An Emerging Role for Enhancer RNAs in Brain Disorders

Achour, M., Le Gras, S., Keime, C., Parmentier, F., Lejeune, F. X., Boutillier, A. L., & Merienne, K. (2015). Neuronal identity genes regulated by super-enhancers are preferentially down-regulated in the striatum of Huntington’s disease mice. Hum Mol Genet, 24(12), 3481–3496. https://doi.org/10.1093/hmg/ddv099

Article  CAS  PubMed  Google Scholar 

Adelman, K., & Lis, J. T. (2012). Promoter-proximal pausing of RNA polymerase II: Emerging roles in metazoans. Nature Reviews Genetics, 13(10), 720–731. https://doi.org/10.1038/nrg3293

Article  CAS  PubMed  PubMed Central  Google Scholar 

Akins, P. T., Liu, P. K., & Hsu, C. Y. (1996). Immediate early gene expression in response to cerebral ischemia. Friend or foe? Stroke, 27(9), 1682–1687. https://doi.org/10.1161/01.str.27.9.1682

Article  CAS  PubMed  Google Scholar 

Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., & Sandelin, A. (2014). An atlas of active enhancers across human cell types and tissues. Nature, 507(7493), 455–461. https://doi.org/10.1038/nature12787

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aoi, Y., Smith, E. R., Shah, A. P., Rendleman, E. J., Marshall, S. A., Woodfin, A. R., & Shilatifard, A. (2020). NELF regulates a promoter-proximal step distinct from RNA Pol II pause-release. Molecular Cell, 78(2), 261-274 e265. https://doi.org/10.1016/j.molcel.2020.02.014

Article  CAS  PubMed  PubMed Central  Google Scholar 

Arner, E., Daub, C. O., Vitting-Seerup, K., Andersson, R., Lilje, B., Drablos, F., & Hayashizaki, Y. (2015). Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science, 347(6225), 1010–1014. https://doi.org/10.1126/science.1259418

Article  CAS  PubMed  PubMed Central  Google Scholar 

Arnold, P. R., Wells, A. D., & Li, X. C. (2019). Diversity and emerging roles of enhancer RNA in regulation of gene expression and cell fate. Frontiers in Cell and Developmental Biology, 7, 377. https://doi.org/10.3389/fcell.2019.00377

Article  PubMed  Google Scholar 

Bharadwaj, R., Jiang, Y., Mao, W., Jakovcevski, M., Dincer, A., Krueger, W., & Akbarian, S. (2013). Conserved chromosome 2q31 conformations are associated with transcriptional regulation of GAD1 GABA synthesis enzyme and altered in prefrontal cortex of subjects with schizophrenia. Journal of Neuroscience, 33(29), 11839–11851. https://doi.org/10.1523/JNEUROSCI.1252-13.2013

Article  CAS  PubMed  Google Scholar 

Bhattarai, S., Akella, A., Gandhi, A., & Dharap, A. (2021). Modulation of brain pathology by enhancer RNAs in cerebral ischemia. Molecular Neurobiology, 58(4), 1482–1490. https://doi.org/10.1007/s12035-020-02194-9

Article  CAS  PubMed  Google Scholar 

Bhattarai, S., Aly, A., Garcia, K., Ruiz, D., Pontarelli, F., & Dharap, A. (2019). Deep sequencing reveals uncharted isoform heterogeneity of the protein-coding transcriptome in cerebral ischemia. Molecular Neurobiology, 56(2), 1035–1043. https://doi.org/10.1007/s12035-018-1147-0

Article  CAS  PubMed  Google Scholar 

Bhattarai, S., Pontarelli, F., Prendergast, E., & Dharap, A. (2017). Discovery of novel stroke-responsive lncRNAs in the mouse cortex using genome-wide RNA-seq. Neurobiology of Diseases, 108, 204–212. https://doi.org/10.1016/j.nbd.2017.08.016

Article  CAS  Google Scholar 

Bohnsack, J. P., Zhang, H., Wandling, G. M., He, D., Kyzar, E. J., Lasek, A. W., & Pandey, S. C. (2022). Targeted epigenomic editing ameliorates adult anxiety and excessive drinking after adolescent alcohol exposure. Science Advances, 8(18), eabn2748. https://doi.org/10.1126/sciadv.abn2748

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bose, D. A., Donahue, G., Reinberg, D., Shiekhattar, R., Bonasio, R., & Berger, S. L. (2017). RNA binding to CBP stimulates histone acetylation and transcription. Cell, 168(1–2), 135–149122. https://doi.org/10.1016/j.cell.2016.12.020

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bullido, M. J., Artiga, M. J., Recuero, M., Sastre, I., Garcia, M. A., Aldudo, J., & Valdivieso, F. (1998). A polymorphism in the regulatory region of APOE associated with risk for Alzheimer’s dementia. Nature Genetics, 18(1), 69–71. https://doi.org/10.1038/ng0198-69

Article  CAS  PubMed  Google Scholar 

Carullo, N. V. N., Phillips Iii, R. A., Simon, R. C., Soto, S. A. R., Hinds, J. E., Salisbury, A. J., & Day, J. J. (2020). Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems. Nucleic Acids Research, 48(17), 9550–9570. https://doi.org/10.1093/nar/gkaa671

Article  CAS  PubMed  PubMed Central  Google Scholar 

Choi, J., Lysakovskaia, K., Stik, G., Demel, C., Soding, J., Tian, T. V., & Cramer, P. (2021). Evidence for additive and synergistic action of mammalian enhancers during cell fate determination. Elife. https://doi.org/10.7554/eLife.65381

Article  PubMed  PubMed Central  Google Scholar 

Consortium, & E. P. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57–74. https://doi.org/10.1038/nature11247

Article  CAS  Google Scholar 

Corradin, O., & Scacheri, P. C. (2014). Enhancer variants: Evaluating functions in common disease. Genome Medicine, 6(10), 85. https://doi.org/10.1186/s13073-014-0085-3

Article  PubMed  PubMed Central  Google Scholar 

Darmanis, S., Sloan, S. A., Zhang, Y., Enge, M., Caneda, C., Shuer, L. M., & Quake, S. R. (2015). A survey of human brain transcriptome diversity at the single cell level. Proceedings of the National Academy of Sciences, 112(23), 7285–7290. https://doi.org/10.1073/pnas.1507125112

Article  CAS  Google Scholar 

Davidson, S., Lear, M., Shanley, L., Hing, B., Baizan-Edge, A., Herwig, A., & MacKenzie, A. (2011). Differential activity by polymorphic variants of a remote enhancer that supports galanin expression in the hypothalamus and amygdala: Implications for obesity, depression and alcoholism. Neuropsychopharmacology, 36(11), 2211–2221. https://doi.org/10.1038/npp.2011.93

Article  CAS  PubMed  PubMed Central  Google Scholar 

de la Torre-Ubieta, L., Stein, J. L., Won, H., Opland, C. K., Liang, D., Lu, D., & Geschwind, D. H. (2018). The dynamic landscape of open chromatin during human cortical neurogenesis. Cell, 172(1–2), 289–304218. https://doi.org/10.1016/j.cell.2017.12.014

Article  CAS  PubMed  PubMed Central  Google Scholar 

De Santa, F., Barozzi, I., Mietton, F., Ghisletti, S., Polletti, S., Tusi, B. K., & Natoli, G. (2010). A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biology, 8(5), e1000384. https://doi.org/10.1371/journal.pbio.1000384

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dharap, A., Bowen, K., Place, R., Li, L. C., & Vemuganti, R. (2009). Transient focal ischemia induces extensive temporal changes in rat cerebral microRNAome. Journal of Cerebral Blood Flow and Metabolism, 29(4), 675–687. https://doi.org/10.1038/jcbfm.2008.157

Article  CAS  PubMed  Google Scholar 

Dharap, A., Nakka, V. P., & Vemuganti, R. (2011). Altered expression of PIWI RNA in the rat brain after transient focal ischemia. Stroke, 42(4), 1105–1109. https://doi.org/10.1161/STROKEAHA.110.598391

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dharap, A., Nakka, V. P., & Vemuganti, R. (2012). Effect of focal ischemia on long noncoding RNAs. Stroke, 43(10), 2800–2802. https://doi.org/10.1161/STROKEAHA.112.669465

Article  CAS  PubMed  PubMed Central  Google Scholar 

Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., & Gingeras, T. R. (2012). Landscape of transcription in human cells. Nature, 489(7414), 101–108. https://doi.org/10.1038/nature11233

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dong, X., Liao, Z., Gritsch, D., Hadzhiev, Y., Bai, Y., Locascio, J. J., & Scherzer, C. R. (2018). Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease. Nature Neuroscience, 21(10), 1482–1492. https://doi.org/10.1038/s41593-018-0223-0

Article  CAS  PubMed  PubMed Central  Google Scholar 

Eckart, N., Song, Q., Yang, R., Wang, R., Zhu, H., McCallion, A. S., & Avramopoulos, D. (2016). Functional characterization of schizophrenia-associated variation in CACNA1C. PLoS ONE, 11(6), e0157086. https://doi.org/10.1371/journal.pone.0157086

Article  CAS  PubMed  PubMed Central  Google Scholar 

Flavell, S. W., & Greenberg, M. E. (2008). Signaling mechanisms linking neuronal activity to gene expression and plasticity of the nervous system. Annual Review of Neuroscience, 31, 563–590. https://doi.org/10.1146/annurev.neuro.31.060407.125631

Article  CAS  PubMed  PubMed Central  Google Scholar 

Francelle, L., Lotz, C., Outeiro, T., Brouillet, E., & Merienne, K. (2017). Contribution of neuroepigenetics to Huntington’s disease. Frontiers in Human Neuroscience, 11, 17. https://doi.org/10.3389/fnhum.2017.00017

Article  CAS  PubMed  PubMed Central  Google Scholar 

Frank, C. L., Liu, F., Wijayatunge, R., Song, L., Biegler, M. T., Yang, M. G., & West, A. E. (2015). Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum. Nature Neuroscience, 18(5), 647–656.

留言 (0)

沒有登入
gif