Abstract:
BACKGROUND:Catalytic RNAs, or ribozymes, are regarded as fossils of a prebiotic RNA world that have remained in the genomes of modern organisms. The simplest ribozymes are the small self-cleaving RNAs, like the hammerhead ribozyme, which have been historically considered biological oddities restricted to some RNA pathogens. Recent data, however, indicate that small self-cleaving ribozymes are widespread in genomes, although their functions are still unknown. RESULTS:We reveal that hammerhead ribozyme sequences in plant genomes form part of a new family of small non-autonomous retrotransposons with hammerhead ribozymes, referred to as retrozymes. These elements contain two long terminal repeats of approximately 350 bp, each harbouring a hammerhead ribozyme that delimitates a variable region of 600-1000 bp with no coding capacity. Retrozymes are actively transcribed, which gives rise to heterogeneous linear and circular RNAs that accumulate differentially depending on the tissue or developmental stage of the plant. Genomic and transcriptomic retrozyme sequences are highly heterogeneous and share almost no sequence homology among species except the hammerhead ribozyme motif and two small conserved domains typical of Ty3-gypsy long terminal repeat retrotransposons. Moreover, we detected the presence of RNAs of both retrozyme polarities, which suggests events of independent RNA-RNA rolling-circle replication and evolution, similarly to that of infectious circular RNAs like viroids and viral satellite RNAs. CONCLUSIONS:Our work reveals that circular RNAs with hammerhead ribozymes are frequently occurring molecules in plant and, most likely, metazoan transcriptomes, which explains the ubiquity of these genomic ribozymes and suggests a feasible source for the emergence of circular RNA plant pathogens.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Cervera A,Urbina D,de la Peña Mdoi
10.1186/s13059-016-1002-4subject
Has Abstractpub_date
2016-06-23 00:00:00pages
135issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-016-1002-4journal_volume
17pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract:BACKGROUND:We propose that a computerized, internet-based graphical description language for systems biology will be essential for describing, archiving and analyzing complex problems of biological function in health and disease. RESULTS:We outline here a conceptual basis for designing such a language and describe Bio...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2001-2-4-research0012
更新日期:2001-01-01 00:00:00
abstract::Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell's native mRNA and result in cross-contamination of transcripts between different cell populations. DecontX is a n...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-1950-6
更新日期:2020-03-05 00:00:00
abstract:BACKGROUND:Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are characterized. In the present study, we systematically evaluate the extent to which errors are incurred dur...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1275-2
更新日期:2017-07-21 00:00:00
abstract::We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. When tested on mouse RNA-seq data, >31,000 splice events were predicted, of which 88% bridged between two regions separated by journal_title:Genome biology pub_type: 杂志文章 doi:10.1186/gb-2010-11-3-r34 更新日期:2010-01-01 00:00:00
abstract:BACKGROUND:The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functio...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0780-4
更新日期:2015-10-21 00:00:00
abstract::Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequencing mixes the signals of sampled populations, diluting the signals of clone-specific aberrations, and complic...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1267-2
更新日期:2017-07-27 00:00:00
abstract::We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genomes to genome-wide m...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1517-y
更新日期:2018-09-25 00:00:00
abstract:BACKGROUND:The annual fish Nothobranchius furzeri is the vertebrate with the shortest known life span in captivity. Fish of the GRZ strain live only three to four months under optimal laboratory conditions, show explosive growth, early sexual maturation and age-dependent physiological and behavioral decline, and expres...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-2-r16
更新日期:2009-02-11 00:00:00
abstract::Short hairpin RNAs can provide stable gene silencing via RNA interference. Recent studies have shown toxicity in vivo that appears to be related to saturation of the endogenous microRNA pathway. Will these findings limit the therapeutic use of such hairpins? ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2006-7-8-231
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:Immunolabeling of metaphase chromosome spreads can map components of the human epigenome at the single cell level. Previously, there has been no systematic attempt to explore the potential of this approach for epigenomic mapping and thereby to complement approaches based on chromatin immunoprecipitation (ChI...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2010-11-11-r110
更新日期:2010-01-01 00:00:00
abstract::The majority of people in the developed world spend more than 90% of their lives indoors. Here, we examine our understanding of the bacteria that co-inhabit our artificial world and how they might influence human health. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2013-14-2-202
更新日期:2013-02-28 00:00:00
abstract::We develop a metagenomic data analysis pipeline, MicroPro, that takes into account all reads from known and unknown microbial organisms and associates viruses with complex diseases. We utilize MicroPro to analyze four metagenomic datasets relating to colorectal cancer, type 2 diabetes, and liver cirrhosis and show tha...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1773-5
更新日期:2019-08-06 00:00:00
abstract:BACKGROUND:Gene duplications have a major role in the evolution of new biological functions. Theoretical studies often assume that a duplication per se is selectively neutral and that, following a duplication, one of the gene copies is freed from purifying (stabilizing) selection, which creates the potential for evolut...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2002-3-2-research0008
更新日期:2002-01-01 00:00:00
abstract::A large number of histone modifications has been implicated in the regulation of gene expression. Together, these modifications have the potential to form a complex combinatorial regulatory code. Genome-wide mapping approaches provide new opportunities to decipher this code, but they may suffer from systematic biases....
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2005-6-6-113
更新日期:2005-01-01 00:00:00
abstract::A recent, genome-wide study shows that the transcriptional program underlying leaf senescence is active and complex, reflecting the activation of more than 2,000 genes in Arabidopsis, with gene products involved in a broad spectrum of regulatory, biochemical and cellular events. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2004-5-3-212
更新日期:2004-01-01 00:00:00
abstract:BACKGROUND:The human lung tissue microbiota remains largely uncharacterized, although a number of studies based on airway samples suggest the existence of a viable human lung microbiota. Here we characterized the taxonomic and derived functional profiles of lung microbiota in 165 non-malignant lung tissue samples from ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-016-1021-1
更新日期:2016-07-28 00:00:00
abstract::Purification of proteins cross-linked to mRNAs has identified 800 mRNA-binding proteins and their characteristics. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb4030
更新日期:2012-07-17 00:00:00
abstract::A report of the First Golden Helix Symposium 'Copy Number Variation (CNV) and Genomic Alterations in Health and Disease', Athens, Greece, 28-29 November 2008. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2009-10-1-301
更新日期:2009-01-01 00:00:00
abstract:BACKGROUND:Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive. RESULTS:By investigating the whole-genome resequencing data of 93 ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1744-x
更新日期:2019-07-12 00:00:00
abstract::Large-scale biology among plant species, as well as comparative genomics of circadian clock architecture and clock-regulated output processes, have greatly advanced our understanding of the endogenous timing system in plants. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2013-14-6-208
更新日期:2013-06-24 00:00:00
abstract::A report on the Keystone symposium 'Non-coding RNAs' held at Snowbird, Utah, USA, 31 March to 5 April 2012. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2012-13-5-315
更新日期:2012-05-25 00:00:00
abstract:BACKGROUND:The vast number of precise intercellular connections within vertebrate nervous systems is only partly explained by the comparatively few known extracellular guidance cues. Large families of neural orphan receptor proteins have been identified and are likely to contribute to these recognition processes but du...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-9-r99
更新日期:2009-01-01 00:00:00
abstract:BACKGROUND:Most studies of molecular evolution are focused on individual genes and proteins. However, understanding the design principles and evolutionary properties of molecular networks requires a system-wide perspective. In the present work we connect molecular evolution on the gene level with system properties of a...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-5-r39
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes and their time of occurrence can shed light on the biology of each species, clade and their evoluti...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1544-8
更新日期:2018-10-05 00:00:00
abstract:BACKGROUND:Obligate pathogenic bacteria lose more genes relative to facultative pathogens, which, in turn, lose more genes than free-living bacteria. It was suggested that the increased gene loss in obligate pathogens may be due to a reduction in the effectiveness of purifying selection. Less attention has been given t...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-8-r164
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:It has been hypothesized that rapid divergence in centromere sequences accompanies rapid karyotypic change during speciation. However, the reuse of breakpoints coincident with centromeres in the evolution of divergent karyotypes poses a potential paradox. In distantly related species where the same centromer...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-8-r170
更新日期:2007-01-01 00:00:00
abstract::The circadian clock determines the rhythmic expression of many different genes throughout a 24-hour period. A recent study investigating the circadian regulation of liver proteins reveals multiple levels of regulation, including transcriptional, post-transcriptional and post-translational mechanisms. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2006-7-9-234
更新日期:2006-01-01 00:00:00
abstract::Gene-expression profiling has yielded important information about simple systems, but complex tissues have not yet been widely profiled. Four recent studies of mammalian skeletal muscles have added to the catalogs of their gene expression differences, but have yet to lead to better understanding of the molecular proce...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2001-2-12-reviews1033
更新日期:2001-01-01 00:00:00
abstract::Chromatin is not a uniform macromolecular entity; it contains different domains characterized by complex signatures of DNA and histone modifications. Such domains are organized both at a linear scale along the genome and spatially within the nucleus. We discuss recent discoveries regarding mechanisms that establish bo...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/s13059-017-1236-9
更新日期:2017-05-23 00:00:00
abstract::To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, we develop CICERO, a local assembly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate ranking. CICERO outperforms commonly used methods, achieving a 95% detection rate for 184 independently validat...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02043-x
更新日期:2020-05-28 00:00:00