Abstract：
BACKGROUND:mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites, when the sequence content is insufficient for this purpose. Previous studies suggested that RNA structure affects mRNA processing. However, the regulatory role of RNA structure in mRNA processing remains unclear. RESULTS:Here, we perform in vivo selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemical profiling on Arabidopsis and generate the in vivo nuclear RNA structure landscape. We find that nuclear mRNAs fold differently from cytosolic mRNAs across translation start and stop sites. Notably, we discover a two-nucleotide single-stranded RNA structure feature upstream of 5' splice sites that is strongly associated with splicing and the selection of alternative 5' splice sites. The regulatory role of this RNA structure feature is further confirmed by experimental validation. Moreover, we find the single-strandedness of branch sites is also associated with 3' splice site recognition. We also identify an RNA structure feature comprising two close-by single-stranded regions that is specifically associated with both polyadenylation and alternative polyadenylation events. CONCLUSIONS:We successfully identify pre-mRNA structure features associated with splicing and polyadenylation at whole-genome scale and validate an RNA structure feature which can regulate splicing. Our study unveils a new RNA structure regulatory mechanism for mRNA processing.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Liu Z,Liu Q,Yang X,Zhang Y,Norris M,Chen X,Cheema J,Zhang H,Ding Ydoi
10.1186/s13059-020-02236-4subject
Has Abstractpub_date
2021-01-04 00:00:00pages
11issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-020-02236-4journal_volume
22pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract：BACKGROUND:Gene duplication followed by divergence is one of the main sources of metabolic versatility. The patchwork and stepwise models of metabolic evolution help us to understand these processes, but their assumptions are relatively simplistic. We used a network-based approach to determine the influence of metaboli...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2007-8-2-r26
更新日期：2007-01-01 00:00:00
abstract：BACKGROUND:Hemispheric asymmetry in neuronal processes is a fundamental feature of the human brain and drives symptom lateralization in Parkinson's disease (PD), but its molecular determinants are unknown. Here, we identify divergent epigenetic patterns involved in hemispheric asymmetry by profiling DNA methylation in ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-020-01960-1
更新日期：2020-03-09 00:00:00
abstract：:The key molecules involved in regulating the assembly and function of the mitotic spindle are shared by evolutionarily divergent species. Studies in different model systems are leading to convergent conclusions about the central role of microtubule nucleation and dynamics and of kinesin-related motor proteins in spind...
journal_title：Genome biology
pub_type： 杂志文章,评审
doi：10.1186/gb-2000-1-1-reviews101
更新日期：2000-01-01 00:00:00
abstract：:DNA transposons are efficient tools in transgenesis and have therefore become popular in the analysis of the regulatory genome in vertebrates via enhancer trap screens. Here, I discuss recent progress in this field of research, with a focus on the application of one of these transposons, namely the medaka fish derived...
journal_title：Genome biology
pub_type： 杂志文章,评审
doi：10.1186/gb-2007-8-s1-s8
更新日期：2007-01-01 00:00:00
abstract：:Our knowledge on tissue- and disease-specific functions of human genes is rather limited and highly context-specific. Here, we have developed a method for the comparison of mRNA expression levels of most human genes across 9,783 Affymetrix gene expression array experiments representing 43 normal human tissue types, 68...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2008-9-9-r139
更新日期：2008-01-01 00:00:00
abstract：:In a recent study, Petrovski and Goldstein reported that (non-Finnish) Europeans have significantly fewer nonsynonymous singletons in Online Mendelian Inheritance in Man (OMIM) disease genes compared with Africans, Latinos, South Asians, East Asians, and other unassigned non-Europeans. We use simulations of Exome Aggr...
journal_title：Genome biology
pub_type： 评论,信件
doi：10.1186/s13059-017-1172-8
更新日期：2017-02-27 00:00:00
abstract：BACKGROUND:Although aberrant DNA methylation has been observed previously in acute lymphoblastic leukemia (ALL), the patterns of differential methylation have not been comprehensively determined in all subtypes of ALL on a genome-wide scale. The relationship between DNA methylation, cytogenetic background, drug resista...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2013-14-9-r105
更新日期：2013-09-24 00:00:00
abstract：:Protein kinases with a conserved catalytic domain make up one of the largest 'superfamilies' of eukaryotic proteins and play many key roles in biology and disease. Efforts to identify and classify all the members of the eukaryotic protein kinase superfamily have recently culminated in the mining of essentially complet...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2003-4-5-111
更新日期：2003-01-01 00:00:00
abstract：BACKGROUND:DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures-each representing a mutagenic process-derived from 3056 patients spanning 19 cancer types to quantify the strand asymmetry of mutational ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-018-1509-y
更新日期：2018-09-10 00:00:00
abstract：BACKGROUND:Nuclear factor I-A (NFI-A), a phylogenetically conserved transcription/replication protein, plays a crucial role in mouse brain development. Previous studies have shown that disruption of the Nfia gene in mice leads to perinatal lethality, corpus callosum agenesis, and hydrocephalus. RESULTS:To identify pot...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2007-8-5-r72
更新日期：2007-01-01 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:Transcription regulatory networks are composed of interactions between transcription factors and their target genes. Whereas unicellular networks have been studied extensively, metazoan transcription regulatory networks remain largely unexplored. Caenorhabditis elegans provides a powerful model to study such...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2005-6-13-r110
更新日期：2005-01-01 00:00:00
abstract：:MiRNAs play important roles in many diseases including cancers. However computational prediction of miRNA target genes is challenging and the accuracies of existing methods remain poor. We report mirMark, a new machine learning-based method of miRNA target prediction at the site and UTR levels. This method uses experi...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-014-0500-5
更新日期：2014-01-01 00:00:00
abstract：BACKGROUND:Parasitism is a highly successful mode of life and one that requires suites of gene adaptations to permit survival within a potentially hostile host. Among such adaptations is the secretion of proteins capable of modifying or manipulating the host environment. Nippostrongylus brasiliensis is a well-studied m...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2004-5-6-r39
更新日期：2004-01-01 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：:ProSplicer is a database of putative alternative splicing information derived from the alignment of proteins, mRNA sequences and expressed sequence tags (ESTs) against human genomic DNA sequences. Proteins, mRNA and ESTs provide valuable evidence that can reveal splice variants of genes. The alternative splicing infor...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2003-4-4-r29
更新日期：2003-01-01 00:00:00
abstract：:Cryptochromes are photoreceptors that regulate entrainment by light of the circadian clock in plants and animals. They also act as integral parts of the central circadian oscillator in animal brains and as receptors controlling photomorphogenesis in response to blue or ultraviolet (UV-A) light in plants. Cryptochromes...
journal_title：Genome biology
pub_type： 杂志文章,评审
doi：10.1186/gb-2005-6-5-220
更新日期：2005-01-01 00:00:00
abstract：:Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction associations for entire metabolic genes in an organism, and can be simulated to predict metabolic fluxes for various systems-level metabolic studies. Since the first GEM for Haemophilus influenzae was reported in 1999, advances have be...
journal_title：Genome biology
pub_type： 杂志文章,评审
doi：10.1186/s13059-019-1730-3
更新日期：2019-06-13 00:00:00
abstract：:We used scaled factorial moments to search for intermittency in the log expression ratios (LERs) for thousands of genes spotted on cDNA microarrays (gene chips). Results indicate varying levels of intermittency in gene expression. The observation of intermittency in the data analyzed provides a complimentary handle on...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2002-3-7-preprint0005
更新日期：2002-05-29 00:00:00
abstract：BACKGROUND:Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-018-1479-0
更新日期：2018-08-17 00:00:00
abstract：BACKGROUND:The direct examination of large, unbiased samples of young gene duplicates in their early stages of evolution is crucial to understanding the origin, divergence and preservation of new genes. Furthermore, comparative analysis of multiple genomes is necessary to determine whether patterns of gene duplication ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2009-10-7-r75
更新日期：2009-01-01 00:00:00
abstract：BACKGROUND:Developmental programs are implemented by regulatory interactions between Transcription Factors (TFs) and their target genes, which remain poorly understood. While recent studies have focused on regulatory cascades of TFs that govern early development, little is known about how the ultimate effectors of cell...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2013-14-8-r86
更新日期：2013-08-23 00:00:00
abstract：BACKGROUND:Differentiation of metazoan cells requires execution of different gene expression programs but recent single-cell transcriptome profiling has revealed considerable variation within cells of seeming identical phenotype. This brings into question the relationship between transcriptome states and cell phenotype...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-015-0683-4
更新日期：2015-06-09 00:00:00
abstract：BACKGROUND:Abundant pseudogenes are a feature of mammalian genomes. Processed pseudogenes (PPs) are reverse transcribed from mRNAs. Recent molecular biological studies show that mammalian long interspersed element 1 (L1)-encoded proteins may have been involved in PP reverse transcription. Here, we present the first com...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2003-4-11-r74
更新日期：2003-01-01 00:00:00
abstract：:The EpiGRAPH web service http://epigraph.mpi-inf.mpg.de/ enables biologists to uncover hidden associations in vertebrate genome and epigenome datasets. Users can upload sets of genomic regions and EpiGRAPH will test multiple attributes (including DNA sequence, chromatin structure, epigenetic modifications and evolutio...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2009-10-2-r14
更新日期：2009-02-10 00:00:00
abstract：BACKGROUND:The relationships between proteins are often asymmetric: one protein (A) depends for its function on another protein (B), but the second protein does not depend on the first. In metabolic networks there are multiple pathways that converge into one central pathway. The enzymes in the converging pathways depen...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2009-10-2-r19
更新日期：2009-02-12 00:00:00
abstract：:As the cost of sequencing continues to decrease and the amount of sequence data generated grows, new paradigms for data storage and analysis are increasingly important. The relative scaling behavior of these evolving technologies will impact genomics research moving forward. ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-016-0917-0
更新日期：2016-03-23 00:00:00
abstract：:Advances in sequencing technology have led to a sharp decrease in the cost of 'data generation'. But is this sufficient to ensure cost-effective and efficient 'knowledge generation'? ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2011-12-8-125
更新日期：2011-08-25 00:00:00
abstract：BACKGROUND:There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challe...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2014-15-3-r53
更新日期：2014-03-25 00:00:00
abstract：:Two landmark studies of cell signaling, by RNA interference and phosphoproteomics, provide complementary global views of the pathways downstream of receptor kinases, including those regulated by Erks. ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2007-8-1-202
更新日期：2007-01-01 00:00:00
