Abstract:
:The lack of long-term evolutionary conservation of microRNA (miRNA) target sites appears to contradict many analyses of their functions. Several hypotheses have been offered, but an attractive one-that the conservation may be a function of taxonomic hierarchy (vertebrates, mammals, primates, etc.)-has rarely been discussed. For such an analysis, we cannot use evolutionary conservation as a criterion of target identification, and hence, have used high confidence target sites in the cross-linking immunoprecipitation (CLIP) data. Assuming that a proportion, p, of target sites in the CLIP data are conserved, we define the evolvability of miRNA targets as 1-p. Genomic data from vertebrate species show that the evolvability between human and fish is very high, at more than 90%. The evolvability decreases to 50% between birds and mammals, 20% among mammalian orders, and only 6% between human and chimpanzee. Within each taxonomic hierarchy, there is a set of targets that are conserved only at that level of evolution. Extrapolating the evolutionary trend, we find the evolvability in any single species to be close to 0%. Thus, all miRNA target sites identified by the CLIP method are evolutionarily conserved in one species, but the conservation is lost step by step in larger taxonomic groups. The changing evolvability of miRNA targets suggests that miRNA-target interactions may play a role in the evolution of organismal diversity.
journal_name
Genome Resjournal_title
Genome researchauthors
Xu J,Zhang R,Shen Y,Liu G,Lu X,Wu CIdoi
10.1101/gr.148916.112subject
Has Abstractpub_date
2013-11-01 00:00:00pages
1810-6issue
11eissn
1088-9051issn
1549-5469pii
gr.148916.112journal_volume
23pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::Chicken B cells create their immunoglobulin repertoire within the Bursa of Fabricius by gene conversion. The high homologous recombination activity is shared by the bursal B-cell-derived DT40 cell line, which integrates transfected DNA constructs at high rates into its endogenous loci. Targeted integration in DT40 is ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.10.12.2062
更新日期:2000-12-01 00:00:00
abstract::Detecting and estimating DNA sample contamination are important steps to ensure high-quality genotype calls and reliable downstream analysis. Existing methods rely on population allele frequency information for accurate estimation of contamination rates. Correctly specifying population allele frequencies for each indi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.246934.118
更新日期:2020-02-01 00:00:00
abstract::Phenotypic differences within populations and between closely related species are often driven by variation and evolution of gene expression. However, most analyses have focused on the effects of genomic variation at cis-regulatory elements such as promoters and enhancers that control transcriptional activity, and lit...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.212563.116
更新日期:2017-03-01 00:00:00
abstract::A large database of copy number profiles from cancer genomes can facilitate the identification of recurrent chromosomal alterations that often contain key cancer-related genes. It can also be used to explore low-prevalence genomic events such as chromothripsis. In this study, we report an analysis of 8227 human cancer...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.140301.112
更新日期:2013-02-01 00:00:00
abstract::Meiotic recombination, including crossovers (COs) and gene conversions (GCs), impacts natural variation and is an important evolutionary force. COs increase genetic diversity by redistributing existing variation, whereas GCs can alter allelic frequency. Here, we sequenced Arabidopsis Landsberg erecta (Ler) and two set...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.127522.111
更新日期:2012-03-01 00:00:00
abstract::Genomics data introduce a substantial computational burden as well as data privacy and ownership issues. Data sets generated by high-throughput sequencing platforms require immense amounts of computational resources to align to reference genomes and to call and annotate genomic variants. This problem is even more pron...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.207464.116
更新日期:2018-09-01 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::The apicomplexan Cryptosporidium parvum is one of the most prevalent protozoan parasites of humans. We report the physical mapping of the genome of the Iowa isolate, sequencing and analysis of chromosome 6, and approximately 0.9 Mbp of sequence sampled from the remainder of the genome. To construct a robust physical m...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1555203
更新日期:2003-08-01 00:00:00
abstract::In comparison to genotypes, knowledge about haplotypes (the combination of alleles present on a single chromosome) is much more useful for whole-genome association studies and for making inferences about human evolutionary history. Haplotypes are typically inferred from population genotype data using computational met...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.077065.108
更新日期:2008-08-01 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::Although more than thirty mammalian genomes have been sequenced to draft quality, very few of these include the Y chromosome. This has limited our understanding of the evolutionary dynamics of gene persistence and loss, our ability to identify conserved regulatory elements, as well our knowledge of the extent to which...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.154286.112
更新日期:2013-09-01 00:00:00
abstract::Despite much research, our understanding of the architecture and cis-regulatory elements of human promoters is still lacking. Here, we devised a high-throughput assay to quantify the activity of approximately 15,000 fully designed sequences that we integrated and expressed from a fixed location within the human genome...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.236075.118
更新日期:2019-02-01 00:00:00
abstract::The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a ch...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.253435.119
更新日期:2019-11-01 00:00:00
abstract::Fetal liver intriguingly consists of hepatic parenchymal cells and hematopoietic stem/progenitor cells. Human fetal liver aged 22 wk of gestation (HFL22w) corresponds to the turning point between immigration and emigration of the hematopoietic system. To gain further molecular insight into its developmental and functi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.175501
更新日期:2001-08-01 00:00:00
abstract::The representation and discovery of transcription factor (TF) sequence binding specificities is critical for understanding gene regulatory networks and interpreting the impact of disease-associated noncoding genetic variants. We present a novel TF binding motif representation, the k-mer set memory (KSM), which consist...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.226852.117
更新日期:2018-06-01 00:00:00
abstract::MicroRNAs (miRNAs) are known to post-transcriptionally regulate target mRNAs through the 3'-UTR, which interacts mainly with the 5'-end of miRNA in animals. Here we identify many endogenous motifs within human 5'-UTRs specific to the 3'-ends of miRNAs. The 3'-end of conserved miRNAs in particular has significant inter...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.089367.108
更新日期:2009-07-01 00:00:00
abstract::Advances in high-throughput technologies, such as ChIP-chip, and the completion of human and mouse genomic sequences now allow analysis of the mechanisms of gene regulation on a systems level. In this study, we have developed a computational genomics approach (termed ChIPModules), which begins with experimentally dete...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5520206
更新日期:2006-12-01 00:00:00
abstract::Single-nucleotide polymorphisms (SNPs) are the most frequently found DNA sequence variations in the human genome. It has been argued that a dense set of SNP markers can be used to identify genetic factors associated with complex disease traits. Because all high-throughput genotyping methods require precise sequence kn...
journal_title:Genome research
pub_type: 杂志文章
doi:
更新日期:1999-05-01 00:00:00
abstract::Large copy number variants (CNVs) have been recently found as structural polymorphisms of the human genome of still unknown biological significance. CNVs are significantly enriched in regions with segmental duplications or low-copy repeats (LCRs). Williams-Beuren syndrome (WBS) is a neurodevelopmental disorder caused ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.073197.107
更新日期:2008-05-01 00:00:00
abstract::In the search for common genetic variants that contribute to prevalent human diseases, patterns of linkage disequilibrium (LD) among linked markers should be considered when selecting SNPs. Genotyping efficiency can be increased by choosing tagging SNPs (tagSNPs) in LD with other SNPs. However, it remains to be seen w...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4138406
更新日期:2006-03-01 00:00:00
abstract::Facio-scapulo-humeral dystrophy (FSHD), a muscular hereditary disease with a prevalence of 1 in 20,000, is caused by a partial deletion of a subtelomeric repeat array on chromosome 4q. Earlier, we demonstrated the existence in the vicinity of the D4Z4 repeat of a nuclear matrix attachment site, FR-MAR, efficient in no...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6620908
更新日期:2008-01-01 00:00:00
abstract::Y chromosome haplotypes are particularly useful in deciphering human evolutionary history because they accentuate the effects of drift, migration, and range expansion. Significant acceleration of Y biallelic marker discovery and subsequent typing involving heteroduplex detection has been achieved by implementing an in...
journal_title:Genome research
pub_type: 信件
doi:10.1101/gr.7.10.996
更新日期:1997-10-01 00:00:00
abstract::Here we use a chromosome-level genome assembly of a prairie rattlesnake (Crotalus viridis), together with Hi-C, RNA-seq, and whole-genome resequencing data, to study key features of genome biology and evolution in reptiles. We identify the rattlesnake Z Chromosome, including the recombining pseudoautosomal region, and...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.240952.118
更新日期:2019-04-01 00:00:00
abstract::Transcription factors (TFs) are key mediators that propagate extracellular and intracellular signals through to changes in gene expression profiles. However, the rules by which promoters decode the amount of active TF into target gene expression are not well understood. To determine the mapping between promoter DNA se...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.212316.116
更新日期:2017-01-01 00:00:00
abstract::Epigenetic mechanisms are believed to play key roles in the establishment of cell-specific transcription programs. Accordingly, the modified bases 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) have been observed in DNA of genomic regulatory regions such as enhancers, and oxidation of 5mC into 5hmC by Ten-e...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.211466.116
更新日期:2017-06-01 00:00:00
abstract::The draft genome ( approximately 160 Mb) of the urochordate ascidian Ciona intestinalis has been sequenced by the whole-genome shotgun method and should provide important insights into the origin and evolution of chordates as well as vertebrates. However, because this genomic data has not yet been mapped onto chromoso...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4156606
更新日期:2006-02-01 00:00:00
abstract::Despite considerable genetic heterogeneity underlying neurodevelopmental diseases, there is compelling evidence that many disease genes will map to a much smaller number of biological subnetworks. We developed a computational method, termed MAGI (merging affected genes into integrated networks), that simultaneously in...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.178855.114
更新日期:2015-01-01 00:00:00
abstract::An important aspect of the development of systems biology approaches in metazoans is the characterization of expression patterns of nearly all genes predicted from genome sequences. Such "localizome" maps should provide information on where (in what cells or tissues) and when (at what stage of development or under wha...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2497604
更新日期:2004-10-01 00:00:00
abstract::DNA transposons, or class 2 transposable elements, have successfully propagated in a wide variety of genomes. However, it is widely believed that DNA transposon activity has ceased in mammalian genomes for at least the last 40 million years. We recently reported evidence for the relatively recent activity of hAT and H...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.071886.107
更新日期:2008-05-01 00:00:00
abstract::Although often considered "minimal" organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete genomic sequence and proteogenomic map for the piscine mycoplasma Mycoplasma mobile, noted for its robust gliding motility. For t...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2674004
更新日期:2004-08-01 00:00:00