Long noncoding RNAs with snoRNA ends.

PubWeight™: 2.71‹?› | Rank: Top 1%

🔗 View Article (PMID 22959273)

Published in Mol Cell on September 06, 2012

Authors

Qing-Fei Yin1, Li Yang, Yang Zhang, Jian-Feng Xiang, Yue-Wei Wu, Gordon G Carmichael, Ling-Ling Chen

Author Affiliations

1: State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

Articles citing this

lincRNAs: genomics, evolution, and mechanisms. Cell (2013) 6.50

Long noncoding RNAs: cellular address codes in development and disease. Cell (2013) 6.01

Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol (2013) 4.57

RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat Rev Mol Cell Biol (2013) 3.47

Dynamic integration of splicing within gene regulatory pathways. Cell (2013) 2.25

Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. Mol Cell (2014) 2.02

Posttranscriptional gene regulation by long noncoding RNA. J Mol Biol (2012) 1.87

Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res (2014) 1.83

Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet (2015) 1.81

Competition between pre-mRNAs for the splicing machinery drives global regulation of splicing. Mol Cell (2013) 1.62

MYC regulates the non-coding transcriptome. Oncotarget (2014) 1.29

A Prader-Willi locus lncRNA cloud modulates diurnal genes and energy expenditure. Hum Mol Genet (2013) 1.19

Long noncoding RNAs: Re-writing dogmas of RNA processing and stability. Biochim Biophys Acta (2015) 1.08

Perspectives on the mechanism of transcriptional regulation by long non-coding RNAs. Epigenetics (2013) 1.08

The regulation and functions of the nuclear RNA exosome complex. Nat Rev Mol Cell Biol (2016) 1.07

Non-coding RNAs: multi-tasking molecules in the cell. Int J Mol Sci (2013) 1.07

Long noncoding RNAs in innate and adaptive immunity. Curr Opin Immunol (2013) 1.06

Integrating the roles of long and small non-coding RNA in brain function and disease. Mol Psychiatry (2014) 1.04

Neighboring gene regulation by antisense long non-coding RNAs. Int J Mol Sci (2015) 1.03

Recommendations for the investigation of animal models of Prader-Willi syndrome. Mamm Genome (2013) 1.01

The role of long non-coding RNAs in neurodevelopment, brain function and neurological disease. Philos Trans R Soc Lond B Biol Sci (2014) 1.01

Epigenetic regulation in human melanoma: past and future. Epigenetics (2015) 0.98

From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. Endocr Rev (2014) 0.98

Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus. Genes Dev (2015) 0.97

Highly restricted deletion of the SNORD116 region is implicated in Prader-Willi Syndrome. Eur J Hum Genet (2014) 0.95

Non-coding RNA: a new frontier in regulatory biology. Natl Sci Rev (2014) 0.95

Single molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev (2014) 0.94

Species-specific alternative splicing leads to unique expression of sno-lncRNAs. BMC Genomics (2014) 0.93

Databases for lncRNAs: a comparative evaluation of emerging tools. RNA (2014) 0.93

Long Noncoding RNAs: A New Regulatory Code in Metabolic Control. Trends Biochem Sci (2015) 0.92

Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nat Rev Mol Cell Biol (2016) 0.91

Long noncoding RNAs, emerging players in muscle differentiation and disease. Skelet Muscle (2014) 0.90

The emerging landscape of small nucleolar RNAs in cell biology. Wiley Interdiscip Rev RNA (2015) 0.89

Lariat intronic RNAs in the cytoplasm of Xenopus tropicalis oocytes. RNA (2014) 0.89

In-gel imaging of RNA processing using broccoli reveals optimal aptamer expression strategies. Chem Biol (2015) 0.88

Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets. Front Bioeng Biotechnol (2015) 0.88

Deciphering the RNA landscape by RNAome sequencing. RNA Biol (2015) 0.88

Long non-coding RNAs as novel targets for therapy in hepatocellular carcinoma. Pharmacol Ther (2016) 0.87

The noncoding RNAs SNORD50A and SNORD50B bind K-Ras and are recurrently deleted in human cancer. Nat Genet (2015) 0.87

ADAR1 is required for differentiation and neural induction by regulating microRNA processing in a catalytically independent manner. Cell Res (2015) 0.87

RNA-guided isomerization of uridine to pseudouridine--pseudouridylation. RNA Biol (2014) 0.87

Small nucleolar RNA 113-1 suppresses tumorigenesis in hepatocellular carcinoma. Mol Cancer (2014) 0.86

The dyskerin ribonucleoprotein complex as an OCT4/SOX2 coactivator in embryonic stem cells. Elife (2014) 0.85

An updated human snoRNAome. Nucleic Acids Res (2016) 0.83

Novel Intronic RNA Structures Contribute to Maintenance of Phenotype in Saccharomyces cerevisiae. Genetics (2016) 0.83

A striatal-enriched intronic GPCR modulates huntingtin levels and toxicity. Elife (2015) 0.83

Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences. BMC Genomics (2013) 0.83

Long non-coding RNAs in haematological malignancies. Int J Mol Sci (2013) 0.83

RNAs of the human chromosome 15q11-q13 imprinted region. Wiley Interdiscip Rev RNA (2012) 0.83

SnoVectors for nuclear expression of RNA. Nucleic Acids Res (2014) 0.83

RNA-RNA interactions and pre-mRNA mislocalization as drivers of group II intron loss from nuclear genomes. Proc Natl Acad Sci U S A (2014) 0.83

Small RNAs with big implications: new insights into H/ACA snoRNA function and their role in human disease. Wiley Interdiscip Rev RNA (2014) 0.83

Formation of nuclear bodies by the lncRNA Gomafu-associating proteins Celf3 and SF1. Genes Cells (2014) 0.82

Long non-coding RNA regulation of reproduction and development. Mol Reprod Dev (2015) 0.82

Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity. Mol Biol Evol (2015) 0.82

Differential regulation of non-protein coding RNAs from Prader-Willi Syndrome locus. Sci Rep (2014) 0.82

Switching cell fate, ncRNAs coming to play. Cell Death Dis (2013) 0.81

Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout. PLoS One (2016) 0.81

Panning for Long Noncoding RNAs. Biomolecules (2013) 0.81

Identification of discrete classes of small nucleolar RNA featuring different ends and RNA binding protein dependency. Nucleic Acids Res (2014) 0.81

Long noncoding RNAs in imprinting and X chromosome inactivation. Biomolecules (2014) 0.81

Alternative processing as evolutionary mechanism for the origin of novel nonprotein coding RNAs. Genome Biol Evol (2013) 0.80

lncRNA-RNA Interactions across the Human Transcriptome. PLoS One (2016) 0.79

Epigenetic marks: regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs. Front Genet (2015) 0.79

Global analysis of biogenesis, stability and sub-cellular localization of lncRNAs mapping to intragenic regions of the human genome. RNA Biol (2015) 0.79

Functional insights into the role of nuclear-retained long noncoding RNAs in gene expression control in mammalian cells. Chromosome Res (2013) 0.79

Developmental regulation of RNA processing by Rbfox proteins. Wiley Interdiscip Rev RNA (2016) 0.78

Transcriptome Analysis Reveals that Vitamin A Metabolism in the Liver Affects Feed Efficiency in Pigs. G3 (Bethesda) (2016) 0.78

Long non-coding RNAs in corticogenesis: deciphering the non-coding code of the brain. EMBO J (2015) 0.78

Non-coding RNAS: A new member of the family. Nat Rev Mol Cell Biol (2012) 0.77

Structure Prediction: New Insights into Decrypting Long Noncoding RNAs. Int J Mol Sci (2016) 0.77

There is a world beyond protein mutations: the role of non-coding RNAs in melanomagenesis. Exp Dermatol (2013) 0.77

Circuitous route to transcription regulation. Mol Cell (2013) 0.77

The persistent contributions of RNA to eukaryotic gen(om)e architecture and cellular function. Cold Spring Harb Perspect Biol (2014) 0.77

Roles for long non-coding RNAs in physiology and disease. Pflugers Arch (2016) 0.76

Long noncoding RNAs as metazoan developmental regulators. Chromosome Res (2013) 0.76

Changes in snoRNA and snRNA Abundance in the Human, Chimpanzee, Macaque, and Mouse Brain. Genome Biol Evol (2016) 0.76

Gene expression profiling of non-polyadenylated RNA-seq across species. Genom Data (2014) 0.75

Stable intronic sequence RNAs have possible regulatory roles in Drosophila melanogaster. J Cell Biol (2015) 0.75

The RNA-binding protein QKI5 regulates primary miR-124-1 processing via a distal RNA motif during erythropoiesis. Cell Res (2017) 0.75

RBFOX1 and RBFOX2 are dispensable in iPSCs and iPSC-derived neurons and do not contribute to neural-specific paternal UBE3A silencing. Sci Rep (2016) 0.75

Integrating Epigenomics into the Understanding of Biomedical Insight. Bioinform Biol Insights (2016) 0.75

Long noncoding RNAs as sinks in Prader-Willi syndrome. Mol Cell (2012) 0.75

RNA-binding protein SAMD4 regulates skeleton development through translational inhibition of Mig6 expression. Cell Discov (2017) 0.75

Splicing noncoding RNAs from the inside out. Wiley Interdiscip Rev RNA (2015) 0.75

Nonsense-mediated RNA decay: at the 'cutting edge' of regulated snoRNA production. Genes Dev (2014) 0.75

Genetics of Prader-Willi syndrome and Prader-Will-Like syndrome. Ann Pediatr Endocrinol Metab (2016) 0.75

Inhaled Pollutants: The Molecular Scene behind Respiratory and Systemic Diseases Associated with Ultrafine Particulate Matter. Int J Mol Sci (2017) 0.75

DIP1 modulates stem cell homeostasis in Drosophila through regulation of sisR-1. Nat Commun (2017) 0.75

The More the Merrier-Complexity in Long Non-Coding RNA Loci. Front Endocrinol (Lausanne) (2017) 0.75

Articles by these authors

I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66

Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39

The developmental transcriptome of Drosophila melanogaster. Nature (2010) 11.85

The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67

Cellular pathophysiology of ischemic acute kidney injury. J Clin Invest (2011) 5.75

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39

LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res (2007) 5.30

Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol (2007) 5.07

Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell (2009) 4.54

IL-21 regulates germinal center B cell differentiation and proliferation through a B cell-intrinsic mechanism. J Exp Med (2010) 4.04

Genome-wide association study identifies 1p36.22 as a new susceptibility locus for hepatocellular carcinoma in chronic hepatitis B virus carriers. Nat Genet (2010) 4.01

RET fusions define a unique molecular and clinicopathologic subtype of non-small-cell lung cancer. J Clin Oncol (2012) 3.72

T regulatory and primed uncommitted CD4 T cells express CD73, which suppresses effector CD4 T cells by converting 5'-adenosine monophosphate to adenosine. J Immunol (2006) 3.40

The changing face of HIV in China. Nature (2008) 3.39

MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins (2008) 3.38

Alu element-mediated gene silencing. EMBO J (2008) 3.22

How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics (2010) 3.22

Graphene at the edge: stability and dynamics. Science (2009) 3.17

Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022). J Bacteriol (2006) 3.14

Responsiveness to reduced dosage of rituximab in Chinese patients with neuromyelitis optica. Neurology (2013) 3.13

IL-17-producing human peripheral regulatory T cells retain suppressive function. Blood (2009) 3.04

Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure (2011) 2.97

Spontaneous molecular reactivation of herpes simplex virus type 1 latency in mice. Proc Natl Acad Sci U S A (2002) 2.94

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins (2012) 2.94

Three-field or two-field resection for thoracic esophageal cancer: a meta-analysis. Ann Thorac Surg (2013) 2.92

Genomewide characterization of non-polyadenylated RNAs. Genome Biol (2011) 2.92

Melamine related bilateral renal calculi in 50 children: single center experience in clinical diagnosis and treatment. J Urol (2010) 2.83

The draft genome of sweet orange (Citrus sinensis). Nat Genet (2012) 2.81

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res (2012) 2.75

Circular intronic long noncoding RNAs. Mol Cell (2013) 2.62

BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Res (2012) 2.56

The transcriptional diversity of 25 Drosophila cell lines. Genome Res (2010) 2.47

Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics (2013) 2.43

Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res (2010) 2.43

Dysregulated T cell expression of TIM3 in multiple sclerosis. J Exp Med (2006) 2.43

Chibby, a nuclear beta-catenin-associated antagonist of the Wnt/Wingless pathway. Nature (2003) 2.42

Functional mesenchymal stem cells derived from human induced pluripotent stem cells attenuate limb ischemia in mice. Circulation (2010) 2.39

Arsenic detoxification and evolution of trimethylarsine gas by a microbial arsenite S-adenosylmethionine methyltransferase. Proc Natl Acad Sci U S A (2006) 2.37

Dominance of HIV-1 subtype CRF01_AE in sexually acquired cases leads to a new epidemic in Yunnan province of China. PLoS Med (2006) 2.37

MicroRNA-101 inhibited postinfarct cardiac fibrosis and improved left ventricular compliance via the FBJ osteosarcoma oncogene/transforming growth factor-β1 pathway. Circulation (2012) 2.36

Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm. Proteins (2004) 2.34

Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res (2010) 2.29

Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys J (2011) 2.24

Structural characterization of N-linked oligosaccharides on monoclonal antibody cetuximab by the combination of orthogonal matrix-assisted laser desorption/ionization hybrid quadrupole-quadrupole time-of-flight tandem mass spectrometry and sequential enzymatic digestion. Anal Biochem (2007) 2.22

Virome analysis for identification of novel mammalian viruses in bat species from Chinese provinces. J Virol (2012) 2.21

Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics (2004) 2.17

HAb18G/CD147 promotes activation of hepatic stellate cells and is a target for antibody therapy of liver fibrosis. J Hepatol (2012) 2.15

Genome-wide association study identifies a susceptibility locus for schizophrenia in Han Chinese at 11p11.2. Nat Genet (2011) 2.13

Comparative evaluation of tandem MS search algorithms using a target-decoy search strategy. Mol Cell Proteomics (2007) 2.13

Clinical pharmacy education in China. Am J Pharm Educ (2008) 2.10

A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics (2008) 2.08

Pattern of lymphatic spread in thoracic esophageal squamous cell carcinoma: A single-institution experience. J Thorac Cardiovasc Surg (2012) 2.08

The microRNA-regulated SBP-Box transcription factor SPL3 is a direct upstream activator of LEAFY, FRUITFULL, and APETALA1. Dev Cell (2009) 2.07

Genome-wide analysis of coordinate expression and evolution of human cis-encoded sense-antisense transcripts. Trends Genet (2005) 2.04

Rare diseases and legislation in China. Lancet (2010) 1.96

Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily. Nat Chem Biol (2008) 1.96

Genome-wide studies reveal that Lin28 enhances the translation of genes important for growth and survival of human embryonic stem cells. Stem Cells (2011) 1.90

REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins (2009) 1.89

Gr-1+CD11b+ myeloid cells tip the balance of immune protection to tumor promotion in the premetastatic lung. Cancer Res (2010) 1.83

Functional MRI in attention-deficit hyperactivity disorder: evidence for hypofrontality. Brain Dev (2005) 1.81

Maternally inherited essential hypertension is associated with the novel 4263A>G mutation in the mitochondrial tRNAIle gene in a large Han Chinese family. Circ Res (2011) 1.81

Mitochondrial 12S rRNA variants in 1642 Han Chinese pediatric subjects with aminoglycoside-induced and nonsyndromic hearing loss. Mitochondrion (2010) 1.80

KIM-1-mediated phagocytosis reduces acute injury to the kidney. J Clin Invest (2015) 1.80

TGF-β signaling in myeloid cells is required for tumor metastasis. Cancer Discov (2013) 1.76

Molecular basis for an attenuated cytoplasmic dsRNA response in human embryonic stem cells. Cell Cycle (2010) 1.71

CT-guided percutaneous chemical ablation of adrenal neoplasms. AJR Am J Roentgenol (2008) 1.70

Inflammation-mediated genetic and epigenetic alterations drive cancer development in the neighboring epithelium upon stromal abrogation of TGF-β signaling. PLoS Genet (2013) 1.69

The role of concurrent chemoradiotherapy in the treatment of locoregionally advanced nasopharyngeal carcinoma among endemic population: a meta-analysis of the phase III randomized trials. BMC Cancer (2010) 1.68

Lysosomal acid lipase deficiency causes respiratory inflammation and destruction in the lung. Am J Physiol Lung Cell Mol Physiol (2003) 1.68

Presynaptic and postsynaptic interaction of the amyloid precursor protein promotes peripheral and central synaptogenesis. J Neurosci (2009) 1.65

Gram-scale synthesis of submicrometer-long polythiophene wires in mesoporous silica matrices. Angew Chem Int Ed Engl (2003) 1.64

Transforming growth factor-beta regulates mammary carcinoma cell survival and interaction with the adjacent microenvironment. Cancer Res (2008) 1.64

Hsa-mir-27a genetic variant contributes to gastric cancer susceptibility through affecting miR-27a and target gene expression. Cancer Sci (2010) 1.63

The molecular etiology of breast cancer: evidence from biomarkers of risk. Int J Cancer (2008) 1.62

A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. Nucleic Acids Res (2006) 1.60

Outcomes of the POG 9340/9341/9342 trials for children with high-risk neuroblastoma: a report from the Children's Oncology Group. Pediatr Blood Cancer (2008) 1.60

Regulation of peripheral inflammation by spinal adenosine: role of somatic afferent fibers. Exp Neurol (2003) 1.60

Control of autophagy maturation by acid sphingomyelinase in mouse coronary arterial smooth muscle cells: protective role in atherosclerosis. J Mol Med (Berl) (2014) 1.59

Characterization of ST-4821 complex, a unique Neisseria meningitidis clone. Genomics (2007) 1.59

MIPSPlantsDB--plant database resource for integrative and comparative plant genome research. Nucleic Acids Res (2007) 1.58

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement. Proteins (2011) 1.58

A Runx2/miR-3960/miR-2861 regulatory feedback loop during mouse osteoblast differentiation. J Biol Chem (2011) 1.57

Effects of length and location on the cellular response to double-stranded RNA. Microbiol Mol Biol Rev (2004) 1.57

A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction. PLoS One (2010) 1.56

Efficacy of contrast-enhanced US and magnetic microbubbles targeted to vascular cell adhesion molecule-1 for molecular imaging of atherosclerosis. Radiology (2011) 1.55

FGF21 and the late adaptive response to starvation in humans. J Clin Invest (2015) 1.55

Palladium-catalyzed enantioselective addition of two distinct nucleophiles across alkenes capable of quinone methide formation. J Am Chem Soc (2009) 1.54

Decoding the function of nuclear long non-coding RNAs. Curr Opin Cell Biol (2010) 1.54

Generating triangulated macromolecular surfaces by Euclidean Distance Transform. PLoS One (2009) 1.54

Protein domain structure uncovers the origin of aerobic metabolism and the rise of planetary oxygen. Structure (2012) 1.53

Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell (2012) 1.52

TRAIL death receptor 4 signaling via lysosome fusion and membrane raft clustering in coronary arterial endothelial cells: evidence from ASM knockout mice. J Mol Med (Berl) (2012) 1.52

Strain-engineering the anisotropic electrical conductance of few-layer black phosphorus. Nano Lett (2014) 1.52

Transforming growth factor-β in the gastrointestinal and hepatic tumor microenvironment. Gastroenterology (2011) 1.51