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Research: Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites
- Fiorella C. Grandi,
- James M. Rosser,
- Simon J. Newkirk,
- Jun Yin,
- Xiaoling Jiang,
- Zhuo Xing,
- Leanne Whitmore,
- Sanum Bashir,
- Zoltán Ivics,
- Zsuzsanna Izsvák,
- Ping Ye,
- Y. Eugene Yu,
- and Wenfeng An
Genome Res. August 2015 25: 1135-1146; Published in Advance May 20, 2015, doi:10.1101/gr.185132.114
...shores”, i.e., a graded influence of hypomethylated CGIs on nearby CpGs within 2 kb from either side of the CGI. No sloping is evident in the more distant CGI shelves and open seas. CpG island shores were first reported in the context of cancer- and tissue-specific methylation (Irizarry et al. 2009...
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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
...displaying CpG dinucleotides (orange lines) forming a CpG island (pink bar). The positions of primers used to assess L1RSPRDM4 methylation via locus-specific bisulfite sequencing in panel C are shown. The second panel displays animal ON22213 ONT read alignments, with unmethylated CpGs colored in blue...
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Research: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice
- Leandros Boukas,
- Teresa Romeo Luperchio,
- Afrooz Razi,
- Kasper D. Hansen,
- and Hans T. Bjornsson
Genome Res. May 2024 34: 696-710; Published in Advance May 3, 2024, doi:10.1101/gr.278416.123
...preferential chromatin disruption at CpG islands and at regulatory elements linked to aging. A sensitive analysis reveals that regulatory elements disrupted in B/T cells do show chromatin accessibility changes in neurons, but these are very subtle and of uncertain functional significance. Finally, we are able...
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Research: Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development
- Patricia Gerdes,
- Dorothy Chan,
- Mischa Lundberg,
- Francisco J. Sanchez-Luque,
- Gabriela O. Bodea,
- Adam D. Ewing,
- Geoffrey J. Faulkner,
- and Sandra R. Richardson
Genome Res. September 2023 33: 1465-1481; Published in Advance October 5, 2023, doi:10.1101/gr.278003.123
..., and 4 monomers (Supplemental Fig. S9). Although methylation was highly variable at most CpG positions, the CpGs flanking the monomer-monomer borders were consistently hypomethylated relative to the CpGs internal to the monomer units. This trend was consistent across L1 TFI elements regardless of monomer...
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Research: Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing
- Russell J. Butterfield,
- Diane M. Dunn,
- Brett Duval,
- Sarah Moldt,
- and Robert B. Weiss
Genome Res. September 2023 33: 1439-1454; Published in Advance October 5, 2023, doi:10.1101/gr.277871.123
...that the lower cost nCATs methodology is currently on par with whole nanopore sequencing for specifically studying the D4Z4 regions.D4Z4 arrays have asymmetric CpG methylation gradientsTo evaluate the extent of hypomethylation that occurs as a result of contraction of the D4Z4 array, we extracted 5-methyl CpG (5...
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Research: L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis
- Stephanie N. Schauer,
- Patricia E. Carreira,
- Ruchi Shukla,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Francisco J. Sanchez-Luque,
- Paola Nicoli,
- Michaela Kindlova,
- Serena Ghisletti,
- Alexandre Dos Santos,
- Delphine Rapoud,
- Didier Samuel,
- Jamila Faivre,
- Adam D. Ewing,
- Sandra R. Richardson,
- and Geoffrey J. Faulkner
Genome Res. May 2018 28: 639-653; Published in Advance April 11, 2018, doi:10.1101/gr.226993.117
...and mobilization is tightly regulated in most cell types and developmental contexts, with CpG methylation of the L1 internal promoter representing a key mechanism for control of L1 activity (Goodier and Kazazian 2008). In the mammalian germline and early embryo, L1 escapes repression to mobilize and create...
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Research: Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters
- Shrutii Sarda,
- Avinash Das,
- Charles Vinson,
- and Sridhar Hannenhalli
Genome Res. April 2017 27: 553-566; Published in Advance February 21, 2017, doi:10.1101/gr.212050.116
...methylation patterns have identified differentially methylated regions (DMRs) even in the shores of CpG islands (Pollard et al. 2009). These regions of lower CpG density in close proximity (up to 2 kb) to CGIs, whose differentialmethylation patterns are strongly related to gene expression, are highly...
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Research: H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells
- Agustín F. Fernández,
- Gustavo F. Bayón,
- Rocío G. Urdinguio,
- Estela G. Toraño,
- María G. García,
- Antonella Carella,
- Sandra Petrus-Reurer,
- Cecilia Ferrero,
- Pablo Martinez-Camblor,
- Isabel Cubillo,
- Javier García-Castro,
- Jesús Delgado-Calle,
- Flor M. Pérez-Campo,
- José A. Riancho,
- Clara Bueno,
- Pablo Menéndez,
- Anouk Mentink,
- Katia Mareschi,
- Fabian Claire,
- Corrado Fagnani,
- Emanuela Medda,
- Virgilia Toccaceli,
- Sonia Brescianini,
- Sebastián Moran,
- Manel Esteller,
- Alexandra Stolzing,
- Jan de Boer,
- Lorenza Nisticò,
- Maria A. Stazi,
- and Mario F. Fraga
Genome Res. January 2015 25: 27-40; Published in Advance September 30, 2014, doi:10.1101/gr.169011.113
...the different regions of the CpG islands (CGIs) (Wu et al. 2010). Interestingly, both hyper- and hypomethylated CpG sites were enriched in non-CGIs (χ2 test; P < 0.001, OR = 2.58 and P < 0.001, OR = 1.76, respectively) (Fig. 1C) and in intragenic DNA regions (χ2 test; P < 0.001, OR = 1.23 and P < 0.001, OR = 1...
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Corrigendum: Corrigendum: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. February 2026 36: 432; doi:10.1101/gr.281294.125
...Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 10.1101/gr.281294.125 ;36/2/432 ;gr.281294.125 432 gr.281294.125 Corrigendum Corrigendum Corrigenda Corrigendum Corrigendum Razavi-Mohseni Milad Huang Weitai Guo Yu A. Shigaki Dustin Ho Shamaine Wei Ting Tan Patrick Skanderup Anders J...
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Research: Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers
- Hyunchul Jung,
- Jung Kyoon Choi,
- and Eunjung Alice Lee
Genome Res. August 2018 28: 1136-1146; Published in Advance July 3, 2018, doi:10.1101/gr.231837.117
...the same patients (Supplemental Table S1). To create a high-confidence insertion set, we included insertion candidates when Tea predicted both target site duplication (TSD) of at least 5 bp and poly(A) tails, the two signatures for target-primed reversed transcription (TPRT)-mediated retrotransposition...
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