Bidirectional analysis of cryba4-crybb1 nascent transcription and nuclear accumulation of crybb3 mrnas in lens fibers

Saima Limi, Yilin Zhao, Peng Guo, Melissa Lopez-Jones, Deyou Zheng, Robert H. Singer, Arthur I. Skoultchi, Ales Cvekl

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)234-244
Number of pages11
JournalInvestigative Ophthalmology and Visual Science
Volume60
Issue number1
DOIs
StatePublished - Jan 1 2019

Fingerprint

Lenses
Genes
Cell Nucleus
Crystallins
Alleles
RNA
Gene Expression
Chromosomes, Human, Pair 5
Messenger RNA
Chromatin Assembly and Disassembly
Gene Expression Profiling
Fluorescence In Situ Hybridization
Transcriptome
Cataract
Cell Differentiation
Genome
Phenotype
Enzymes

Keywords

  • Crystallin
  • Denucleation
  • Differentiation
  • Head-to-head genes
  • Lens
  • Nucleus
  • RNA FISH
  • Splicing

ASJC Scopus subject areas

  • Ophthalmology
  • Sensory Systems
  • Cellular and Molecular Neuroscience

Cite this

@article{198b1957405246f69e6791f947ee4a2a,
title = "Bidirectional analysis of cryba4-crybb1 nascent transcription and nuclear accumulation of crybb3 mrnas in lens fibers",
abstract = "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.",
keywords = "Crystallin, Denucleation, Differentiation, Head-to-head genes, Lens, Nucleus, RNA FISH, Splicing",
author = "Saima Limi and Yilin Zhao and Peng Guo and Melissa Lopez-Jones and Deyou Zheng and Singer, {Robert H.} and Skoultchi, {Arthur I.} and Ales Cvekl",
year = "2019",
month = "1",
day = "1",
doi = "10.1167/iovs.18-25921",
language = "English (US)",
volume = "60",
pages = "234--244",
journal = "Investigative Ophthalmology and Visual Science",
issn = "0146-0404",
publisher = "Association for Research in Vision and Ophthalmology Inc.",
number = "1",

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TY - JOUR

T1 - Bidirectional analysis of cryba4-crybb1 nascent transcription and nuclear accumulation of crybb3 mrnas in lens fibers

AU - Limi, Saima

AU - Zhao, Yilin

AU - Guo, Peng

AU - Lopez-Jones, Melissa

AU - Zheng, Deyou

AU - Singer, Robert H.

AU - Skoultchi, Arthur I.

AU - Cvekl, Ales

PY - 2019/1/1

Y1 - 2019/1/1

N2 - 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.

AB - 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.

KW - Crystallin

KW - Denucleation

KW - Differentiation

KW - Head-to-head genes

KW - Lens

KW - Nucleus

KW - RNA FISH

KW - Splicing

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U2 - 10.1167/iovs.18-25921

DO - 10.1167/iovs.18-25921

M3 - Article

VL - 60

SP - 234

EP - 244

JO - Investigative Ophthalmology and Visual Science

JF - Investigative Ophthalmology and Visual Science

SN - 0146-0404

IS - 1

ER -