Large-scale identification and mapping of nuclear matrix-attachment regions in the distal imprinted domain of mouse chromosome 7

Wahyu Purbowasito, Chikako Suda, Takaaki Yokomine, Mohamad Zubair, Takashi Sado, Ken Tsutsui, Hiroyuki Sasaki

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)391-407
Number of pages17
JournalDNA Research
Volume11
Issue number6
DOIs
Publication statusPublished - Dec 1 2004
Externally publishedYes

Fingerprint

Matrix Attachment Regions
Nuclear Matrix
Chromosomes, Human, Pair 7
Cosmids
Intergenic DNA
Software

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Large-scale identification and mapping of nuclear matrix-attachment regions in the distal imprinted domain of mouse chromosome 7. / Purbowasito, Wahyu; Suda, Chikako; Yokomine, Takaaki; Zubair, Mohamad; Sado, Takashi; Tsutsui, Ken; Sasaki, Hiroyuki.

In: DNA Research, Vol. 11, No. 6, 01.12.2004, p. 391-407.

Research output: Contribution to journalArticle

Purbowasito, Wahyu ; Suda, Chikako ; Yokomine, Takaaki ; Zubair, Mohamad ; Sado, Takashi ; Tsutsui, Ken ; Sasaki, Hiroyuki. / Large-scale identification and mapping of nuclear matrix-attachment regions in the distal imprinted domain of mouse chromosome 7. In: DNA Research. 2004 ; Vol. 11, No. 6. pp. 391-407.
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