Daniel Lim, MD, PhD

Professor in Residence
Department of Neurosurgery
Research Overview: 

Chromatin regulators in neural development and disease

The ability of stem cells to self-renew and produce multiple daughter cell lineages requires the expression of certain sets of genes, repression of other loci, and transcriptional “plasticity” of many others. In normal development, such genome-wide transcriptional programs are in part regulated by chromatin structure – the “packaged” state of DNA with histone proteins. Genomic studies of neurodevelopmental and psychiatric disorders have revealed mutations in many chromatin regulators. Furthermore, chromatin regulators are frequently mutated or aberrantly expressed in brain tumors.

The Polycomb group (PcG) and trithorax group (trxG) factors are part of an evolutionarily conserved cellular “memory” system that specify cell identity by regulating the chromatin state of specific loci. We found that trxG member MLL1 is required for neurogenesis – but not gliogenesis – from neural stem cells (NSCs) in the adult mouse brain ventricular-subventricular zone (V-SVZ) (Lim, Nature, 2009; Potts, Neurosurgery, 2014). Without MLL1, key neurogenic genes are enriched with histone-3 lysine-27 trimethylation (H3K27me3), a chromatin modification that correlates with local transcriptional repression. In our studies of EZH2 – a PcG factor that catalyzes H3K27me3 – it does not appear that EZH2 is downregulated during neurogenesis (Hwang, eLIFE, 2014), suggesting that active removal of H3K27me3 is required for transcriptional activation. In support of this model, we discovered that the H3K27-demethylase JMJD3 is required for V-SVZ neurogenesis, de-repressing the chromatin state of transcriptional promoters and enhancers of neurogenic genes (Park, Cell Rep., 2014). Interestingly, in Mll1-deleted V-SVZ cells, JMJD3 does not localize to a key neurogenic enhancer, suggesting that MLL1 is required for the local recruitment of this H3K27-demethylase. Understanding the potential physical interactions between MLL1, JMJD3, and EZH2 at promoters and enhancers, and whether these factors interact with transcription factors for targeting to specific DNA regions represent current mechanistic research aims. Based on our studies of these chromatin regulators as well as Ink4a/Arf (Price, J Neurosci., 2014) – the locus most frequently inactivated in brain tumors – we are now working to determine whether these chromatin regulators are ideal therapeutic targets.

The brain develops from NSCs that have distinct regional identities, and defects in the positional information of NSCs result in abnormal brain development. Mutations in MLL1 have been identified as a cause of Wiedemann-Steiner syndrome, a disorder that includes developmental delay and autism. Our current data suggest that MLL1 maintains NSC regional identity during embryonic brain growth. The mechanisms that enable the “scaling” of developmental patterns during tissue growth are poorly understood. Given that the human brain grows to a very large size, the mechanisms of scaling are especially relevant to our understanding of human neurodevelopmental disorders.

Long non-coding RNAs (lncRNAs) in neural development

The mammalian genome transcribes many thousands of lncRNAs – transcripts >200 nucleotides long with no evidence of protein codingpotential, and it is now clear that lncRNAs can have critical biological functions and roles in human neurological disease. Many lncRNAs interact with chromatin regulators and appear to regulate their function. In our recent annotation and genome-wide analysis of lncRNAs in the adult V-SVZ (Ramos et al, Cell Stem Cell 2013), we identified Pnky, a novel lncRNA transcript that is a potent regulator of neural stem cells in the embryonic and postnatal brain (Ramos, Andersen et al., Cell Stem Cell 2015). Using mass spectrometry, Western blot, and RNA immunoprecipitation analysis, we identified proteins that specifically interact with this lncRNA. We are continuing to determine the function of this lncRNA in vivo and the molecular mechanisms by which it regulates neurogenesis.

Primary Thematic Area: 
Developmental & Stem Cell Biology
Secondary Thematic Area: 
Cancer Biology & Cell Signaling
Research Summary: 
Chromatin regulators and long noncoding RNAs (lncRNAs) in neural development and disease


Featured Publications: 

Maintenance of neural stem cell positional identity by mixed-lineage leukemia 1.

Science (New York, N.Y.)

Delgado RN, Mansky B, Ahanger SH, Lu C, Andersen RE, Dou Y, Alvarez-Buylla A, Lim DA

CRISPRi-based radiation modifier screen identifies long non-coding RNA therapeutic targets in glioma.

Genome biology

Liu SJ, Malatesta M, Lien BV, Saha P, Thombare SS, Hong SJ, Pedraza L, Koontz M, Seo K, Horlbeck MA, He D, Birk HS, Jain M, Olsen HE, Akeson M, Weissman JS, Monje M, Gupta N, Raleigh DR, Ullian EM, Lim DA

The Long Noncoding RNA Pnky Is a Trans-acting Regulator of Cortical Development In Vivo.

Developmental cell

Andersen RE, Hong SJ, Lim JJ, Cui M, Harpur BA, Hwang E, Delgado RN, Ramos AD, Liu SJ, Blencowe BJ, Lim DA

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells.

Science (New York, N.Y.)

Liu SJ, Horlbeck MA, Cho SW, Birk HS, Malatesta M, He D, Attenello FJ, Villalta JE, Cho MY, Chen Y, Mandegar MA, Olvera MP, Gilbert LA, Conklin BR, Chang HY, Weissman JS, Lim DA

The long noncoding RNA Pnky regulates neuronal differentiation of embryonic and postnatal neural stem cells.

Cell stem cell

Ramos AD, Andersen RE, Liu SJ, Nowakowski TJ, Hong SJ, Gertz C, Salinas RD, Zarabi H, Kriegstein AR, Lim DA