Developing Human Brain Transcript Browser

To get started with the browser, begin typing the name of a gene of interest above. Genes for which data is available will be suggested in a drop-down list. Upon submitting a gene name, two tabs for bulk and single cell datasets will become accessible. Several options affecting the display of the transcript isoforms are available; please hover over the info icons to learn more. Some options are specific to one or the other tab and will be grayed out if they do not apply to the current view.

Both the bulk and single cell datasets come from full-length, long-read sequencing (PacBio Iso-Seq) of the developing human neocortex at mid-gestation (six unique donors, post-conception weeks 15-17). Tissue was microdissected into the cortical plate (CP) and germinal zone (GZ) regions. The single cell dataset consists of 4,281 single cells with barcodes matched to previous short-read sequencing of the same libraries. Single cell barcodes were matched to 16 cell-type clusters previously identified from short-read (gene-based clustering) or used to identify 15 distinct cell-type clusters based on long-read as part of this study (isoform-based clustering).

Bug reports, questions, and comments regarding this web app are welcome and may be directed to:

Connor Jops

connor.jops@pennmedicine.upenn.edu

Cell-type-specificity of isoform diversity in the developing human neocortex informs mechanisms of neurodevelopmental disorders

Ashok Patowary⁺, Pan Zhang⁺, Connor Jops⁺, Celine K. Vuong, Xinzhu Ge, Kangcheng Hou, Minsoo Kim, Naihua Gong, Michael Margolis, Daniel Vo, Xusheng Wang, Chunyu Liu, Bogdan Pasaniuc, Jingyi Jessica Li, Michael J. Gandal^*, Luis de la Torre-Ubieta^*

Human brain development is under tight molecular genetic control and the recent advent of single-cell genomics has revolutionized our ability to elucidate the diverse underlying cell-types and states. Although RNA splicing is highly prevalent in the brain and has strong links to neuropsychiatric disorders, previous work has not systematically investigated the role of cell-type-specific splicing or transcript-isoform diversity during human brain development. Here, we leverage single molecule long-read sequencing to deeply profile the full-length transcriptome of the germinal zone (GZ) and cortical plate (CP) regions of the developing human neocortex at tissue and single-cell resolution. We identify 214,516 unique isoforms, corresponding to 22,391 genes. Remarkably, we find that 72.6% of these are novel and together with >7,000 novel-spliced exons expands the proteome by 92,422 proteoforms. We uncover myriad novel isoform switches during cortical neurogenesis, implicating previously-uncharacterized RNA-binding protein-mediated and other regulatory mechanisms in cellular identity and disease. Early-stage excitatory neurons exhibit the greatest isoform diversity and isoform-based single-cell clustering identifies previously uncharacterized cell states. Leveraging this resource, we re-prioritize thousands of rare de novo risk variants associated with neurodevelopmental disorders (NDDs) and reveal that risk genes are strongly associated with the number of unique isoforms observed per gene. Altogether, this work uncovers a substantial contribution of transcript-isoform diversity in cellular identity in the developing neocortex, elucidates novel genetic risk mechanisms for neurodevelopmental and neuropsychiatric disorders, and provides a comprehensive isoform-centric gene annotation for the developing human brain.