ArticlePLoS genetics2011
Repetitive elements may comprise over two-thirds of the human genome.
Article in PLoS genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 633 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
633 citing papers in PubMed, 1 synthesis or guideline pooled it, 1,132 citations in OpenAlex.
- Integrated genomic analyses of acral and mucosal melanomas nominate novel driver genes.Genome medicine · 2022Pooled it
- The therapeutic potential of transposable element activity modulation.EMBO molecular medicine · 2026Review
- Disruption of RNA metabolism and its impact on protein homeostasis.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2026Review
- Article
- Active Human Transposable Elements: Long-Read Sequencing Technologies, Computational Analysis, and Implications for Human Disease.Biomolecules · 2026Review
- LINE-1 Epigenetic Repression and Regulation of Immunity.Viruses · 2026Review
- Gene regulatory innovations from transposable elements in primate cerebellum development.Nature communications · 2026Article
- LINE-1 Retrotransposons and Amyotrophic Lateral Sclerosis.International journal of molecular sciences · 2026Review
- Transcriptional landscapes of dengue patients reveal associations between HERV activity and disease severity.NAR molecular medicine · 2026Article
- Fiber-TEnCATS reveals haplotype-specific chromatin accessibility and DNA methylation at human L1HS loci.bioRxiv : the preprint server for biology · 2026Article
- Stones in genomic storms: transposable element-driven variation in Prunus fruit trees.Mobile DNA · 2026Review
- Host-Parasite Interactions Revisited: Evidence of Horizontal Transfer of a Transposable Element Between a Snail and Its Parasite.Genome biology and evolution · 2026Article
- Transposable elements shape stemness in normal and leukemic hematopoiesis.Nature genetics · 2026Article
- Article
- Therapeutic Stress-Induced Remodeling of Transposable Elements and TE-Gene Chimeras in KYSE150 Esophageal Squamous Cell Carcinoma Cells.International journal of molecular sciences · 2026Article
- Protocol for efficient CRISPRi-mediated silencing of retrotransposons in human pluripotent stem cells.STAR protocols · 2026Article
- Positive Selection Targeted Primate Genes that Encode Transposable Element Repressors.Genome biology and evolution · 2026Article
- The role of KRAB zinc-finger proteins in expanding the domestication potential of transposable elements.Nature genetics · 2026Review
- SFPQ directs histone H3.3 deposition to R-loops in DNA repeats to protect genome stability.Nature communications · 2026Article
- PRIME-BSPre: a genome-wide protein-RNA binding sites prediction method based on templates.BMC genomics · 2026Article
573 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Transposable elements (TEs) are conventionally identified in eukaryotic genomes by alignment to consensus element sequences. Using this approach, about half of the human genome has been previously identified as TEs and low-complexity repeats. We recently developed a highly sensitive alternative de novo strategy, P-clouds, that instead searches for clusters of high-abundance oligonucleotides that are related in sequence space (oligo "clouds"). We show here that P-clouds predicts >840 Mbp of additional repetitive sequences in the human genome, thus suggesting that 66%-69% of the human genome is repetitive or repeat-derived. To investigate this remarkable difference, we conducted detailed analyses of the ability of both P-clouds and a commonly used conventional approach, RepeatMasker (RM), to detect different sized fragments of the highly abundant human Alu and MIR SINEs. RM can have surprisingly low sensitivity for even moderately long fragments, in contrast to P-clouds, which has good sensitivity down to small fragment sizes (∼25 bp). Although short fragments have a high intrinsic probability of being false positives, we performed a probabilistic annotation that reflects this fact. We further developed "element-specific" P-clouds (ESPs) to identify novel Alu and MIR SINE elements, and using it we identified ∼100 Mb of previously unannotated human elements. ESP estimates of new MIR sequences are in good agreement with RM-based predictions of the amount that RM missed. These results highlight the need for combined, probabilistic genome annotation approaches and suggest that the human genome consists of substantially more repetitive sequence than previously believed.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.