PMID- 25556833 OWN - NLM STAT- MEDLINE VI - 85 IP - 2 TI - DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex. PG - 275-288 CI - Copyright © 2015 Elsevier Inc. All rights reserved. LA - eng PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Neuron JT - Neuron JID - 8809320 IS - 1097-4199 (Electronic) LID - 10.1016/j.neuron.2014.12.024 [doi] FAU - Molyneaux, Bradley J AU - Molyneaux BJ AD - Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States. FAU - Goff, Loyal A AU - Goff LA AD - Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States. AD - Broad Institute of MIT and Harvard, Cambridge, MA, 02139, United States. AD - Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States. FAU - Brettler, Andrea C AU - Brettler AC AD - Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States. FAU - Chen, Hsu-Hsin AU - Chen HH AD - Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States. FAU - Hrvatin, Siniša AU - Hrvatin S AD - Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States. FAU - Rinn, John L AU - Rinn JL AD - Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States. AD - Broad Institute of MIT and Harvard, Cambridge, MA, 02139, United States. AD - Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, United States. FAU - Arlotta, Paola AU - Arlotta P AD - Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States. AD - Broad Institute of MIT and Harvard, Cambridge, MA, 02139, United States. IS - 0896-6273 (Linking) RN - 0 (Bcl11b protein, mouse) RN - 0 (Matrix Attachment Region Binding Proteins) RN - 0 (RNA, Long Noncoding) RN - 0 (RNA, Messenger) RN - 0 (Repressor Proteins) RN - 0 (SATB2 protein, mouse) RN - 0 (Tle4 protein, mouse) RN - 0 (Transcription Factors) RN - 0 (Tumor Suppressor Proteins) SB - IM MH - Animals MH - Base Sequence MH - Cell Differentiation/*genetics MH - Corpus Callosum/cytology MH - Flow Cytometry MH - Gene Expression Profiling MH - Gene Expression Regulation, Developmental/*genetics MH - Matrix Attachment Region Binding Proteins/metabolism MH - Mice MH - Molecular Sequence Data MH - Motor Neurons MH - Neocortex/*metabolism MH - Neurogenesis/genetics MH - Neurons/metabolism MH - Pyramidal Cells/*metabolism MH - Pyramidal Tracts/cytology MH - RNA, Long Noncoding/*genetics MH - RNA, Messenger/*genetics MH - Repressor Proteins/metabolism MH - Transcription Factors/metabolism MH - *Transcriptome MH - Tumor Suppressor Proteins/metabolism PMC - PMC4430475 DCOM- 20150324 LR - 20181113 DP - 2015 Jan 21 DEP - 20141231 AB - UNLABELLED: Neuronal development requires a complex choreography of transcriptional decisions to obtain specific cellular identities. Realizing the ultimate goal of identifying genome-wide signatures that define and drive specific neuronal fates has been hampered by enormous complexity in both time and space during development. Here, we have paired high-throughput purification of pyramidal neuron subclasses with deep profiling of spatiotemporal transcriptional dynamics during corticogenesis to resolve lineage choice decisions. We identified numerous features ranging from spatial and temporal usage of alternative mRNA isoforms and promoters to a host of mRNA genes modulated during fate specification. Notably, we uncovered numerous long noncoding RNAs with restricted temporal and cell-type-specific expression. To facilitate future exploration, we provide an interactive online database to enable multidimensional data mining and dissemination. This multifaceted study generates a powerful resource and informs understanding of the transcriptional regulation underlying pyramidal neuron diversity in the neocortex. VIDEO ABSTRACT: