Evaluation sequence motifs found in scaffold/matrix-attached regions (S/MARs)

Nucleic Acids Research

Volumn 30, Issue 15, 2002, Pages 3433-3442

  Liebich, I ^a   Bode, J ^a   Reuter, I ^a,b   Wingender, E ^a,b  

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^b BIOBASE GMBH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; HOMEODOMAIN PROTEIN; NONHISTONE PROTEIN; SCAFFOLD MATRIX ATTACHED REGION; THYMINE; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; AT RICH SEQUENCE; BINDING SITE; CONTROLLED STUDY; EVALUATION; EXON; NUCLEOTIDE SEQUENCE; PRACTICE GUIDELINE; PRIORITY JOURNAL; PROTEIN MOTIF; RANDOMIZATION; REGULATORY MECHANISM; SEQUENCE ANALYSIS; SEQUENCE DATABASE;

EID: 0036682334     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkf446     Document Type: Article

References (62)

1. Cohabitation of scaffold binding regions with upstream/enhancer elements of three developmentally regulated genes of D. melanogaster
2. The nuclear matrix: A heuristic model for investigating genomic organization and function in the cell nucleus
3. Scaffold/matrix-attached regions: Topological switches with multiple regulatory functions
4. Chromatin domain surrounding the human interferon-beta gene as defined by scaffold-attached regions
5. Hierarchical binding of DNA fragments derived from scaffold-attached regions: Correlation of properties in vitro and function in vivo
6. Facilitation of chromatin dynamics by SARs
7. Chromosome topology-organizing genes by loops and bounds
8. Scaffold-associated regions: Cis-acting determinants of chromatin structural loops and functional domains
9. Scaffold/matrix-attached regions act upon transcription in a context-dependent manner
10. Biological significance of unwinding capability of nuclear matrix-associating DNAs
11. High-level transgene expression in plant cells: Effects of a strong scaffold attachment region from tobacco
12. Immunoglobulin kappa gene expression after stable integration. I. Role of the intronic MAR and enhancer in plasmacytoma cells
13. A plant scaffold attached region detected close to a T-DNA integration site is active in mammalian cells
14. The limits of the DNaseI-sensitive domain of the human apolipoprotein B gene coincide with the locations of chromosomal anchorage loops and define the 5′ and 3′ boundaries of the gene
15. The β-phaseolin gene is flanked by matrix attachment regions
16. Position-independent transgene expression mediated by boundary elements from the apolipoprotein B chromatin domain
17. Human matrix attachment regions insulate transgene expression from chromosomal position effects in Drosophila melanogaster
18. The 5′ boundary of the human apolipoprotein B chromatin domain in intestinal cells
19. High affinity MAR-DNA binding is a common property of murine and human mutant p53
20. Chromosomal loop anchorage of the kappa immunoglobin gene occurs next to the enhancer in a region containing topoisomerase II sites
21. Homeodomain protein binding sites, inverted repeats and nuclear matrix attachment regions along the human beta-globin gene complex
22. Analysis of the chromatin domain organisation around the plastocyanin gene reveals a MAR-specific sequence element in Arabidopsis thaliana
23. TRANSFAC: An integrated system for gene expression regulation
24. S/MARt DB: A database on scaffold/matrix attached regions
25. The eukaryotic promoter database (EPD): Recent developments
26. The EMBL nucleotide sequence database
27. Transcription regulatory region analysis using signal detection and fuzzy clustering
28. MatInd and MatInspector: New fast and versatile tools for detection of consensus matches in nucleotide sequence data
29. The TRANSFAC system on gene expression regulation
30. Nature of DNA sequences at the attachment regions of genes to the nuclear matrix
31. Characterization of matrix attachment sites in the upstream region of a tobacco chitinase gene
32. A glimpse of a chromosomal order
33. Specific inhibition of DNA binding to nuclear scaffolds and histone H1 by distamycin. The role of oligo(dA)·oligo(dT) tracts
34. Nucleolin is a matrix attachment region DNA-binding protein that specifically recognizes a region with high base-unpairing potential
35. The hitchhiking principle: Optimizing episomal vectors for the use in gene therapy and biotechnology
36. Organization of the 3′-boundary of the chicken alpha globin gene domain and characterization of a CR 1-specific protein binding site
37. Sequence-specific DNA-binding proteins are components of a nuclear matrix-attachment site
38. Interaction of the nuclear matrix-associated region (MAR)-binding proteins, SATB1 and CDP/Cux, with a MAR element (L2a) in an upstream regulatory region of the mouse CD8a gene
39. Classification scheme of eukaryotic transcription factors
40. Cux/CDP homeoprotein is a component of NF-μNR and represses the immunoglobulin heavy chain intronic enhancer by antagonizing the Bright transcription activator
41. Transcription-promoting genomic sites in mammalia: Their elucidation and architectural principles
42. A scaffold-associated DNA region is located downstream of the pea plastocyanin gene
43. A-T-rich scaffold attachment regions flank the haematopoietic serine protease genes clustered on chromosome 14q11.2
44. Double strand DNA cleavage by type II DNA topoisomerase from Drosophila melanogaster
45. A consensus sequence for cleavage by vertebrate DNA topoisomerase II
46. Drosophila scaffold-attached regions bind nuclear scaffolds and can function as ARS elements in both budding and fission yeast
47. In silico prediction of scaffold/matrix attachment regions in large genomic sequences
48. Characterization of SAF-A, a novel nuclear DNA binding protein from HeLa cells with high affinity for nuclear matrix/scaffold attachment DNA elements
49. UTRdb and UTRsite: Specialized databases of sequences and functional elements of 5′ and 3′ untranslated regions of eukaryotic mRNAs. Update 2002
50. Statistical mining of S/MARt Database
51. Synthetic concatemers as artificial MAR: Importance of a particular configuration of short AT-tracts for protein recognition
52. Characterization of randomly-obtained matrix attachment regions (MARs) from higher plants
53. Sequences of DNA fragments contacting the nuclear lamina in vivo
54. Anatomy of highly expressing chromosomal sites targeted by retroviral vectors
55. A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition
56. The immunoglobulin heavy-chain matrix-associating regions are bound by Bright: A B cell-specific trans-activator that describes a new DNA-binding protein family
57. Nuclear scaffold attachment sites in the human globin gene complexes
58. The association of the human epsilon-globin gene with the nuclear matrix: A reconsideration
59. 2+
60. Computer assisted search for sites of nuclear matrix attachment
61. Mathematical model to predict regions of chromatin attachment to the nuclear matrix
62. Stress-induced duplex DNA destabilization in scaffold/matrix attachment regions