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Bidirectional Analysis of Cryba4-Crybb1 Nascent Transcription and Nuclear Accumulation of Crybb3 mRNAs in Lens Fibers
PURPOSE: Crystallin gene expression during lens fiber cell differentiation is tightly spatially and temporally regulated. A significant fraction of mammalian genes is transcribed from adjacent promoters in opposite directions (“bidirectional” promoters). It is not known whether two proximal genes lo...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Association for Research in Vision and Ophthalmology
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6336207/ https://www.ncbi.nlm.nih.gov/pubmed/30646012 http://dx.doi.org/10.1167/iovs.18-25921 |
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author | Limi, Saima Zhao, Yilin Guo, Peng Lopez-Jones, Melissa Zheng, Deyou Singer, Robert H. Skoultchi, Arthur I. Cvekl, Ales |
author_facet | Limi, Saima Zhao, Yilin Guo, Peng Lopez-Jones, Melissa Zheng, Deyou Singer, Robert H. Skoultchi, Arthur I. Cvekl, Ales |
author_sort | Limi, Saima |
collection | PubMed |
description | PURPOSE: Crystallin gene expression during lens fiber cell differentiation is tightly spatially and temporally regulated. A significant fraction of mammalian genes is transcribed from adjacent promoters in opposite directions (“bidirectional” promoters). It is not known whether two proximal genes located on the same allele are simultaneously transcribed. METHODS: Mouse lens transcriptome was analyzed for paired genes whose transcriptional start sites are separated by less than 5 kbp to identify coexpressed bidirectional promoter gene pairs. To probe these transcriptional mechanisms, nascent transcription of Cryba4, Crybb1, and Crybb3 genes from gene-rich part of chromosome 5 was visualized by RNA fluorescent in situ hybridizations (RNA FISH) in individual lens fiber cell nuclei. RESULTS: Genome-wide lens transcriptome analysis by RNA-seq revealed that the Cryba4-Crybb1 pair has the highest Pearson correlation coefficient between their steady-state mRNA levels. Analysis of Cryba4 and Crybb1 nascent transcription revealed frequent simultaneous expression of both genes from the same allele. Nascent Crybb3 transcript visualization in “early” but not “late” differentiating lens fibers show nuclear accumulation of the spliced Crybb3 transcripts that was not affected in abnormal lens fiber cell nuclei depleted of chromatin remodeling enzyme Snf2h (Smarca5). CONCLUSIONS: The current study shows for the first time that two highly expressed lens crystallin genes, Cryba4 and Crybb1, can be simultaneously transcribed from adjacent bidirectional promoters and do not show nuclear accumulation. In contrast, spliced Crybb3 mRNAs transiently accumulate in early lens fiber cell nuclei. The gene pairs coexpressed during lens development showed significant enrichment in human “cataract” phenotype. |
format | Online Article Text |
id | pubmed-6336207 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | The Association for Research in Vision and Ophthalmology |
record_format | MEDLINE/PubMed |
spelling | pubmed-63362072019-01-22 Bidirectional Analysis of Cryba4-Crybb1 Nascent Transcription and Nuclear Accumulation of Crybb3 mRNAs in Lens Fibers Limi, Saima Zhao, Yilin Guo, Peng Lopez-Jones, Melissa Zheng, Deyou Singer, Robert H. Skoultchi, Arthur I. Cvekl, Ales Invest Ophthalmol Vis Sci Biochemistry and Molecular Biology PURPOSE: Crystallin gene expression during lens fiber cell differentiation is tightly spatially and temporally regulated. A significant fraction of mammalian genes is transcribed from adjacent promoters in opposite directions (“bidirectional” promoters). It is not known whether two proximal genes located on the same allele are simultaneously transcribed. METHODS: Mouse lens transcriptome was analyzed for paired genes whose transcriptional start sites are separated by less than 5 kbp to identify coexpressed bidirectional promoter gene pairs. To probe these transcriptional mechanisms, nascent transcription of Cryba4, Crybb1, and Crybb3 genes from gene-rich part of chromosome 5 was visualized by RNA fluorescent in situ hybridizations (RNA FISH) in individual lens fiber cell nuclei. RESULTS: Genome-wide lens transcriptome analysis by RNA-seq revealed that the Cryba4-Crybb1 pair has the highest Pearson correlation coefficient between their steady-state mRNA levels. Analysis of Cryba4 and Crybb1 nascent transcription revealed frequent simultaneous expression of both genes from the same allele. Nascent Crybb3 transcript visualization in “early” but not “late” differentiating lens fibers show nuclear accumulation of the spliced Crybb3 transcripts that was not affected in abnormal lens fiber cell nuclei depleted of chromatin remodeling enzyme Snf2h (Smarca5). CONCLUSIONS: The current study shows for the first time that two highly expressed lens crystallin genes, Cryba4 and Crybb1, can be simultaneously transcribed from adjacent bidirectional promoters and do not show nuclear accumulation. In contrast, spliced Crybb3 mRNAs transiently accumulate in early lens fiber cell nuclei. The gene pairs coexpressed during lens development showed significant enrichment in human “cataract” phenotype. The Association for Research in Vision and Ophthalmology 2019-01 /pmc/articles/PMC6336207/ /pubmed/30646012 http://dx.doi.org/10.1167/iovs.18-25921 Text en Copyright 2019 The Authors 2018 http://creativecommons.org/licenses/by-nc-nd/4.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. |
spellingShingle | Biochemistry and Molecular Biology Limi, Saima Zhao, Yilin Guo, Peng Lopez-Jones, Melissa Zheng, Deyou Singer, Robert H. Skoultchi, Arthur I. Cvekl, Ales Bidirectional Analysis of Cryba4-Crybb1 Nascent Transcription and Nuclear Accumulation of Crybb3 mRNAs in Lens Fibers |
title | Bidirectional Analysis of Cryba4-Crybb1 Nascent Transcription and Nuclear Accumulation of Crybb3 mRNAs in Lens Fibers |
title_full | Bidirectional Analysis of Cryba4-Crybb1 Nascent Transcription and Nuclear Accumulation of Crybb3 mRNAs in Lens Fibers |
title_fullStr | Bidirectional Analysis of Cryba4-Crybb1 Nascent Transcription and Nuclear Accumulation of Crybb3 mRNAs in Lens Fibers |
title_full_unstemmed | Bidirectional Analysis of Cryba4-Crybb1 Nascent Transcription and Nuclear Accumulation of Crybb3 mRNAs in Lens Fibers |
title_short | Bidirectional Analysis of Cryba4-Crybb1 Nascent Transcription and Nuclear Accumulation of Crybb3 mRNAs in Lens Fibers |
title_sort | bidirectional analysis of cryba4-crybb1 nascent transcription and nuclear accumulation of crybb3 mrnas in lens fibers |
topic | Biochemistry and Molecular Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6336207/ https://www.ncbi.nlm.nih.gov/pubmed/30646012 http://dx.doi.org/10.1167/iovs.18-25921 |
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