The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Systematic Discovery of Xist RNA Binding Proteins
Open accessAbstract
Summary Noncoding RNAs (ncRNAs) function with associated proteins to effect complex structural and regulatory outcomes. To reveal the composition and dynamics of specific noncoding RNA- protein complexes (RNPs) in vivo, we developed comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS). ChIRP-MS analysis of four ncRNAs captures key protein interactors, including a U1-specific link to the 3′ RNA processing machinery. Xist, an essential lncRNA for X-chromosome inactivation (XCI), interacts with 81 proteins from chromatin modification, nuclear matrix, and RNA remodeling pathways. The Xist RNA-protein particle assembles in two steps coupled with the transition from pluripotency to differentiation. Specific interactors include HnrnpK that participates in Xist-mediated gene silencing and histone modifications, but not Xist localization and Drosophila Split ends homolog Spen that interacts via the A-repeat domain of Xist and is required for gene silencing. Thus, Xist lncRNA engages with proteins in a modular and developmentally controlled manner to coordinate chromatin spreading and silencing.
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A compendium of RNA-binding motifs for decoding gene regulation
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Structure-based prediction of protein–protein interactions on a genome-wide scale
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“Together the two snRNAs retrieved 79% of the human spliceosome components (Figure 2A) and 8 of 9 direct U1 binding proteins verified by crystal structure (Pomeranz Krummel et al., 2009; Stark et al., 2001; Zhang et al., 2012).”
BackgroundSelf-citationU1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation
Kaida, D., Berg, M. G., Younis, I., Kasim, M., Singh, L. N., Wan, L., & Dreyfuss, G. (2010) · Nature · doi:10.1038/nature09479 · Cited by 638
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“NuRD-mediated deacetylation of H3K27ac also permits PRC2mediated H3K27me3 and gene silencing (Reynolds et al., 2012).”
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Cited by
m6A RNA methylation promotes XIST-mediated transcriptional repression
Patil, D. P., Chen, C.-K., Pickering, B. F., Chow, A., Jackson, C., Guttman, M., & Jaffrey, S. R. (2016) · Nature · doi:10.1038/nature19342 · Cited by 1,747
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)
Van Nostrand, E. L., Pratt, G. A., Shishkin, A. A., Gelboin-Burkhart, C., Fang, M. Y., Sundararaman, B., Blue, S. M., Nguyen, T. B., Surka, C., Elkins, K., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3810 · Cited by 1,397
Linking Long Noncoding RNA Localization and Function
Chen, L.-L. (2016) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2016.07.003 · Cited by 1,052
The 3D Genome as Moderator of Chromosomal Communication
Dekker, J., & Mirny, L. (2016) · Cell · doi:10.1016/j.cell.2016.02.007 · Cited by 937
the 4D Nucleome Network, Dekker, J., Belmont, A. S., Guttman, M., Leshyk, V. O., Lis, J. T., Lomvardas, S., Mirny, L. A., O’Shea, C. C., Park, P. J., et al. (2017) · Nature · doi:10.1038/nature23884 · Cited by 732
Metadata
- Authors
- Chu, C., Zhang, Q. C., da Rocha, S. T., Flynn, R. A., Bharadwaj, M., Calabrese, J. M., Magnuson, T., Heard, E., & Chang, H. Y.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2015-04
- Volume
- 161
- Issue
- 2
- Pages
- 404-416
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2041770101
- Cited by
- 1,101
- References
- 5
- FWCI
- 31.40
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Chu, C., Zhang, Q. C., da Rocha, S. T., Flynn, R. A., Bharadwaj, M., Calabrese, J. M., Magnuson, T., Heard, E., & Chang, H. Y. (2015). Systematic Discovery of Xist RNA Binding Proteins. Cell. https://doi.org/10.1016/j.cell.2015.03.025
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