ASCOT identifies key regulators of neuronal subtype-specific splicing

Ling, Jonathan P.; Wilks, Christopher; Charles, Rone; Ghosh, Dipak; Jiang, Lizhi; Santiago, Clayton; Pang, Bo; Venkataraman, Anand; Clark, Brian S.; Nellore, Abhinav; Langmead, Ben; Blackshaw, Seth

doi:10.1101/501882

Cited by 19 publications

(46 citation statements)

References 69 publications

(75 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We analyzed the expression of Musashi proteins in various tissues from adult mice. Out of all the tissues we tested, retina showed the highest expression of MSI1 and MSI2 proteins ( Figure 1A), in line with the previously reported high transcript levels for Msi1 and Msi2 in rod photoreceptors (9). Quantitative RT-PCR of Msi1 and Msi2 levels in the tissues shown on Figure 1A further confirmed significantly higher levels of expression of the two transcripts in retina ( Figure 1B).…”

Section: Validation Of the Conditional Knockout Mouse Modelssupporting

confidence: 88%

The Musashi proteins MSI1 and MSI2 are required for photoreceptor morphogenesis and vision in mice

Sundar

Matalkah

Jeong

et al. 2021

Journal of Biological Chemistry

View full text Add to dashboard Cite

The Musashi family of RNA-binding proteins is known for its role in stem-cell renewal and are negative regulators of cell differentiation. Interestingly, in the retina, the Musashi proteins MSI1 and MSI2 are differentially expressed throughout the cycle of retinal development, with MSI2 protein displaying robust expression in the adult retinal tissue. In this study, we investigated the importance of Musashi proteins in the development and function of photoreceptor neurons in the retina. We generated a pan-retinal and rod photoreceptor neuron-specific conditional knockout mouse lacking MSI1 and MSI2. Independent of sex, photoreceptor neurons with simultaneous deletion of Msi1 and Msi2 were unable to respond to light and displayed severely disrupted photoreceptor outer segment morphology and ciliary defects. Mice lacking MSI1 and MSI2 in the retina exhibited neuronal degeneration, with complete loss of photoreceptors within six months. In concordance with our earlier studies that proposed a role for Musashi proteins in regulating alternative splicing, the loss of MSI1 and MSI2 prevented the use of photoreceptor-specific exons in transcripts critical for OS morphogenesis, ciliogenesis and synaptic transmission. Overall, we demonstrate a critical role for Musashi proteins in the morphogenesis of terminally differentiated photoreceptor neurons. This role is in stark contrast with the canonical function of these two proteins in the maintenance and renewal of stem cells.

show abstract

Section: Validation Of the Conditional Knockout Mouse Modelssupporting

confidence: 88%

The Musashi proteins MSI1 and MSI2 are required for photoreceptor morphogenesis and vision in mice

Sundar

Matalkah

Jeong

et al. 2021

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…We analyzed the expression of Musashi proteins in various tissues from adult mice. Out of all the tissues we tested, retina showed the highest expression of MSI1 and MSI2 proteins ( Figure 1A), in line with the previously reported high transcript levels for Msi1 and Msi2 in rod photoreceptors (9). To test the biological significance of Musashi protein expression in the murine retina, we used Cre-LoxP conditional recombination to remove either Msi1, Msi2, or both the Msi1 and Msi2 genes throughout the entire retina and ventral forebrain using the Six3 Cre transgene (26).…”

Section: Validation Of the Conditional Knockout Mouse Modelssupporting

confidence: 90%

“…In addition, Musashi promotes the splicing of several photoreceptor specific exons when over-expressed in cultured cells (8). Recently, analysis of a comprehensive gene expression data set demonstrated that photoreceptors utilize a unique set of alternative exons that are primarily regulated by MSI1 and MSI2 (9).…”

Section: Introductionmentioning

confidence: 99%

A critical role for Musashi in photoreceptor morphogenesis and Vision

Sundar

Matalkah

Jeong

et al. 2020

Preprint

View full text Add to dashboard Cite

23We previously proposed a role for the Musashi proteins, MSI1 and MSI2, in 24 photoreceptor cell development that is mediated by their ability to control alternative splicing. 25 Photoreceptors with simultaneous deletion of Msi1 and Msi2 did not respond to light, displayed 26 severely disrupted OS morphology and axonemal defects. At postnatal day 5, we observed an 27 increase in proliferating retinal progenitor cells in the knockout animals, suggesting delay in 28 photoreceptor development. The loss of Musashi prevented the use of photoreceptor-specific 29 exons in transcripts important for OS morphogenesis, ciliogenesis and synaptic transmission.30 However, deletion of the photoreceptor-specific exons in Ttc8, Cc2d2a, Cep290, Cacna2d4, and 31 Slc17a7 did not impair retinal development or visual function. We demonstrate a critical role for 32 Musashi in the morphogenesis of terminally differentiated photoreceptor neurons. This role is in 33 stark contrast with the canonical function of the two proteins in maintenance and renewal of stem 34 cells. 35 36 37 38 42Alternative splicing is particularly prevalent in vertebrate neurons and is critical for the 43 development and function of vertebrate nervous systems 2-7 . 44 We previously showed that photoreceptor neurons exploit a unique splicing program 8 . 45Motif enrichment analysis suggested that Musashi-1 (MSI1) and Musashi-2 (MSI2), promote the 46 use of photoreceptor specific exons 8 . We further showed that MSI1 is critical for utilization of 47 photoreceptor specific exon in Tetratricopeptide repeat domain protein-8 (Ttc8) 8 . In addition, 48 Musashi promotes the splicing of several photoreceptor specific exons when over-expressed in 49 cultured cells 8 . Recently, analysis of a comprehensive gene expression data set that spanned 50 multiple tissues and cell types from mice and human proved that photoreceptors utilize a unique 51 set of alternative exons that are primarily regulated by MSI1 and MSI2 9 . Furthermore, the work 52 by Ling et. al. demonstrated that Msi1 transcript levels are upregulated in the developing rod 53 photoreceptors and reach exceptionally high levels compared to all other cell types or tissues in 54 the data set. 55 The MSI1 and MSI2 proteins have two highly conserved RNA binding domains (RBDs) 56 in the N-terminal region which show close to 90% sequence identity and recognize a similar 57 UAG motif in RNA 10 . The two RBDs of MSI1 and MSI2 are followed by a less conserved C-58 terminal region which shows approximately 70% sequence identity 11 . The high degree of 59 sequence identity between the MSI1 and MSI2 results in functional redundancy between the two 60 proteins 12,13 . The canonical function of the Musashi proteins is to control mRNA translation in 61 4 the cytosol 14,15 , where they can either block or enhance translation of mRNA depending on 62 cellular context 16-21 . 63 Vertebrate photoreceptors are neurons specialized in detecting and transducing light 64 stimuli. Photoreceptors are characterized by segmented morp...

show abstract

“…In order to identify cells that show adipocyte signatures, key adipocyte-enriched genes were first extracted from GTEx dataset from ascot.cs.jhu.edu, 22 relying on both robustness (NAUC > 20) and specificity (expressed only in both adipocytes dataset or in tissues that are enriched with adipocytes, such as mammary tissues). These genes were then used to train the dataset using Garnett 23 to identify differentiated adipocytes.…”

Section: Single-nucleus Rna-seqmentioning

confidence: 99%

Transcriptomic Profiling of Control and Thyroid-Associated Orbitopathy (TAO) Orbital Fat and TAO Orbital Fibroblasts Undergoing Adipogenesis

Kim

Taneja

Hoang

et al. 2021

Invest. Ophthalmol. Vis. Sci.

Self Cite

View full text Add to dashboard Cite

PURPOSE.Orbital fat hyperplasia commonly occurs in thyroid-associated orbitopathy (TAO). To understand molecular mechanisms underlying orbital adipogenesis, we used transcriptomics to compare gene expression in controls and patients with TAO, as well as in orbital fibroblasts (OFs) undergoing adipogenic differentiation. METHODS.We performed bulk RNA sequencing (RNA-Seq) on intraconal orbital fat from controls and patients with TAO. We treated cultured OFs derived from patients with TAO with adipogenic media to induce adipogenesis. We used single nucleus RNA-Seq (snRNA-Seq) to profile treated and control OFs, identifying genes that are dynamically expressed during orbital adipogenesis in vitro, and compared these results to data from control and TAO orbital fat. RESULTS.Gene expression profiles in control and TAO orbital fat are distinct. Signaling pathways including PI3K-Akt signaling, cAMP signaling, AGE-RAGE signaling, regulation of lipolysis, and thyroid hormone signaling are enriched in orbital fat isolated from patients with TAO. SnRNA-Seq of orbital fibroblasts undergoing adipogenesis reveals differential expression of the adipocyte-specific genes FABP4/5, APOE, PPARG, and ADIPOQ during adipogenic differentiation. The insulin-like growth factor-1 receptor and Wnt signaling pathways appear to be enriched early in adipogenesis. Gene modules that are enriched in TAO orbital fat are upregulated in orbital adipocytes during differentiation in vitro, whereas genes that are enriched in control orbital fat are enriched in undifferentiated OFs. CONCLUSIONS.We identified pathways enriched in TAO orbital fat, and dynamic changes in gene expression that occur during adipogenic differentiation of orbital fibroblasts. These findings may help guide functional studies of genes and pathways critical for orbital adipogenesis.

show abstract

ASCOT identifies key regulators of neuronal subtype-specific splicing

Cited by 19 publications

References 69 publications

The Musashi proteins MSI1 and MSI2 are required for photoreceptor morphogenesis and vision in mice

The Musashi proteins MSI1 and MSI2 are required for photoreceptor morphogenesis and vision in mice

A critical role for Musashi in photoreceptor morphogenesis and Vision

Transcriptomic Profiling of Control and Thyroid-Associated Orbitopathy (TAO) Orbital Fat and TAO Orbital Fibroblasts Undergoing Adipogenesis

Contact Info

Product

Resources

About