In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants.


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.


Genome Biol


Genome biology


Liu Z,Liu Q,Yang X,Zhang Y,Norris M,Chen X,Cheema J,Zhang H,Ding Y




Has Abstract


2021-01-04 00:00:00














  • Multi-species integrative biclustering.

    abstract::We describe an algorithm, multi-species cMonkey, for the simultaneous biclustering of heterogeneous multiple-species data collections and apply the algorithm to a group of bacteria containing Bacillus subtilis, Bacillus anthracis, and Listeria monocytogenes. The algorithm reveals evolutionary insights into the surpris...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Waltman P,Kacmarczyk T,Bate AR,Kearns DB,Reiss DJ,Eichenberger P,Bonneau R

    更新日期:2010-01-01 00:00:00

  • Common gene expression strategies revealed by genome-wide analysis in yeast.

    abstract:BACKGROUND:Gene expression is a two-step synthesis process that ends with the necessary amount of each protein required to perform its function. Since the protein is the final product, the main focus of gene regulation should be centered on it. However, because mRNA is an intermediate step and the amounts of both mRNA ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: García-Martínez J,González-Candelas F,Pérez-Ortín JE

    更新日期:2007-01-01 00:00:00

  • Anticipatory evolution and DNA shuffling.

    abstract::DNA shuffling has proven to be a powerful technique for the directed evolution of proteins. A mix of theoretical and applied research has now provided insights into how recombination can be guided to more efficiently generate proteins and even organisms with altered functions. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Bacher JM,Reiss BD,Ellington AD

    更新日期:2002-07-31 00:00:00

  • Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation.

    abstract:BACKGROUND:Protein synthesis is tightly regulated and alterations to translation are characteristic of many cancers.Translation regulation is largely exerted at initiation through the eukaryotic translation initiation factor 4 F (eIF4F). eIF4F is pivotal for oncogenic signaling as it integrates mitogenic signals to amp...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Rubio CA,Weisburd B,Holderfield M,Arias C,Fang E,DeRisi JL,Fanidi A

    更新日期:2014-01-01 00:00:00

  • Decode-seq: a practical approach to improve differential gene expression analysis.

    abstract::Many differential gene expression analyses are conducted with an inadequate number of biological replicates. We describe an easy and effective RNA-seq approach using molecular barcoding to enable profiling of a large number of replicates simultaneously. This approach significantly improves the performance of different...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Li Y,Yang H,Zhang H,Liu Y,Shang H,Zhao H,Zhang T,Tu Q

    更新日期:2020-03-23 00:00:00

  • Genome-wide mapping of FOXM1 binding reveals co-binding with estrogen receptor alpha in breast cancer cells.

    abstract:BACKGROUND:The forkhead transcription factor FOXM1 is a key regulator of the cell cycle. It is frequently over-expressed in cancer and is emerging as an important therapeutic target. In breast cancer FOXM1 expression is linked with estrogen receptor (ERα) activity and resistance to endocrine therapies, with high levels...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Sanders DA,Ross-Innes CS,Beraldi D,Carroll JS,Balasubramanian S

    更新日期:2013-01-24 00:00:00

  • Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function.

    abstract:BACKGROUND:Many eukaryotic genomes encode cis-natural antisense transcripts (cis-NATs). Sense and antisense transcripts may form double-stranded RNAs that are processed by the RNA interference machinery into small interfering RNAs (siRNAs). A few so-called nat-siRNAs have been reported in plants, mammals, Drosophila, a...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Zhang X,Xia J,Lii YE,Barrera-Figueroa BE,Zhou X,Gao S,Lu L,Niu D,Chen Z,Leung C,Wong T,Zhang H,Guo J,Li Y,Liu R,Liang W,Zhu JK,Zhang W,Jin H

    更新日期:2012-01-01 00:00:00

  • Surveying genome replication.

    abstract::Two recent studies have added microarrays to the toolkit used to analyze the origins of replication in yeast chromosomes, providing a fuller picture of how genomic DNA replication is organized. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Kearsey S

    更新日期:2002-01-01 00:00:00

  • Dating branches on the tree of life using DNA.

    abstract::The use of DNA sequences to estimate the timing of evolutionary events is increasingly popular, although it is fraught with practical difficulties. But the exponential growth of relevant information and improved methods of analysis are providing increasingly reliable sequence-derived dates, and it may become possible ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Wray GA

    更新日期:2002-01-01 00:00:00

  • The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes.

    abstract:BACKGROUND:Comparisons between C3 and C4 grasses often utilize C3 species from the subfamilies Ehrhartoideae or Pooideae and C4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C3 panicoid grass Dichanthelium oligosanthes from the independent C4 lineages ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Studer AJ,Schnable JC,Weissmann S,Kolbe AR,McKain MR,Shao Y,Cousins AB,Kellogg EA,Brutnell TP

    更新日期:2016-10-28 00:00:00

  • Dynamic systems.

    abstract::A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011. ...

    journal_title:Genome biology



    authors: Bakal C

    更新日期:2012-01-30 00:00:00

  • Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features.

    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


    authors: Yu G,Gail MH,Consonni D,Carugno M,Humphrys M,Pesatori AC,Caporaso NE,Goedert JJ,Ravel J,Landi MT

    更新日期:2016-07-28 00:00:00

  • A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila.

    abstract:BACKGROUND:Population genetic theory predicts that rapid adaptation is largely driven by complex traits encoded by many loci of small effect. Because large-effect loci are quickly fixed in natural populations, they should not contribute much to rapid adaptation. RESULTS:To investigate the genetic architecture of therm...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Mallard F,Nolte V,Tobler R,Kapun M,Schlötterer C

    更新日期:2018-08-20 00:00:00

  • A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1.

    abstract:BACKGROUND:The cell-cycle checkpoint kinase Chk1 is essential in mammalian cells due to its roles in controlling processes such as DNA replication, mitosis and DNA-damage responses. Despite its paramount importance, how Chk1 controls these functions remains unclear, mainly because very few Chk1 substrates have hitherto...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Blasius M,Forment JV,Thakkar N,Wagner SA,Choudhary C,Jackson SP

    更新日期:2011-08-18 00:00:00

  • SCALE: modeling allele-specific gene expression by single-cell RNA sequencing.

    abstract::Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing allows the comparison of expression distribution between the two alleles of a diploid organism and the characterization of allele-specific bursting. Here, we propose SC...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Jiang Y,Zhang NR,Li M

    更新日期:2017-04-26 00:00:00

  • Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity.

    abstract::We describe a bioinformatic tool, Tumor Aberration Prediction Suite (TAPS), for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. It includes detailed visualization of genomic segment characteristics and iterative pattern recognition for copy number identificati...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Rasmussen M,Sundström M,Göransson Kultima H,Botling J,Micke P,Birgisson H,Glimelius B,Isaksson A

    更新日期:2011-10-24 00:00:00

  • Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23.

    abstract:BACKGROUND:The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potential therapeutic targets. Using novel chromatin interaction detection techniques and allele specific as...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: McGovern A,Schoenfelder S,Martin P,Massey J,Duffus K,Plant D,Yarwood A,Pratt AG,Anderson AE,Isaacs JD,Diboll J,Thalayasingam N,Ospelt C,Barton A,Worthington J,Fraser P,Eyre S,Orozco G

    更新日期:2016-11-01 00:00:00

  • Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding.

    abstract:BACKGROUND:The C2H2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent or diverse in other eukaryotes. The biochemical and evolutionary mechanisms that underlie the diversity of this DNA-binding domain exclusively in metazoans are, however, mostly unknown. RESULTS:Here,...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Najafabadi HS,Garton M,Weirauch MT,Mnaimneh S,Yang A,Kim PM,Hughes TR

    更新日期:2017-09-06 00:00:00

  • Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency.

    abstract::Understanding the functional impact of genomic variants is a major goal of modern genetics and personalized medicine. Although many synonymous and non-coding variants act through altering the efficiency of pre-mRNA splicing, it is difficult to predict how these variants impact pre-mRNA splicing. Here, we describe a ma...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Adamson SI,Zhan L,Graveley BR

    更新日期:2018-06-01 00:00:00

  • xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features.

    abstract::The eXtensible Genome Data Broker (xGDB) provides a software infrastructure consisting of integrated tools for the storage, display, and analysis of genome features in their genomic context. Common features include gene structure annotations, spliced alignments, mapping of repetitive sequence, and microarray probes, b...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Schlueter SD,Wilkerson MD,Dong Q,Brendel V

    更新日期:2006-01-01 00:00:00

  • Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells.

    abstract:BACKGROUND:Estrogens and their receptors are important in human development, physiology and disease. In this study, we utilized an integrated genome-wide molecular and computational approach to characterize the interaction between the activated estrogen receptor (ER) and the regulatory elements of candidate target gene...

    journal_title:Genome biology

    pub_type: 杂志文章,meta分析


    authors: Lin CY,Ström A,Vega VB,Kong SL,Yeo AL,Thomsen JS,Chan WC,Doray B,Bangarusamy DK,Ramasamy A,Vergara LA,Tang S,Chong A,Bajic VB,Miller LD,Gustafsson JA,Liu ET

    更新日期:2004-01-01 00:00:00

  • A novel and universal method for microRNA RT-qPCR data normalization.

    abstract::Gene expression analysis of microRNA molecules is becoming increasingly important. In this study we assess the use of the mean expression value of all expressed microRNAs in a given sample as a normalization factor for microRNA real-time quantitative PCR data and compare its performance to the currently adopted approa...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Mestdagh P,Van Vlierberghe P,De Weer A,Muth D,Westermann F,Speleman F,Vandesompele J

    更新日期:2009-01-01 00:00:00

  • Networks for all.

    abstract::A report on the Cold Spring Harbor Laboratory/Wellcome Trust conference on Network Biology, Hinxton, UK, 27-31 August 2008. ...

    journal_title:Genome biology



    authors: Ahnert SE,Teichmann SA

    更新日期:2008-10-27 00:00:00

  • Ancient DNA and the rewriting of human history: be sparing with Occam's razor.

    abstract::Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA. ...

    journal_title:Genome biology

    pub_type: 历史文章,杂志文章,评审


    authors: Haber M,Mezzavilla M,Xue Y,Tyler-Smith C

    更新日期:2016-01-11 00:00:00

  • Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations.

    abstract:BACKGROUND:Short-term laboratory evolution of bacteria followed by genomic sequencing provides insight into the mechanism of adaptive evolution, such as the number of mutations needed for adaptation, genotype-phenotype relationships, and the reproducibility of adaptive outcomes. RESULTS:In the present study, we descri...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Conrad TM,Joyce AR,Applebee MK,Barrett CL,Xie B,Gao Y,Palsson BØ

    更新日期:2009-01-01 00:00:00

  • The cryptochromes.

    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


    authors: Lin C,Todo T

    更新日期:2005-01-01 00:00:00

  • DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution.

    abstract:BACKGROUND:Analysis of somatic mutations provides insight into the mutational processes that have shaped the cancer genome, but such analysis currently requires large cohorts. We develop deconstructSigs, which allows the identification of mutational signatures within a single tumor sample. RESULTS:Application of decon...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Rosenthal R,McGranahan N,Herrero J,Taylor BS,Swanton C

    更新日期:2016-02-22 00:00:00

  • Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes.

    abstract:BACKGROUND:DNA methylation and the Polycomb repression system are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests that DNA methylation can attenuate the binding of Polycomb protein components to chromatin and thus plays a role in determining their geno...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Reddington JP,Perricone SM,Nestor CE,Reichmann J,Youngson NA,Suzuki M,Reinhardt D,Dunican DS,Prendergast JG,Mjoseng H,Ramsahoye BH,Whitelaw E,Greally JM,Adams IR,Bickmore WA,Meehan RR

    更新日期:2013-03-25 00:00:00

  • Protein recoding by ADAR1-mediated RNA editing is not essential for normal development and homeostasis.

    abstract:BACKGROUND:Adenosine-to-inosine (A-to-I) editing of dsRNA by ADAR proteins is a pervasive epitranscriptome feature. Tens of thousands of A-to-I editing events are defined in the mouse, yet the functional impact of most is unknown. Editing causing protein recoding is the essential function of ADAR2, but an essential rol...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Heraud-Farlow JE,Chalk AM,Linder SE,Li Q,Taylor S,White JM,Pang L,Liddicoat BJ,Gupte A,Li JB,Walkley CR

    更新日期:2017-09-05 00:00:00

  • Altered retinal microRNA expression profile in a mouse model of retinitis pigmentosa.

    abstract:BACKGROUND:The role played by microRNAs (miRs) as common regulators in physiologic processes such as development and various disease states was recently highlighted. Retinitis pigmentosa (RP) linked to RHO (which encodes rhodopsin) is the most frequent form of inherited retinal degeneration that leads to blindness, for...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Loscher CJ,Hokamp K,Kenna PF,Ivens AC,Humphries P,Palfi A,Farrar GJ

    更新日期:2007-01-01 00:00:00