Abstract:
:Transposable elements (TEs) are an integral part of the host transcriptome. TE-containing noncoding RNAs (ncRNAs) show considerable tissue specificity and play important roles during development, including stem cell maintenance and cell differentiation. Recent advances in single-cell RNA-seq (scRNA-seq) revolutionized cell type-specific gene expression analysis. However, effective scRNA-seq quantification tools tailored for TEs are lacking, limiting our ability to dissect TE expression dynamics at single-cell resolution. To address this issue, we established a TE expression quantification pipeline that is compatible with scRNA-seq data generated across multiple technology platforms. We constructed TE-containing ncRNA references using bulk RNA-seq data and showed that quantifying TE expression at the transcript level effectively reduces noise. As proof of principle, we applied this strategy to mouse embryonic stem cells and successfully captured the expression profile of endogenous retroviruses in single cells. We further expanded our analysis to scRNA-seq data from early stages of mouse embryogenesis. Our results illustrated the dynamic TE expression at preimplantation stages and revealed 146 TE-containing ncRNA transcripts with substantial tissue specificity during gastrulation and early organogenesis.
journal_name
Genome Resjournal_title
Genome researchauthors
Shao W,Wang Tdoi
10.1101/gr.265173.120subject
Has Abstractpub_date
2021-01-01 00:00:00pages
88-100issue
1eissn
1088-9051issn
1549-5469pii
gr.265173.120journal_volume
31pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::Advanced prostate cancer can progress to systemic metastatic tumors, which are generally androgen insensitive and ultimately lethal. Here, we report a comprehensive genomic survey for somatic events in systemic metastatic prostate tumors using both high-resolution copy number analysis and targeted mutational survey of...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.107961.110
更新日期:2011-01-01 00:00:00
abstract::UEV proteins are enzymatically inactive variants of the E2 ubiquitin-conjugating enzymes that regulate noncanonical elongation of ubiquitin chains. In Saccharomyces cerevisiae, UEV is part of the RAD6-mediated error-free DNA repair pathway. In mammalian cells, UEV proteins can modulate c-FOS transcription and the G2-M...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.gr-1405r
更新日期:2000-11-01 00:00:00
abstract::Long sequencing reads generated by single-molecule sequencing technology offer the possibility of dramatically improving the contiguity of genome assemblies. The biggest challenge today is that long reads have relatively high error rates, currently around 15%. The high error rates make it difficult to use this data al...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.213405.116
更新日期:2017-05-01 00:00:00
abstract::Histone modifications are now well-established mediators of transcriptional programs that distinguish cell states. However, the kinetics of histone modification and their role in mediating rapid, signal-responsive gene expression changes has been little studied on a genome-wide scale. Vascular endothelial growth facto...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.149674.112
更新日期:2013-06-01 00:00:00
abstract::Chronic neuropathic pain is affected by specifics of the precipitating neural pathology, psychosocial factors, and by genetic predisposition. Little is known about the identity of predisposing genes. Using an integrative approach, we discovered that CACNG2 significantly affects susceptibility to chronic pain following...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.104976.110
更新日期:2010-09-01 00:00:00
abstract::The discovery of the genetic code was one of the most important advances of modern biology. But there is more to a DNA code than protein sequence; DNA carries signals for splicing, localization, folding, and regulation that are often embedded within the protein-coding sequence. In this issue, Itzkovitz and Alon show t...
journal_title:Genome research
pub_type: 评论,杂志文章,评审
doi:10.1101/gr.6144007
更新日期:2007-04-01 00:00:00
abstract::The maternal and paternal copies of the genome are both required for mammalian development, and this is primarily due to imprinted genes, those that are monoallelically expressed based on parent-of-origin. Typically, this pattern of expression is regulated by differentially methylated regions (DMRs) that are establish...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.196139.115
更新日期:2016-06-01 00:00:00
abstract::Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the p...
journal_title:Genome research
pub_type: 信件
doi:10.1101/gr.6902
更新日期:2002-05-01 00:00:00
abstract::Transcription factors canonically bind nucleosome-free DNA, making the positioning of nucleosomes within regulatory regions crucial to the regulation of gene expression. Using the assay of transposase accessible chromatin (ATAC-seq), we observe a highly structured pattern of DNA fragment lengths and positions around n...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.192294.115
更新日期:2015-11-01 00:00:00
abstract::Disturbance of DNA methylation leading to aberrant gene expression has been implicated in the etiology of many diseases. Whereas variation at the genetic level has been studied extensively, less is known about the extent and function of epigenetic variation. To explore variation and heritability of DNA methylation, we...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.119685.110
更新日期:2011-11-01 00:00:00
abstract::The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes (cis-eQTLs). More research is needed to identify effects of genetic variation on distant genes (trans-eQTLs) and understand their...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.216754.116
更新日期:2017-11-01 00:00:00
abstract::Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of post-transcriptional gene regulatory evolution are largely unknown. Here we used ri...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.164996.113
更新日期:2014-03-01 00:00:00
abstract::Gene amplification occurs in most solid tumors and is associated with poor prognosis. Amplification of 20q13.2 is common to several tumor types including breast cancer. The 1 Mb of sequence spanning the 20q13.2 breast cancer amplicon is one of the most exhaustively studied segments of the human genome. These studies h...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.gr1743r
更新日期:2001-06-01 00:00:00
abstract::Many thousands of proteins encoded by the genome of Plasmodium falciparum, the causal organism of the deadliest form of human malaria, are of unknown function. It is of utmost importance that these proteins be characterized if we are to develop combative strategies against malaria based on the biology of the parasite....
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4573206
更新日期:2006-04-01 00:00:00
abstract::Variation in the composition of the human oral microbiome in health and disease has been observed. We have characterized inter- and intra-individual variation of microbial communities of 107 individuals in one of the largest cohorts to date (264 saliva samples), using culture-independent 16S rRNA pyrosequencing. We ex...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.140608.112
更新日期:2012-11-01 00:00:00
abstract::The genetic positions of the five Arabidopsis thaliana centromere regions have been identified by mapping size polymorphisms in the centromeric 180-bp repeat arrays. Structural and genetic analysis indicates that 180-bp repeat arrays of up to 1000 kb are found in the centromere region of each chromosome. The genetic b...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7.11.1045
更新日期:1997-11-01 00:00:00
abstract::The vomeronasal system of mice is thought to be specialized in the detection of pheromones. Two multigene families have been identified that encode proteins with seven putative transmembrane domains and that are expressed selectively in subsets of neurons of the vomeronasal organ. The products of these vomeronasal rec...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.10.12.1958
更新日期:2000-12-01 00:00:00
abstract::Single-cell sequencing (SCS) is a powerful new tool for investigating evolution and diversity in cancer and understanding the role of rare cells in tumor progression. These methods have begun to unravel key questions in cancer biology that have been difficult to address with bulk tumor measurements. Over the past five...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.191098.115
更新日期:2015-10-01 00:00:00
abstract::The genomic alterations associated with cancers are numerous and varied, involving both isolated and large-scale complex genomic rearrangements (CGRs). Although the underlying mechanisms are not well understood, CGRs have been implicated in tumorigenesis. Here, we introduce CouGaR, a novel method for characterizing th...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.211201.116
更新日期:2017-01-01 00:00:00
abstract::We have conducted a phylogenetic analysis of the Ribonuclease HI (RNH) domains present in Eubacteria, Eukarya, all long-term repeat (LTR)-bearing retrotransposons, and several late-branching clades of non-LTR retrotransposons. Analysis of this simple yet highly conserved enzymatic domain from these disparate sources p...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.185101
更新日期:2001-07-01 00:00:00
abstract::In plants there are several classes of 21-24-nt short RNAs that regulate gene expression. The most conserved class is the microRNAs (miRNAs), although some miRNAs are found only in specific species. We used high-throughput pyrosequencing to identify conserved and nonconserved miRNAs and other short RNAs in tomato frui...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.080127.108
更新日期:2008-10-01 00:00:00
abstract::Despite recent progress in genome topology knowledge, the role of repeats, which make up the majority of mammalian genomes, remains elusive. Satellite repeats are highly abundant sequences that cluster around centromeres, attract pericentromeric heterochromatin, and aggregate into nuclear chromocenters. These nuclear ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.186643.114
更新日期:2015-07-01 00:00:00
abstract::It is believed that most modern mammalian lineages arose from a series of rapid speciation events near the Cretaceous-Tertiary boundary. It is shown that such a phylogeny makes the common ancestral genome sequence an ideal target for reconstruction. Simulations suggest that with methods currently available, we can exp...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2800104
更新日期:2004-12-01 00:00:00
abstract::Targeted genotyping of transcriptome-scale genetic markers is highly attractive for genetic, ecological, and evolutionary studies, but achieving this goal in a cost-effective manner remains a major challenge, especially for laboratories working on nonmodel organisms. Here, we develop a high-throughput, sequencing-base...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.235820.118
更新日期:2018-12-01 00:00:00
abstract::Natural killer (NK) cells contribute to the essential functions of innate immunity and reproduction. Various genes encode NK cell receptors that recognize the major histocompatibility complex (MHC) Class I molecules expressed by other cells. For primate NK cells, the killer-cell immunoglobulin-like receptors (KIR) are...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.085738.108
更新日期:2009-05-01 00:00:00
abstract::Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using integrated artificial transposons and automated fluorescent sequencing. Mapping and assembly tools represent important compone...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7.5.551
更新日期:1997-05-01 00:00:00
abstract::There are numerous examples from the genomes of viruses, mitochondria, and chromosomes that adjacent genes can overlap, sharing at least one nucleotide. Overlaps have been hypothesized to be involved in genome size minimization and as a regulatory mechanism of gene expression. Here we show that overlapping genes are a...
journal_title:Genome research
pub_type: 信件
doi:10.1101/gr.2433104
更新日期:2004-11-01 00:00:00
abstract::Essential genes refer to those whose null mutation leads to lethality or sterility. Theoretical reasoning and empirical data both suggest that the fatal effect of inactivating an essential gene can be attributed to either the loss of indispensable core cellular function (Type I), or the gain of fatal side effects afte...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.205955.116
更新日期:2016-10-01 00:00:00
abstract::Human genomic data of many types are readily available, but the complexity and scale of human molecular biology make it difficult to integrate this body of data, understand it from a systems level, and apply it to the study of specific pathways or genetic disorders. An investigator could best explore a particular prot...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.082214.108
更新日期:2009-06-01 00:00:00
abstract::Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here, we present sequential ChIP-bisulfite-sequencing (ChIP-BS-seq) as an approach to quantitatively assess DNA methylat...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.133728.111
更新日期:2012-06-01 00:00:00