Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification

scientific article published on 6 July 2014

Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1038/NBT.2943
P932PMC publication ID4175979
P698PubMed publication ID24997788

P50authorIbrahim IlikQ83379404
P2093author name stringHoward Y Chang
Asifa Akhtar
Kun Qu
Plamen Georgiev
Jeffrey J Quinn
Ci Chu
P2860cites workModel-based analysis of ChIP-Seq (MACS)Q21183902
Mfold web server for nucleic acid folding and hybridization predictionQ24498105
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profilesQ24536351
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasisQ24607308
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIPQ24630900
Fitting a mixture model by expectation maximization to discover motifs in biopolymersQ27860556
Long non-coding RNAs: insights into functionsQ28131764
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammalsQ28131802
CLIP: a method for identifying protein-RNA interaction sites in living cellsQ28284054
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expressionQ29614326
Modular regulatory principles of large non-coding RNAsQ29617829
Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactionsQ29617830
lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs.Q33666551
ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regionsQ33970447
The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosomeQ34037436
The Drosophila MSL complex activates the transcription of target genes.Q34055907
The roX genes encode redundant male-specific lethal transcripts required for targeting of the MSL complexQ34086038
Three-dimensional folding and functional organization principles of the Drosophila genomeQ34248756
Activating RNAs associate with Mediator to enhance chromatin architecture and transcriptionQ34328232
Promoter-bound trinucleotide repeat mRNA drives epigenetic silencing in fragile X syndromeQ34407383
Functional redundancy within roX1, a noncoding RNA involved in dosage compensation in Drosophila melanogaster.Q34618051
Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31Q34644225
An evolutionarily conserved domain of roX2 RNA is sufficient for induction of H4-Lys16 acetylation on the Drosophila X chromosomeQ34718369
The genomic binding sites of a noncoding RNA.Q35651163
Mapping the human miRNA interactome by CLASH reveals frequent noncanonical bindingQ36833119
Long noncoding RNAs: cellular address codes in development and diseaseQ36837377
A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosomeQ37034847
The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensationQ37064594
Transcription rate of noncoding roX1 RNA controls local spreading of the Drosophila MSL chromatin remodeling complexQ37138024
The dosage compensation complex shapes the conformation of the X chromosome in DrosophilaQ37426760
High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation.Q37524878
Dosage compensation in Drosophila melanogaster: epigenetic fine-tuning of chromosome-wide transcriptionQ37976525
X-Inactivation, Imprinting, and Long Noncoding RNAs in Health and DiseaseQ38090112
Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in DrosophilaQ39977345
Regulation of viral and cellular gene expression by Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA.Q40528266
Chromatin Isolation by RNA Purification (ChIRP)Q41846416
Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in DrosophilaQ42939992
ATP-dependent roX RNA remodeling by the helicase maleless enables specific association of MSL proteinsQ44708171
P433issue9
P304page(s)933-940
P577publication date2014-07-06
P1433published inNature BiotechnologyQ1893837
P1476titleRevealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification
P478volume32

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cites work (P2860)
Q91970577A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division
Q47099046A mutually exclusive stem-loop arrangement in roX2 RNA is essential for X-chromosome regulation in Drosophila
Q89664223A nomogram combining long non-coding RNA expression profiles and clinical factors predicts survival in patients with bladder cancer
Q37231014Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on Chromatin
Q47416156Catching RNAs on chromatin using hybridization capture methods.
Q64917839Chromatin That Guides Dosage Compensation Is Modulated by the siRNA Pathway in Drosophila melanogaster.
Q55039880Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts.
Q92503341Chromatin-associated RNAs as facilitators of functional genomic interactions
Q35906316Comprehensive prediction of lncRNA-RNA interactions in human transcriptome
Q58049785Current Advances in Noncoding RNA Relevant to Epigenetic Mechanisms
Q57807472Current status and strategies of long noncoding RNA research for diabetic cardiomyopathy
Q33112269DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome.
Q58608005Differential Expression Pattern of Exosome Long Non-Coding RNAs (lncRNAs) and MicroRNAs (miRNAs) in Vascular Endothelial Cells Under Heat Stroke
Q90208763Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatin
Q39182098Epigenetic Regulation: A New Frontier for Biomedical Engineers
Q38771104Epigenetic and lncRNA regulation of cardiac pathophysiology
Q36726403High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila
Q40499080Histone locus regulation by the Drosophila dosage compensation adaptor protein CLAMP.
Q37478463Identification of mRNA-Interacting Factors by MS2-TRAP (MS2-Tagged RNA Affinity Purification).
Q38753861Improving understanding of chromatin regulatory proteins and potential implications for drug discovery
Q91404418In-cell identification and measurement of RNA-protein interactions
Q36447611Insight into lncRNA biology using hybridization capture analyses
Q26782744Linking RNA biology to lncRNAs
Q37445925LncRNAs in vertebrates: advances and challenges
Q50187327Long Noncoding RNA Discovery in Cardiovascular Disease: Decoding Form to Function
Q28083390Long Noncoding RNAs: A New Regulatory Code in Metabolic Control
Q26801406Long non-coding RNA and chromatin remodeling
Q35016600Long non-coding RNAs in cancer and development: where do we go from here?
Q36394663Long non-coding RNAs in corticogenesis: deciphering the non-coding code of the brain
Q38961358Long non-coding RNAs in human early embryonic development and their potential in ART.
Q46259490Long non-coding RNAs involve in resistance to Verticillium dahliae, a fungal disease in cotton
Q38990786Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression
Q42332574Long noncoding RNA: noncoding and not coded
Q50589433Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.).
Q34626174Long noncoding RNAs: an emerging link between gene regulation and nuclear organization
Q38845439Methods to Study Long Noncoding RNA Biology in Cancer
Q63976761Multi-Omics Approaches to Study Long Non-coding RNA Function in Atherosclerosis
Q36998286Non-coding RNA LINC00857 is predictive of poor patient survival and promotes tumor progression via cell cycle regulation in lung cancer
Q55469742Non-coding RNA-linked epigenetic regulation in cardiac hypertrophy.
Q87421729Non-coding RNA: Zooming in on lncRNA functions
Q38667231Non-coding RNAs in Mammary Gland Development and Disease
Q47880484Noncoding RNAs in neurodegeneration
Q47099658Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes
Q37642818Overexpression of FAM83H-AS1 indicates poor patient survival and knockdown impairs cell proliferation and invasion via MET/EGFR signaling in lung cancer
Q34580795PAN's Labyrinth: Molecular biology of Kaposi's sarcoma-associated herpesvirus (KSHV) PAN RNA, a multifunctional long noncoding RNA.
Q64326917Platforms for Investigating LncRNA Functions
Q40955031Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species.
Q39458571Probing Long Non-coding RNA-Protein Interactions.
Q36480899Rapid evolutionary turnover underlies conserved lncRNA-genome interactions
Q26799764SINEUPs: A new class of natural and synthetic antisense long non-coding RNAs that activate translation
Q27727988Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment
Q39385283State of the art technologies to explore long non-coding RNAs in cancer.
Q37285424Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization
Q38552806Study strategies for long non-coding RNAs and their roles in regulating gene expression
Q39629883Systemic genome screening identifies the outcome associated focal loss of long noncoding RNA PRAL in hepatocellular carcinoma
Q52426930Targeting LncRNAs in Cardiovascular Disease: Options and Expeditions
Q42777373Technological Developments in lncRNA Biology
Q38309696Technologies to probe functions and mechanisms of long noncoding RNAs
Q47251709The Drosophila CLAMP protein associates with diverse proteins on chromatin
Q46920734The functions and unique features of long intergenic non-coding RNA.
Q33633347The long noncoding RNA SPRIGHTLY acts as an intranuclear organizing hub for pre-mRNA molecules
Q51472031Understanding RNA-Chromatin Interactions Using Chromatin Isolation by RNA Purification (ChIRP).
Q26766143Understanding Spatial Genome Organization: Methods and Insights
Q38668939Unique features of long non-coding RNA biogenesis and function
Q85794047Unraveling the lncRNA mystery
Q93074975Unveiling the druggable RNA targets and small molecule therapeutics
Q26779139Unveiling the hidden function of long non-coding RNA by identifying its major partner-protein
Q93010867lncRedibly versatile: biochemical and biological functions of long noncoding RNAs

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