The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions
Open accessAbstract
SUMMARY Long intergenic noncoding RNAs (lincRNAs) are key regulators of chromatin state, yet the nature and sites of RNA-chromatin interaction are mostly unknown. Here we introduce Chromatin Isolation by RNA Purification (ChIRP), where tiling oligonucleotides retrieve specific lincRNAs with bound protein and DNA sequences, which are enumerated by deep sequencing. ChIRP-seq of three lincRNAs reveal that RNA occupancy sites in the genome are focal, sequence-specific, and numerous. Drosophila roX2 RNA occupies male X-linked gene bodies with increasing tendency toward the 3’ end, peaking at CES sites. Human telomerase RNA TERC occupies telomeres and Wnt pathway genes. HOTAIR lincRNA preferentially occupies a GA-rich DNA motif to nucleate broad domains of Polycomb occupancy and histone H3 lysine 27 trimethylation. HOTAIR occupancy occurs independently of EZH2, suggesting the order of RNA guidance of Polycomb occupancy. ChIRP-seq is generally applicable to illuminate the intersection of RNA and chromatin with newfound precision genome-wide.
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Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
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Long non-coding RNAs: insights into functions
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Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes
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“HOTAIR also binds the LSD1-coREST-REST complex that can target DNA (Tsai et al., 2010), and multiple mechanisms may operate together to target lncRNAs.”
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Telomerase modulates Wnt signalling by association with target gene chromatin
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“It is known that TERT can bind to and coactivate Wnt target genes at chromatin (Park et al., 2009), and we hypothesized that TERC, as a component of the TERT complex, may also co-occupy some of the same genes.”
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A Human Telomerase Holoenzyme Protein Required for Cajal Body Localization and Telomere Synthesis
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Cited by
Gene regulation by long non-coding RNAs and its biological functions
Statello, L., Guo, C.-J., Chen, L.-L., & Huarte, M. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-00315-9 · Cited by 4,991
Long non-coding RNAs: new players in cell differentiation and development
Fatica, A., & Bozzoni, I. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3606 · Cited by 2,980
Exon-intron circular RNAs regulate transcription in the nucleus
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Long Noncoding RNAs: Cellular Address Codes in Development and Disease
Batista, P. J., & Chang, H. Y. (2013) · Cell · doi:10.1016/j.cell.2013.02.012 · Cited by 2,531
Self-citationLong noncoding RNAs: past, present, and future
Kung, J. T. Y., Colognori, D., & Lee, J. T. (2013) · Genetics · doi:10.1534/genetics.112.146704 · Cited by 1,874
Metadata
- Authors
- Chu, C., Qu, K., Zhong, F. L., Artandi, S. E., & Chang, H. Y.
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2011-11
- Volume
- 44
- Issue
- 4
- Pages
- 667-678
- ISSN
- 1097-2765 (ISSN-L)
- OpenAlex
- W1979768717
- Cited by
- 1,269
- References
- 11
- FWCI
- 26.10
- Type
- journal article
- Language
- en
- Open access
- bronze
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