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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...al. (2022) were among the first to demonstrate the utility of targeted LRS in investigating imprinted loci. They studied a family with autosomal dominant pseudohypoparathyroidism type 1b (PHP-1b) demonstrating the loss of methylation in GNAS was due to a maternally inherited retrotransposon insertion...
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Research: Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA
- Seung Cho Lee,
- Evan Ernst,
- Benjamin Berube,
- Filipe Borges,
- Jean-Sebastien Parent,
- Paul Ledon,
- Andrea Schorn,
- and Robert A. Martienssen
Genome Res. April 2020 30: 576-588; Published in Advance April 17, 2020, doi:10.1101/gr.259044.119
...version: In this window In a new window Figure 5. Small RNA profiles of representative LTR retrotransposons; 21-, 22-, 23-, and 24-nt small RNA levels in inflorescence tissues and pollen of WT and ddm1. Reads per million (RPM) were calculated from entire elements, including LTR and coding sequences...
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Research: Genomic analysis of Rad26 and Rad1–Rad10 reveals differences in their dependence on Mediator and RNA polymerase II
- Diyavarshini Gopaul,
- Cyril Denby Wilkes,
- Arach Goldar,
- Nathalie Giordanengo Aiach,
- Marie-Bénédicte Barrault,
- Elizaveta Novikova,
- and Julie Soutourina
Genome Res. August 2022 32: 1516-1528; Published in Advance June 23, 2022, doi:10.1101/gr.276371.121
...equally to this work. Corresponding author: julie.soutourina@cea.frAbstractMediator is a conserved coregulator playing a key role in RNA polymerase (Pol) II transcription. Mediator also links transcription and nucleotide excision repair (NER) via a direct contact with Rad2/ERCC5(XPG) endonuclease...
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Method: Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus
- Sara B. Linker,
- Lynne Randolph-Moore,
- Kalyani Kottilil,
- Fan Qiu,
- Baptiste N. Jaeger,
- Jerika Barron,
- and Fred H. Gage
Genome Res. November 2020 30: 1643-1654; Published in Advance October 29, 2020, doi:10.1101/gr.262196.120
...this method to identify SINE activation in a context that is relevant for normal learning and memory.Retrotransposons are a class of transposable elements (TEs) that integrate into the host through an RNA intermediate (Craig et al. 2015). It is important to be able to examine the transcription of TE RNA...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...(RdDM). Best studied in Arabidopsis thaliana, during RdDM, H3K9me2 and DNA methylation recruit the plant-specific RNA polymerases (Pol) IV and V. Pol IV transcripts are processed into 24 nt siRNAs, which, loaded into members of the AGO4/6 clade, target Pol V transcripts to guide the sequence...
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Research: Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains
- Vivek Hari Sundar G,
- Chenna Swetha,
- Debjani Basu,
- Kannan Pachamuthu,
- Steffi Raju,
- Tania Chakraborty,
- Rebecca A. Mosher,
- and P.V. Shivaprasad
Genome Res. May 2023 33: 715-728; Published in Advance June 5, 2023, doi:10.1101/gr.277353.122
...-transcriptional levels (Baulcombe 2004). Small RNAs (sRNAs), predominant effectors of plant RNA silencing, confer both specificity and amplification modality in silencing. The production of sRNAs associated with transcriptional silencing is primarily initiated by plant-specific RNA Pol II paralog RNA polymerase IV (Pol...
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Research: Profiling neural editomes reveals a molecular mechanism to regulate RNA editing during development
- Suba Rajendren,
- Alfa Dhakal,
- Pranathi Vadlamani,
- Jack Townsend,
- Sarah N. Deffit,
- and Heather A. Hundley
Genome Res. January 2021 31: 27-39; Published in Advance December 18, 2020, doi:10.1101/gr.267575.120
...modification is a molecular process that regulates gene expression by shaping the transcriptional profiles of cells in a multicellular organism. Individual nucleosides in RNA can be deleted or inserted, can undergo base modifications (which together are historically referred to as “RNA editing” events), or can...
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Research: Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites
- Kurt Patterson,
- Farbod Shavarebi,
- Christophe Magnan,
- Ivan Chang,
- Xiaojie Qi,
- Pierre Baldi,
- Virginia Bilanchone,
- and Suzanne B. Sandmeyer
Genome Res. August 2019 29: 1298-1309; Published in Advance June 27, 2019, doi:10.1101/gr.240861.118
...site selection. The Saccharomyces cerevisiae Ty3 retrotransposon inserts proximal to the transcription start sites (TSS) of genes transcribed by RNA polymerase III (RNAP3). In this study, differential patterns of insertion were profiled -wide using a random barcode-tagged Ty3. Saturation transposition...
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Research: Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family
- Alex de Mendoza,
- Jahnvi Pflueger,
- and Ryan Lister
Genome Res. August 2019 29: 1277-1286; Published in Advance June 25, 2019, doi:10.1101/gr.243774.118
...from silencing mechanisms and targeting by the host. Among transposable elements, there are two main types depending on their replication strategy: DNA transposons, which are excised and copied in the as DNA, and retrotransposons, which have an intermediate RNA step before retrotranscription to DNA...
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Research: The origin and evolution of a distinct mechanism of transcription initiation in yeasts
- Zhaolian Lu and
- Zhenguo Lin
Genome Res. January 2021 31: 51-63; Published in Advance November 20, 2020, doi:10.1101/gr.264325.120
...and phenotypic traits (Lin and Li 2012).Most studies of the RNA Polymerase II (Pol II) transcription machinery have focused on promoters containing a TATA box (Patikoglou et al. 1999), which was the first identified core promoter element (Smale and Kadonaga 2003). The process of transcription initiation from...

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