Complex architecture and regulated expression of the Sox2ot locus during vertebrate development
Open accessAbstract
The Sox2 gene is a key regulator of pluripotency embedded within an intron of a long noncoding RNA (ncRNA), termed Sox2 overlapping transcript (Sox2ot), which is transcribed in the same orientation. However, this ncRNA remains uncharacterized. Here we show that Sox2ot has multiple transcription start sites associated with genomic features that indicate regulated expression, including highly conserved elements (HCEs) and chromatin marks characteristic of gene promoters. To identify biological processes in which Sox2ot may be involved, we analyzed its expression in several developmental systems, compared to expression of Sox2. We show that Sox2ot is a stable transcript expressed in mouse embryonic stem cells, which, like Sox2, is down-regulated upon induction of embryoid body (EB) differentiation. However, in contrast to Sox2, Sox2ot is up-regulated during EB mesoderm-lineage differentiation. In adult mouse, Sox2ot isoforms were detected in tissues where Sox2 is expressed, as well as in different tissues, supporting independent regulation of expression of the ncRNA. Sox2dot, an isoform of Sox2ot transcribed from a distal HCE located >500 kb upstream of Sox2, was detected exclusively in the mouse brain, with enrichment in regions of adult neurogenesis. In addition, Sox2ot isoforms are transcribed from HCEs upstream of Sox2 in other vertebrates, including in several regions of the human brain. We also show that Sox2ot is dynamically regulated during chicken and zebrafish embryogenesis, consistently associated with central nervous system structures. These observations provide insight into the structure and regulation of the Sox2ot gene, and suggest conserved roles for Sox2ot orthologs during vertebrate development.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
SOX2-OT is a heavily spliced, evolutionarily conserved lncRNA with predominant brain expression and is a hub of these oligodendrocyte modules.
“SOX2-OT is a heavily spliced, evolutionarily-conserved lncRNA exhibiting predominant brain expression and a hub of these oligodendrocyte modules, without previous mechanistic links to myelination (75, 76).”
From Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder (2018) · cites this paper as [75]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Takahashi, K., & Yamanaka, S. (2006) · Cell · doi:10.1016/j.cell.2006.07.024 · Cited by 26,673 · see citing works
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696 · see citing works
Stages of embryonic development of the zebrafish
Kimmel, C. B., Ballard, W. W., Kimmel, S. R., Ullmann, B., & Schilling, T. F. (1995) · Developmental Dynamics · doi:10.1002/aja.1002030302 · Cited by 12,037 · see citing works
Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells
Boyer, L. A., Lee, T. I., Cole, M. F., Johnstone, S. E., Levine, S. S., Zucker, J. P., Guenther, M. G., Kumar, R. M., Murray, H. L., Jenner, R. G., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.020 · Cited by 4,505 · see citing works
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. H., Brugmann, S. A., Goodnough, L. H., Helms, J. A., Farnham, P., Segal, E., et al. (2007) · Cell · doi:10.1016/j.cell.2007.05.022 · Cited by 4,246 · see citing works
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129 · see citing works
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 · see citing works
The Transcriptional Landscape of the Mammalian Genome
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C. A., et al. (2005) · Science · doi:10.1126/science.1112014 · Cited by 3,492 · see citing works
Mechanisms and Functional Implications of Adult Neurogenesis
Zhao, C., Deng, W., & Gage, F. H. (2008) · Cell · doi:10.1016/j.cell.2008.01.033 · Cited by 3,007 · see citing works
Khalil, 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 · see citing works
Chen, X., Han, X., Yuan, P., Fang, F., Huss, M., Vega, V. B., Wong, E., Orlov, Y. L., Zhang, W., Jiang, J., et al. (2008) · Cell · doi:10.1016/j.cell.2008.04.043 · Cited by 2,474 · see citing works
Mattick, J. S., & Makunin, I. V. (2006) · Human Molecular Genetics · doi:10.1093/hmg/ddl046 · Cited by 2,471 · see citing works
Self-citationMultipotent cell lineages in early mouse development depend on SOX2 functionPreprint
Avilion, A. A., Nicolis, S. K., Pevny, L., Pérez, L., Vivian, N., & Lovell-Badge, R. H. (2003) · Genes & Development · doi:10.1101/gad.224503 · Cited by 2,372 · see citing works
Generation of Mouse Induced Pluripotent Stem Cells Without Viral Vectors
Okita, K., Nakagawa, M., Hong, H., Ichisaka, T., & Yamanaka, S. (2008) · Science · doi:10.1126/science.1164270 · Cited by 2,002 · see citing works
The UCSC Genome Browser database: update 2011
Fujita, P. A., Rhead, B. L., Zweig, A. S., Hinrichs, A. S., Karolchik, D., Cline, M., Goldman, M. J., Barber, G. P., Clawson, H., Coelho, A., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq963 · Cited by 1,836 · see citing works
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences
Mammalian Gene Collection (MGC) Program Team* (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.242603899 · Cited by 1,742 · see citing works
The UCSC Genome Browser Database: update 2006
Hinrichs, A. S. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj144 · Cited by 1,646 · see citing works
MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation
Tay, Y., Zhang, J., Thomson, A. M., Lim, B., & Rigoutsos, I. (2008) · Nature · doi:10.1038/nature07299 · Cited by 1,385 · see citing works
Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells
Masui, S., Nakatake, Y., Toyooka, Y., Shimosato, D., Yagi, R., Takahashi, K., Okochi, H., Okuda, A., Matoba, R., Sharov, A., et al. (2007) · Nature Cell Biology · doi:10.1038/ncb1589 · Cited by 1,333 · see citing works
An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells
Kim, J., Chu, J., Shen, X., Wang, J., & Orkin, S. H. (2008) · Cell · doi:10.1016/j.cell.2008.02.039 · Cited by 1,321 · see citing works
Yanai, I., Benjamin, H., Shmoish, M., Chalifa-Caspi, V., Shklar, M., Ophir, R., Bar-Even, A., Horn-Saban, S., Safran, M., Domany, E., et al. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti042 · Cited by 1,300 · see citing works
Pandey, R. R., Mondal, T., Mohammad, F., Enroth, S., Redrup, L., Komorowski, J., Nagano, T., Mancini‐DiNardo, D., & Kanduri, C. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.08.022 · Cited by 1,192 · see citing works
In vivo enhancer analysis of human conserved non-coding sequences
Pennacchio, L. A., Ahituv, N., Moses, A. M., Prabhakar, S., Nobrega, M. A., Shoukry, M., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K. D., et al. (2006) · Nature · doi:10.1038/nature05295 · Cited by 1,165 · see citing works
Specific expression of long noncoding RNAs in the mouse brain
Mercer, T. R., Dinger, M. E., Sunkin, S. M., Mehler, M. F., & Mattick, J. S. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706729105 · Cited by 1,103 · see citing works
Self-citationCawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., et al. (2004) · Cell · doi:10.1016/s0092-8674(04)00127-8 · Cited by 1,095 · see citing works
The non-coding Air RNA is required for silencing autosomal imprinted genes
Sleutels, F., Zwart, R., & Barlow, D. P. (2002) · Nature · doi:10.1038/415810a · Cited by 1,071 · see citing works
Stem cell transcriptome profiling via massive-scale mRNA sequencing
Cloonan, N., Forrest, A. R. R., Kolle, G., Gardiner, B. B. A., Faulkner, G. J., Brown, M. K., Taylor, D. F., Steptoe, A. L., Wani, S., Bethel, G., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1223 · Cited by 1,035 · cited 1× · see citing works
“Moreover, analysis of RNA deep sequencing (RNA-Seq) data (Cloonan et al. 2008; Mortazavi et al. 2008) showed the presence of alternative splicing isoforms of Sox2ot in mouse brain, as well as in pluripotent and differentiating embryonic stem cells (Fig.”
BackgroundSelf-citationAn RNA gene expressed during cortical development evolved rapidly in humans
Pollard, K. S., Salama, S. R., Lambert, N., Lambot, M.-A., Coppens, S., Pedersen, J. S., Katzman, S., King, B., Onodera, C., Siepel, A., et al. (2006) · Nature · doi:10.1038/nature05113 · Cited by 1,005 · see citing works
Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription
Wang, X., Arai, S., Song, X., Reichart, D. R., Du, K., Pascual, G., Tempst, P., Rosenfeld, M. G., Glass, C. K., & Kurokawa, R. (2008) · Nature · doi:10.1038/nature06992 · Cited by 988 · see citing works
Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development
Woolfe, A., Goodson, M., Goode, D. K., Snell, P., McEwen, G. K., Vavouri, T., Smith, S. F., North, P., Callaway, H., Kelly, K., et al. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0030007 · Cited by 970 · see citing works
Vertebrate neurogenesis is counteracted by Sox1–3 activity
Bylund, M., Andersson, E., Novitch, B. G., & Muhr, J. (2003) · Nature Neuroscience · doi:10.1038/nn1131 · Cited by 825 · see citing works
Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA
Yu, W., Gius, D. R., Onyango, P. O., Muldoon‐Jacobs, K., Karp, J. E., Feinberg, A. P., & Cui, H. (2008) · Nature · doi:10.1038/nature06468 · Cited by 801 · see citing works
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAsPreprint
Ponjavic, J., Ponting, C. P., & Lunter, G. A. (2007) · Genome Research · doi:10.1101/gr.6036807 · Cited by 731 · see citing works
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiationPreprint
Dinger, M. E., Amaral, P., Mercer, T. R., Pang, K. C., Bruce, S. J., Gardiner, B., Askarian-Amiri, M., Ru, K., Soldà, G., Simons, C., et al. (2008) · Genome Research · doi:10.1101/gr.078378.108 · Cited by 729 · see citing works
Self-citationRepression of the human dihydrofolate reductase gene by a non-coding interfering transcript
Martianov, I., Ramadass, A., Barros, A. S., Chow, N., & Akoulitchev, A. V. (2007) · Nature · doi:10.1038/nature05519 · Cited by 728 · see citing works
Feng, J., Bi, C., Clark, B. S., Mady, R., Shah, P., & Kohtz, J. D. (2006) · Genes & Development · doi:10.1101/gad.1416106 · Cited by 712 · see citing works
The Genetic Signatures of Noncoding RNAs
Mattick, J. S. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000459 · Cited by 704 · see citing works
Self-citationBeltran-Nebot, M., Puig, I., Peña, C., García, J. M., Álvarez, A. B., Peña, R., Bonilla, F., & de Herreros, A. G. (2008) · Genes & Development · doi:10.1101/gad.455708 · Cited by 677 · see citing works
Neural stem cells and neurospheres—re-evaluating the relationship
Reynolds, B. A., & Rietze, R. L. (2005) · Nature Methods · doi:10.1038/nmeth758 · Cited by 674 · see citing works
Sox2 deficiency causes neurodegeneration and impaired neurogenesis in the adult mouse brain
Ferri, L., Cavallaro, M., Braida, D., Cristofano, A. D., Canta, A., Vezzani, A., Ottolenghi, S., Pandolfi, P. P., Sala, M., Debiasi, S., et al. (2004) · Development · doi:10.1242/dev.01204 · Cited by 666 · see citing works
Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function
Pang, K. C., Frith, M. C., & Mattick, J. S. (2005) · Trends in Genetics · doi:10.1016/j.tig.2005.10.003 · Cited by 653 · see citing works
Self-citationSunwoo, H., Dinger, M. E., Wilusz, J. E., Amaral, P., Mattick, J. S., & Spector, D. L. (2008) · Genome Research · doi:10.1101/gr.087775.108 · Cited by 649 · see citing works
Self-citationAceView: a comprehensive cDNA-supported gene and transcripts annotation
Thierry-Mieg, D., & Thierry-Mieg, J. (2006) · Genome Biology · doi:10.1186/gb-2006-7-s1-s12 · Cited by 629 · see citing works
The Eukaryotic Genome as an RNA Machine
Amaral, P., Dinger, M. E., Mercer, T. R., & Mattick, J. S. (2008) · Science · doi:10.1126/science.1155472 · Cited by 621 · see citing works
Self-citationRNAalifold: improved consensus structure prediction for RNA alignments
Bernhart, S. H., Hofacker, I. L., Will, S., Gruber, A. R., & Stadler, P. F. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-474 · Cited by 595 · see citing works
SOX2 is a dose-dependent regulator of retinal neural progenitor competencePreprint
Taranova, O., Magness, S. T., Fagan, B. M., Wu, Y., Surzenko, N., Hutton, S. R., & Pevny, L. H. (2006) · Genes & Development · doi:10.1101/gad.1407906 · Cited by 554 · see citing works
Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities
Dinger, M. E., Pang, K. C., Mercer, T. R., & Mattick, J. S. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000176 · Cited by 538 · see citing works
Self-citationMutations in SOX2 cause anophthalmia
Fantes, J. A., Ragge, N., Lynch, S. A., McGill, N. I., Collin, J. R. O., Howard‐Peebles, P. N., Hayward, C., Vivian, A. J., Williamson, K. A., van Heyningen, V., et al. (2003) · Nature Genetics · doi:10.1038/ng1120 · Cited by 538 · see citing works
Ravasi, T., Suzuki, H., Pang, K. C., Katayama, S., Furuno, M., Okunishi, R., Fukuda, S., Ru, K., Frith, M. C., Gongora, M., et al. (2005) · Genome Research · doi:10.1101/gr.4200206 · Cited by 522 · see citing works
Self-citationBall, R. K., Friis, R. R., Schoenenberger, C., Doppler, W., & Groner, B. (1988) · The EMBO Journal · doi:10.1002/j.1460-2075.1988.tb03048.x · Cited by 506 · see citing works
Kimura, K., Wakamatsu, A., Suzuki, Y., Ota, T., Nishikawa, T., Yamashita, R., Yamamoto, J.-I., Sekine, M., Tsuritani, K., Wakaguri, H., et al. (2006) · Genome Research · doi:10.1101/gr.4039406 · Cited by 506 · see citing works
Amaral, P., & Mattick, J. S. (2008) · Mammalian Genome · doi:10.1007/s00335-008-9136-7 · Cited by 479 · see citing works
Self-citationMizuseki, K., Kishi, M., Matsui, M., Nakanishi, S., & Sasai, Y. (1998) · Development · doi:10.1242/dev.125.4.579 · Cited by 463 · see citing works
Generation of human-induced pluripotent stem cells
Park, I.-H., Lerou, P., Zhao, R., Huo, H.-G., & Daley, G. (2008) · Nature Protocols · doi:10.1038/nprot.2008.92 · Cited by 451 · see citing works
CRITICA: coding region identification tool invoking comparative analysis
Badger, J. H., & Olsen, G. J. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026133 · Cited by 433 · see citing works
From stem cells to neurons and glia: a Soxist's view of neural development
Wegner, M., & Stolt, C. C. (2005) · Trends in Neurosciences · doi:10.1016/j.tins.2005.08.008 · Cited by 426 · see citing works
Bond, A. M., VanGompel, M. J. W., Sametsky, E. A., Clark, M. F., Savage, J. C., Disterhoft, J. F., & Kohtz, J. D. (2009) · Nature Neuroscience · doi:10.1038/nn.2371 · Cited by 399 · see citing works
Uchikawa, M., Ishida, Y., Takemoto, T., Kamachi, Y., & Kondoh, H. (2003) · Developmental Cell · doi:10.1016/s1534-5807(03)00088-1 · Cited by 397 · see citing works
Pax6 and SOX2 form a co-DNA-binding partner complex that regulates initiation of lens developmentPreprint
Kamachi, Y., Uchikawa, M., Tanouchi, A., Sekido, R., & Kondoh, H. (2001) · Genes & Development · doi:10.1101/gad.887101 · Cited by 394 · see citing works
RNA regulation of epigenetic processes
Mattick, J. S., Amaral, P., Dinger, M. E., Mercer, T. R., & Mehler, M. F. (2009) · BioEssays · doi:10.1002/bies.080099 · Cited by 381 · see citing works
Self-citationStefan Washietl, A., Hofacker, I. L., Lukasser, M., Hüttenhofer, A., & Stadler, P. F. (2005) · Nature Biotechnology · doi:10.1038/nbt1144 · Cited by 379 · see citing works
Zhang, X., Lian, Z., Padden, C., Gerstein, M., Rozowsky, J. S., Snyder, M. P., Gingeras, T., Kapranov, P., Weissman, S. M., & Newburger, P. E. (2009) · Blood · doi:10.1182/blood-2008-06-162164 · Cited by 374 · see citing works
Kelberman, D. (2006) · Journal of Clinical Investigation · doi:10.1172/jci28658 · Cited by 370 · see citing works
Eminli, S., Utikal, J. S., Arnold, K., Jaenisch, R., & Hochedlinger, K. (2008) · Stem Cells · doi:10.1634/stemcells.2008-0317 · Cited by 349 · see citing works
Zappone, M., Galli, R., Catena, R., Meani, N., Biasi, S. D., Mattei, E., Tiveron, C., Vescovi, A. L., Lovell-Badge, R. H., Ottolenghi, S., et al. (2000) · Development · doi:10.1242/dev.127.11.2367 · Cited by 349 · see citing works
Small Increases in the Level of Sox2 Trigger the Differentiation of Mouse Embryonic Stem Cells
Kopp, J. L., Ormsbee, B. D., Desler, M. M., & Rizzino, A. (2008) · Stem Cells · doi:10.1634/stemcells.2007-0951 · Cited by 338 · see citing works
Regulation of Self-Renewal and Pluripotency by Sox2 in Human Embryonic Stem Cells
Fong, H., Hohenstein, K. A., & Donovan, P. J. (2008) · Stem Cells · doi:10.1634/stemcells.2007-1002 · Cited by 305 · see citing works
Complex Loci in Human and Mouse Genomes
Engström, P. G., Suzuki, H., Ninomiya, N., Akalin, A., Sessa, L., Lavorgna, G., Brozzi, A., Luzi, L., Tan, S. L., Yang, L., et al. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020047 · Cited by 294 · see citing works
Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs
Hirota, K., Miyoshi, T., Kugou, K., Hoffman, C. S., Shibata, T., & Ohta, K. (2008) · Nature · doi:10.1038/nature07348 · Cited by 275 · see citing works
Role of Sox2 in the development of the mouse neocortex
Bani‐Yaghoub, M., Tremblay, R. G., Lei, J. X., Zhang, D., Zurakowski, B., Sandhu, J. K., Smith, B., Ribecco‐Lutkiewicz, M., Kennedy, J. A., Walker, P. R., et al. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.03.007 · Cited by 271 · see citing works
Strengths and Limitations of the Neurosphere Culture System
Jensen, J. B., & Parmar, M. (2006) · Molecular Neurobiology · doi:10.1385/mn:34:3:153 · Cited by 254 · see citing works
Ripples from neighbouring transcription
Ebisuya, M., Yamamoto, T., Nakajima, M., & Nishida, E. (2008) · Nature Cell Biology · doi:10.1038/ncb1771 · Cited by 253 · see citing works
SOX9 Regulates Prostaglandin D Synthase Gene Transcription in Vivo to Ensure Testis Development
Wilhelm, D., Hiramatsu, R., Mizusaki, H., et al. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m609578200 · Cited by 235 · see citing works
Nakaya, H. I., Amaral, P., Louro, R., Lopes, A., Fachel, Â. A., Moreira, Y. B., El-Jundi, T. A., da Silva, A. M., Reis, E. M. R., & Verjovski‐Almeida, S. (2007) · Genome biology · doi:10.1186/gb-2007-8-3-r43 · Cited by 234 · see citing works
Self-citationA DNA microarray survey of gene expression in normal human tissues
Shyamsundar, R., Kim, Y. H., Higgins, J., Montgomery, K. D., Jorden, M. A., Sethuraman, A., van de Rijn, M., Botstein, D., Brown, P. O., & Pollack, J. R. (2005) · Genome biology · doi:10.1186/gb-2005-6-3-r22 · Cited by 226 · see citing works
Neural Stem Cell Isolation and Characterization
Rietze, R. L., & Reynolds, B. A. (2006) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(06)19001-1 · Cited by 223 · see citing works
Denœud, F., Kapranov, P., Ucla, C., Frankish, A., Castelo, R., Drenkow, J., Lagarde, J., Alioto, T., Manzano, C., Chrast, J., et al. (2007) · Genome Research · doi:10.1101/gr.5660607 · Cited by 199 · see citing works
Sox-2 is expressed by neural progenitors and astroglia in the adult rat brain
Komitova, M., & Eriksson, P. S. (2004) · Neuroscience Letters · doi:10.1016/j.neulet.2004.07.035 · Cited by 193 · see citing works
Properties of a Fetal Multipotent Neural Stem Cell (NEP Cell)
Cai, J., Wu, Y., Mirua, T., Pierce, J. L., Lucero, M. T., Albertine, K. H., Spangrude, G. J., & Rao, M. S. (2002) · Developmental Biology · doi:10.1006/dbio.2002.0828 · Cited by 188 · see citing works
Impaired generation of mature neurons by neural stem cells from hypomorphic Sox2 mutants
Cavallaro, M., Mariani, J., Lancini, C., Latorre, E., Caccia, R., Gullo, F., Valotta, M., Debiasi, S., Spinardi, L., Ronchi, A. E., et al. (2008) · Development · doi:10.1242/dev.010801 · Cited by 187 · see citing works
Manak, J. R., Dike, S., Sementchenko, V. I., Kapranov, P., Biemar, F., Long, J. C., Cheng, J., Bell, I., Ghosh, S., Piccolboni, A., et al. (2006) · Nature Genetics · doi:10.1038/ng1875 · Cited by 182 · see citing works
SOX2 Plays a Critical Role in the Pituitary, Forebrain, and Eye during Human Embryonic Development
Kelberman, D., de Castro, S. C., Huang, S., Crolla, J. A., Palmer, R. W., Gregory, J. W., Taylor, D. S. I., Cavallo, L., Faienza, M. F., Fischetto, R., et al. (2008) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/jc.2007-2337 · Cited by 181 · see citing works
Ebralidze, A. K., Guibal, F. C., Steidl, U. G., Zhang, P., Lee, S., Bartholdy, B., Alberich-Jordà, M., Petkova, V., Rosenbauer, F., Huang, G., et al. (2008) · Genes & Development · doi:10.1101/gad.1654808 · Cited by 176 · see citing works
Okuda, Y., Yoda, H., Uchikawa, M., Furutani‐Seiki, M., Takeda, H., Kondoh, H., & Kamachi, Y. (2006) · Developmental Dynamics · doi:10.1002/dvdy.20678 · Cited by 166 · see citing works
Torarinsson, E., Sawera, M., Havgaard, J. H., Fredholm, M., & Gorodkin, J. (2006) · Genome Research · doi:10.1101/gr.5226606 · Cited by 164 · see citing works
RNAdb 2.0--an expanded database of mammalian non-coding RNAs
Pang, K. C., Stephen, S. J., Dinger, M. E., Engström, P. G., Lenhard, B., & Mattick, J. S. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl926 · Cited by 164 · see citing works
Self-citationCatena, R., Tiveron, C., Ronchi, A. E., Porta, S., Ferri, L., Tatangelo, L., Cavallaro, M., Favaro, R., Ottolenghi, S., Reinbold, R. A., et al. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m405514200 · Cited by 160 · see citing works
Willingham, A. T., & Gingeras, T. (2006) · Cell · doi:10.1016/j.cell.2006.06.009 · Cited by 159 · see citing works
A Susceptibility Locus for Papillary Thyroid Carcinoma on Chromosome 8q24
He, H., Nagy, R. S., Liyanarachchi, S., Jiao, H., Li, W., Suster, S. M., Kere, J., & de la Chapelle, A. (2009) · Cancer Research · doi:10.1158/0008-5472.can-08-1071 · Cited by 149 · see citing works
Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA CollectionPreprint
Numata, K., Kanai, A., Saito, R., Kondo, S., Adachi, J., Wilming, L. G., Hume, D. A., RIKEN GER Group, Members, G., Hayashizaki, Y., et al. (2003) · Genome Research · doi:10.1101/gr.1011603 · Cited by 145 · see citing works
Mortazavi, A., Thompson, E. C. L., Garcia, S. T., Myers, R. M., & Wold, B. (2006) · Genome Research · doi:10.1101/gr.4997306 · Cited by 141 · see citing works
Vavouri, T., Walter, K., Gilks, W. R., Lehner, B., & Elgar, G. S. (2007) · Genome biology · doi:10.1186/gb-2007-8-2-r15 · Cited by 137 · see citing works
Transposon-free regions in mammalian genomesPreprint
Simons, C., Pheasant, M., Makunin, I. V., & Mattick, J. S. (2005) · Genome Research · doi:10.1101/gr.4624306 · Cited by 125 · see citing works
Self-citationStephen, S. J., Pheasant, M., Makunin, I. V., & Mattick, J. S. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm268 · Cited by 119 · see citing works
Self-citationBoer, B., Kopp, J. L., Mallanna, S. K., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm059 · Cited by 113 · see citing works
Discrimination of Non-Protein-Coding Transcripts from Protein-Coding mRNA
Frith, M. C., Bailey, T. L., Kasukawa, T., et al. (2006) · RNA Biology · doi:10.4161/rna.3.1.2789 · Cited by 110 · see citing works
Shirasawa, S., Harada, H., Furugaki, K., Akamizu, T., Ishikawa, N., Ito, K., Ito, K., Tamai, H., Kuma, K., Kubota, S., et al. (2004) · Human Molecular Genetics · doi:10.1093/hmg/ddh245 · Cited by 109 · see citing works
Regulation of neural macroRNAs by the transcriptional repressor REST
Johnson, R., Teh, C. H.-L., Jia, H., Vanisri, R. R., Pandey, T., Lu, Z.-H., Buckley, N. J., Stanton, L. W., & Lipovich, L. (2008) · RNA · doi:10.1261/rna.1127009 · Cited by 107 · see citing works
Miyagi, S., Saito, T., Mizutani, K., Masuyama, N., Gotoh, Y., Iwama, A., Nakauchi, H., Masui, S., Niwa, H., Nishimoto, M., et al. (2004) · Molecular and Cellular Biology · doi:10.1128/mcb.24.10.4207-4220.2004 · Cited by 101 · see citing works
The Sox2 Regulatory Region 2 Functions as a Neural Stem Cell-specific Enhancer in the Telencephalon
Miyagi, S., Nishimoto, M., Saito, T., Ninomiya, M., Sawamoto, K., Okano, H., Muramatsu, M., Oguro, H., Iwama, A., & Okuda, A. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m512669200 · Cited by 100 · see citing works
Role of SOX2 Mutations in Human Hippocampal Malformations and Epilepsy
Sisodiya, S. M., Ragge, N., Cavalleri, G. L., Hever, A. M., Lorenz, B., Schneider, A. S., Williamson, K. A., Stevens, J., Free, S. L., Thompson, P. J., et al. (2006) · Epilepsia · doi:10.1111/j.1528-1167.2006.00464.x · Cited by 92 · see citing works
Uchikawa, M., Takemoto, T., Kamachi, Y., & Kondoh, H. (2004) · Mechanisms of Development · doi:10.1016/j.mod.2004.05.009 · Cited by 81 · see citing works
Androgen responsive intronic non-coding RNAs
Louro, R., Nakaya, H. I., Amaral, P., Festa, F., Sogayar, M. C., da Silva, A. M., Verjovski‐Almeida, S., & Reis, E. M. R. (2007) · BMC Biology · doi:10.1186/1741-7007-5-4 · Cited by 78 · see citing works
Self-citationAndrew, T., Maniatis, N., Carbonaro, F., Liew, S. H. M., Lau, W., Spector, T. D., & Hammond, C. J. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000220 · Cited by 72 · see citing works
Sikorska, M., Sandhu, J. K., Deb‐Rinker, P., Jezierski, A., Leblanc, J. E., Charlebois, C., Ribecco‐Lutkiewicz, M., Bani‐Yaghoub, M., & Walker, P. R. (2008) · Journal of Neuroscience Research · doi:10.1002/jnr.21635 · Cited by 70 · see citing works
Bruce, S. J., Gardiner, B., Burke, L. J., Gongora, M., Grimmond, S. M., & Perkins, A. C. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-365 · Cited by 70 · see citing works
Self-citationCONDOR: a database resource of developmentally associated conserved non-coding elements
Woolfe, A., Goode, D. K., Cooke, J. E., Callaway, H., Smith, S. F., Snell, P., McEwen, G. K., & Elgar, G. S. (2007) · BMC Developmental Biology · doi:10.1186/1471-213x-7-100 · Cited by 69 · see citing works
Kohtz, J. D., & Fishell, G. (2004) · Gene Expression Patterns · doi:10.1016/j.modgep.2004.01.007 · Cited by 58 · see citing works
Mtx2 directs zebrafish morphogenetic movements during epiboly by regulating microfilament formation
Wilkins, S. J., Yoong, S., Verkade, H. M., Mizoguchi, T., Plowman, S. J., Hancock, J. F., Kikuchi, Y., Heath, J. K., & Perkins, A. C. (2007) · Developmental Biology · doi:10.1016/j.ydbio.2007.10.050 · Cited by 32 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
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 · see citing works
Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder
Gandal, M. J., Zhang, P., Hadjimichael, E., Walker, R. L., Chen, C., Liu, S., Won, H., van Bakel, H., Varghese, M., Wang, Y., et al. (2018) · Science · doi:10.1126/science.aat8127 · Cited by 1,247 · see citing works
An Emerging Role for Long Non-Coding RNA Dysregulation in Neurological Disorders
Fenoglio, C., Ridolfi, E., Galimberti, D., & Scarpini, E. (2013) · International Journal of Molecular Sciences · doi:10.3390/ijms141020427 · Cited by 68 · see citing works
Klocke, C., Sherina, V., Graham, U. M., Gunderson, J., Allen, J. L., Sobolewski, M., Blum, J. L., Zelikoff, J. T., & Cory-Slechta, D. A. (2018) · Inhalation Toxicology · doi:10.1080/08958378.2018.1533053 · Cited by 41 · see citing works
- Authors
- Amaral, P. P., Neyt, C., Wilkins, S. J., Askarian-Amiri, M. E., Sunkin, S. M., Perkins, A. C., & Mattick, J. S.
- Affiliations
- The University of Queensland (AU)
- Allen Institute for Brain Science (US)
- ORCID
- Venue
- RNA
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2009-09-18
- Volume
- 15
- Issue
- 11
- Pages
- 2013-2027
- ISSN
- 1355-8382 (ISSN-L)
- 1469-9001
- PMC
- PMC2764477
- OpenAlex
- W2163141464
- Cited by
- 209
- References
- 109
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 5 · 2023: 18 · 2022: 9 · 2021: 16 · 2020: 18 · 2019: 13 · 2018: 19 · 2017: 22 · 2016: 15 · 2015: 12 · 2014: 13 · 2013: 17 · 2012: 10
- FWCI
- 3.36
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- RNA (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- ResearchSpace (University of Auckland) (submittedVersion)
- Funders
- University of Queensland
- Australian Research Council (FF0561986)
- National Health and Medical Research Council (455871)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- SOX2OT, SOX2, long non-coding RNA, transcription start sites, gene expression regulation, pluripotency, embryoid body differentiation, mesoderm differentiation, mouse embryonic stem cells, adult neurogenesis, brain, vertebrate embryonic development, central nervous system, chickens, zebrafish
- MeSH terms
- Amino Acid Sequence, Animals, Cell Differentiation, Cell Line, Embryo, Mammalian, Genes, Overlapping, Humans, Neurons, Organ Specificity, Transcription, Genetic, Zebrafish, Gene Expression Regulation, Developmental, Cell Lineage, Zebrafish Proteins, Mice, SOX Transcription Factors, SOXB1 Transcription Factors
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review