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 little is understood about the influence of post-transcriptional processes on transcript evolution. Post-transcriptional modification of RNA by N6-methyladenosine (m6A) has been shown to be widespread throughout the transcriptome, and this reversible mark can affect transcript stability and translation dynamics. Here we analyze m6A mRNA modifications in lymphoblastoid cell lines (LCLs) from human, chimpanzee and rhesus, and we identify patterns of m6A evolution among species. We find that m6A evolution occurs in parallel with evolution of consensus RNA sequence motifs known to be associated with the enzymatic complexes that regulate m6A dynamics, and expression evolution of m6A-modified genes occurs in parallel with m6A evolution.
journal_name
Genome Resjournal_title
Genome researchauthors
Ma L,Zhao B,Chen K,Thomas A,Tuteja JH,He X,He C,White KPdoi
10.1101/gr.212563.116subject
Has Abstractpub_date
2017-03-01 00:00:00pages
385-392issue
3eissn
1088-9051issn
1549-5469pii
gr.212563.116journal_volume
27pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::Aberrations of protein-coding genes are a focus of cancer genomics; however, the impact of oncogenes on expression of the ~50% of transcripts without protein-coding potential, including long noncoding RNAs (lncRNAs), has been largely uncharacterized. Activating mutations in the BRAF oncogene are present in >70% of mel...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.140061.112
更新日期:2012-06-01 00:00:00
abstract::In positional cloning the initial assignment of a gene to a specific chromosomal locus is followed by physical mapping of the critical region. The construction of a high-resolution physical map still involves considerable effort. However, new high-resolution fluorescence in situ hybridization (FISH) techniques have fa...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.10.1002
更新日期:1996-10-01 00:00:00
abstract::Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumula...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.191338.115
更新日期:2016-01-01 00:00:00
abstract::Telomeres shorten with each cell division and can ultimately become substrates for nonhomologous end-joining repair, leading to large-scale genomic rearrangements of the kind frequently observed in human cancers. We have characterized more than 1400 telomere fusion events at the single-molecule level, using a combinat...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.200840.115
更新日期:2016-05-01 00:00:00
abstract::Recent advances toward the characterization of Alzheimer's disease (AD) have permitted the identification of a dozen of genetic risk factors, although many more remain undiscovered. In parallel, works in the field of network biology have shown a strong link between protein connectivity and disease. In this manuscript,...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.114280.110
更新日期:2011-03-01 00:00:00
abstract::We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, th...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.213802
更新日期:2002-03-01 00:00:00
abstract::Hammerhead ribozymes previously were found in satellite RNAs from plant viroids and in repetitive DNA from certain species of newts and schistosomes. To determine if this catalytic RNA motif has a wider distribution, we decided to scrutinize the GenBank database for RNAs that contain hammerhead or hammerhead-like moti...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.10.7.1011
更新日期:2000-07-01 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::Most mammalian RNA polymerase II initiation events occur at CpG islands, which are rich in CpGs and devoid of DNA methylation. Despite their relevance for gene regulation, it is unknown to what extent the CpG dinucleotide itself actually contributes to promoter activity. To address this question, we determined the tra...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.241653.118
更新日期:2019-04-01 00:00:00
abstract::The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis of 24,398 expressed sequence tags (ESTs) generated from 15 different adult and juvenile Fugu tissues, 74% of which match...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1691503
更新日期:2003-12-01 00:00:00
abstract::Sequencing of the human Y chromosome has uncovered the peculiarities of the genomic organization of a heterogametic sex chromosome of old evolutionary age, and has led to many insights into the evolutionary changes that occurred during its long history. We have studied the genomic organization of the medaka fish Y chr...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5016106
更新日期:2006-07-01 00:00:00
abstract::Insertion of the human non-LTR retrotransposon LINE-1 (L1) into chromosomal DNA is thought to be initiated by a mechanism called target-primed reverse transcription (TPRT). This mechanism readily accounts for the attachment of the 3'-end of an L1 copy to the genomic target, but the subsequent integration steps leading...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3421505
更新日期:2005-06-01 00:00:00
abstract::Although much is known about genetic variation in human and African great ape (chimpanzee, bonobo, and gorilla) genomes, substantially less is known about variation in gene-expression profiles within and among these species. This information is necessary for defining transcriptional regulatory networks that contribute...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1289803
更新日期:2003-07-01 00:00:00
abstract::The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that is being developed as a resource for mammalian systems genetics. Here we describe an experiment that uses partially inbred CC lines to evaluate the genetic properties and utility of this emerging resource. Genome-wide analysis of the incipien...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.111310.110
更新日期:2011-08-01 00:00:00
abstract::CLONEPICKER is a software pipeline that integrates sequence data with BAC clone fingerprints to dynamically select a minimal overlapping clone set covering the whole genome. In the Rat Genome Sequencing Project (RGSP), a hybrid strategy of "clone by clone" and "whole genome shotgun" approaches was used to maximize the...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2171704
更新日期:2004-04-01 00:00:00
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::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::Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward thi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.212696.116
更新日期:2017-06-01 00:00:00
abstract::Careful titration of Vent polymerase activity allows efficient amplification of full-length plasmids (12 kb). The high processivity and fidelity of this enzyme made oligonucleotide-directed site-specific mutagenesis of plasmids a straight-forward process. Using only two primers, a mutagenic and a complementary, single...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5.4.404
更新日期:1995-11-01 00:00:00
abstract::Mammalian genomes are partitioned into domains that replicate in a defined temporal order. These domains can replicate at similar times in all cell types (constitutive) or at cell type-specific times (developmental). Genome-wide chromatin conformation capture (Hi-C) has revealed sub-megabase topologically associating ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.183699.114
更新日期:2015-08-01 00:00:00
abstract::Dystroglycan is a laminin binding protein, which provides a structural link between the subsarcolemmal cytoskeleton and the extracellular matrix. It is also involved in the organization of basement membranes. So far the genomic organization of the dystroglycan gene DAG1 has not been completely investigated. Here we re...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.10.3.295
更新日期:2000-03-01 00:00:00
abstract::Identifying genes in the genomic context is central to a cell's ability to interpret the genome. Yet, in general, the signals used to define eukaryotic genes are poorly described. Here, we derived simple classifiers that identify where transcription will initiate and terminate using nucleic acid sequence features dete...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.164327.113
更新日期:2014-01-01 00:00:00
abstract::Biological products of importance in food (e.g., milk) and medical (e.g., donor blood-derived products) sciences often correspond to mixtures of samples contributed by multiple individuals. Identifying which individuals contributed to the mixture and in what proportions may be of interest in several circumstances. We ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.256172.119
更新日期:2020-08-01 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::Quantification of mRNA levels in human cortical brain biopsies and autopsies was performed using a fluorogenic 5' nuclease assay. The reproducibility of the assay using replica plates was 97%-99%. Relative quantities of mRNA from 16 different genes were evaluated using a statistical approach based on ANCOVA analysis. ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.10.8.1219
更新日期:2000-08-01 00:00:00
abstract::We have constructed a detailed map of the genomic region containing the ETS-variant gene 6 (ETV6), involved in translocations and deletions associated with hematologic malignancies. Thirty-eight cosmids were characterized belonging to two contigs spanning 340 kb, and an EcoRl restriction map was developed. The gap bet...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.5.404
更新日期:1996-05-01 00:00:00
abstract::Large numbers of expressed sequence tags (ESTs) continue to fill public and private databases with partial cDNA sequences. However, using this huge amount of ESTs to facilitate gene finding in genomic sequence imposes a challenge, especially to wet-lab scientists who often have limited computing resources. In an effor...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.8.3.268
更新日期:1998-03-01 00:00:00
abstract::A contiguous high-resolution map of 44 loci from a 35-Mb portion of the distal region of the long arm of human chromosome 5, q21-q35, was produced using radiation hybrid (RH) mapping in conjunction with a natural deletion mapping panel. The map includes 30 genes, four sequence-tagged site (STS) loci, and 10 DNA marker...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.7.628
更新日期:1996-07-01 00:00:00
abstract::Short tandem repeats (STRs) have a wide range of applications, including medical genetics, forensics, and genetic genealogy. High-throughput sequencing (HTS) has the potential to profile hundreds of thousands of STR loci. However, mainstream bioinformatics pipelines are inadequate for the task. These pipelines treat S...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.135780.111
更新日期:2012-06-01 00:00:00
abstract::As part of a recent high-density linkage disequilibrium (LD) study of chromosome 20, we obtained genotypes for approximately 30,000 SNPs at a density of 1 SNP/2 kb on four different population samples (47 CEPH founders; 91 UK unrelateds [unrelated white individuals of western European ancestry]; 97 African Americans; ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4217605
更新日期:2005-11-01 00:00:00