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From trans to cis: transcriptional regulatory networks in neocortical development
Open accessAbstract
Transcriptional mechanisms mediated by the binding of transcription factors (TFs) to cis-acting regulatory elements (CREs) in DNA play crucial roles in directing gene expression. While TFs have been extensively studied, less effort has gone towards the identification and functional characterization of CREs and associated epigenetic modulation. However, owing to methodological and analytical advances, more comprehensive studies of regulatory elements and mechanisms are now possible. We summarize recent progress in integrative analyses of these regulatory components in the development of the cerebral neocortex, the part of the brain involved in cognition and complex behavior. These studies are uncovering not only the underlying transcriptional regulatory networks, but also how these networks are altered across species and in neurological and psychiatric disorders.
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“In 12-year-olds, the path length of resting-state networks has a heritability of 42%155.”
From Imaging structural and functional brain development in early childhood (2018) · cites this paper as [155]
In the citing paper
“Comparative genomic studies have shown that many of the genes encoding transcription factors and associated regulatory networks involved in the specification and differentiation of different subtypes of neurons and glia are highly conserved across mammals (Nord et al., 2015; Shibata et al., 2015).”
From The Cellular and Molecular Landscapes of the Developing Human Central Nervous System (2016) · cites this paper as Shibata et al., 2015
In the citing paper
“The spatio-temporal patterns of gene expression discussed above are achieved through complex regulatory processes involving several players that function in a combinatorial way (Nord et al., 2015; Shibata et al., 2015).”
From The Cellular and Molecular Landscapes of the Developing Human Central Nervous System (2016) · cites this paper as Shibata et al., 2015
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“For instance, many of the genes previously implicated in the generation and specification of distinct subtypes of cortical projection neurons (Leone et al., 2008; Molyneaux et al., 2007; Shibata et al., 2015) and interneurons (Southwell et al., 2014) have well conserved expression gradients and domains among neural stem/progenitor cells in the VZ/SVZ or neurons in the SP and CP (Bayatti et al., 2”
From The Cellular and Molecular Landscapes of the Developing Human Central Nervous System (2016) · cites this paper as Shibata et al., 2015
In the citing paper
“Epigenetic mechanisms, acting in concert with trans- and cis-components of the regulatory circuitry, play a critical role in regulating spatio-temporal expression patterns (Maze et al., 2014; Nord et al., 2015; Shibata et al., 2015).”
From The Cellular and Molecular Landscapes of the Developing Human Central Nervous System (2016) · cites this paper as Shibata et al., 2015
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Cites
Multiplex Genome Engineering Using CRISPR/Cas Systems
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls
The Wellcome Trust Case Control Consortium, Management Committee, Burton, P. R., Clayton, D. G., Cardon, L. R., Craddock, N., Deloukas, P., Duncanson, A., Kwiatkowski, D. P., McCarthy, M. I., et al. (2007) · Nature · doi:10.1038/nature05911 · Cited by 9,442
High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.035 · Cited by 4,143
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716
Super-enhancers in the control of cell identity and disease
Hnisz, D., Abraham, B. J., Lee, T. I., Lau, A., Saint-André, V., Sigova, A. A., Hoke, H. A., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.09.053 · Cited by 3,662
Wang, H., Yang, H., Shivalila, C. S., Dawlaty, M. M., Cheng, A. W., Zhang, F., & Jaenisch, R. (2013) · Cell · doi:10.1016/j.cell.2013.04.025 · Cited by 3,495
Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398
Cahoy, J. D., Emery, B., Kaushal, A., Foo, L. C., Zamanian, J. L., Christopherson, K. S., Xing, Y., Lubischer, J. L., Krieg, P. A., Krupenko, S. A., et al. (2008) · The Journal of Neuroscience · doi:10.1523/jneurosci.4178-07.2008 · Cited by 3,129
Genome-Wide Mapping of in Vivo Protein-DNA Interactions
Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927
King, M.-C., & Wilson, A. C. (1975) · Science · doi:10.1126/science.1090005 · Cited by 2,815
The contribution of de novo coding mutations to autism spectrum disorder
Iossifov, I., O’Roak, B. J., Sanders, S. J., Ronemus, M., Krumm, N., Levy, D., Stessman, H. A., Witherspoon, K. T., Vives, L., Patterson, K. E., et al. (2014) · Nature · doi:10.1038/nature13908 · Cited by 2,585
Widespread transcription at neuronal activity-regulated enhancers
Kim, T.-K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) · Nature · doi:10.1038/nature09033 · Cited by 2,450
Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells
Lee, T. I., Jenner, R. G., Boyer, L. A., Guenther, M. G., Levine, S. S., Kumar, R., Chevalier, B. S., Johnstone, S. E., Cole, M. F., Isono, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.043 · Cited by 2,296
Transcription factors: from enhancer binding to developmental control
Spitz, F., & Furlong, E. E. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3207 · Cited by 2,227
Spatio-temporal transcriptome of the human brain
Kang, H. J., Kawasawa, Y. I., Cheng, F., Zhu, Y., Xu, X., Li, M., Sousa, A. M. M., Pletikos, M., Meyer, K. A., Sedmak, G., et al. (2011) · Nature · doi:10.1038/nature10523 · Cited by 2,084
Self-citationDe novo mutations revealed by whole-exome sequencing are strongly associated with autism
Sanders, S. J., Murtha, M. T., Gupta, A. R., Murdoch, J. D., Raubeson, M. J., Willsey, A. J., Ercan-Sencicek, A. G., DiLullo, N. M., Parikshak, N. N., Stein, J. L., et al. (2012) · Nature · doi:10.1038/nature10945 · Cited by 2,084
Genome-wide association study identifies five new schizophrenia loci
The Schizophrenia Psychiatric Genome-Wide Association Study (GWAS) Consortium (2011) · Nature Genetics · doi:10.1038/ng.940 · Cited by 1,919
A comparative encyclopedia of DNA elements in the mouse genome
Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., Sandstrom, R., Ma, Z., Davis, C., Pope, B. D., et al. (2014) · Nature · doi:10.1038/nature13992 · Cited by 1,781
Transcriptional Regulation and Its Misregulation in Disease
Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.014 · Cited by 1,676
ChIP-seq accurately predicts tissue-specific activity of enhancers
Visel, A., Blow, M. J., Li, Z., Zhang, T., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F., et al. (2009) · Nature · doi:10.1038/nature07730 · Cited by 1,639
A census of human transcription factors: function, expression and evolution
Vaquerizas, J. M., Kummerfeld, S. K., Teichmann, S. A., & Luscombe, N. M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2538 · Cited by 1,573
Kadoch, C., Hargreaves, D. C., Hodges, H. C., Elias, L., Ho, L., Ranish, J. A., & Crabtree, G. R. (2013) · Nature Genetics · doi:10.1038/ng.2628 · Cited by 1,493
Psychiatric GWAS Consortium Bipolar Disorder Working Group, Sklar, P., Ripke, S., Scott, L. J., Andreassen, O. A., Cichon, S., Craddock, N., Edenberg, H. J., Nurnberger, J. I., Rietschel, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.943 · Cited by 1,344
Development and Evolution of the Human Neocortex
Lui, J. H., Hansen, D. V., & Kriegstein, A. R. (2011) · Cell · doi:10.1016/j.cell.2011.06.030 · Cited by 1,342
Polycomb silencers control cell fate, development and cancer
Sparmann, A., & van Lohuizen, M. (2006) · Nature reviews. Cancer · doi:10.1038/nrc1991 · Cited by 1,339
Transcriptional landscape of the prenatal human brain
Miller, J. A., Ding, S.-L., Sunkin, S. M., Smith, K. A., Ng, L., Szafer, A., Ebbert, A., Riley, Z. L., Royall, J. J., Aiona, K., et al. (2014) · Nature · doi:10.1038/nature13185 · Cited by 1,325
Self-citationCis-regulatory elements: Molecular mechanisms and evolutionary processes underlying divergence
Wittkopp, P. J., & Kalay, G. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3095 · Cited by 1,231
Cohesin mediates transcriptional insulation by CCCTC-binding factor
Wendt, K. S., Yoshida, K., Itoh, T., Bando, M., Koch, B., Schirghuber, E., Tsutsumi, S., Nagae, G., Ishihara, K., Mishiro, T., et al. (2008) · Nature · doi:10.1038/nature06634 · Cited by 1,193
Neuronal Subtype-Specific Genes that Control Corticospinal Motor Neuron Development In Vivo
Arlotta, P., Molyneaux, B. J., Chen, J., Inoue, J., Kominami, R., & Macklis, J. D. (2005) · Neuron · doi:10.1016/j.neuron.2004.12.036 · Cited by 1,161
Interneuron cell types are fit to function
Kepecs, A., & Fishell, G. (2014) · Nature · doi:10.1038/nature12983 · Cited by 1,110
A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees
Nielsen, R., Bustamante, C. D., Clark, A. G., Glanowski, S., Sackton, T. B., Hubisz, M. J., Fledel-Alon, A., Tanenbaum, D. M., Civello, D., White, T. J., et al. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030170 · Cited by 998
The origin and specification of cortical interneurons
Wonders, C. P., & Anderson, S. A. (2006) · Nature Reviews Neuroscience · doi:10.1038/nrn1954 · Cited by 980
Willsey, A. J., Sanders, S. J., Li, M., Dong, S., Tebbenkamp, A. T., Muhle, R. A., Reilly, S. K., Lin, L., Fertuzinhos, S., Miller, J. A., et al. (2013) · Cell · doi:10.1016/j.cell.2013.10.020 · Cited by 934
Molecular logic of neocortical projection neuron specification, development and diversity
Greig, L. C., Woodworth, M. B., Galazo, M. J., Padmanabhan, H., & Macklis, J. D. (2013) · Nature Reviews Neuroscience · doi:10.1038/nrn3586 · Cited by 863
Tbr1 regulates differentiation of the preplate and layer 6
Hevner, R. F., Shi, L., Justice, N., Hsueh, Y.-P., Sheng, M., Smiga, S., Bulfone, A., Goffinet, A. M., Campagnoni, A. T., & Rubenstein, J. L. R. (2001) · Neuron · doi:10.1016/s0896-6273(01)00211-2 · Cited by 857
Gene regulatory networks for development
Levine, M., & Davidson, E. H. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408031102 · Cited by 796
Natural selection on protein-coding genes in the human genome
Bustamante, C. D., Fledel-Alon, A., Williamson, S., Nielsen, R., Hubisz, M. J., Glanowski, S., Tanenbaum, D. M., White, T. J., Sninsky, J. J., Hernandez, R. D., et al. (2005) · Nature · doi:10.1038/nature04240 · Cited by 794
Structure and evolution of transcriptional regulatory networks
Babu, M. M., Luscombe, N. M., Aravind, L., Gerstein, M., & Teichmann, S. A. (2004) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2004.05.004 · Cited by 780
Developmental genetics of vertebrate glial–cell specification
Rowitch, D. H., & Kriegstein, A. R. (2010) · Nature · doi:10.1038/nature09611 · Cited by 774
Imayoshi, I., Sakamoto, M., Yamaguchi, M., Mori, K., & Kageyama, R. (2010) · The Journal of Neuroscience · doi:10.1523/jneurosci.4987-09.2010 · Cited by 716
Melnikov, A., Murugan, A., Zhang, X., Tesileanu, T., Wang, L., Rogov, P., Feizi, S., Gnirke, A., Callan, C. G., Kinney, J. B., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2137 · Cited by 711
Temporal dynamics and genetic control of transcription in the human prefrontal cortex
Colantuoni, C., Lipska, B. K., Ye, T., Hyde, T. M., Tao, R., Leek, J. T., Colantuoni, E. A., Elkahloun, A. G., Herman, M. M., Weinberger, D. R., et al. (2011) · Nature · doi:10.1038/nature10524 · Cited by 685
Neurogenin promotes neurogenesis and inhibits glial differentiation by independent mechanisms.
Sun, Y., Nadal-Vicens, M., Misono, S., Lin, M. Z., Zubiaga, A., Hua, X., Fan, G., & Greenberg, M. E. (2001) · Cell · doi:10.1016/s0092-8674(01)00224-0 · Cited by 681
Satb2 Is a Postmitotic Determinant for Upper-Layer Neuron Specification in the Neocortex
Britanova, O., de Juan Romero, C., Cheung, A., Kwan, K. Y., Schwark, M., Gyorgy, A., Vogel, T., Akopov, S., Mitkovski, M., Agoston, D., et al. (2008) · Neuron · doi:10.1016/j.neuron.2007.12.028 · Cited by 674
Self-citationInferring Nonneutral Evolution from Human-Chimp-Mouse Orthologous Gene Trios
Clark, A. G., Glanowski, S., Nielsen, R., Thomas, P. D., Kejariwal, A., Todd, M. A., Tanenbaum, D. M., Civello, D., Lu, F., Murphy, B., et al. (2003) · Science · doi:10.1126/science.1088821 · Cited by 667
Satb2 Regulates Callosal Projection Neuron Identity in the Developing Cerebral Cortex
Alcamo, E. A., Chirivella, L., Dautzenberg, M., Dobreva, G., Fariñas, I., Grosschedl, R., & McConnell, S. K. (2008) · Neuron · doi:10.1016/j.neuron.2007.12.012 · Cited by 658
Neural progenitors, neurogenesis and the evolution of the neocortex
Florio, M., & Huttner, W. Β. (2014) · Development · doi:10.1242/dev.090571 · Cited by 654
Genetic variability in the regulation of gene expression in ten regions of the human brain
UK Brain Expression Consortium, Ramasamy, A., North American Brain Expression Consortium, Trabzuni, D., Guelfi, S., Varghese, V., Smith, C., Walker, R., De, T., Coin, L., et al. (2014) · Nature Neuroscience · doi:10.1038/nn.3801 · Cited by 644
Enhancers: five essential questions
Pennacchio, L. A., Bickmore, W. A., Dean, A., Nóbrega, M. A., & Bejerano, G. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3458 · Cited by 625
Takizawa, T., Nakashima, K., Namihira, M., Ochiai, W., Uemura, A., Yanagisawa, M., Fujita, N., Nakao, M., & Taga, T. (2001) · Developmental Cell · doi:10.1016/s1534-5807(01)00101-0 · Cited by 620
Johnson, M. B., Kawasawa, Y. I., Mason, C. E., Krsnik, Ž., Coppola, G., Bogdanović, D., Geschwind, D. H., Mane, S. M., State, M. W., & Šestan, N. (2009) · Neuron · doi:10.1016/j.neuron.2009.03.027 · Cited by 603
Talkowski, M. E., Rosenfeld, J. A., Blumenthal, I., Pillalamarri, V., Chiang, C., Heilbut, A., Ernst, C., Hanscom, C., Rossin, E., Lindgren, A. M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.03.028 · Cited by 577
Human-specific loss of regulatory DNA and the evolution of human-specific traits
McLean, C. Y., Reno, P. L., Pollen, A. A., Bassan, A. I., Capellini, T. D., Guenther, C., Indjeian, V. B., Lim, X., Menke, D. B., Schaar, B. T., et al. (2011) · Nature · doi:10.1038/nature09774 · Cited by 535
Neuronal Activity-Regulated Gene Transcription in Synapse Development and Cognitive Function
West, A. E., & Greenberg, M. E. (2011) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a005744 · Cited by 532
Fezl Is Required for the Birth and Specification of Corticospinal Motor Neurons
Molyneaux, B. J., Arlotta, P., Hirata, T., Hibi, M., & Macklis, J. D. (2005) · Neuron · doi:10.1016/j.neuron.2005.08.030 · Cited by 491
Accelerated Evolution of Conserved Noncoding Sequences in Humans
Prabhakar, S., Noonan, J. P., Pääbo, S., & Rubin, E. M. (2006) · Science · doi:10.1126/science.1130738 · Cited by 481
Transcriptional co-regulation of neuronal migration and laminar identity in the neocortex
Kwan, K. Y., Šestan, N., & Anton, E. S. (2012) · Development · doi:10.1242/dev.069963 · Cited by 414
Sansom, S. N., Griffiths, D. S., Faedo, A., Kleinjan, D., Ruan, Y., Smith, J. C., van Heyningen, V., Rubenstein, J. L. R., & Livesey, F. J. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000511 · Cited by 401
Sequential phases of cortical specification involve Neurogenin‐dependent and ‐independent pathways
Schuurmans, C. J., Armant, O., Nieto, M., Stenman, J. M., Britz, O., Klenin, N., Brown, C. E., Langevin, L.-M., Seibt, J., Tang, H., et al. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600278 · Cited by 399
Sessa, A., Mao, C., Hadjantonakis, A., Klein, W. H., & Broccoli, V. (2008) · Neuron · doi:10.1016/j.neuron.2008.09.028 · Cited by 389
The determination of projection neuron identity in the developing cerebral cortex
Leone, D. P., Srinivasan, K., Chen, B., Alcamo, E., & McConnell, S. K. (2008) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2008.05.006 · Cited by 382
Olig2 Targets Chromatin Remodelers to Enhancers to Initiate Oligodendrocyte Differentiation
Yu, Y., Chen, Y., Kim, B., Wang, H., Zhao, C., He, X., Liu, L., Liu, W., Wu, L. M. N., Mao, M., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.006 · Cited by 375
Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development
Nord, A. S., Blow, M. J., Attanasio, C., Akiyama, J. A., Holt, A., Hosseini, R., Phouanenavong, S., Plajzer-Frick, I., Shoukry, M., Afzal, V., et al. (2013) · Cell · doi:10.1016/j.cell.2013.11.033 · Cited by 375
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analysesPreprint
Fullwood, M. J., Wei, C., Liu, E. T., & Ruan, Y. (2009) · Genome Research · doi:10.1101/gr.074906.107 · Cited by 373
Petryniak, M. A., Potter, G. B., Rowitch, D. H., & Rubenstein, J. L. R. (2007) · Neuron · doi:10.1016/j.neuron.2007.06.036 · Cited by 371
Emx1 and Emx2 functions in development of dorsal telencephalon
Yoshida, M., Suda, Y., Matsuo, I., Miyamoto, N., Takeda, N., Kuratani, S., & Aizawa, S. (1997) · Development · doi:10.1242/dev.124.1.101 · Cited by 364
Hand, R., Bortone, D. S., Mattar, P. A., Nguyen, L., Heng, J. I., Guerrier, S., Boutt, E., Peters, E. C., Barnes, A. P., Parras, C. M., et al. (2005) · Neuron · doi:10.1016/j.neuron.2005.08.032 · Cited by 363
Chen, B., Schaevitz, L. R., & McConnell, S. K. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0508732102 · Cited by 353
Committed Neuronal Precursors Confer Astrocytic Potential on Residual Neural Precursor Cells
Namihira, M., Kohyama, J., Semi, K., Sanosaka, T., Deneen, B., Taga, T., & Nakashima, K. (2009) · Developmental Cell · doi:10.1016/j.devcel.2008.12.014 · Cited by 345
MicroRNA-9 Regulates Neurogenesis in Mouse Telencephalon by Targeting Multiple Transcription Factors
Shibata, M., Nakao, H., Kiyonari, H., Abe, T., & Aizawa, S. (2011) · The Journal of Neuroscience · doi:10.1523/jneurosci.5085-10.2011 · Cited by 342
Self-citationKieffer-Kwon, K.-R., Tang, Z., Mathé, E. A., Qian, J., Sung, M., Li, G., Resch, W., Baek, S., Pruett, N. D., Grøntved, L., et al. (2013) · Cell · doi:10.1016/j.cell.2013.11.039 · Cited by 337
Tbr1 regulates regional and laminar identity of postmitotic neurons in developing neocortex
Bedogni, F., Hodge, R. D., Elsen, G. E., Nelson, B. R., Daza, R. A. M., Beyer, R. P., Bammler, T. K., Rubenstein, J. L. R., & Hevner, R. F. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002285107 · Cited by 322
Haygood, R., Fedrigo, O. D., Hanson, B., Yokoyama, K.-D., & Wray, G. A. (2007) · Nature Genetics · doi:10.1038/ng2104 · Cited by 311
SOX5 Controls the Sequential Generation of Distinct Corticofugal Neuron Subtypes
Lai, T. S., Jabaudon, D., Molyneaux, B. J., Azim, E., Arlotta, P., Menezes, J. R. L., & Macklis, J. D. (2008) · Neuron · doi:10.1016/j.neuron.2007.12.023 · Cited by 307
Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue
Lovatt, D., Ruble, B. K., Lee, J., Dueck, H., Kim, T. K., Fisher, S., Francis, C., Spaethling, J. M., Wolf, J. A., Grady, M. S., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2804 · Cited by 287
Genome-wide identification and characterization of functional neuronal activity–dependent enhancers
Malik, A. N., Vierbuchen, T., Hemberg, M., Rubin, A. A., Ling, E., Couch, C. H., Stroud, H., Spiegel, I., Farh, K. K., Harmin, D. A., et al. (2014) · Nature Neuroscience · doi:10.1038/nn.3808 · Cited by 279
Neurogenin 2 controls cortical neuron migration through regulation of Rnd2
Heng, J. I., Nguyen, L., Castro, D. S., Zimmer, C., Wildner, H., Armant, O., Skowronska‐Krawczyk, D., Bedogni, F., Matter, J.-M., Hevner, R. F., et al. (2008) · Nature · doi:10.1038/nature07198 · Cited by 276
Transcriptional Regulation of Cortical Neuron Migration by POU Domain Factors
McEvilly, R. J., de Diaz, M. O., Schonemann, M. D., Hooshmand, F., & Rosenfeld, M. G. (2002) · Science · doi:10.1126/science.1067132 · Cited by 271
Kwan, K. Y., Lam, M. M. S., Krsnik, Ž., Kawasawa, Y. I., Lefebvre, V., & Šestan, N. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806791105 · Cited by 271
Brn-1 and Brn-2 share crucial roles in the production and positioning of mouse neocortical neurons
Sugitani, Y., Nakai, S., Minowa, O., Nishi, M., Jishage, K.-I., Kawano, H., Mori, K., Ogawa, M., & Noda, T. (2002) · Genes & Development · doi:10.1101/gad.978002 · Cited by 259
A High-Resolution Enhancer Atlas of the Developing Telencephalon
Visel, A., Taher, L., Girgis, H., May, D., Golonzhka, O., Hoch, R. V., McKinsey, G. L., Pattabiraman, K., Silberberg, S. N., Blow, M. J., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.041 · Cited by 257
Tbr1 and Fezf2 Regulate Alternate Corticofugal Neuronal Identities during Neocortical Development
McKenna, W. L., Betancourt, J., Larkin, K. A., Abrams, B., Guo, C., Rubenstein, J. L. R., & Chen, B. (2011) · The Journal of Neuroscience · doi:10.1523/jneurosci.4131-10.2011 · Cited by 252
Chen, J.-G., Rašin, M.-R., Kwan, K. Y., & Šestan, N. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509032102 · Cited by 246
Genomic approaches towards finding cis-regulatory modules in animals
Hardison, R. C., & Taylor, J. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3242 · Cited by 246
Pruunsild, P., Sepp, M., Orav, E., Koppel, I., & Timmusk, T. (2011) · Journal of Neuroscience · doi:10.1523/jneurosci.4540-10.2011 · Cited by 239
Direct and concentration-dependent regulation of the proneural gene Neurogenin2 by Pax6
Scardigli, R., Bäumer, N., Gruss, P., Guillemot, F., & Roux, I. L. (2003) · Development · doi:10.1242/dev.00539 · Cited by 239
Cheung, I., Shulha, H. P., Jiang, Y., Matevossian, A., Wang, J., Weng, Z., & Akbarian, S. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1001702107 · Cited by 235
Glial Development: The Crossroads of Regeneration and Repair in the CNS
Gallo, V., & Deneen, B. (2014) · Neuron · doi:10.1016/j.neuron.2014.06.010 · Cited by 232
Quinn, J. C., Molinek, M., Martynoga, B., Zaki, P. A., Faedo, A., Bulfone, A., Hevner, R. F., West, J. D., & Price, D. J. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.08.035 · Cited by 231
Temporal Specification and Bilaterality of Human Neocortical Topographic Gene Expression
Pletikos, M., Sousa, A. M. M., Sedmak, G., Meyer, K. A., Zhu, Y., Cheng, F., Li, M., Kawasawa, Y. I., & Šestan, N. (2014) · Neuron · doi:10.1016/j.neuron.2013.11.018 · Cited by 228
Ninkovic, J., Steiner-Mezzadri, A., Jawerka, M., Akinci, U., Masserdotti, G., Petricca, S., Fischer, J., von Holst, A., Beckers, J., Lie, D. C., et al. (2013) · Cell stem cell · doi:10.1016/j.stem.2013.07.002 · Cited by 216
The Cell-Intrinsic Requirement of Sox6 for Cortical Interneuron Development
Batista-Brito, R., Rossignol, E., Hjerling-Leffler, J., Denaxa, M., Wegner, M., Lefebvre, V., Pachnis, V., & Fishell, G. (2009) · Neuron · doi:10.1016/j.neuron.2009.08.005 · Cited by 214
SOX6 controls dorsal progenitor identity and interneuron diversity during neocortical development
Azim, E., Jabaudon, D., Fame, R. M., & Macklis, J. D. (2009) · Nature Neuroscience · doi:10.1038/nn.2387 · Cited by 209
Molecular insights into human brain evolution
Hill, R. S., & Walsh, C. A. (2005) · Nature · doi:10.1038/nature04103 · Cited by 208
Han, W., Kwan, K. Y., Shim, S., Lam, M. M. S., Shin, Y., Xu, X., Zhu, Y., Li, M., & Šestan, N. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016723108 · Cited by 206
Hanashima, C., Shen, L., Li, S. C., & Lai, E. (2002) · Journal of Neuroscience · doi:10.1523/jneurosci.22-15-06526.2002 · Cited by 194
Wang, X., & Hayes, J. J. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.01245-07 · Cited by 193
Rubenstein, J. L. R. (2010) · Journal of Child Psychology and Psychiatry · doi:10.1111/j.1469-7610.2010.02307.x · Cited by 184
Cis-regulatory control of corticospinal system development and evolution
Shim, S., Kwan, K. Y., Li, M., Lefebvre, V., & Šestan, N. (2012) · Nature · doi:10.1038/nature11094 · Cited by 183
Self-citationGuo, C., Eckler, M. J., McKenna, W. L., McKinsey, G. L., Rubenstein, J. L. R., & Chen, B. (2013) · Neuron · doi:10.1016/j.neuron.2013.09.037 · Cited by 181
Chromatin Regulation by BAF170 Controls Cerebral Cortical Size and Thickness
Tuoc, T. C., Boretius, S., Sansom, S. N., Pitulescu, M.-E., Frahm, J., Livesey, F. J., & Stoykova, A. (2013) · Developmental Cell · doi:10.1016/j.devcel.2013.04.005 · Cited by 177
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Britz, O., Mattar, P. A., Nguyen, L., Langevin, L.-M., Zimmer, C., Alam, S., Guillemot, F., & Schuurmans, C. (2006) · Cerebral Cortex · doi:10.1093/cercor/bhj168 · Cited by 175
Small Deletions of SATB2 Cause Some of the Clinical Features of the 2q33.1 Microdeletion Syndrome
Rosenfeld, J. A., Ballif, B. C., Lucas, A. M., Spence, E. J., Powell, C. M., Aylsworth, A. S., Torchia, B. A., & Shaffer, L. G. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006568 · Cited by 174
Srinivasan, K., Leone, D. P., Bateson, R. K., Dobreva, G., Kohwi, Y., Kohwi-Shigematsu, T., Grosschedl, R., & McConnell, S. K. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1216793109 · Cited by 171
Farkas, L. M., Haffner, C., Giger, T., Khaitovich, P., Nowick, K., Birchmeier, C., Pääbo, S., & Huttner, W. Β. (2008) · Neuron · doi:10.1016/j.neuron.2008.09.020 · Cited by 162
The role of BAF (mSWI/SNF) complexes in mammalian neural development
Son, E., & Crabtree, G. R. (2014) · American Journal of Medical Genetics Part C Seminars in Medical Genetics · doi:10.1002/ajmg.c.31416 · Cited by 148
SATB2 interacts with chromatin‐remodeling molecules in differentiating cortical neurons
Gyorgy, A. B., Szemes, M., Romero, C. D. J., Tarabykin, V. S., & Ágoston, D. V. (2008) · European Journal of Neuroscience · doi:10.1111/j.1460-9568.2008.06061.x · Cited by 146
Species-dependent posttranscriptional regulation of NOS1 by FMRP in the developing cerebral cortex
Kwan, K. Y., Lam, M. M. S., Johnson, M. B., Dube, U., Shim, S., Rašin, M.-R., Sousa, A. M. M., Fertuzinhos, S., Chen, J.-G., Arellano, J. I., et al. (2012) · Cell · doi:10.1016/j.cell.2012.02.060 · Cited by 137
Id4regulates neural progenitor proliferation and differentiation in vivo
Yun, K., Mantani, A., Garel, S., Rubenstein, J. L. R., & Israel, M. A. (2004) · Development · doi:10.1242/dev.01430 · Cited by 126
Human-Specific Histone Methylation Signatures at Transcription Start Sites in Prefrontal Neurons
Shulha, H. P., Crisci, J. L., Reshetov, D. A., Tushir, J. S., Cheung, I. K., Bharadwaj, R. A., Chou, H.-J., Houston, I. B., Peter, C. J., Mitchell, A., et al. (2012) · PLoS Biology · doi:10.1371/journal.pbio.1001427 · Cited by 124
Ghanem, N., Yu, M., Long, J. E., Hatch, G., Rubenstein, J. L. R., & Ekker, M. (2007) · Journal of Neuroscience · doi:10.1523/jneurosci.4725-06.2007 · Cited by 113
Personal and population genomics of human regulatory variationPreprint
Vernot, B., Stergachis, A. B., Maurano, M. T., Vierstra, J. D., Neph, S. J., Thurman, R. E., Stamatoyannopoulos, J. A., & Akey, J. M. (2012) · Genome Research · doi:10.1101/gr.134890.111 · Cited by 110
Lamb, A. N., Rosenfeld, J. A., Neill, N. J., Talkowski, M. E., Blumenthal, I., Girirajan, S., Keelean-Fuller, D., Fan, Z., Pouncey, J., Stevens, C., et al. (2012) · Human Mutation · doi:10.1002/humu.22037 · Cited by 107
Transcriptional Regulation of Enhancers Active in Protodomains of the Developing Cerebral Cortex
Pattabiraman, K., Golonzhka, O., Lindtner, S., Nord, A. S., Taher, L., Hoch, R. V., Silberberg, S. N., Zhang, D., Chen, B., Zeng, H., et al. (2014) · Neuron · doi:10.1016/j.neuron.2014.04.014 · Cited by 102
Toma, K., Kumamoto, T., & Hanashima, C. (2014) · Journal of Neuroscience · doi:10.1523/jneurosci.2334-14.2014 · Cited by 102
Two-tier transcriptional control of oligodendrocyte differentiation
Li, H., He, Y., Richardson, W. D., & Casaccia, P. (2009) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2009.08.004 · Cited by 102
AP2γ regulates basal progenitor fate in a region- and layer-specific manner in the developing cortex
Pinto, L., Drechsel, D., Schmid, M.-T., Ninkovic, J., Irmler, M., Brill, M. S., Restani, L., Gianfranceschi, L., Cerri, C., Weber, S. N., et al. (2009) · Nature Neuroscience · doi:10.1038/nn.2399 · Cited by 100
ChIA-PET analysis of transcriptional chromatin interactions
Zhang, J., Poh, H. M., Peh, S. Q., Sia, Y. Y., Li, G., Mulawadi, F. H., Goh, Y., Fullwood, M. J., Sung, W.-K. K., Ruan, X., et al. (2012) · Methods · doi:10.1016/j.ymeth.2012.08.009 · Cited by 96
Mechanisms of astrocytogenesis in the mammalian brain
Namihira, M., & Nakashima, K. (2013) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2013.06.002 · Cited by 93
MicroRNA-92b regulates the development of intermediate cortical progenitors in embryonic mouse brain
Nowakowski, T. J., Fotaki, V., Pollock, A., Sun, T., Pratt, T., & Price, D. J. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1219385110 · Cited by 93
Large-Scale Identification of Coregulated Enhancer Networks in the Adult Human Brain
Vermunt, M. W., Reinink, P., Korving, J., de Bruijn, E., Creyghton, P. M., Başak, O., Geeven, G., Toonen, P. W., Lansu, N. R., Meunier, C., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.09.023 · Cited by 86
Olig1 Function Is Required to Repress Dlx1/2 and Interneuron Production in Mammalian Brain
Silbereis, J. C., Nobuta, H., Tsai, H., Heine, V. M., McKinsey, G. L., Meijer, D. H., Howard, M. A., Petryniak, M. A., Potter, G. B., Alberta, J. A., et al. (2014) · Neuron · doi:10.1016/j.neuron.2013.11.024 · Cited by 82
Ohtaka‐Maruyama, C., Hirai, S., Miwa, A., Heng, J. I., Shitara, H., Ishii, R., Taya, C., Kawano, H., Kasai, M., Nakajima, K., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.01.012 · Cited by 81
Xiang, C., Baubet, V., Pal, S., Holderbaum, L., Tatard-Leitman, V. M., Jiang, P., Davuluri, R. V., & Dahmane, N. (2011) · Cell Death and Differentiation · doi:10.1038/cdd.2011.144 · Cited by 79
Shimizu, T., Nakazawa, M., Kani, S., Bae, Y., Shimizu, T., Kageyama, R., & Hibi, M. (2010) · Development · doi:10.1242/dev.047167 · Cited by 79
Büttner, N., Johnsen, S. A., Kügler, S., & Vogel, T. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0912041107 · Cited by 66
Role for Lhx2 in corticogenesis through regulation of progenitor differentiation
Chou, S., & O’Leary, D. D. M. (2013) · Molecular and Cellular Neuroscience · doi:10.1016/j.mcn.2013.02.006 · Cited by 61
Cux‐1 and Cux‐2 control the development of Reelin expressing cortical interneurons
Cubelos, B., Sebastián‐Serrano, Á., Kim, S., Redondo, J. M., Walsh, C. A., & Nieto, M. (2008) · Developmental Neurobiology · doi:10.1002/dneu.20626 · Cited by 53
Tashiro, K., Teissier, A., Kobayashi, N., Nakanishi, A., Sasaki, T., Yan, K., Tarabykin, V. S., Vigier, L., Sumiyama, K., Hirakawa, M., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028497 · Cited by 53
Chapter 6 Global Control Regions and Regulatory Landscapes in Vertebrate Development and Evolution
Spitz, F., & Duboule, D. (2008) · Advances in genetics · doi:10.1016/s0065-2660(07)00006-5 · Cited by 52
Heng, J. I., Qu, Z., Ohtaka‐Maruyama, C., Okado, H., Kasai, M., Castro, D. S., Guillemot, F., & Tan, S. (2013) · Cerebral Cortex · doi:10.1093/cercor/bht277 · Cited by 48
In vivo function of Rnd2 in the development of neocortical pyramidal neurons
Nakamura, K., Yamashita, Y., Tamamaki, N., Katoh, H., Kaneko, T., & Negishi, M. (2005) · Neuroscience Research · doi:10.1016/j.neures.2005.10.008 · Cited by 40
Wenger, A. M., Clarke, S. L., Notwell, J. H., Chung, T. R., Tuteja, G., Guturu, H., Schaar, B. T., & Bejerano, G. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003728 · Cited by 37
Ohtaka‐Maruyama, C., Hirai, S., Miwa, A., Takahashi, A., & Okado, H. (2011) · Neuroscience · doi:10.1016/j.neuroscience.2011.11.006 · Cited by 15
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Silbereis, J. C., Pochareddy, S., Zhu, Y., Li, M., & Sestan, N. (2016) · Neuron · doi:10.1016/j.neuron.2015.12.008 · Cited by 818
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Li, M., Santpere, G., Imamura Kawasawa, Y., Evgrafov, O. V., Gulden, F. O., Pochareddy, S., Sunkin, S. M., Li, Z., Shin, Y., Zhu, Y., et al. (2018) · Science · doi:10.1126/science.aat7615 · Cited by 810
Self-citationEvolution of the Human Nervous System Function, Structure, and Development
Sousa, A. M. M., Meyer, K. A., Santpere, G., Gulden, F. O., & Sestan, N. (2017) · Cell · doi:10.1016/j.cell.2017.06.036 · Cited by 517
Self-citationAkbarian, S., Liu, C., Knowles, J. A., Vaccarino, F. M., Farnham, P. J., Crawford, G. E., Jaffe, A. E., Pinto, D., Dracheva, S., Geschwind, D. H., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.4156 · Cited by 451
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Metadata
- Authors
- Shibata, M., Gulden, F. O., & Sestan, N.
- Affiliations
- Yale University (US)
- Venue
- Trends in Genetics
- Publisher
- Elsevier BV
- Published
- 2015-02
- Volume
- 31
- Issue
- 2
- Pages
- 77-87
- ISSN
- 0168-9525 (ISSN-L)
- PMC
- PMC4382006
- OpenAlex
- W2113267995
- Cited by
- 109
- References
- 138
- Citations by year
- 2026: 4 · 2025: 3 · 2024: 6 · 2023: 6 · 2022: 5 · 2021: 3 · 2020: 5 · 2019: 7 · 2018: 57 · 2017: 7 · 2016: 3 · 2015: 3
- FWCI
- 2.26
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Trends in Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health
- National Institute of Mental Health (U01MH103339, P50MH106934, U01MH081896, U01MH105972)
- National Institute of Neurological Disorders and Stroke (R01NS054273)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- transcriptional regulatory networks, cis-regulatory elements, transcription factors, neocortex development, epigenetic regulation, gene expression regulation, species differences, neurological disorders, mental illness
- MeSH terms
- Animals, Mental Disorders, Cell Differentiation, Cell Movement, Gene Expression Regulation, Humans, Nerve Net, Nervous System Diseases, Neuroglia, Neurons, Regulatory Sequences, Nucleic Acid, Transcription, Genetic, Neocortex, Regulatory Elements, Transcriptional, Gene Regulatory Networks, Neurogenesis
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