Specialization of the photoreceptor transcriptome by Srrm3-dependent microexons is required for outer segment maintenance and vision

ABSTRACTRetinal photoreceptors differ in their transcriptomic profiles from other neuronal subtypes, likely as a reflection of their unique cellular morphology and function in the detection of light thorough the ciliary outer segment. We discovered a new layer of this molecular specialization by revealing that the vertebrate retina expresses the largest number of tissue-enriched microexons of all tissue types. A subset of these microexons is included exclusively in photoreceptor transcripts, particularly in genes involved in cilia biogenesis and in vesicle-mediated transport. This microexon program is regulated by Srrm3, a paralog of the neural microexon regulator Srrm4. Despite both proteins positively regulate retina microexons in vitro, only Srrm3 is highly expressed in mature photoreceptors and its deletion in zebrafish results in widespread downregulation of microexon inclusion, severe photoreceptor alterations and blindness. These results shed light into photoreceptor’s transcriptomic specialization and functionality, uncovering new cell type-specific roles for Srrm3 and microexons with implication for retinal diseases.

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Btbd11 is an inhibitory interneuron specific synaptic scaffolding protein that supports excitatory synapse structure and function

10.1101/2021.11.01.466782 ◽

2021 ◽

Author(s):

Alexei M. Bygrave ◽

Ayesha Sengupta ◽

Ella P. Jackert ◽

Mehroz Ahmed ◽

Beloved Adenuga ◽

...

Keyword(s):

Inhibitory Interneuron ◽

Nmda Receptor Antagonist ◽

Specific Protein ◽

Network Activity ◽

Scaffolding Protein ◽

Inhibitory Interneurons ◽

Cell Type ◽

Cell Type Specific

Synapses in the brain exhibit cell–type–specific differences in basal synaptic transmission and plasticity. Here, we evaluated cell–type–specific differences in the composition of glutamatergic synapses, identifying Btbd11, as an inhibitory interneuron–specific synapse–enriched protein. Btbd11 is highly conserved across species and binds to core postsynaptic proteins including Psd–95. Intriguingly, we show that Btbd11 can undergo liquid–liquid phase separation when expressed with Psd–95, supporting the idea that the glutamatergic post synaptic density in synapses in inhibitory and excitatory neurons exist in a phase separated state. Knockout of Btbd11 from inhibitory interneurons decreased glutamatergic signaling onto parvalbumin–positive interneurons. Further, both in vitro and in vivo, we find that Btbd11 knockout disrupts network activity. At the behavioral level, Btbd11 knockout from interneurons sensitizes mice to pharmacologically induced hyperactivity following NMDA receptor antagonist challenge. Our findings identify a cell–type–specific protein that supports glutamatergic synapse function in inhibitory interneurons–with implication for circuit function and animal behavior.

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Profound functional and molecular diversity of mitochondria revealed by cell type-specific profiling in vivo

10.1101/403774 ◽

2018 ◽

Cited By ~ 1

Author(s):

Caroline Fecher ◽

Laura Trovò ◽

Stephan A. Müller ◽

Nicolas Snaidero ◽

Jennifer Wettmarshausen ◽

...

Keyword(s):

Molecular Diversity ◽

Molecular Level ◽

Cell Types ◽

Long Chain Fatty Acids ◽

Cell Type ◽

Mitochondrial Proteome ◽

Novel Approach ◽

Cell Type Specific ◽

And Function

AbstractMitochondria vary in morphology and function in different tissues, however little is known about their molecular diversity among cell types. To investigate mitochondrial diversity in vivo, we developed an efficient protocol to isolate cell type-specific mitochondria based on a new MitoTag mouse. We profiled the mitochondrial proteome of three major neural cell types in cerebellum and identified a substantial number of differential mitochondrial markers for these cell types in mice and humans. Based on predictions from these proteomes, we demonstrate that astrocytic mitochondria metabolize long-chain fatty acids more efficiently than neurons. Moreover, we identified Rmdn3 as a major determinant of ER-mitochondria proximity in Purkinje cells. Our novel approach enables exploring mitochondrial diversity on the functional and molecular level in many in vivo contexts.

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Identification of the cell-type-specific ER membrane protein Tanmp expressed in hypothalamic tanycytes and subsets of neurons

10.1101/2021.07.06.451253 ◽

2021 ◽

Author(s):

Osamu Takahashi ◽

Mayuko Tanahashi ◽

Saori Yokoi ◽

Mari Kaneko ◽

Tomoko Tokuhara ◽

...

Keyword(s):

Third Ventricle ◽

Functional Domains ◽

Mitochondrial Atpase ◽

Cell Type ◽

Rna Probes ◽

Cell Type Specific ◽

Ventral Wall ◽

Fine Morphology ◽

Normal Laboratory

Genomes of higher eukaryotes encode many uncharacterized proteins, and the functions of these proteins cannot be predicted from the primary sequences due to a lack of conserved functional domains. During a screening of novel noncoding RNAs abundantly expressed in mouse brains, we incidentally identified a gene termed Tanmp, which encoded an endoplasmic reticulum (ER) protein without known functional domains. Tanmp is specifically expressed in the nervous system, and the highest expression was observed in a specialized cell type called tanycyte that aligns the ventral wall of the third ventricle in the hypothalamus. Immunostaining of Tanmp revealed the fine morphology of tanycytes with highly branched apical ER membranes. Immunoprecipitation revealed that Tanmp associates with mitochondrial ATPase at least in vitro, and ER and mitochondrial signals occasionally overlapped in tanycytes. Mutant mice lacking Tanmp did not exhibit overt phenotypes, suggesting that Tanmp is not essential in mice reared under normal laboratory conditions. We also found that RNA probes that are predicted to uniquely detect Tanmp mRNA cross-reacted with uncharacterized RNAs, highlighting the importance of experimental validation of the specificity of probes during the hybridization-based study of RNA localization.

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Cell-type Specific Protoporphyrin IX Metabolism in Human Bladder Cancer in vitro¶

Photochemistry and Photobiology ◽

10.1562/0031-8655(2000)072<0226:ctspim>2.0.co;2 ◽

2000 ◽

Vol 72 (2) ◽

pp. 226 ◽

Cited By ~ 84

Author(s):

René C. Krieg ◽

Sonja Fickweiler ◽

Otto S. Wolfbeis ◽

Ruth Knuechel

Keyword(s):

Bladder Cancer ◽

Protoporphyrin Ix ◽

Human Bladder Cancer ◽

Cell Type ◽

Human Bladder ◽

Cell Type Specific

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Revisiting the role of IRF3 in inflammation and immunity by conditional and specifically targeted gene ablation in mice

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1803936115 ◽

2018 ◽

Vol 115 (20) ◽

pp. 5253-5258 ◽

Cited By ~ 19

Author(s):

Hideyuki Yanai ◽

Shiho Chiba ◽

Sho Hangai ◽

Kohei Kometani ◽

Asuka Inoue ◽

...

Keyword(s):

Immune Cell ◽

Cell Types ◽

Type I ◽

Type I Ifn ◽

Cell Type ◽

Gene Ablation ◽

Cell Type Specific

IFN regulatory factor 3 (IRF3) is a transcription regulator of cellular responses in many cell types that is known to be essential for innate immunity. To confirm IRF3’s broad role in immunity and to more fully discern its role in various cellular subsets, we engineered Irf3-floxed mice to allow for the cell type-specific ablation of Irf3. Analysis of these mice confirmed the general requirement of IRF3 for the evocation of type I IFN responses in vitro and in vivo. Furthermore, immune cell ontogeny and frequencies of immune cell types were unaffected when Irf3 was selectively inactivated in either T cells or B cells in the mice. Interestingly, in a model of lipopolysaccharide-induced septic shock, selective Irf3 deficiency in myeloid cells led to reduced levels of type I IFN in the sera and increased survival of these mice, indicating the myeloid-specific, pathogenic role of the Toll-like receptor 4–IRF3 type I IFN axis in this model of sepsis. Thus, Irf3-floxed mice can serve as useful tool for further exploring the cell type-specific functions of this transcription factor.

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Retinal Diseases with Ciliopathies

Güncel Retina Dergisi (Current Retina Journal) ◽

10.37783/crj-0270 ◽

2021 ◽

pp. 271-278

Keyword(s):

Retinitis Pigmentosa ◽

Outer Segment ◽

Usher Syndrome ◽

Joubert Syndrome ◽

Retinal Diseases ◽

Bardet Biedl Syndrome ◽

Retinal Photoreceptors ◽

Underlying Mechanisms ◽

Larsson Syndrome ◽

Functional Defects

Ciliopathies are a group of diseases that affects cells containing the cilia organel. Retinal involvement is frequent in ciliopathies. The outer segment of retinal photoreceptors is composed of the cilium. Functional defects limited to the photoreceptors cilia, in particular, are classified as non-syndromic ciliopathies like Leber congenital amaurosis and retinitis pigmentosa. Photoreceptor disease also manifests as a part of syndromic ciliopathies with the involvement of multiple tissues as Usher syndrome, Joubert syndrome, Meckel-Gruber syndrome, Senior-Loken syndrome, Sjögren-Larsson syndrome, Bardet-Biedl syndrome, and Alstrom syndrome. Underlying mechanisms of pathology remain largely unclear in these diseases. Symptoms are treated using current methods. This paper describes the pathogenesis, clinics, diagnosis, and treatment of retinal diseases occurring due to ciliopathy.

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