标题
Methods to Analyze the Non-Coding RNA Interactome—Recent Advances and Challenges
作者
关键词
-
出版物
Frontiers in Genetics
Volume 13, Issue -, Pages -
出版商
Frontiers Media SA
发表日期
2022-03-17
DOI
10.3389/fgene.2022.857759
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- In vivo discovery of RNA proximal proteins via proximity-dependent biotinylation
- (2021) Xianzhi Lin et al. RNA Biology
- Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans
- (2021) Huifen Cao et al. BMC BIOLOGY
- iDRiP for the systematic discovery of proteins bound directly to noncoding RNA
- (2021) Hsueh-Ping Chu et al. Nature Protocols
- RNA promotes the formation of spatial compartments in the nucleus
- (2021) Sofia A. Quinodoz et al. CELL
- Hybridization-proximity labeling reveals spatially ordered interactions of nuclear RNA compartments
- (2021) Karen Yap et al. MOLECULAR CELL
- Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6.
- (2020) Michael Heskett et al. RNA
- RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions
- (2020) Alessandro Bonetti et al. Nature Communications
- A CRISPR/Cas13-based approach demonstrates biological relevance of vlinc class of long non-coding RNAs in anticancer drug response
- (2020) Dongyang Xu et al. Scientific Reports
- RIC-seq for global in situ profiling of RNA–RNA spatial interactions
- (2020) Zhaokui Cai et al. NATURE
- Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics
- (2020) Alexey A Gavrilov et al. NUCLEIC ACIDS RESEARCH
- CRISPR-assisted detection of RNA–protein interactions in living cells
- (2020) Wenkai Yi et al. NATURE METHODS
- RNA–protein interaction mapping via MS2- or Cas13-based APEX targeting
- (2020) Shuo Han et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- RNA nucleation by MSL2 induces selective X chromosome compartmentalization
- (2020) Claudia Isabelle Keller Valsecchi et al. NATURE
- Genome-wide colocalization of RNA–DNA interactions and fusion RNA pairs
- (2019) Zhangming Yan et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Atlas of Subcellular RNA Localization Revealed by APEX-Seq
- (2019) Furqan M. Fazal et al. CELL
- RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus
- (2019) Jörg Morf et al. NATURE BIOTECHNOLOGY
- Proximity labeling to detect RNA ‐protein interactions in live cells
- (2019) Mingxing Lu et al. FEBS Open Bio
- Proximity RNA Labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules
- (2019) Alejandro Padrón et al. MOLECULAR CELL
- Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors
- (2018) Silvana Konermann et al. CELL
- Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus
- (2018) Sofia A. Quinodoz et al. CELL
- RNA–protein interaction detection in living cells
- (2018) Muthukumar Ramanathan et al. NATURE METHODS
- Strategies to Annotate and Characterize Long Noncoding RNAs: Advantages and Pitfalls
- (2018) Huifen Cao et al. TRENDS IN GENETICS
- Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
- (2018) Jason C Bell et al. eLife
- COMRADES determines in vivo RNA structures and interactions
- (2018) Omer Ziv et al. NATURE METHODS
- RNA targeting with CRISPR–Cas13
- (2017) Omar O. Abudayyeh et al. NATURE
- GRID-seq reveals the global RNA–chromatin interactome
- (2017) Xiao Li et al. NATURE BIOTECHNOLOGY
- RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure
- (2016) Zhipeng Lu et al. CELL
- In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation
- (2016) Jong Ghut Ashley Aw et al. MOLECULAR CELL
- Global Mapping of Human RNA-RNA Interactions
- (2016) Eesha Sharma et al. MOLECULAR CELL
- Mapping RNA–RNA interactome and RNA structure in vivo by MARIO
- (2016) Tri C. Nguyen et al. Nature Communications
- A Hox-Embedded Long Noncoding RNA: Is It All Hot Air?
- (2016) Licia Selleri et al. PLoS Genetics
- Hotair Is Dispensible for Mouse Development
- (2016) Ana Rita Amândio et al. PLoS Genetics
- Does every transcript originate from a gene?
- (2015) Carsten A. Raabe et al. Annals of the New York Academy of Sciences
- Systematic Discovery of Xist RNA Binding Proteins
- (2015) Ci Chu et al. CELL
- Formaldehyde Crosslinking: A Tool for the Study of Chromatin Complexes
- (2015) Elizabeth A. Hoffman et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- High-throughput determination of RNA structure by proximity ligation
- (2015) Vijay Ramani et al. NATURE BIOTECHNOLOGY
- A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation
- (2015) A. Minajigi et al. SCIENCE
- A vlincRNA participates in senescence maintenance by relieving H2AZ-mediated repression at the INK4 locus
- (2015) Sandra Lazorthes et al. Nature Communications
- RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites
- (2014) Jesse M. Engreitz et al. CELL
- The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites
- (2014) Jason A. West et al. MOLECULAR CELL
- Directed evolution of APEX2 for electron microscopy and proximity labeling
- (2014) Stephanie S Lam et al. NATURE METHODS
- A novel antisense long noncoding RNA within the IGF1R gene locus is imprinted in hematopoietic malignancies
- (2014) Jingnan Sun et al. NUCLEIC ACIDS RESEARCH
- The Case for Junk DNA
- (2014) Alexander F. Palazzo et al. PLoS Genetics
- Long non-coding RNAs: modulators of nuclear structure and function
- (2013) Jan H Bergmann et al. CURRENT OPINION IN CELL BIOLOGY
- The dark matter rises: the expanding world of regulatory RNAs
- (2013) Michael B. Clark et al. Essays in Biochemistry
- Long Noncoding RNAs: Past, Present, and Future
- (2013) J. T. Y. Kung et al. GENETICS
- Functional transcriptomics in the post-ENCODE era
- (2013) J. M. Mudge et al. GENOME RESEARCH
- Structure and function of long noncoding RNAs in epigenetic regulation
- (2013) Tim R Mercer et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Is junk DNA bunk? A critique of ENCODE
- (2013) W. F. Doolittle PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome
- (2013) J. M. Engreitz et al. SCIENCE
- Proteomic Mapping of Mitochondria in Living Cells via Spatially Restricted Enzymatic Tagging
- (2013) H.-W. Rhee et al. SCIENCE
- Long noncoding RNAs: fresh perspectives into the RNA world
- (2013) Lin Yang et al. TRENDS IN BIOCHEMICAL SCIENCES
- Targeted Disruption of Hotair Leads to Homeotic Transformation and Gene Derepression
- (2013) Lingjie Li et al. Cell Reports
- VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer
- (2013) Georges St Laurent et al. GENOME BIOLOGY
- Can ENCODE tell us how much junk DNA we carry in our genome?
- (2012) Deng-Ke Niu et al. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
- The C-value paradox, junk DNA and ENCODE
- (2012) Sean R. Eddy CURRENT BIOLOGY
- Landscape of transcription in human cells
- (2012) Sarah Djebali et al. NATURE
- Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy
- (2012) Jeffrey D Martell et al. NATURE BIOTECHNOLOGY
- Loss of the abundant nuclear non-coding RNAMALAT1is compatible with life and development
- (2012) Moritz Eißmann et al. RNA Biology
- Malat1 is not an essential component of nuclear speckles in mice
- (2012) S. Nakagawa et al. RNA
- The lncRNA Malat1 Is Dispensable for Mouse Development but Its Transcription Plays a cis-Regulatory Role in the Adult
- (2012) Bin Zhang et al. Cell Reports
- Genomic “Dark Matter”: Implications for Understanding Human Disease Mechanisms, Diagnostics, and Cures
- (2012) Philipp Kapranov et al. Frontiers in Genetics
- The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA
- (2011) Philipp Kapranov et al. BMC BIOLOGY
- Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions
- (2011) Ci Chu et al. MOLECULAR CELL
- Gracefully ageing at 50, X-chromosome inactivation becomes a paradigm for RNA and chromatin control
- (2011) Jeannie T. Lee NATURE REVIEWS MOLECULAR CELL BIOLOGY
- The genomic binding sites of a noncoding RNA
- (2011) M. D. Simon et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- X Chromosome Dosage Compensation: How Mammals Keep the Balance
- (2008) Bernhard Payer et al. Annual Review of Genetics
- A Sequence Motif within Chromatin Entry Sites Directs MSL Establishment on the Drosophila X Chromosome
- (2008) Artyom A. Alekseyenko et al. CELL
- Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome
- (2008) J. Zhao et al. SCIENCE
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