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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...examples of L1 co-option for vertebrate proteins have been reported. Here, we describe protein isoforms, in which the L1 retrotransposons are incorporated into host genes as protein-coding exons by alternative splicing. L1 ORF1 protein (ORF1p) is an RNA-binding protein that binds to L1 RNA and is required...
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Methods: Identification of transposable elements using multiple alignments of related genomes
- Anat Caspi and
- Lior Pachter
Genome Res. February 2006 16: 260-270; Published in Advance December 14, 2005, doi:10.1101/gr.4361206
...on the host genome, and improve the quality of assembled genomes. Using the availability of several nearly complete Drosophila genomes and developments in whole genome alignment methods, we introduce a large-scale comparative method for identifying repetitive mobile DNA regions. These regions are highly...
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LETTER: HIV integration site selection: Analysis by massively parallel pyrosequencing reveals association with epigenetic modifications
- Gary P. Wang,
- Angela Ciuffi,
- Jeremy Leipzig,
- Charles C. Berry,
- and Frederic D. Bushman
Genome Res. August 2007 17: 1186-1194; Published in Advance June 1, 2007, doi:10.1101/gr.6286907
...integration. Another possibility is that the A/T-rich sequences facilitate binding of the integration cofactor PSIP1/LEDGF/p75 (discussed further below). Primary sequences at genomic locations hosting multiple integration events We found 41 sites that hosted two independent integration events at exactly...
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REVIEW: Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health
- Victoria P. Belancio,
- Dale J. Hedges,
- and Prescott Deininger
Genome Res. March 2008 18: 343-358; Published in Advance February 6, 2008, doi:10.1101/gr.5558208
...of mobile elements to their host genomes, these discoveries have occurred alongside growing evidence of the role of TEs in human disease and genetic instability. Here we examine, with a particular emphasis on human retrotransposon activity, several newly discovered aspects of mammalian retrotransposon...
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Resource: Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
- Jiawei Shen,
- Siyuan Cheng,
- Deepak Purushotham,
- Xiaoyu Zhuo,
- Alan Y Du,
- Wenjin Zhang,
- Daofeng Li,
- and Ting Wang
Genome Res. February 21, 2025 gr.279764.124; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124
...dictates algorithms: recent developments in read alignment. Genome Biology 22. Bao W, Kojima KK, Kohany O. 2015. Repbase Update, a database of repetitive elements in eukaryotic s. Mobile DNA 6: 11. Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, Imbeault M, Izsvák Z, Levin HL, Macfarlan...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...type during embryonic mitosis.Recent characterization of haploids produced from CENH3-mediated elimination has revealed the presence of mini-chromosomes that include the endogenous centromeres, which can be maintained through multiple subsequent generations (Tan et al. 2023). Mini-chromosomes in plants...
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Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
- Jonas de Tribolet-Hardy,
- Christian W. Thorball,
- Romain Forey,
- Evarist Planet,
- Julien Duc,
- Alexandre Coudray,
- Bara Khubieh,
- Sandra Offner,
- Cyril Pulver,
- Jacques Fellay,
- Michael Imbeault,
- Priscilla Turelli,
- and Didier Trono
Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
...more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. Here, we present a comprehensive survey...
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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
.... 2001; de Koning et al. 2011). Mammalian TEs are grouped into two major classes according to their mode of mobilization—the “copy and paste” retrotransposons and the “cut and paste” DNA transposons. Retrotransposons are further classified into three types—long interspersed elements (LINEs), short...
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Research: DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity
- Steven R. Eichten,
- Tim Stuart,
- Akanksha Srivastava,
- Ryan Lister,
- and Justin O. Borevitz
Genome Res. November 2016 26: 1520-1531; Published in Advance September 9, 2016, doi:10.1101/gr.205468.116
...by transposon insertion polymorphisms in which the presence or absence of an element dictates methylation levels in flanking low-copy sequence. Recent work across more than 200 natural Arabidopsis thaliana accessions have indicated that a large number of novel transposable element insertions and deletions...
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LETTER: Active Alu retrotransposons in the human genome
- E. Andrew Bennett,
- Heiko Keller,
- Ryan E. Mills,
- Steffen Schmidt,
- John V. Moran,
- Oliver Weichenrieder,
- and Scott E. Devine
Genome Res. December 2008 18: 1875-1883; Published in Advance October 3, 2008, doi:10.1101/gr.081737.108
...largely dictates its mobilization capacity ( Figs. 1 , 2 ), though other factors influence mobilization as well (see below). Resurrection of ancient Alu J and Alu S elements We next determined that sequence variation is ultimately responsible for the functional extinction of older Alu elements...

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