A Novel Cis-Regulatory lncRNA, <i>Kalnc2</i>, Downregulates <i>Kalrn</i> Protein-Coding Transcripts in Mouse Neuronal Cells
The <i>KALRN</i> gene encodes several multi-domain protein isoforms that localize to neuronal synapses, conferring the ability to grow and retract dendritic spines and shaping axonal outgrowth, dendrite morphology, and dendritic spine re-modeling. The <i>KALRN</i> genomic loc...
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MDPI AG
2023-01-01
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| Series: | Non-Coding RNA |
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| Online Access: | https://www.mdpi.com/2311-553X/9/1/7 |
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| author | Muneesh Pal Divya Chaubey Mohit Tanwar Beena Pillai |
| author_facet | Muneesh Pal Divya Chaubey Mohit Tanwar Beena Pillai |
| author_sort | Muneesh Pal |
| collection | DOAJ |
| description | The <i>KALRN</i> gene encodes several multi-domain protein isoforms that localize to neuronal synapses, conferring the ability to grow and retract dendritic spines and shaping axonal outgrowth, dendrite morphology, and dendritic spine re-modeling. The <i>KALRN</i> genomic locus is implicated in several neurodevelopmental and neuropsychiatric diseases, including autism, schizophrenia, bipolar disease, and intellectual disability. We have previously shown that a novel brain-specific long non-coding RNA (lncRNA) arising from the 5′ end of the <i>kalrna</i> gene, called <i>durga</i>, regulates neuronal morphology in zebrafish. Here, we characterized mammalian <i>Kalrn</i> loci, annotating and experimentally validating multiple novel non-coding RNAs, including linear and circular variants. Comparing the mouse and human loci, we show that certain non-coding RNAs and <i>Kalrn</i> protein-coding isoforms arising from the locus show similar expression dynamics during development. In humans, mice, and zebrafish, the 5′ end of the <i>Kalrn</i> locus gives rise to a chromatin-associated lncRNA that is present in adult ovaries, besides being expressed during brain development and enriched in certain regions of the adult brain. Ectopic expression of this lncRNA led to the downregulation of all the major <i>Kalrn</i> mRNA isoforms. We propose that this lncRNA arising from the 5′ end of the <i>Kalrn</i> locus is functionally the mammalian ortholog of zebrafish lncRNA <i>durga</i>. |
| first_indexed | 2024-03-11T08:20:08Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2311-553X |
| language | English |
| last_indexed | 2024-03-11T08:20:08Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Non-Coding RNA |
| spelling | doaj.art-ac6f91ce3a204e649890f177e644b91e2023-11-16T22:28:57ZengMDPI AGNon-Coding RNA2311-553X2023-01-0191710.3390/ncrna9010007A Novel Cis-Regulatory lncRNA, <i>Kalnc2</i>, Downregulates <i>Kalrn</i> Protein-Coding Transcripts in Mouse Neuronal CellsMuneesh Pal0Divya Chaubey1Mohit Tanwar2Beena Pillai3CSIR-Institute of Genomics and Integrative Biology, Delhi 110025, IndiaCSIR-Institute of Genomics and Integrative Biology, Delhi 110025, IndiaCSIR-Institute of Genomics and Integrative Biology, Delhi 110025, IndiaCSIR-Institute of Genomics and Integrative Biology, Delhi 110025, IndiaThe <i>KALRN</i> gene encodes several multi-domain protein isoforms that localize to neuronal synapses, conferring the ability to grow and retract dendritic spines and shaping axonal outgrowth, dendrite morphology, and dendritic spine re-modeling. The <i>KALRN</i> genomic locus is implicated in several neurodevelopmental and neuropsychiatric diseases, including autism, schizophrenia, bipolar disease, and intellectual disability. We have previously shown that a novel brain-specific long non-coding RNA (lncRNA) arising from the 5′ end of the <i>kalrna</i> gene, called <i>durga</i>, regulates neuronal morphology in zebrafish. Here, we characterized mammalian <i>Kalrn</i> loci, annotating and experimentally validating multiple novel non-coding RNAs, including linear and circular variants. Comparing the mouse and human loci, we show that certain non-coding RNAs and <i>Kalrn</i> protein-coding isoforms arising from the locus show similar expression dynamics during development. In humans, mice, and zebrafish, the 5′ end of the <i>Kalrn</i> locus gives rise to a chromatin-associated lncRNA that is present in adult ovaries, besides being expressed during brain development and enriched in certain regions of the adult brain. Ectopic expression of this lncRNA led to the downregulation of all the major <i>Kalrn</i> mRNA isoforms. We propose that this lncRNA arising from the 5′ end of the <i>Kalrn</i> locus is functionally the mammalian ortholog of zebrafish lncRNA <i>durga</i>.https://www.mdpi.com/2311-553X/9/1/7<i>Kalrn</i>lncRNA<i>durga</i>neurondendritechromatin |
| spellingShingle | Muneesh Pal Divya Chaubey Mohit Tanwar Beena Pillai A Novel Cis-Regulatory lncRNA, <i>Kalnc2</i>, Downregulates <i>Kalrn</i> Protein-Coding Transcripts in Mouse Neuronal Cells Non-Coding RNA <i>Kalrn</i> lncRNA <i>durga</i> neuron dendrite chromatin |
| title | A Novel Cis-Regulatory lncRNA, <i>Kalnc2</i>, Downregulates <i>Kalrn</i> Protein-Coding Transcripts in Mouse Neuronal Cells |
| title_full | A Novel Cis-Regulatory lncRNA, <i>Kalnc2</i>, Downregulates <i>Kalrn</i> Protein-Coding Transcripts in Mouse Neuronal Cells |
| title_fullStr | A Novel Cis-Regulatory lncRNA, <i>Kalnc2</i>, Downregulates <i>Kalrn</i> Protein-Coding Transcripts in Mouse Neuronal Cells |
| title_full_unstemmed | A Novel Cis-Regulatory lncRNA, <i>Kalnc2</i>, Downregulates <i>Kalrn</i> Protein-Coding Transcripts in Mouse Neuronal Cells |
| title_short | A Novel Cis-Regulatory lncRNA, <i>Kalnc2</i>, Downregulates <i>Kalrn</i> Protein-Coding Transcripts in Mouse Neuronal Cells |
| title_sort | novel cis regulatory lncrna i kalnc2 i downregulates i kalrn i protein coding transcripts in mouse neuronal cells |
| topic | <i>Kalrn</i> lncRNA <i>durga</i> neuron dendrite chromatin |
| url | https://www.mdpi.com/2311-553X/9/1/7 |
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