ArticlePlant physiology2004
Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression.
Article in Plant physiology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 55 citations in OpenAlex.
- Circle-seq analysis reveals the involvement of eccDNAs in salt stress response of bermudagrass (Cynodon dactylon).BMC genomics · 2026Article
- A novel geminivirus-derived 3' flanking sequence of terminator mediates the gene expression enhancement.Plant biotechnology journal · 2025Article
- Salt stress activates the CDK8-AHL10-SUVH2/9 module to dynamically regulate salt tolerance in Arabidopsis.Nature communications · 2025Article
- Transposable elements as scaffold/matrix attachment regions: shaping organization and functions in genomes.Frontiers in molecular biosciences · 2023Article
- Dynamics of nuclear matrix attachment regions during 5BMC genomics · 2022Article
- Ectopic application of the repressive histone modification H3K9me2 establishes post-zygotic reproductive isolation inGenes & development · 2017Article
- Article
- Genome-WideFrontiers in cellular and infection microbiology · 2016Article
- In vivo mapping of arabidopsis scaffold/matrix attachment regions reveals link to nucleosome-disfavoring poly(dA:dT) tracts.The Plant cell · 2014Article
- The AT-hook motif-containing protein AHL22 regulates flowering initiation by modifying FLOWERING LOCUS T chromatin in Arabidopsis.The Journal of biological chemistry · 2012Article
- Identification of Scaffold/Matrix Attachment (S/MAR) like DNA element from the gastrointestinal protozoan parasite Giardia lamblia.BMC genomics · 2010Article
- Coordinated regulation of p53 apoptotic targets BAX and PUMA by SMAR1 through an identical MAR element.The EMBO journal · 2010Article
- Regions associated with repression of the barley (Hordeum vulgare) VERNALIZATION1 gene are not required for cold induction.Molecular genetics and genomics : MGG · 2009Article
- Association of the matrix attachment region recognition signature with coding regions in Caenorhabditis elegans.BMC genomics · 2007Article
- Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana.PLoS computational biology · 2006Review
- Unintended consequences of plant transformation: a molecular insight.Journal of applied genetics · 2006Review
- In-silico prediction and observations of nuclear matrix attachment.Cellular & molecular biology letters · 2006Article
- A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription.The Plant cell · 2005Article
- Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid.Genetics · 2004Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We carried out a genome-wide prediction of scaffold/matrix attachment regions (S/MARs) in Arabidopsis. Results indicate no uneven distribution on the chromosomal level but a clear underrepresentation of S/MARs inside genes. In cases where S/MARs were predicted within genes, these intragenic S/MARs were preferentially located within the 5'-half, most prominently within introns 1 and 2. Using Arabidopsis whole-genome expression data generated by the massively parallel signature sequencing methodology, we found a negative correlation between S/MAR-containing genes and transcriptional abundance. Expressed sequence tag data correlated the same way with S/MAR-containing genes. Thus, intragenic S/MARs show a negative correlation with transcription level. For various genes it has been shown experimentally that S/MARs can function as transcriptional regulators and that they have an implication in stabilizing expression levels within transgenic plants. On the basis of a genome-wide in silico S/MAR analysis, we found a significant correlation between the presence of intragenic S/MARs and transcriptional down-regulation.
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