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Research: Switching roles for DNA and histone methylation depend on evolutionary ages of human endogenous retroviruses
- Hitoshi Ohtani,
- Minmin Liu,
- Wanding Zhou,
- Gangning Liang,
- and Peter A. Jones
Genome Res. August 2018 28: 1147-1157; Published in Advance July 3, 2018, doi:10.1101/gr.234229.118
...D, Tang JX, Shinkai Y, Mager DL, Jones S, Hirst M, et al. 2011. DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements and chimaeric transcripts in mouse ES cells. Cell Stem Cell 8: 676–687. ↵Kassiotis G, Stoye JP. 2016. Immune responses to endogenous...
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Research: Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis
- Ozren Bogdanović,
- Steven W. Long,
- Simon J. van Heeringen,
- Arie B. Brinkman,
- Jose Luis Gómez-Skarmeta,
- Hendrik G. Stunnenberg,
- Peter L. Jones,
- and Gert Jan C. Veenstra
Genome Res. August 2011 21: 1313-1327; Published in Advance June 2, 2011, doi:10.1101/gr.114843.110
...and the epigenetic regulation of pluripotency and differentiation and suggest a relatively open, pliable chromatin state in early embryos followed by reestablished methylation-dependent transcriptional repression during organogenesis and differentiation. Footnotes ↵ 4 Corresponding author. E-mail g...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...-regulated TEs. Long terminal repeat (LTR) retroelements are most transcriptionally active immediately following zygotic activation, whereas DNA transposons are enriched among transcripts expressed in later stages of development. Single-cell analysis reveals several endogenous retroviruses expressed in specific...
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Method: The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells
- Mireia Jordà,
- Anna Díez-Villanueva,
- Izaskun Mallona,
- Berta Martín,
- Sergi Lois,
- Víctor Barrera,
- Manel Esteller,
- Tanya Vavouri,
- and Miguel A. Peinado
Genome Res. January 2017 27: 118-132; Published in Advance December 20, 2016, doi:10.1101/gr.207522.116
...cells. In normal cells, unmethylated Alu elements tend to locate in the vicinity of functionally rich regions and display epigenetic features consistent with a direct impact on regulation. In cancer cells, Alu repeats are more resistant to hypomethylation than other retroelements. Genome segmentation...
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Research: Combinatorial DNA methylation codes at repetitive elements
- Christophe Papin,
- Abdulkhaleg Ibrahim,
- Stéphanie Le Gras,
- Amandine Velt,
- Isabelle Stoll,
- Bernard Jost,
- Hervé Menoni,
- Christian Bronner,
- Stefan Dimitrov,
- and Ali Hamiche
Genome Res. June 2017 27: 934-946; Published in Advance March 27, 2017, doi:10.1101/gr.213983.116
...C/CG densities and transcription levels in control and Tdg-deficient MEFs at B1m retroelements ranked by conservation score (n = 185,667). (E) Curves representing cytosine modification densities and transcription levels of B1m SINEs as a function of their conservation. B1m retroelements were sorted...
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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...Human pluripotent cells support endogenous L1 demethylation, transcription, and mobilization (Garcia-Perez et al. 2007; Klawitter et al. 2016; Macia et al. 2017; Sanchez-Luque et al. 2019). Although accurate TE locus-specific measurement of transcription with short-read RNA-seq is extremely challenging (Lanciano...
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Research: LTRs activated by Epstein-Barr virus–induced transformation of B cells alter the transcriptome
- Amy Leung,
- Candi Trac,
- Hiroyuki Kato,
- Kevin R. Costello,
- Zhaoxia Chen,
- Rama Natarajan,
- and Dustin E. Schones
Genome Res. December 2018 28: 1791-1798; Published in Advance October 31, 2018, doi:10.1101/gr.233585.117
...of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nat Genet 46: 558–566. doi:10.1038/ng.2965 ↵Göke J, Lu X, Chan YS, Ng HH, Ly LH, Sachs F, Szczerbinska I. 2015. Dynamic transcription of distinct classes of endogenous retroviral elements marks specific...
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Method: Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data
- Wanqing Shao and
- Ting Wang
Genome Res. January 2021 31: 88-100; Published in Advance December 21, 2020, doi:10.1101/gr.265173.120
...and early embryogenesis. For instance, endogenous retroviruses (ERVs) are highly expressed in ESCs and ERV-derived transcripts are involved in the maintenance of pluripotency (Macfarlan et al. 2012; Santoni et al. 2012; Fort et al. 2014; Lu et al. 2014; Ohnuki et al. 2014; Wang et al. 2014). During mouse...
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Research: Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes
- Vedran Franke,
- Sravya Ganesh,
- Rosa Karlic,
- Radek Malik,
- Josef Pasulka,
- Filip Horvat,
- Maja Kuzman,
- Helena Fulka,
- Marketa Cernohorska,
- Jana Urbanova,
- Eliska Svobodova,
- Jun Ma,
- Yutaka Suzuki,
- Fugaku Aoki,
- Richard M. Schultz,
- Kristian Vlahovicek,
- and Petr Svoboda
Genome Res. August 2017 27: 1384-1394; Published in Advance May 18, 2017, doi:10.1101/gr.216150.116
...-length Dicer1 transcripts (Fig. 5C). Thus, unlike inmice, Dicer1O mRNA comprises a minority of Dicer1 transcripts in hamster oocytes. TheMTCLTR inDicer1 is essential for fertility, and its loss correlates with up-regulation of transcripts targeted by endogenous RNAi (Flemr et al. 2013). Interestingly, after...
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Research: Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures
- Yuliya A. Sytnikova,
- Reazur Rahman,
- Gung-wei Chirn,
- Josef P. Clark,
- and Nelson C. Lau
Genome Res. December 2014 24: 1977-1990; Published in Advance September 29, 2014, doi:10.1101/gr.178129.114
...-seq approach, we profiled PIWI-regulated endogenous transcripts fromOSS cells treated with siRNAs knocking down PIWI compared to cells receiving a negative control siRNA (siGFP). In addition to total mRNA, we measured cytoplasmic, nucleoplasmic, and nascent RNAs to determine the compartmentswherePIWI regulates...

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