNA transposon showed varied enrichment of YY1 binding in mESCs (Fig.6C-D). Three families (ERV1, ERV2/ERVK, and ERV3/ERVL) make up mouse LTR class of TEs (46), and they contributed to 22, 60 and 17 subfamilies enriched for YY1 occupancy, respectively but with modest fold changes. Intracisternal A-type particle (IAP) subfamilies belong to family ERV2/ERVK.…”

Section: Resultsmentioning

confidence: 99%

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YY1 is a transcriptional activator of mouse LINE-1 Tf subfamily

Saha,

Nielsen,

Nandani

et al. 2024

Preprint

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Long interspersed element type 1 (LINE-1, L1) is an active autonomous transposable element (TE) in the human genome. The first step of L1 replication is transcription, which is controlled by an internal RNA polymerase II promoter in the 5' untranslated region (UTR) of a full-length L1. It has been shown that transcription factor YY1 binds to a conserved sequence motif at the 5' end of the human L1 5'UTR and dictates where transcription initiates but not the level of transcription. Putative YY1-binding motifs have been predicted in the 5'UTRs of two distinct mouse L1 subfamilies, Tf and Gf. Using site-directed mutagenesis, in vitro binding, and gene knockdown assays, we experimentally tested the role of YY1 in mouse L1 transcription. Our results indicate that Tf, but not Gf subfamily, harbors functional YY1-binding sites in its 5'UTR monomers. In contrast to its role in human L1, YY1 functions as a transcriptional activator for the mouse Tf subfamily. Furthermore, YY1-binding motifs are solely responsible for the synergistic interaction between monomers, consistent with a model wherein distant monomers act as enhancers for mouse L1 transcription. The abundance of YY1-binding sites in Tf elements also raise important implications for gene regulation at the genomic level.

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Section: Resultsmentioning

confidence: 99%

“…6C-D). Three families (ERV1, ERV2/ERVK, and ERV3/ERVL) make up mouse LTR class of TEs (46), and they contributed to 22, 60 and 17 subfamilies enriched for YY1 occupancy, respectively but with modest fold changes. Intracisternal A-type particle (IAP) subfamilies belong to family ERV2/ERVK.…”

Section: Gf_i Monomers Lack Functional Yy1-binding Motifmentioning

confidence: 99%

YY1 is a transcriptional activator of mouse LINE-1 Tf subfamily

Saha,

Nielsen,

Nandani

et al. 2024

Preprint

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Insertion of short L1 sequences generates inter-strain histone acetylation differences in the mouse

Boyboy,

Ichiyanagi

2024

Mobile DNA

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Background Gene expression divergence between populations and between individuals can emerge from genetic variations within the genes and/or in the cis regulatory elements. Since epigenetic modifications regulate gene expression, it is conceivable that epigenetic variations in cis regulatory elements can also be a source of gene expression divergence. Results In this study, we compared histone acetylation (namely, H3K9ac) profiles in two mouse strains of different subspecies origin, C57BL/6 J (B6) and MSM/Ms (MSM), as well as their F1 hybrids. This identified 319 regions of strain-specific acetylation, about half of which were observed between the alleles of F1 hybrids. While the allele-specific presence of the interferon regulatory factor 3 (IRF3) binding sequence was associated with allele-specific histone acetylation, we also revealed that B6-specific insertions of a short 3′ fragment of LINE-1 (L1) retrotransposon occur within or proximal to MSM-specific acetylated regions. Furthermore, even in hyperacetylated domains, flanking regions of non-polymorphic 3′ L1 fragments were hypoacetylated, suggesting a general activity of the 3′ L1 fragment to induce hypoacetylation. Indeed, we confirmed the binding of the 3′ region of L1 by three Krüppel-associated box domain-containing zinc finger proteins (KZFPs), which interact with histone deacetylases. These results suggest that even a short insertion of L1 would be excluded from gene- and acetylation-rich regions by natural selection. Finally, mRNA-seq analysis for F1 hybrids was carried out, which disclosed a link between allele-specific promoter/enhancer acetylation and gene expression. Conclusions This study disclosed a number of genetic changes that have changed the histone acetylation levels during the evolution of mouse subspecies, a part of which is associated with gene expression changes. Insertions of even a very short L1 fragment can decrease the acetylation level in their neighboring regions and thereby have been counter-selected in gene-rich regions, which may explain a long-standing mystery of discrete genomic distribution of LINEs and SINEs.

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Mouse retrotransposons: sequence structure, evolutionary age, genomic distribution and function

Cited by 2 publications

References 125 publications

YY1 is a transcriptional activator of mouse LINE-1 Tf subfamily

YY1 is a transcriptional activator of mouse LINE-1 Tf subfamily

Insertion of short L1 sequences generates inter-strain histone acetylation differences in the mouse

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