Use of Laser Capture Microdissection for Analysis of Retinal mRNA/miRNA Expression and DNA Methylation

Avidin Ltd, Szeged, Hungary.
Methods in molecular biology (Clifton, N.J.) (Impact Factor: 1.29). 06/2012; 884:289-304. DOI: 10.1007/978-1-61779-848-1_21
Source: PubMed


Laser capture microdissection (LCM) is a useful method to isolate specific cells or cell layers of interest from heterogeneous tissues, such as the retina. The collected cells can be used for DNA, RNA, or protein analysis. We have applied LCM technology to isolate cells from the outer nuclear, inner nuclear, and ganglion cell layers of the retina for mRNA and microRNA (miRNA) expression and epigenetic (DNA methylation) analysis. Here, we describe the methods we have employed for sample preparation, LCM-based isolation of retinal layers, RNA/DNA extraction, RNA quality check, microRNA analysis by quantitative PCR, and DNA methylation analysis by bisulfite sequencing.

  • Source
    • "PCR was performed using 1 µl of bisulfite-converted DNA and HotStarTaq DNA Polymerase (Qiagen) under the following cycling conditions: 95°C for 15 min; 45 cycles of [94°C for 30 s, annealing temperature (56.3°C for rat, 58.3°C for mouse) 30 s, 72°C for 60 s]; 72°C for 3 min; 4°C hold followed by storage at −20°C. Amplicons were analyzed on a PyroMark Q24 Pyrosequencer as per the manufacturers’ protocols, and methylation at the CpG sites was quantified using the PyroMark Q24 software version 2.0.6 (34). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The exact role of intragenic DNA methylation in regulating tissue-specific gene regulation is unclear. Recently, the DNA-binding protein CTCF has been shown to participate in the regulation of alternative splicing in a DNA methylation-dependent manner. To globally evaluate the relationship between DNA methylation and tissue-specific alternative splicing, we performed genome-wide DNA methylation profiling of mouse retina and brain. In protein-coding genes, tissue-specific differentially methylated regions (T-DMRs) were preferentially located in exons and introns. Gene ontology and evolutionary conservation analysis suggest that these T-DMRs are likely to be biologically relevant. More than 14% of alternatively spliced genes were associated with a T-DMR. T-DMR-associated genes were enriched for developmental genes, suggesting that a specific set of alternatively spliced genes may be regulated through DNA methylation. Novel DNA sequences motifs overrepresented in T-DMRs were identified as being associated with positive and/or negative regulation of alternative splicing in a position-dependent context. The majority of these evolutionarily conserved motifs contain a CpG dinucleotide. Some transcription factors, which recognize these motifs, are known to be involved in splicing. Our results suggest that DNA methylation-dependent alternative splicing is widespread and lay the foundation for further mechanistic studies of the role of DNA methylation in tissue-specific splicing regulation.
    Nucleic Acids Research 07/2013; 41(18). DOI:10.1093/nar/gkt652 · 9.11 Impact Factor
  • Source
    • "All mice were treated in accordance with the Guide for the Care and Use of Laboratory Animals and the Animal Welfare Act as well as the guidelines of the Institutional Animal Care and Use Committee at Johns Hopkins University. Tissues of individual retinal layers of adult C57BL/6J mice were collected by laser capture microdissection (LCM) as previously described [41-43]. Briefly, after the cornea and lens were removed, the eyecups were immersed in 10%, 15%, and 25% sucrose for 30 min each, and frozen in optimal cutting temperature compound (OCT) with 25% sucrose. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Ras-like without CAAX 2 (RIT2), a member of the Ras superfamily of small guanosine triphosphatases, is involved in regulating neuronal function. RIT2 is a unique member of the Ras family in that RIT2 is preferentially expressed in various neurons, including retinal neurons. The mechanisms that regulate RIT2 expression in neurons were studied. Reverse transcription-quantitative PCR (RT-qPCR), immunohistochemistry, western blotting, bioinformatic prediction, electrophoretic mobility shift assay (EMSA), and cell transfection methods were used. With immunohistochemistry of the mouse retina, RIT2 protein was detected in the ganglion cell layer (GCL), inner plexiform layer, inner nuclear layer, and outer plexiform layer, with the strongest staining in the GCL and the inner plexiform layer. RT-qPCR combined with laser capture microdissection detected Rit2 messenger RNA in the GCL and the inner nuclear layer. Western blot analysis showed a large increase in the RIT2 protein in the retina during maturation from newborn to adult. Transient transfection identified the 1.3 kb upstream region of human RIT2 as capable of driving expression in neuronal cell lines. Based on the known expression pattern and biological activity, we hypothesized that POU4 family factors might modulate RIT2 expression in retinal ganglion cells (RGCs). Bioinformatic analyses predicted six POU4 factor-binding sites within the 1.3 kb human RIT2 promoter region. EMSA analyses showed binding of POU4 proteins to three of the six predicted sites. Cotransfection with expression vectors demonstrated that POU4 proteins can indeed modulate the human RIT2 promoter, and that ISL1, a LIM homeodomain factor, can further modulate the activity of the POU4 factors. These studies confirm the expression of RIT2 in retinal neuronal cells, including RGCs, begin to reveal the mechanisms responsible for neuronal expression of RIT2, and suggest a role for the POU4 family factors in modulating RIT2 expression in RGCs.
    Molecular vision 06/2013; 19:1371-1386. · 1.99 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Laser capture microdissection (LCM) is a superior method for non-destructive collection of specific cell populations from tissue sections. While DNA, RNA and protein have been analyzed from LCM-procured samples, epigenetic analyses, particularly of fetal, highly hydrated tissue, have not been attempted. A standardized protocol with quality assurance measures was established to procure cells by LCM of the medial edge epithelia (MEE) of the fetal palatal processes for isolation of intact microRNA for expression analyses and genomic DNA for CpG methylation analyses. MicroRNA preparations, obtained using the RNAqueous(®) Micro kit (Life Technologies), exhibited better yields and higher quality than those obtained using the Arcturus(®) PicoPure(®) RNA Isolation kit (Life Technologies). The approach was validated using real-time PCR to determine expression of selected microRNAs (miR-99a and miR-200b) and pyrosequencing to determine CpG methylation status of selected genes (Aph1a and Dkk4) in the MEE. These studies describe an optimized approach for employing LCM of epithelial cells from fresh frozen fetal tissue that enables quantitative analyses of miRNA expression levels and CpG methylation.
    Analytical Biochemistry 07/2013; 442(1). DOI:10.1016/j.ab.2013.07.029 · 2.22 Impact Factor
Show more