The regulated retrotransposon transcriptome of mammalian cells

By G. Faulkner, Y. Kimura, Carsten O. Daub, Shivangi Wani, C. Plessy, K. Irvine, Kate Schroder, N. Cloonan, Anita L. Steptoe, Timo Lassmann and 12 more. Nature Genetics, 2009

796 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/3ae44b7d80d1a116878f8ddd4c17f25fbdf62606

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Citations in the corpus

The functional role of long non-coding RNA in human carcinomas (2011, neutral): “Retrotransposon-derived RNAs RE-RNAs [231,232]”
The Landscape of long non-coding RNA classification (2015, positive): “Promoters within repeats drive expression of many ncRNAs [75], especially in pluripotent [29, 76, 77] and cancerous cells [29].”
Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs (2013, background): “Several instances of TEs co-opted for cellular function on a genome-wide scale have been documented, notably as a source of cis-elements regulating adjacent host genes, such as promoters [53,54], transcription factor binding sites [55–57], enhancers [58,59] or insulators [60,61].”
The rise of regulatory RNA (2014, background): “…is evidence that plasticity has been superimposed on RNA-directed epigenetic networks by the expansion of RNA editing, especially during cognitive evolution 296,297 , and by retrotransposon utilization and mobility 114,298–301 , which harks back to the insights of McClintock and Britten & Davidson.”
KRAB zinc finger proteins (2017, background): “First, deep transcriptome analyses indicate that some TE loci can be transcriptionally active in adult tissues, providing alternative promoters or fulfilling other regulatory functions (Faulkner et al., 2009; Belancio et al., 2010).”
The impact of retrotransposons on human genome evolution (2009, neutral): “The functional promoter sequences of L1 and Alu elements can also initiate sense or antisense transcription through other gene”
Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa (2010, background): “However, we failed to observe a correlation between enhanced nucleosomal retention and the expression status of individual repeats in human testis or embryonic tissues (data not shown”
CpG islands and the regulation of transcription. (2011, neutral): “2008), and CAGE tags (Faulkner et al. 2009).”
LINE-1 Elements in Structural Variation and Disease (2011, background): “Interestingly, L1 ASP-derived chimeric transcripts have proven useful in the identification of expressed L1s from human embryonic stem cells, embryonic carcinoma cell lines, and somatic human tissues (77, 149, 223).”
Endogenous viruses: insights into viral evolution and impact on host biology (2012, background): “Promoters acquired from LTRs typically function as alternative, tissue-specific promoters in addition to the broadly used ancestral promoter”
Landscape of transcription in human cells (2012, neutral): “miRNA 1,756 497 (28) 59 (12) 147 (30) 454 (454) 175 (175) 18 snoRNA 1,521 458 (30) 73 (16) 223 (49) NA NA 60 snRNA 1,944 378 (19) 123 (33) 41 (11) NA NA 36 tRNA 624 465 (75) 29 (6) 197 (42) NA NA 52 Other{ 1,209 191 (16) 69 (36) 24 (13) NA NA 32 Total GENCODE 7,054 1,989 (28) 353 (18) 632 (32) NA NA”
Somatic retrotransposition alters the genetic landscape of the human brain (2011, methodology): “Several lines of evidence support this model, including L1 transcription 8-9 and CNV in brain tissues from human donors of various ages 10-11 as well as mobilization of engineered L1s in vitro and in transgenic rodents 10,12 .”
The emergence of lncRNAs in cancer biology (2011, background): “Although many RNA species are >200 bp long, such as repeat or pseudogene-derived transcripts (15), the abbreviated term lncRNA (also referred to as lincRNA, for long intergenic ncRNA) does not uniformly apply to all of these (Box 1).”
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. (2011, background): “…due to limitations in the TSS-seq process, we may have missed or under-represented transcripts of poly(A ) RNAs (Kapranov et al. 2007a) and TSCs located in perfectly matching repetitive genomic sequences, which are estimated to contain 6%–30% of the capped RNAs in humans (Faulkner et al. 2009).”
A Comparative Encyclopedia of DNA Elements in the Mouse Genome (2014, background): “Previous studies have shown that endogenous retroviral elements can be transcribed in tissue-specific manner 63,64 , with a fraction of them derived from enhancers and necessary for transcription of genes involved in pluripotency 65,66 .”
Adaptive seeds tame genomic sequence comparison. (2011, background): “Onthe other hand, repeat-masking may be undesirable when mapping DNA reads to a genome, because the repetitive reads can some-times be mapped successfully and they can reveal interesting biology (Faulkner et al. 2009).”