Searching journal content for articles similar to Payer et al. 31 (12): 2236.

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  1. Research: Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing
    • Jesper Eisfeldt,
    • Edward J. Higginbotham,
    • Felix Lenner,
    • Jennifer Howe,
    • Bridget A. Fernandez,
    • Anna Lindstrand,
    • Stephen W. Scherer,
    • and Lars Feuk
    Genome Res. November 2024 34: 1763-1773; Published in Advance October 29, 2024, doi:10.1101/gr.279263.124
    ...of families 1 and 2, and consists of an 8 nt stretch of seemingly random sequence. Two BPJs are located within matching repeats: BPJ 1 in family 3, as well as BPJ 1 in family 5. In both cases, the matched repeats are Alu elements. None of the BPJs carry signatures of small deletions.View this table...
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  2. Method: Predicting human genes susceptible to genomic instability associated with Alu/Alu-mediated rearrangements
    • Xiaofei Song,
    • Christine R. Beck,
    • Renqian Du,
    • Ian M. Campbell,
    • Zeynep Coban-Akdemir,
    • Shen Gu,
    • Amy M. Breman,
    • Pawel Stankiewicz,
    • Grzegorz Ira,
    • Chad A. Shaw,
    • and James R. Lupski
    Genome Res. August 2018 28: 1228-1242; Published in Advance June 15, 2018, doi:10.1101/gr.229401.117
    ...CNVs, we emphasize a potentially underappreciated role of Alu in causing variants in these genes as AAMR events are easily missed by routine short-read genomic sequencing techniques.View this table: In this window In a new window Table 2. Human disease-associated genes in predicted AAMR hotspots...
  3. Research: Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes
    • Alexandra J. Scott,
    • Colby Chiang,
    • and Ira M. Hall
    Genome Res. December 2021 31: 2249-2257; Published in Advance September 20, 2021, doi:10.1101/gr.275488.121
    ...were merged as previously described (Chiang et al. 2017). Additionally, we ran MELT v2.1.4 using MELT-SPLIT to identify Alu, SVA, and LINE-1 insertions into the test s (Gardner et al. 2017). We retained MELT calls categorized as “PASS” in the VCF info field that had an ASSESS score of three or more...
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  4. Method: A framework to score the effects of structural variants in health and disease
    • Philip Kleinert and
    • Martin Kircher
    Genome Res. April 2022 32: 766-777; Published in Advance February 23, 2022, doi:10.1101/gr.275995.121
    ...-specificity of regulatory elements and genes. Further, the putatively different mechanisms of phenotypic effects of deletions compared to insertions or duplications complicates a generalized approach for variant effect prediction, as the effect can be mediated by copy number alterations of redundant or unique genomic...
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  5. 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
    ...HMAR) ( Fig. 6 C; Supplemental Tables S14 , S15 ). Similar differences were observed at the gene expression level, with the highest transcriptional activity outside HMARs ( Fig. 6 C). Regarding DNA methylation, Alu repeats showed slightly different behaviors inside and outside HMAR: Lower levels...
  6. Research: Alu repeat discovery and characterization within human genomes
    • Fereydoun Hormozdiari,
    • Can Alkan,
    • Mario Ventura,
    • Iman Hajirasouliha,
    • Maika Malig,
    • Faraz Hach,
    • Deniz Yorukoglu,
    • Phuong Dao,
    • Marzieh Bakhshi,
    • S. Cenk Sahinalp,
    • and Evan E. Eichler
    Genome Res. June 2011 21: 840-849; Published in Advance December 3, 2010, doi:10.1101/gr.115956.110
    ...distinct categories of Alu subfamilies are recognized (Mills et al. 2007) with AluYa5 and AluYb8 being most active in the human lineage (Carroll et al. 2001). Alu retrotranspositions have numerous consequences leading to insertional mutations, gene conversion, recombination, alterations in gene expression...
  7. 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
    ...from mutating the left half of the Alu structure. Several of the random right halves selected from old, Sx, Alu subfamily members negatively impacted insertion efficiency while others did not. These influences were post-transcriptional as we did not alter the promoter and saw only minimal variation...
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  8. Method: Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays
    • Shaleen Shrestha,
    • Jared Allan Sewell,
    • Clarissa Stephanie Santoso,
    • Elena Forchielli,
    • Sebastian Carrasco Pro,
    • Melissa Martinez,
    • and Juan Ignacio Fuxman Bass
    Genome Res. September 2019 29: 1533-1544; doi:10.1101/gr.248823.119
    ...within gene promoters, enhancers, and introns and have been shown to play key roles in gene regulation (Batzer and Deininger 2002; Deininger 2011). In addition, Alu sequences are often silenced by mechanisms that are not fully understood, which could in part be mediated by transcriptional repressors...
  9. Method: Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations
    • David J. Witherspoon,
    • Yuhua Zhang,
    • Jinchuan Xing,
    • W. Scott Watkins,
    • Hongseok Ha,
    • Mark A. Batzer,
    • and Lynn B. Jorde
    Genome Res. July 2013 23: 1170-1181; Published in Advance April 18, 2013, doi:10.1101/gr.148973.112
    .... In one case, a validated novel singleton Alu interrupts a proteincoding exon of FAM187B. This implies that exonic Alu insertions are generally deleterious and thus eliminated by natural selection, but not so quickly that they cannot be observed as extremely rare variants. [Supplemental material...
  10. Research: ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters
    • Nina L. Haring,
    • Elisabeth J. van Bree,
    • Whitney S. Jordaan,
    • Judith R.E. Roels,
    • Gonzalo Congrains Sotomayor,
    • Tiziana M. Hey,
    • Fred T.G. White,
    • Marc D. Galland,
    • Marten P. Smidt,
    • and Frank M.J. Jacobs
    Genome Res. April 2021 31: 551-563; Published in Advance March 15, 2021, doi:10.1101/gr.265348.120
    ...contributed an extra layer of species-specific gene regulation by providing novel transcription factor binding sites. In humans, SINE-VNTR-Alu (SVA) elements are one of three still active TE families; approximately 2800 SVA insertions exist in the human , half of which are human-specific. TEs are often...
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