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Article: Diverse cis factors controlling Alu retrotransposition: What causes Alu elements to die?
- Matthew S. Comeaux,
- Astrid M. Roy-Engel,
- Dale J. Hedges,
- and Prescott L. Deininger
Genome Res. April 2009 19: 545-555; Published in Advance March 9, 2009, doi:10.1101/gr.089789.108
...of the active Alu elements belong to the younger subfamilies. We present a systematic analysis evaluating the observed sequence variation in the different sections of an Alu element on retrotransposition. The length of the longest number of uninterrupted adenines in the A-tail, the degree of A-tail...
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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
...is necessary for Alu mobilization, although the binding of two heterodimers provides more efficient mobilization. Alu RNPs, once formed, can dock on ribosomes. As L1 mRNA is translated, the poly(A) tail of an SRP9/14-bound Alu competes for nascent L1 ORF2 reverse transcriptase ( Sinnett et al. 1991 ; Boeke...
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Research: A matter of life or death: How microsatellites emerge in and vanish from the human genome
- Yogeshwar D. Kelkar,
- Kristin A. Eckert,
- Francesca Chiaromonte,
- and Kateryna D. Makova
Genome Res. December 2011 21: 2038-2048; Published in Advance October 12, 2011, doi:10.1101/gr.122937.111
...frequency of births/deaths over their entire length, while GC-rich Alu s only in their 3′ poly(A) tails and middle A-stretches, with differences depending on transposable element integration timing. Births/deaths were strongly selected against in coding regions. Births/deaths occurred in genomic regions...
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LETTER: Differential Alu Mobilization and Polymorphism Among the Human and Chimpanzee Lineages
- Dale J. Hedges,
- Pauline A. Callinan,
- Richard Cordaux,
- Jinchuan Xing,
- Erin Barnes,
- and Mark A. Batzer
Genome Res. June 2004 14: 1068-1075; doi:10.1101/gr.2530404
...in retrotransposition capability has been observed in members of the L1 subfamily ( Lutz et al. 2003 ) and within Alu may be attributable to variation at PolIII promoter efficiency, variation in target-primed reverse transcription, oligo dA tail instability ( Roy-Engel et al. 2002b ), and insertion status polymorphism...
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Method: Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome
- Ju Heon Maeng,
- H. Josh Jang,
- Alan Y. Du,
- Shin-Cheng Tzeng,
- and Ting Wang
Genome Res. December 2023 33: 2143-2155; Published in Advance December 8, 2023, doi:10.1101/gr.277061.122
.... 2022). To investigate full-length transcripts, we used LRCAGE reads to call transcripts because LRCAGE reads span from the 5′ end to poly(A) tail. Then, we filtered out transcripts whose 5′ ends were not supported by the merged peaks of LRCAGE and nanoCAGE peaks, resulting in 43,665 full...
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Research: Discovery of a new repeat family in the Callithrix jacchus genome
- Miriam K. Konkel,
- Brygg Ullmer,
- Erika L. Arceneaux,
- Sreeja Sanampudi,
- Sarah A. Brantley,
- Robert Hubley,
- Arian F.A. Smit,
- and Mark A. Batzer
Genome Res. May 2016 26: 649-659; Published in Advance February 25, 2016, doi:10.1101/gr.199075.115
.... 2009; Konkel et al. 2010). A full-length Alu element is ∼300 bp in length and terminates in an adenosine-rich tail (A-tail), a typical characteristic of non-LTR retrotransposons (Batzer and Deininger 2002). L1 predates the origin of primates, has been active throughout the radiation of primates...
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Research: The human genome contains over a million autonomous exons
- Nicholas Stepankiw,
- Ally W.H. Yang,
- and Timothy R. Hughes
Genome Res. November 2023 33: 1865-1878; Published in Advance November 9, 2023, doi:10.1101/gr.277792.123
...DNA Fragmentase, mix by vortexing, incubate at 37°C for 20 min, stop with 15 µL 0.5M EDTA mixed by pipetting). The resulting fragmented DNA was purified with Zymo Clean and Concentrator 5 µg and eluted with NEB DNA elution buffer. We then end repaired the DNA using NEB end repair kit and added dA tails using NEB...
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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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Method: TIGRA: A targeted iterative graph routing assembler for breakpoint assembly
- Ken Chen,
- Lei Chen,
- Xian Fan,
- John Wallis,
- Li Ding,
- and George Weinstock
Genome Res. February 2014 24: 310-317; Published in Advance December 4, 2013, doi:10.1101/gr.162883.113
...indicates that the majority of these insertions (predominately Alu) were assembled near their full length (;300 bp). Manual inspection (Methods) of TIGRA contigs confirmed that many Alu elements were completely assembled not only with polyA tails but also with flanking sequences attached on both ends...
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Letter: 5′-Transducing SVA retrotransposon groups spread efficiently throughout the human genome
- Annette Damert,
- Julija Raiz,
- Axel V. Horn,
- Johannes Löwer,
- Hui Wang,
- Jinchuan Xing,
- Mark A. Batzer,
- Roswitha Löwer,
- and Gerald G. Schumann
Genome Res. November 2009 19: 1992-2008; Published in Advance August 3, 2009, doi:10.1101/gr.093435.109
...of the env gene and the 39-LTR of the endogenous retrovirus HERVK-10 (Ono et al. 1987). A poly(A) tail is positioned downstream of the predicted conserved polyadenylation signal AATAAA (Ostertag et al. 2003). The origin of SVA elements can be traced back to the beginnings of hominid primate evolution, only...

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