Transcription defined

Okabe M, Miyabe S, Nagatsuka H, et al. MECT1-MAML2 fusion transcript defines a favorable subset of mucoepidermoid carcinoma. Clin Cancer Res. 2006 12(13) 3902-3907. 

Zoubek, A., Dockhorn-Dworniczak, B., Delattre, O. (1996) Does expression of different EWS chimeric transcripts define clinically distinct risk groups of Ewing tumor patients. J Clin Oncol, 14, 1245— 1251. 

BROWN, D.W., YU, J.-H., KELKER, H.S., FERNANDES, M., NESBITT, T.C., KELLER, N.P., ADAMS, T.H., LEONARD, T.J., Twenty-five coregulated transcripts define a sterigmatocystin gene cluster in Aspergillus nidulans, Proc. Natl. Acad. Sci. USA, 1996,93,1418-1422. 

Figure 9.12 Schematic diagram of the structure of the heterodimeric yeast transcription factor Mat a2-Mat al bound to DNA. Both Mat o2 and Mat al are homeodomains containing the helix-turn-helix motif. The first helix in this motif is colored blue and the second, the recognition helix, is red. (a) The assumed structure of the Mat al homeodomain in the absence of DNA, based on Its sequence similarity to other homeodomains of known structure, (b) The structure of the Mat o2 homeodomain. The C-terminal tail (dotted) is flexible in the monomer and has no defined structure, (c) The structure of the Mat a 1-Mat a2-DNA complex. The C-terminal domain of Mat a2 (yellow) folds into an a helix (4) in the complex and interacts with the first two helices of Mat a2, to form a heterodimer that binds to DNA. (Adapted from B.J. Andrews and M.S. Donoviel, Science 270 251-253, 1995.)...

Find the translation and transcription initiation sites, find promoter sites, define open reading rames (ORF)... 

The N-terminal A/B region whose structure has not yet been defined contains a transcriptional activation function, referred to as activation function 1 (AF-1), which can operate autonomously. The length and sequence of the A/B region in the different NRs are highly variable, revealing a very weak evolutionary... 

Fig. 3.14 Model for polyamide inhibition of the p55/p50 heterodimeric transcription factor NF-kB. Polyamides designed to target both the p65 and p50 DNA subsites (NF-kB site in bracket) demonstrated that only those targeting the p50 subsite effectively inhibit heterodimer binding. Symbols are defined in Fig. 3.4...

The multiple sites that serve as origins for DNA replication in eukaryotes are poorly defined except in a few animal viruses and in yeast. However, it is clear that initiation is regulated both spatially and temporaUy, since clusters of adjacent sites initiate rephcation synchronously. There are suggestions that functional domains of chromatin replicate as intact units, implying that the origins of rephcation are specificaUy located with respect to transcription units. 

It is clear that the signals in DNA which control transcription in eukaryotic cells are of several types. Two types of sequence elements are promoter-proximal. One of these defines where transcription is to commence... 

TBP binds to the TATA box in the minor groove of DNA (most transcription factors bind in the major groove) and causes an approximately 100-degree bend or kink of the DNA helix. This bending is thought to facilitate the interaction of TBP-associated factors with other components of the transcription initiation complex and possibly with factors bound to upstream elements. Although defined as a component of class II gene promoters, TBP, by virtue of its association with... 

Pol II associates with other proteins to form a holoenzyme complex. In yeast, at least nine gene products—called Srb (for suppressor of RNA polymerase B)—bind to the CTD. The Srb proteins—or mediators, as they are also called—are essential for pol II transcription, though their exact role in this process has not been defined. Related proteins comprising even more complex forms of RNA polymerase II have been described in human cells. 

Transcription Domains Can Be Defined by Locus Control Regions Insulators... 

By selectively affecting gene transcription and the consequent production of appropriate target mRNAs, the amounts of specific proteins are changed and metabolic processes are influenced. The influence of each of these hormones is quite specific generally, the hormone affects less than 1% of the genes, mRNA, or proteins in a target cell sometimes only a few are affected. The nuclear actions of steroid, thyroid, and retinoid hormones are quite well defined. Most evidence sug-... 

DNA binding proteins. Since these proteins have no homology with proteins of the other families of transcriptional regulators, they define a new family of regulatory proteins. 

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