Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: a novel context analysis approach

Scherf, Matthias; Klingenhoff, Andreas; Werner, Thomas

doi:10.1006/jmbi.2000.3589

Cited by 255 publications

(154 citation statements)

References 17 publications

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“…Computational analysis of the Gal1 locus (chr22:36,400,510-36,406,802, alignment with Human NCBI Genome assembly v36, March 2006) was performed with the publicly available version of Genomatix suite (www.genomatix.de) (43) and rVISTA (http://rvista.dcode.org) (44), and a putative downstream regulatory element (enhancer) containing a conserved AP1-binding site was identified (1567-1675). To generate a series of Gal1 promoter-enhancer reporter constructs, we first PCR-amplified the Gal1 promoter region (Ϫ403 to ϩ67) and ligated this sequence into the pGL3 promoterless reporter vector (Promega, Madison, WI), generating pGL3-Gal1Ϫ403ϩ67-Luc.…”

Section: Analysis Of Regulatory Elements In the Gal1 Locus And Generamentioning

confidence: 99%

The AP1-dependent secretion of galectin-1 by Reed–Sternberg cells fosters immune privilege in classical Hodgkin lymphoma

Juszczyński

Ouyang

Monti

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

290

301

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Section: Analysis Of Regulatory Elements In the Gal1 Locus And Generamentioning

confidence: 99%

The AP1-dependent secretion of galectin-1 by Reed–Sternberg cells fosters immune privilege in classical Hodgkin lymphoma

Juszczyński

Ouyang

Monti

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

290

301

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“…Promoter Search-An analysis of putative promoter regions was undertaken using the TRANSFAC data base, in conjunction with the MatInspector program (32), and an in silico promoter search was performed using two pieces of software, Promoter Inspector (33) and Eponine (34).…”

Section: Nomenclature For or Genes-the Human Nomenclature Committeementioning

confidence: 99%

Complex Transcription and Splicing of Odorant Receptor Genes

Volz

Ehlers

Younger

et al. 2003

Journal of Biological Chemistry

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Human major histocompatibility (human leucocyte antigen (HLA)) complex-linked odorant receptor (OR) genes are among the best characterized OR genes in the human genome. In addition to their functions as odorant receptors in olfactory epithelium, they have been suggested to play a role in the fertilization process. Here, we report the first in-depth analysis of their expression and regulation within testicular tissue. Sixteen HLA-linked OR and three non-HLA-linked OR were analyzed. One OR gene (hs6M1-16, in positive transcriptional orientation) exhibited six different transcriptional start sites combined with extensive alternative splicing within the 5 -untranslated region, the coding exon, and the 3 -untranslated region. Long distance splicing, exon sharing, and premature polyadenylation were features of another three OR loci (hs6M1-18, -21, and -27, all upstream of hs6M1-16, but in negative transcriptional orientation). Determination of the transcriptional start sites of these OR genes identified a region of 81 bp with potential bi-directional transcriptional activity. The results demonstrate that HLA-linked OR genes are subject to unusually complex transcriptional regulatory mechanisms.

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“…Genomic sequences were analyzed with the latest version of REPEATMASKER (A. F. A. Smit and P. Green, www.repeatmasker.org). Promoter analysis was performed with PROMOTERINSPECTOR (16) and MATINSPECTOR RELEASE 7.2 (17). The protein parameters were analyzed by using the PROTPARAM, CLUSTALW, PROSITE, and PREDICT PROTEIN programs.…”

Section: Methodsmentioning

confidence: 99%

GTF2IRD2 is located in the Williams–Beuren syndrome critical region 7q11.23 and encodes a protein with two TFII-I-like helix–loop–helix repeats

Makeyev

Erdenechimeg²,

Mungunsukh³

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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Williams-Beuren syndrome (also known as Williams syndrome) is caused by a deletion of a 1.55-to 1.84-megabase region from chromosome band 7q11.23. GTF2IRD1 and GTF2I, located within this critical region, encode proteins of the TFII-I family with multiple helix-loop-helix domains known as I repeats. In the present work, we characterize a third member, GTF2IRD2, which has sequence and structural similarity to the GTF2I and GTF2IRD1 paralogs. The ORF encodes a protein with several features characteristic of regulatory factors, including two I repeats, two leucine zippers, and a single Cys-2͞His-2 zinc finger. The genomic organization of human, baboon, rat, and mouse genes is well conserved. Our exon-by-exon comparison has revealed that GTF2IRD2 is more closely related to GTF2I than to GTF2IRD1 and apparently is derived from the GTF2I sequence. The comparison of GTF2I and GTF2IRD2 genes revealed two distinct regions of homology, indicating that the helix-loop-helix domain structure of the GTF2IRD2 gene has been generated by two independent genomic duplications. We speculate that GTF2I is derived from GTF2IRD1 as a result of local duplication and the further evolution of its structure was associated with its functional specialization. Comparison of genomic sequences surrounding GTF2IRD2 genes in mice and humans allows refinement of the centromeric breakpoint position of the primatespecific inversion within the Williams-Beuren syndrome critical region.

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Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: a novel context analysis approach

Cited by 255 publications

References 17 publications

The AP1-dependent secretion of galectin-1 by Reed–Sternberg cells fosters immune privilege in classical Hodgkin lymphoma

The AP1-dependent secretion of galectin-1 by Reed–Sternberg cells fosters immune privilege in classical Hodgkin lymphoma

Complex Transcription and Splicing of Odorant Receptor Genes

GTF2IRD2 is located in the Williams–Beuren syndrome critical region 7q11.23 and encodes a protein with two TFII-I-like helix–loop–helix repeats

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