Transcription Regulatory Regions Database (TRRD): its status in 2000

Kolchanov, Nikolay А.; Podkolodnaya, O. A.; Ananko, E. A.; Ignatieva, E. V.; Степаненко, И. Л.; Kel-Margoulis, Olga V.; Kel, Alexander; Меркулова, Т. И.; Goryachkovskaya, T. N.; Busygina, T. V.; Kolpakov, Fedor A.; Podkolodny, N. L.; Naumochkin, A. N.; Korostishevskaya, I. M.; Romashchenko, A. G.; Overton, Gail

doi:10.1093/nar/28.1.298

Cited by 49 publications

(13 citation statements)

References 9 publications

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“…This sort of ability to function in both orientations and in different locations is a classical feature of enhancer elements (Banerji et al 1981). However, database searches using BLAST (Altschul et al 1990), PLACE (Higo et al 1999), and TRRD (Kolchanov et al 2000) failed to identify any previously defined enhancer motif in the 937-bp fragment that had been inverted, or in the rest of intron 5, or in intron 3.…”

Section: Enhancer Elements Are Present In Introns 3 Andmentioning

confidence: 99%

Two enhancers and one silencer located in the introns of regA control somatic cell differentiation in Volvox carteri

Stark¹,

Kirk²,

Schmitt³

2001

Genes Dev.

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The regA gene plays a central role in germ-soma differentiation of Volvox carteri by suppressing all reproductive functions in somatic cells. Here we show that the minimal promoter of regA consists of only 42 bp immediately upstream of the transcription start site, and that it contains no discernible regulatory elements. However, introns 3 and 5 are both required for regA expression in somatic cells, and intron 7 is essential for silencing regA in gonidia (asexual reproductive cells). A regA gene lacking intron 7 rescues the normal phenotype of mutant somatic cells, but also results in gonidia that reproduce only weakly and soon die out. The same phenotype is observed when a regA gene containing intron 7 is placed under control of a constitutive promoter, suggesting that the silencing activity of intron 7 is promoter specific. Intron 7 is unusual in that it contains a potential ORF that is in frame with exons 7 and 8, and some transcripts are produced in which intron 7 is retained. However, a regulatory role for the intron 7 translation product can be ruled out, because a construct in which intron 7 must be translated, and one in which it cannot be translated, both result in wild-type development of both cell types. Furthermore, intron 7 is unable to act in trans to silence regA, but is able to exert its normal effect when placed in a different location within the gene. Therefore, it appears that intron 7 functions in gonidia as a classical cell-type-specific and promoter-specific enhancer, of the inhibitory type that is often referred to as a silencer.

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Section: Enhancer Elements Are Present In Introns 3 Andmentioning

confidence: 99%

Two enhancers and one silencer located in the introns of regA control somatic cell differentiation in Volvox carteri

Stark¹,

Kirk²,

Schmitt³

2001

Genes Dev.

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“…A consensus sequence of each of the 20 abundant classes was compared to known regulatory signals from TRANSFAC and TRRD databases (12,13). Consensuses of 10 classes were found to be similar to known motifs of regulatory factors and signals ( Table 1).…”

Section: Resultsmentioning

confidence: 99%

Classification of common conserved sequences in mammalian intergenic regions

Kondrashov

Shabalina

2002

Human Molecular Genetics

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Comparisons between orthologous intergenic regions of related genomes reveal numerous hits, i.e. pairs of relatively short highly similar sequences that evolved slowly, perhaps due to selective constraint. We analyzed and classified 2638 hits found within 100 pairs of complete, orthologous intergenic regions of human and murine genomes. We identified all common fragments of hits that align well with many other hits and constructed their classification. Our analysis revealed 20 abundant classes each containing 10 or more fragments. Fragments of the same class may perform the same function, e.g. bind a particular protein. Ten of the abundant classes apparently correspond to known functional consensuses, whereas others may represent novel conserved sites. Thus, large-scale comparative analysis of slowly evolving intergenic sequences can provide valuable insights into their function.

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“…This also holds true for the GENE flat file, which connects S/MARt DB to Transcription Regulatory Region Database (TRRD) as well (11). Besides that, S/MARt DB contains hyperlinked cross-references to MEDLINE/PubMed, to the EMBL data library (12) and, where appropriate, entries are also linked to SWISS-PROT and PIR (13,14).…”

Section: Links To Other Databasesmentioning

confidence: 98%

S/MARt DB: a database on scaffold/matrix attached regions

Liebich¹

2002

Nucleic Acids Research

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Transcription Regulatory Regions Database (TRRD): its status in 2000

Cited by 49 publications

References 9 publications

Two enhancers and one silencer located in the introns of regA control somatic cell differentiation in Volvox carteri

Two enhancers and one silencer located in the introns of regA control somatic cell differentiation in Volvox carteri

Classification of common conserved sequences in mammalian intergenic regions

S/MARt DB: a database on scaffold/matrix attached regions

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