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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

AT Rich Sequence

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Disease relevance of AT Rich Sequence


High impact information on AT Rich Sequence

  • Missing nucleoside experiments showed that SATB1 selectively binds in a special AT-rich sequence context where one strand consists of mixed A's, T's, and C's, excluding G's (ATC sequences) [4].
  • Deletion mutants indicate that multiple AT-rich sequences, if contained in a minimal approximately 350 bp MAR fragment, can lead to efficient binding of ARBP [5].
  • These fragments do not result from bulk nucleosome phasing in vivo, but arise from micrococcal nuclease cleavages internal to the core particle, at roughly 10-base pair intervals and at AT-rich sequences [6].
  • SATB1 ('special AT-rich sequence binding 1'), a protein found predominantly in thymocytes, regulates genes by folding chromatin into loop domains, tethering specialized DNA elements to an SATB1 network structure [7].
  • Despite its clear preference for AT-rich sequences, TBP can mediate TFIIIB assembly at diverse DNA sequences, including stretches containing only G and C. However, a mutant TBP, m3, which recognizes TATAAA and TGTAAA and is active for Pol III transcription, utilizes other sequences only poorly [8].

Biological context of AT Rich Sequence


Anatomical context of AT Rich Sequence


Associations of AT Rich Sequence with chemical compounds

  • Treatment of cells with distamycin selectively enhances cleavage at nucleosome linker sites of the SAR and satellite regions, suggesting that AT-rich sequences flanking cleavage sites may be involved in determining topoisomerase II activity in the cell [18].
  • Distamycin A is a well known polyamide antibiotic that can bind in the minor groove of duplex DNA primarily at AT-rich sequences both as a monomer or as a side-by-side antiparallel dimer [19].
  • Guanine at position 3 determines DnaA-ATP preference, and changing this base to thymine at both I sites allows DnaA-ADP to bind and open oriC, although DNA strand separation is not precisely localized in the AT-rich region [20].
  • A factor present in nuclear extracts from endothelial and nonendothelial cells binds to an AT-rich sequence located between nt -133 and -125 [21].
  • The AT-rich region often contained ATTTA motifs, 5'-AAT-3' or 5'-TAA-3' trinucleotides which were reported to be involved in rapidly degrading mRNA [22].

Gene context of AT Rich Sequence

  • Surprisingly, we found that an AT-rich region 5' to the GC box also is important for MIG1 binding [23].
  • A near homogeneous 20-kDa DNA-binding protein purified from rat brain was able to bind to these AT-rich regions of both Ng/RC3 and PKC-gamma genes with footprints containing ATTA, ATAA, and AATA sequences [24].
  • Synergism between STAT3 or STAT3-C and c-Jun is impaired by mutation of the APRE (SIE) or either AP1 site, as well as by mutations that alter the AT-rich regions or their phasing [25].
  • The binding of EGR1 to the GC-rich region prevented TBP binding to the AT-rich region [26].
  • HMGA1 proteins belong to a family of nonhistone chromatin proteins able to bind DNA in AT-rich regions and to interact with various transcription factors thus enhancing or inhibiting gene transcription by acting as architectural proteins [27].

Analytical, diagnostic and therapeutic context of AT Rich Sequence

  • In vitro footprinting and quantitative gel shift analyses showed that PF1 binds preferentially to the PE1 element but also at lower affinity to two other AT-rich regions upstream of PE1 [28].
  • STS mapping narrowed the 1p21.2 breakpoint to a 1990 bp AT-rich region, and junction fragments were amplified by nested PCR [29].
  • Primer extension, S1 nuclease protection, and genomic and cDNA sequence analysis demonstrate that gene transcripts are initiated within a conserved AT-rich sequence element immediately preceding the ATG translation initiation codon and the short 5' untranslated region is not extended by transsplicing [30].
  • Isothermal titration calorimetry (ITC) profiles of berenil bound to different DNAs show that, despite the strong preference of berenil for AT-rich regions in DNA, it can bind to other DNA sequences significantly [31].


  1. Stoichiometry of DnaA and DnaB protein in initiation at the Escherichia coli chromosomal origin. Carr, K.M., Kaguni, J.M. J. Biol. Chem. (2001) [Pubmed]
  2. Polymorphisms at - 174 and in the 3' flanking region of interleukin-6 (IL-6) gene in patients with myasthenia gravis. Huang, D., Zheng, C., Giscombe, R., Matell, G., Pirskanen, R., Lefvert, A.K. J. Neuroimmunol. (1999) [Pubmed]
  3. Structural elements of the Streptomyces oriC region and their interactions with the DnaA protein. Jakimowicz, D., Majka, J., Messer, W., Speck, C., Fernandez, M., Martin, M.C., Sanchez, J., Schauwecker, F., Keller, U., Schrempf, H., Zakrzewska-Czerwińska, J. Microbiology (Reading, Engl.) (1998) [Pubmed]
  4. A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition. Dickinson, L.A., Joh, T., Kohwi, Y., Kohwi-Shigematsu, T. Cell (1992) [Pubmed]
  5. A matrix/scaffold attachment region binding protein: identification, purification, and mode of binding. von Kries, J.P., Buhrmester, H., Strätling, W.H. Cell (1991) [Pubmed]
  6. Another potential artifact in the study of nucleosome phasing by chromatin digestion with micrococcal nuclease. McGhee, J.D., Felsenfeld, G. Cell (1983) [Pubmed]
  7. SATB1 targets chromatin remodelling to regulate genes over long distances. Yasui, D., Miyano, M., Cai, S., Varga-Weisz, P., Kohwi-Shigematsu, T. Nature (2002) [Pubmed]
  8. Alternative outcomes in assembly of promoter complexes: the roles of TBP and a flexible linker in placing TFIIIB on tRNA genes. Joazeiro, C.A., Kassavetis, G.A., Geiduschek, E.P. Genes Dev. (1996) [Pubmed]
  9. Isoform-specific amino-terminal domains dictate DNA-binding properties of ROR alpha, a novel family of orphan hormone nuclear receptors. Giguère, V., Tini, M., Flock, G., Ong, E., Evans, R.M., Otulakowski, G. Genes Dev. (1994) [Pubmed]
  10. The LIM-homeodomain transcription factor Lmx1b plays a crucial role in podocytes. Rohr, C., Prestel, J., Heidet, L., Hosser, H., Kriz, W., Johnson, R.L., Antignac, C., Witzgall, R. J. Clin. Invest. (2002) [Pubmed]
  11. Archaebacteria: transcription and processing of ribosomal RNA sequences in Halobacterium cutirubrum. Chant, J., Dennis, P. EMBO J. (1986) [Pubmed]
  12. Specific binding of high-mobility-group I (HMGI) protein and histone H1 to the upstream AT-rich region of the murine beta interferon promoter: HMGI protein acts as a potential antirepressor of the promoter. Bonnefoy, E., Bandu, M.T., Doly, J. Mol. Cell. Biol. (1999) [Pubmed]
  13. LCR-regulated transgene expression levels depend on the Oct-1 site in the AT-rich region of beta -globin intron-2. Bharadwaj, R.R., Trainor, C.D., Pasceri, P., Ellis, J. Blood (2003) [Pubmed]
  14. Identification of sequences within the murine granulocyte-macrophage colony-stimulating factor mRNA 3'-untranslated region that mediate mRNA stabilization induced by mitogen treatment of EL-4 thymoma cells. Iwai, Y., Bickel, M., Pluznik, D.H., Cohen, R.B. J. Biol. Chem. (1991) [Pubmed]
  15. High mobility group-I(Y) protein facilitates nuclear factor-kappaB binding and transactivation of the inducible nitric-oxide synthase promoter/enhancer. Perrella, M.A., Pellacani, A., Wiesel, P., Chin, M.T., Foster, L.C., Ibanez, M., Hsieh, C.M., Reeves, R., Yet, S.F., Lee, M.E. J. Biol. Chem. (1999) [Pubmed]
  16. Involvement of the homeodomain-containing transcription factor PDX-1 in islet amyloid polypeptide gene transcription. Watada, H., Kajimoto, Y., Kaneto, H., Matsuoka, T., Fujitani, Y., Miyazaki, J., Yamasaki, Y. Biochem. Biophys. Res. Commun. (1996) [Pubmed]
  17. High-mobility group protein 2 may be involved in the locus control region regulation of the beta-globin gene cluster. Lv, X., Xu, D.D., Liu, D.P., Li, L., Hao, D.L., Liang, C.C. Biochem. Cell Biol. (2002) [Pubmed]
  18. In vivo topoisomerase II cleavage of the Drosophila histone and satellite III repeats: DNA sequence and structural characteristics. Käs, E., Laemmli, U.K. EMBO J. (1992) [Pubmed]
  19. On the kinetics of distamycin binding to its target sites on duplex DNA. Baliga, R., Crothers, D.M. Proc. Natl. Acad. Sci. U.S.A. (2000) [Pubmed]
  20. Two discriminatory binding sites in the Escherichia coli replication origin are required for DNA strand opening by initiator DnaA-ATP. McGarry, K.C., Ryan, V.T., Grimwade, J.E., Leonard, A.C. Proc. Natl. Acad. Sci. U.S.A. (2004) [Pubmed]
  21. Oct-1 is involved in the transcriptional repression of the von willebrand factor gene promoter. Schwachtgen, J.L., Remacle, J.E., Janel, N., Brys, R., Huylebroeck, D., Meyer, D., Kerbiriou-Nabias, D. Blood (1998) [Pubmed]
  22. Rat liver cholesterol 7 alpha-hydroxylase. Pretranslational regulation for circadian rhythm. Noshiro, M., Nishimoto, M., Okuda, K. J. Biol. Chem. (1990) [Pubmed]
  23. Importance of a flanking AT-rich region in target site recognition by the GC box-binding zinc finger protein MIG1. Lundin, M., Nehlin, J.O., Ronne, H. Mol. Cell. Biol. (1994) [Pubmed]
  24. Structure and regulation of the gene encoding the neuron-specific protein kinase C substrate neurogranin (RC3 protein). Sato, T., Xiao, D.M., Li, H., Huang, F.L., Huang, K.P. J. Biol. Chem. (1995) [Pubmed]
  25. Synergistic activity of STAT3 and c-Jun at a specific array of DNA elements in the alpha 2-macroglobulin promoter. Yoo, J.Y., Wang, W., Desiderio, S., Nathans, D. J. Biol. Chem. (2001) [Pubmed]
  26. Effect of DNA-binding drugs on early growth response factor-1 and TATA box-binding protein complex formation with the herpes simplex virus latency promoter. Chiang, S.Y., Welch, J.J., Rauscher, F.J., Beerman, T.A. J. Biol. Chem. (1996) [Pubmed]
  27. HMGA1 protein expression sensitizes cells to cisplatin-induced cell death. Baldassarre, G., Belletti, B., Battista, S., Nicoloso, M.S., Pentimalli, F., Fedele, M., Croce, C.M., Fusco, A. Oncogene (2005) [Pubmed]
  28. PF1: an A-T hook-containing DNA binding protein from rice that interacts with a functionally defined d(AT)-rich element in the oat phytochrome A3 gene promoter. Nieto-Sotelo, J., Ichida, A., Quail, P.H. Plant Cell (1994) [Pubmed]
  29. A palindrome-mediated mechanism distinguishes translocations involving LCR-B of chromosome 22q11.2. Gotter, A.L., Shaikh, T.H., Budarf, M.L., Rhodes, C.H., Emanuel, B.S. Hum. Mol. Genet. (2004) [Pubmed]
  30. Isolation and characterization of a NADP-dependent glutamate dehydrogenase gene from the primitive eucaryote Giardia lamblia. Yee, J., Dennis, P.P. J. Biol. Chem. (1992) [Pubmed]
  31. Heterogeneous DNA binding modes of berenil. Barceló, F., Ortiz-Lombardía, M., Portugal, J. Biochim. Biophys. Acta (2001) [Pubmed]
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