Large-scale identification and mapping of nuclear matrix-attachment regions in the distal imprinted domain of mouse chromosome 7.
Mammalian imprinted genes, which are expressed from only one of the parental alleles, have a tendency to form clusters and are regulated by long-range mechanisms. Nuclear matrix-attachment regions (MARs), the anchor points of loop domains, are involved in coordination of gene expression and could play a role in regulation of imprinted domains. We have identified and mapped a total of 52 MARs in a 1-Mb imprinted domain on mouse distal chromosome 7 using our cosmid contigs and an in vitro MAR assay. We find two MAR clusters (comprising 20 and 19 MARs), one of which is mapped in the Th-Ins2 intergenic region, coincident with the boundary between the two imprinted subdomains. However, the imprinted/non-imprinted boundaries are not associated with a MAR. Based on the sequence information, we find that many of the MARs are rich in long interspersed nuclear elements. In addition, comparisons of the results obtained with several MAR-prediction software programs reveal good performance of ChrClass in terms of both sensitivity and specificity. This study presents the first large-scale mapping of MARs in an imprinted domain and provides a platform for understanding the roles of MARs in imprinting.
Purbowasito
Wahyu
W
Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima 411-8540, Japan.
Suda
Chikako
C
Yokomine
Takaaki
T
Zubair
Mohamad
M
Sado
Takashi
T
Tsutsui
Ken
K
Sasaki
Hiroyuki
H
D000818:Animals; D001667:Binding, Competitive; D002467:Cell Nucleus / Q000378:metabolism*; D002874:Chromosome Mapping; D003198:Computer Simulation; D020451:Contig Mapping; D003360:Cosmids / Q000235:genetics; D004305:Dose-Response Relationship, Drug; D005786:Gene Expression Regulation; D018392:Genomic Imprinting; D020084:Long Interspersed Nucleotide Elements; D045170:Matrix Attachment Regions / Q000235:genetics*; D051379:Mice; D008957:Models, Genetic; D008969:Molecular Sequence Data; D005810:Multigene Family; D015530:Nuclear Matrix / Q000378:metabolism; D017434:Protein Structure, Tertiary; D012984:Software