Methylation profiles of genomic DNA of mouse developmental brain detected by restriction landmark genomic scanning (RLGS) method

Abstract

Restriction landmark genomic scanning using methylation-sensitive endonucleases (RLGS-M) is a newly developed powerful method for systematic detection of DNA methylation. Using this method, we scanned mouse brain genomic DNAs from various developmental stages to detect the transcriptionally active regions. This approach is based on the assumption that CpG methylation, particularly of CpG islands, might be associated with gene transcriptional regulation. Genomic DNAs were prepared from telencephalons of 9.5-, 13.5- and 16.5-day embryos, 1- and 10-day neonates and adults, followed by subjecting them to RLGS-M and comparing their patterns with each other or with that of the adult liver. We used NotI as a methylation-sensitive restriction enzyme and surveyed the methylation states of 2,600 NotI sites, almost of which should correspond to gene loci. Although almost all RLGS spots (98%) were present constantly at every developmental stages, only a few percent of spots reproducibly appeared and disappeared at different developmental stages of the brain (44 spots, 1.7%) and some were tissue-specific (10 spots, 0.7%). These data suggest that DNA methylation associated with gene transcription is a well-programmed event during the central nervous system (CNS) development. Thus, RLGS-M can offer a means for detecting systematically the genes in which the state of DNA methylation changes during development of the higher organism.

The ‘golden age’ of DNA methylation in neurodegenerative diseases

“…The restriction landmark genomic scanning (RLGS) was one of the earliest approaches used for genome-wide analyses [ 31 ]. In this assay, genomic DNA is digested with a rare sensitive-methylation restriction enzyme, radioactively end-labeled at the cleavage sites and size-fractionated in one dimension.…”

Reactivating the expression of methylation silenced genes in human cancer

“…A second approach for examining DNA methylation abnormalities in human cancer is known as restriction landmark genomic scanning (RLGS) (Kawai et al, 1993). The RLGS method is based on the differential cutting of CpG island-rich genomic DNA libraries with the methylation-sensitive enzyme NotI.…”

Methylation analysis of the human multidrug resistance 1 gene in normal and leukemic hematopoietic cells

“…16 Exceptions include methylated CpG islands of silenced genes associated with imprinting, Xchromosome inactivation, fragile-X syndrome, and tumorigenesis. [17][18][19][20][21] A CpG-rich domain, approximately 1 kb in size, encompasses the MDR1 promoter region, exon I, and intron I. Several contradictory preliminary reports have associated MDR1 gene expression with either low or high levels of methylation in this CpG-rich domain in various primary and cultured cell types.…”