The DOI matches its Crossref record; 42 of the 42 references it cites were found in a registry or an index.
An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment
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SUMMARY Here, we generated the first genome-scale shRNA library targeting lincRNAs in the mouse. We performed an unbiased loss-of-function study in mouse embryonic stem cells (mESCs) and identified 20 novel lincRNAs involved in the maintenance of pluripotency. Among these, TUNA (Tcl1 Upstream Neuron-Associated lincRNA), was required for pluripotency and formed a complex with three RNA-binding proteins (RBPs). The TUNA–RBP complex was detected at the promoters of Nanog, Sox2, and Fgf4, and knockdown of TUNA or the individual RBPs inhibited neural differentiation of mESCs. TUNA showed striking evolutionary conservation of both sequence and central nervous system-restricted expression in vertebrates. Accordingly, knockdown of tuna in zebrafish caused impaired locomotor function, and TUNA expression in the brains of Huntington’s patients was significantly associated with disease grade. Our results suggest that the lincRNA TUNA plays a vital role in pluripotency and neural differentiation of ESCs and is associated with neurological function of adult vertebrates.
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1 retracted
RETRACTED: hnRNP K: An HDM2 Target and Transcriptional Coactivator of p53 in Response to DNA Damage
Moumen, A., Masterson, P., O'Connor, M. J., & Jackson, S. P. (2005) · Cell · doi:10.1016/j.cell.2005.09.032 · Cited by 350
RetractedTakahashi, K., & Yamanaka, S. (2006) · Cell · doi:10.1016/j.cell.2006.07.024 · Cited by 26,673
Landscape of transcription in human cells
Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. (2012) · Nature · doi:10.1038/nature11233 · Cited by 5,187
Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D. G., et al. (2012) · Genome Research · doi:10.1101/gr.132159.111 · Cited by 5,061
Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs
Rinn, J. L., Kertesz, M., Wang, J. K., Squazzo, S. L., Xu, X., Brugmann, S. A., Goodnough, L. H., Helms, J. A., Farnham, P. J., Segal, E., et al. (2007) · Cell · doi:10.1016/j.cell.2007.05.022 · Cited by 4,244
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., et al. (2009) · Nature · doi:10.1038/nature07672 · Cited by 4,098
Genome Regulation by Long Noncoding RNAs
Rinn, J. L., & Chang, H. Y. (2012) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-051410-092902 · Cited by 4,005
Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes
Tsai, M.-C., Manor, O., Wan, Y., Mosammaparast, N., Wang, J. K., Lan, F., Shi, Y., Segal, E., & Chang, H. Y. (2010) · Science · doi:10.1126/science.1192002 · Cited by 3,290 · cited 4×
“Recent studies have suggested that the conserved motifs in lincRNAsmay serve as functional units to modulate RNA-protein or RNA-DNA interactions (Chu et al., 2011; Tsai et al., 2010).”
InfluentialKhalil, A. M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B. E., van Oudenaarden, A., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904715106 · Cited by 2,872
Walker, F. O. (2007) · The Lancet · doi:10.1016/s0140-6736(07)60111-1 · Cited by 2,603
Neuropathological Classification of Huntingtonʼs Disease
VONSATTEL, J.-P., MYERS, R. H., STEVENS, T. J., FERRANTE, R. J., BIRD, E. D., & RICHARDSON, E. P. (1985) · Journal of Neuropathology and Experimental Neurology · doi:10.1097/00005072-198511000-00003 · Cited by 2,227
A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response
Huarte, M., Guttman, M., Feldser, D., Garber, M., Koziol, M. J., Kenzelmann-Broz, D., Khalil, A. M., Zuk, O., Amit, I., Rabani, M., et al. (2010) · Cell · doi:10.1016/j.cell.2010.06.040 · Cited by 2,053
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
Wang, K. C., Yang, Y. W., Liu, B., Sanyal, A., Corces-Zimmerman, R., Chen, Y., Lajoie, B. R., Protacio, A., Flynn, R. A., Gupta, R. A., et al. (2011) · Nature · doi:10.1038/nature09819 · Cited by 1,976
lincRNAs act in the circuitry controlling pluripotency and differentiation
Guttman, M., Donaghey, J., Carey, B. W., Garber, M., Grenier, J. K., Munson, G., Young, G., Lucas, A. B., Ach, R., Bruhn, L., et al. (2011) · Nature · doi:10.1038/nature10398 · Cited by 1,858
Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions
Chu, C., Qu, K., Zhong, F. L., Artandi, S. E., & Chang, H. Y. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.08.027 · Cited by 1,269
Epigenetic Regulation by Long Noncoding RNAs
Lee, J. T. (2012) · Science · doi:10.1126/science.1231776 · Cited by 1,259
Guttman, M., Garber, M., Levin, J. Z., Donaghey, J., Robinson, J., Adiconis, X., Fan, L., Koziol, M. J., Gnirke, A., Nusbaum, C., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1633 · Cited by 1,253
Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution
Ulitsky, I., Shkumatava, A., Jan, C. H., Sive, H., & Bartel, D. P. (2011) · Cell · doi:10.1016/j.cell.2011.11.055 · Cited by 1,179
Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells
Loewer, S., Cabili, M. N., Guttman, M., Loh, Y.-H., Thomas, K., Park, I. H., Garber, M., Curran, M., Onder, T., Agarwal, S., et al. (2010) · Nature Genetics · doi:10.1038/ng.710 · Cited by 976
Dissecting self-renewal in stem cells with RNA interference
Ivanova, N., Dobrin, R., Lu, R., Kotenko, I., Levorse, J., DeCoste, C., Schafer, X., Lun, Y., & Lemischka, I. R. (2006) · Nature · doi:10.1038/nature04915 · Cited by 959
Regional and cellular gene expression changes in human Huntington's disease brain
Hodges, A., Strand, A. D., Aragaki, A. K., Kuhn, A., Sengstag, T., Hughes, G., Elliston, L. A., Hartog, C., Goldstein, D. R., Thu, D., et al. (2006) · Human Molecular Genetics · doi:10.1093/hmg/ddl013 · Cited by 804
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
Dinger, M. E., Amaral, P. P., Mercer, T. R., Pang, K. C., Bruce, S. J., Gardiner, B. B., Askarian-Amiri, M. E., Ru, K., Soldà, G., Simons, C., et al. (2008) · Genome Research · doi:10.1101/gr.078378.108 · Cited by 731
Synthetic spike-in standards for RNA-seq experiments
Jiang, L., Schlesinger, F., Davis, C. A., Zhang, Y., Li, R., Salit, M., Gingeras, T. R., & Oliver, B. (2011) · Genome Research · doi:10.1101/gr.121095.111 · Cited by 653
In situ hybridization; a practical approach
(1993) · Comparative Biochemistry and Physiology Part A: Physiology · doi:10.1016/0300-9629(93)90060-h · Cited by 648
Genes controlling and mediating locomotion behavior of the zebrafish embryo and larva
Granato, M., Eeden, F. J. M. V., Schach, U., Trowe, T., Brand, M., Furutani-Seiki, M., Haffter, P., Hammerschmidt, M., Heisenberg, C.-P., Jiang, Y.-J., et al. (1996) · Development · doi:10.1242/dev.123.1.399 · Cited by 644
Molecular dissection of nucleolin's role in growth and cell proliferation: new insights
Srivastava, M., & Pollard, H. B. (1999) · The FASEB Journal · doi:10.1096/fasebj.13.14.1911 · Cited by 494
A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity
Chia, N.-Y., Chan, Y.-S., Feng, B., Lu, X., Orlov, Y. L., Moreau, D., Kumar, P., Yang, L., Jiang, J., Lau, M.-S., et al. (2010) · Nature · doi:10.1038/nature09531 · Cited by 461
Sequentially acting Sox transcription factors in neural lineage development
Bergsland, M., Ramsköld, D., Zaouter, C., Klum, S., Sandberg, R., & Muhr, J. (2011) · Genes & Development · doi:10.1101/gad.176008.111 · Cited by 311
Cell Cycle Control of Embryonic Stem Cells
White, J., & Dalton, S. (2005) · Stem Cell Reviews · doi:10.1385/scr:1:2:131 · Cited by 310
Ding, L., Paszkowski-Rogacz, M., Nitzsche, A., Slabicki, M. M., Heninger, A.-K., Vries, I. D., Kittler, R., Junqueira, M., Shevchenko, A., Schulz, H., et al. (2009) · Cell Stem Cell · doi:10.1016/j.stem.2009.03.009 · Cited by 261
Nucleolin is a histone chaperone with FACT‐like activity and assists remodeling of nucleosomes
Angelov, D., Bondarenko, V. A., Almagro, S., Menoni, H., Mongélard, F., Hans, F., Mietton, F., Studitsky, V. M., Hamiche, A., Dimitrov, S., et al. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601046 · Cited by 258
PSD-95 is post-transcriptionally repressed during early neural development by PTBP1 and PTBP2
Zheng, S., Gray, E. E., Chawla, G., Porse, B. T., O'Dell, T. J., & Black, D. L. (2012) · Nature Neuroscience · doi:10.1038/nn.3026 · Cited by 254
Neuronal regulation of pre-mRNA splicing by polypyrimidine tract binding proteins, PTBP1 and PTBP2
Keppetipola, N., Sharma, S., Li, Q., & Black, D. L. (2012) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409238.2012.691456 · Cited by 201
Dempsey, L. A., Sun, H., Hanakahi, L. A., & Maizels, N. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.2.1066 · Cited by 188
The role of REST in transcriptional and epigenetic dysregulation in Huntington's disease
Buckley, N. J., Johnson, R., Zuccato, C., Bithell, A., & Cattaneo, E. F. (2010) · Neurobiology of Disease · doi:10.1016/j.nbd.2010.02.003 · Cited by 160
Yano, M., Okano, H. J., & Okano, H. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m411119200 · Cited by 131
Kim, K., Choi, J., Heo, K., Kim, H., Levens, D., Kohno, K., Johnson, E. M., Brock, H. W., & An, W. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m708205200 · Cited by 122
Purification and Characterization of Nucleolin and Its Identification as a Transcription Repressor
Yang, T. H., Tsai, W. H., LEE, Y.-M., et al. (1994) · Molecular and Cellular Biology · doi:10.1128/mcb.14.9.6068 · Cited by 108
Sox3 regulates both neural fate and differentiation in the zebrafish ectoderm
Dee, C. T., Hirst, C. S., Shih, Y.-H., Tripathi, V. B., Patient, R. K., & Scotting, P. J. (2008) · Developmental Biology · doi:10.1016/j.ydbio.2008.05.542 · Cited by 99
Nucleolin Maintains Embryonic Stem Cell Self-renewal by Suppression of p53 Protein-dependent Pathway
Yang, A., Shi, G., Zhou, C., Lu, R., Li, H., Sun, L., & Jin, Y. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.225185 · Cited by 55
Hutchins, A. P., Choo, S. H., Mistri, T. K., Rahmani, M., Woon, C. T., Ng, C. K. L., Jauch, R., & Robson, P. (2012) · Stem Cells · doi:10.1002/stem.1279 · Cited by 45
Matsui, M., Prakash, T. P., & Corey, D. R. (2012) · ACS Chemical Biology · doi:10.1021/cb300490j · Cited by 23
Cited by
CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells
Liu, S. J., Horlbeck, M. A., Cho, S. W., Birk, H. S., Malatesta, M., He, D., Attenello, F. J., Villalta, J. E., Cho, M. Y., Chen, Y., et al. (2017) · Science · doi:10.1126/science.aah7111 · Cited by 746
Single-nucleus and single-cell transcriptomes compared in matched cortical cell types
Bakken, T. E., Hodge, R. D., Miller, J. A., Yao, Z., Nguyen, T. N., Aevermann, B., Barkan, E., Bertagnolli, D., Casper, T., Dee, N., et al. (2018) · PLoS ONE · doi:10.1371/journal.pone.0209648 · Cited by 608
Raj, B., & Blencowe, B. J. (2015) · Neuron · doi:10.1016/j.neuron.2015.05.004 · Cited by 475
Briggs, J. A., Wolvetang, E. J., Mattick, J. S., Rinn, J. L., & Barry, G. (2015) · Neuron · doi:10.1016/j.neuron.2015.09.045 · Cited by 447
Ramos, A. D., Andersen, R. E., Liu, S. J., Nowakowski, T. J., Hong, S. J., Gertz, C. C., Salinas, R. D., Zarabi, H., Kriegstein, A. R., & Lim, D. A. (2015) · Cell stem cell · doi:10.1016/j.stem.2015.02.007 · Cited by 359
Metadata
- Authors
- Lin, N., Chang, K.-Y., Li, Z., Gates, K., Rana, Z. A., Dang, J., Zhang, D., Han, T., Yang, C.-S., Cunningham, T. J., Head, S. R., Duester, G., Dong, P. D. S., & Rana, T. M.
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2014-03
- Volume
- 53
- Issue
- 6
- Pages
- 1005-1019
- ISSN
- 1097-2765 (ISSN-L)
- OpenAlex
- W2008695914
- Cited by
- 393
- References
- 42
- FWCI
- 11.76
- Type
- journal article
- Language
- en
- Open access
- bronze
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