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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...

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Autores principales: Limi, Saima, Zhao, Yilin, Guo, Peng, Lopez-Jones, Melissa, Zheng, Deyou, Singer, Robert H., Skoultchi, Arthur I., Cvekl, Ales
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Association for Research in Vision and Ophthalmology 2019
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.
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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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