Searching journal content for articles similar to Attig et al. 29 (10): 1578.

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  1. 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
    ...of TE transcripts by 2.7-fold but not that of non-TE transcripts (Fig. 5A; Supplemental Fig. S18A). This was primarily by activation of LTR-derived promoters (Supplemental Fig. S18B). Because LTRs could function as promoters of GENCODE genes, proviral human endogenous retrovirus (HERV) or unannotated...
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  2. Method: Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data
    • Wanqing Shao and
    • Ting Wang
    Genome Res. January 2021 31: 88-100; Published in Advance December 21, 2020, doi:10.1101/gr.265173.120
    ...distinct sequence composition. For instance, TE transcripts enriched in extraembryonic ectoderm, extraembryonic endoderm, parietal endoderm, and visceral endoderm are almost exclusively composed of LTRs, although we did find that several highly expressed transcripts in extraembryonic ectoderm are derived...
  3. Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
    • Ni-Chen Chang,
    • Quirze Rovira,
    • Jonathan Wells,
    • Cédric Feschotte,
    • and Juan M. Vaquerizas
    Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
    ...-regulated TEs. Long terminal repeat (LTR) retroelements are most transcriptionally active immediately following zygotic activation, whereas DNA transposons are enriched among transcripts expressed in later stages of development. Single-cell analysis reveals several endogenous retroviruses expressed in specific...
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  4. Research: Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain
    • Christopher J. Playfoot,
    • Julien Duc,
    • Shaoline Sheppard,
    • Sagane Dind,
    • Alexandre Coudray,
    • Evarist Planet,
    • and Didier Trono
    Genome Res. September 2021 31: 1531-1545; Published in Advance August 16, 2021, doi:10.1101/gr.275133.120
    ...(LHPP; 0.9% vs. 97%) (Fig. 3A), the host of intronic single-nucleotide polymorphisms (SNPs) associated with major depressive disorder (Neff et al. 2009; Cui et al. 2016). The previously reported LTR12C-driven transcript of semaphorin 4D (SEMA4D), the product of which participates in axon guidance...
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