Xinyu Zhao, PhD – Slide of the Week

Xinyu Zhao, PhD - Slide of the Week

Title: Identification of FMR1-regulated molecular networks in human neurodevelopment

Legend: Generation of FMR1-FLAG hPSCs using one-step seamless genome editing using CRISPR-Cas9, Neural differentiation of hPSCs into forebrain dorsal NPCs (dNPC) and ventral MGE-like NPCs (vNPC), Flow chart of ireCLIP-seq (modified crosslink immunoprecipitation followed by RNA sequencing), Identification of FMRP targets in human neurons

Citation: Li M, Shin J, Risgaard RD, Parries MJ, Wang J, Chasman D, Liu S, Roy S, Bhattacharyya A, Zhao X. (2020).Identification of FMR1-regulated molecular networks in human neurodevelopment.  Genome Res. 2020 Mar;30(3):361-374. doi: 10.1101/gr.251405.119.

Abstract: RNA-binding proteins (RNA-BPs) play critical roles in development and disease to regulate gene expression. However, genome-wide identification of their targets in primary human cells has been challenging. Here, we applied a modified CLIP-seq strategy to identify genome-wide targets of the FMRP translational regulator 1 (FMR1), a brain-enriched RNA-BP, whose deficiency leads to Fragile X Syndrome (FXS), the most prevalent inherited intellectual disability. We identified FMR1 targets in human dorsal and ventral forebrain neural progenitors and excitatory and inhibitory neurons differentiated from human pluripotent stem cells. In parallel, we measured the transcriptomes of the same four cell types upon FMR1 gene deletion. We discovered that FMR1 preferentially binds long transcripts in human neural cells. FMR1 targets include genes unique to human neural cells and associated with clinical phenotypes of FXS and autism. Integrative network analysis using graph diffusion and multitask clustering of FMR1 CLIP-seq and transcriptional targets reveals critical pathways regulated by FMR1 in human neural development. Our results demonstrate that FMR1 regulates a common set of targets among different neural cell types but also operates in a cell type-specific manner targeting distinct sets of genes in human excitatory and inhibitory neural progenitors and neurons. By defining molecular subnetworks and validating specific high-priority genes, we identify novel components of the FMR1 regulation program. Our results provide new insights into gene regulation by a critical neuronal RNA-BP in human neurodevelopment.

About the Lab: Research in the Zhao laboratory focuses on understanding the molecular mechanisms that regulate neural stem cells and neurodevelopment with the goal of applying this knowledge for the treatment of neurological disorders and injuries. Neurodevelopmental disorders are a highly heterogeneous constellation of disorders, both in terms of etiology and clinical manifestations. Using neural stem cells as model systems, the lab is investigating the molecular mechanisms that regulate neuronal development during the postnatal period and their implications in human neurodevelopmental disorders such as Rett syndrome, autism, and fragile X syndrome.

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