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Developmental regulation of human cortex transcription and its clinical relevance at single base resolution
Open accessAbstract
Transcriptome analysis of human brain provides fundamental insight into development and disease, but it largely relies on existing annotation. We sequenced transcriptomes of 72 prefrontal cortex samples across six life stages and identified 50,650 differentially expression regions (DERs) associated with developmental and aging, agnostic of annotation. While many DERs annotated to non-exonic sequence (41.1%), most were similarly regulated in cytosolic mRNA extracted from independent samples. The DERs were developmentally conserved across 16 brain regions and in the developing mouse cortex, and were expressed in diverse cell and tissue types. The DERs were further enriched for active chromatin marks and clinical risk for neurodevelopmental disorders such as schizophrenia. Lastly, we demonstrate quantitatively that these DERs associate with a changing neuronal phenotype related to differentiation and maturation. These data show conserved molecular signatures of transcriptional dynamics across brain development, have potential clinical relevance and highlight the incomplete annotation of the human brain transcriptome.
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“Transcriptomic analyses suggest that genes associated with psychiatric disorders are highly expressed during development 5,6 ,”
From Developmental timing and critical windows for the treatment of psychiatric disorders (2016) · cites this paper as [6]
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“We highlight two primate-specific lncRNAs, LINC00693 and LINC00689. Both interact with miRNA processing complexes and are typically downregulated during development12, but are upregulated in ASD cortex (Fig. 1c, d, Extended Data Fig. 2n).”
From Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism (2016) · cites this paper as [12]
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“Lines above the plot indicate pairwise significance with a one-sided Wilcoxon rank-sum test between brain and the other tissues.”
From Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism (2016) · cites this paper as [12]
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Cites
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Liao, Y., Smyth, G. K., & Shi, W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt656 · Cited by 27,219
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L. (2013) · Genome Biology · doi:10.1186/gb-2013-14-4-r36 · Cited by 12,668
Database resources of the National Center for Biotechnology Information: update
Wheeler, D. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,695
Biological insights from 108 schizophrenia-associated genetic loci
Schizophrenia Working Group of the Psychiatric Genomics Consortium (2014) · Nature · doi:10.1038/nature13595 · Cited by 7,577
Derrien, T., Johnson, R., Bussotti, G., Andrea 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 5,135
Empirical threshold values for quantitative trait mapping.
Churchill, G. A., & Doerge, R. W. (1994) · Genetics · doi:10.1093/genetics/138.3.963 · Cited by 4,935
Aryee, M. J., Jaffe, A. E., Bravo, H. C., Ladd‐Acosta, C., Feinberg, A. P., Hansen, K. D., & Irizarry, R. A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu049 · Cited by 4,389
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(EADI), E. A. D. I., Lambert, J.-C., (GERAD), G. A. E. R. I. A. D., Alzheimer's Disease Genetic Consortium (ADGC), (CHARGE), C. F. H. A. A. R. I. G. E., Ibrahim-Verbaas, C. A., Harold, D., Naj, A. C., Sims, R., Bellenguez, C., et al. (2013) · Nature Genetics · doi:10.1038/ng.2802 · Cited by 4,336
Bioinformatics and Computational Biology Solutions Using R and Bioconductor
Gentleman, R. C., Carey, V. J., Huber, W. K., Irizarry, R. A., & Dudoit, S. (2005) · Statistics in the health sciences · doi:10.1007/0-387-29362-0 · Cited by 3,470
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Self-citationKahn, R. S., Sommer, I. E., Murray, R. M., Meyer‐Lindenberg, A., Weinberger, D. R., Cannon, T. D., O’Donovan, M. C., Correll, C. U., Kane, J. M., van Os, J., et al. (2015) · Nature Reviews Disease Primers · doi:10.1038/nrdp.2015.67 · Cited by 1,163
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Ursini, G., Punzi, G., Chen, Q., Marenco, S., Robinson, J. F., Porcelli, A., Hamilton, E. G., Mitjans, M., Maddalena, G., Begemann, M., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0021-y · Cited by 276
Self-citationRenner, H., Grabos, M., Becker, K., Kagermeier, T., Wu, J., Otto, M., Peischard, S., Zeuschner, D., Tsytsyura, Y., Disse, P., et al. (2020) · eLife · doi:10.7554/elife.52904 · Cited by 229
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Del-Aguila, J. L., Li, Z., Dube, U., Mihindukulasuriya, K. A., Budde, J. P., Fernandez, M. V., Ibanez, L., Bradley, J., Wang, F., Bergmann, K., et al. (2019) · Alzheimer's Research & Therapy · doi:10.1186/s13195-019-0524-x · Cited by 183
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Hwang, T., Park, C., Leung, A. K. L., Gao, Y., Hyde, T. M., Kleinman, J. E., Rajpurohit, A., Tao, R., Shin, J. H., & Weinberger, D. R. (2016) · Nature Neuroscience · doi:10.1038/nn.4337 · Cited by 184
Self-citationLi, M., Jaffe, A. E., Straub, R. E., Tao, R., Shin, J. H., Wang, Y., Chen, Q., Li, C., Jia, Y., Ohi, K., et al. (2016) · Nature Medicine · doi:10.1038/nm.4096 · Cited by 163
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Self-citationChatterton, Z., Hartley, B. J., Seok, M.-H., Mendelev, N., Chen, S., Milekic, M. H., Rosoklija, G. B., Stankov, A., Trencevsja-Ivanovska, I., Brennand, K., et al. (2017) · Epigenetics & Chromatin · doi:10.1186/s13072-017-0111-y · Cited by 97
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van de Leemput, J., Hess, J., Glatt, S. J., & Tsuang, M. T. (2016) · Advances in genetics · doi:10.1016/bs.adgen.2016.08.001 · Cited by 71
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Birnbaum, R., Jaffe, A. E., Chen, Q., Shin, J. H., BrainSeq Consortium, Schubert, C. R., O'Donnell, P., Quan, J., Wendland, J. R., Xi, H. S., et al. (2018) · Molecular Psychiatry · doi:10.1038/mp.2017.89 · Cited by 67
Self-citationDillman, A., Majounie, E., Ding, J., Gibbs, J. R., Hernandez, D. G., Arepalli, S., Traynor, B. J., Singleton, A., Galter, D., & Cookson, M. R. (2017) · Scientific Reports · doi:10.1038/s41598-017-17322-0 · Cited by 65
Zhang, D., Guelfi, S., García-Ruiz, S., Costa, B., Reynolds, R. H., D’Sa, K., Liu, W., Courtin, T., Peterson, A., Jaffe, A. E., et al. (2020) · Science Advances · doi:10.1126/sciadv.aay8299 · Cited by 60
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Self-citationMasjosthusmann, S., Becker, D., Petzuch, B., Klose, J., Siebert, C., Deenen, R., Barenys, M., Baumann, J., Dach, K., Tigges, J., et al. (2018) · Toxicology and Applied Pharmacology · doi:10.1016/j.taap.2018.05.009 · Cited by 42
Steward, C. A., Roovers, J., Suner, M., González, J. M., Uszczyńska-Ratajczak, B., Pervouchine, D. D., Fitzgerald, S. F., Viola, M., Stamberger, H., Hamdan, F. F., et al. (2019) · npj Genomic Medicine · doi:10.1038/s41525-019-0106-7 · Cited by 37
Price, A. J., Hwang, T., Tao, R., Burke, E. E., Rajpurohit, A., Shin, J. H., Hyde, T. M., Kleinman, J. E., Jaffe, A. E., & Weinberger, D. R. (2019) · Genome Research · doi:10.1101/gr.250217.119 · Cited by 32
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Ohi, K., Shimada, T., Nitta, Y., Kihara, H., Okubo, H., Uehara, T., & Kawasaki, Y. (2016) · Schizophrenia Research · doi:10.1016/j.schres.2016.03.032 · Cited by 32
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Guelfi, S., D’Sa, K., Botía, J. A., Vandrovcová, J., Reynolds, R. H., Zhang, D., Trabzuni, D., Collado‐Torres, L., Thomason, A., Leyton, P. Q., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14483-x · Cited by 31
Self-citationZhang, C., Xiao, X., Zhang, Z., Hu, Z., & Li, M. (2021) · Molecular Psychiatry · doi:10.1038/s41380-021-01037-w · Cited by 33
Davis, K. N., Tao, R., Li, C., Gao, Y., Gondré‐Lewis, M. C., Lipska, B. K., Shin, J. H., Xie, B., Ye, T., Weinberger, D. R., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0148558 · Cited by 33
Self-citationMobley, C. B., Fox, C. D., Thompson, R. M., Healy, J. C., Santucci, V., Kephart, W. C., McCloskey, A. E., Kim, M., Pascoe, D. D., Martin, J. S., et al. (2016) · Amino Acids · doi:10.1007/s00726-015-2121-z · Cited by 32
Morgan, L. Z., Rollins, B. L., Sequeira, A., Byerley, W., DeLisi, L. E., Schatzberg, A. F., Barchas, J. D., Myers, R., Watson, S. J., Akil, H., et al. (2016) · Microarrays · doi:10.3390/microarrays5010006 · Cited by 32
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Heighway, J., Sedó, A., Garg, A., Eldershaw, L., Perreau, V. M., Berecki, G., Reid, C. A., Petrou, S., & Maljevic, S. (2022) · Neurobiology of Disease · doi:10.1016/j.nbd.2022.105622 · Cited by 32
Sokolowski, M., Wasserman, J., & Wasserman, D. (2018) · American Journal of Medical Genetics Part B: Neuropsychiatric Genetics · doi:10.1002/ajmg.b.32694 · Cited by 30
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Schneider, E., Dittrich, M. T., Böck, J., Nanda, I., Müller, T., Seidmann, L., Tralau, T., Galetzka, D., Hajj, N. E., & Haaf, T. (2016) · Gene · doi:10.1016/j.gene.2016.07.058 · Cited by 29
McKinney, B. C., Ding, Y., Lewis, D. A., & Sweet, R. A. (2017) · Translational Psychiatry · doi:10.1038/tp.2016.297 · Cited by 29
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Self-citationPergola, G., Parihar, M., Sportelli, L., Bharadwaj, R. A., Borcuk, C., Radulescu, E., Bellantuono, L., Blasi, G., Chen, Q., Kleinman, J. E., et al. (2023) · Science Advances · doi:10.1126/sciadv.ade2812 · Cited by 26
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Homberg, J. R., Kyzar, E. J., Stewart, A., Nguyen, M., Poudel, M. K., Echevarria, D. J., Collier, A. D., Gaikwad, S., Клименко, В. М., Norton, W., et al. (2015) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2016.1115834 · Cited by 24
Kroeze, Y., Oti, M., van Beusekom, E., Cooijmans, R. H. M., van Bokhoven, H., Kolk, S. M., Homberg, J. R., & Zhou, H. (2017) · Cerebral Cortex · doi:10.1093/cercor/bhw407 · Cited by 22
Ha, T. J., Zhang, P. G. Y., Robert, R., Yeung, J., Swanson, D. J., Mathelier, A., Wasserman, W. W., Im, S., Itoh, M., Kawaji, H., et al. (2019) · BMC Genomics · doi:10.1186/s12864-019-6063-9 · Cited by 21
Vornholt, E., Luo, D., Qiu, W., McMichael, G. O., Liu, Y., Gillespie, N. A., Ma, C., & Vladimirov, V. I. (2019) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2019.04.015 · Cited by 23
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Self-citationSawada, T., Barbosa, A. R., Araújo, B. H. S., McCord, A. E., D’Ignazio, L., Benjamin, K. J., Sheehan, B., Zabolocki, M., Feltrin, A. S., Arora, R., et al. (2023) · American Journal of Psychiatry · doi:10.1176/appi.ajp.20220723 · Cited by 21
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Kraushar, M. L., Popovitchenko, T., Volk, N. L., & Rašin, M. (2016) · International Journal of Developmental Neuroscience · doi:10.1016/j.ijdevneu.2016.02.003 · Cited by 20
Patil, V. S., Pal, J., Mahalingam, K., & Somasundaram, K. (2020) · PeerJ · doi:10.7717/peerj.9755 · Cited by 17
Charles, S., Jackson, E., Sun, G., Zhou, Y., Siciliano, B., Niu, W., Han, H., Nikitina, A. A., Kemp, M. L., Wen, Z., et al. (2024) · Advanced Materials Technologies · doi:10.1002/admt.202400473 · Cited by 19
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Ogawa, Y., Yamaguchi, J., Yano, M., Uchiyama, Y., & Okano, H. J. (2018) · Neuroscience Research · doi:10.1016/j.neures.2018.03.008 · Cited by 17
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Silvennoinen, K., Gaweł, K., Tsortouktzidis, D., Pitsch, J., Alhusaini, S., van Loo, K. M. J., Picardo, R., Michalak, Z., Pagni, S., Custodio, H. M., et al. (2022) · Acta Neuropathologica · doi:10.1007/s00401-022-02429-0 · Cited by 17
Wen, C. H., Margolis, M. P., Dai, R., Zhang, P., Przytycki, P. F., Vo, D., Bhattacharya, A., Kim, M., Matoba, N., Tsai, E. A., et al. (2023) · medRxiv · doi:10.1101/2023.03.03.23286706 · Cited by 16
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Metadata
- Authors
- Jaffe, A. E., Shin, J., Collado-Torres, L., Leek, J. T., Tao, R., Li, C., Gao, Y., Jia, Y., Maher, B. J., Hyde, T. M., Kleinman, J. E., & Weinberger, D. R.
- Affiliations
- Johns Hopkins University (US)
- Corresponding author
- Jaffe, Andrew E
- Weinberger, Daniel R
- ORCID
- Venue
- Nature Neuroscience
- Published
- 2014-12-15
- Volume
- 18
- Issue
- 1
- Pages
- 154-161
- ISSN
- 1097-6256 (ISSN-L)
- 1546-1726
- PMC
- PMC4281298
- OpenAlex
- W2002097805
- Cited by
- 156
- References
- 63
- Citations by year
- 2026: 7 · 2025: 6 · 2024: 7 · 2023: 10 · 2022: 5 · 2021: 4 · 2020: 20 · 2019: 19 · 2018: 18 · 2017: 20 · 2016: 27 · 2015: 13
- FWCI
- 8.21
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Neuroscience (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of Mental Health (R03MH096539, R21MH102791)
- National Institute of General Medical Sciences (R01GM105705)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Keywords
- human prefrontal cortex, brain development, brain aging, transcriptome annotation, neurodevelopmental disorders, schizophrenia, mouse cortex, neuronal differentiation, neuronal maturation
- MeSH terms
- Aging, Animals, Cerebral Cortex, Chromatin, Female, Fetus, Humans, Infant, Infant, Newborn, Neurons, Pregnancy, Conserved Sequence, Gene Expression Regulation, Developmental, Mice, Transcriptome
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