Chromatin Structure and Transcription Activation

In the previous considerations the function of chromatin structure on transcription activation has been ignored. Generally it holds true that chromatin structure is decisive for gene activity and certain configurations of chromatin are associated with transcription repression. 

The basic structural imit of chromatin is the nucleosome, in which the DNA is wrapped 1.65 turns aroimd the histone octamer (H2A, H2B, H3, H4)2. The chromatin is further condensed to a so-called solenoid with the aid of histone HI. The following observations are relevant to the discussions about the role of chromatin structure in gene regulation (Lewin, 1994, Workman and Kingston, 1997, Kadonaga, 1998)  

In view of the size of the nucleosome, it appears very difficult to carry out transcription initiation and elongation on nucleosome-covered DNA. The special role played by the nucleosome in the total transcription process is confirmed by the following experimental findings  

Proteins of the yeast SWFSNF family can initiate a modification of nucleosome structure to enable the interaction of the transcription factors with the nucleosome-bound DNA. Proteins of this class can function as anti-repressors by opposing the general repression of chromatin structure. The SWl/SNF proteins are contained in a large protein complex. They can modify nucleosome structure under ATP hydrolysis in such a way as to strengthen the binding of transcription factors, such as GAL4 or the TATA box binding protein, to nucleosome-bound DNA (Cote et al., 1994,). 

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The nucleosomes are further packaged into higher-order structures, among which the so-called solenoid is best characterized. Linker histones like histone HI are involved in this organization. Formation of the higher-order structures generally has a repressive influence on transcription. 

Histones are subject to the folowing covalent modifications (Fig. 1.33 review Lee and Young, 2000)  

Often these modifications are found at the N-terminal tails of the histones, and their presence correlates with a transcriptionally active state of the chromatin. The multiple modifications of histone tails may serve as a combinatorial code for instructing cellular actions on the DNA template during mitosis, transcription or replication. Of the different modifications, the acetylation of histones is of outstanding importance for transcription regulation and will be discussed later (see Section 1.4.7.1). Furthermore, histone methylation has now been recognized as another important regulatory tool for transcriptional control (see Section 1.4.7.2). 

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Regulating mono-ubiquitination of proteins by DUBs is important in histone modification where ubiquitination is thought to modulate chromatin structure and transcriptional activity. Normally, about 10% of the histone core octomers contain ubiquitinated histones and the ubiquitin is removed at mitosis by DUB activity. UBP8 has been demonstrated to regulate the ubiquitination of histone H2B, which is important in transcriptional activation of many genes [88]. 

Dover GJ, Brusilow S, Charache S (1994) Induction of fetal hemoglobin production in subjects with sickle cell anemia by oral sodium phenylbutyrate. Blood 84 339-343 El Kharroubi A, Martin MA (1996) cis-acting sequences located downstream of the human immunodeficiency virus type 1 promoter affect its chromatin structure and transcriptional activity. Mol Cell Biol 16 2958-2966... 

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One of the most-studied covalent modifications is the acetylation of the lysine residues of histone tails. The acetylation state of lysines of nucleosomal histones modulates chromatin structure and regulates gene transcriptional activity. The balance of lysine acetylation is controlled by the antagonistic action of two enzyme families histone deacetylases (HDACs) and histone acetyltransferases (HATs). In humans there are essentially three main HDAC subclasses [6]. 

Boffa, L.C., Walker, J., Chen, T.A., Sterner, R., Mariani, M.R., and Allfrey, V.G. (1990) Factors effecting nucleosome structure in transcriptionally active chromatin. Histone acetylation, nascent RNA and inhibitors of RNA synthesis. Eur. J. Biochem. 194, 811-823. 

The amino terminal tads of the four core histones contain lysines that are acetylated by HATs and deacetylated by HDACs. The histone octamer (H2A, H2B, H3, H4)2 is represented as a cylinder wrapped by DNA. It is thought that neutrahzation of the positive charges on the histone tads results in alterations of the nucleosome structure that may lead to a higher mobdity of the nucleosome and/or an improved accessibdity of the bound DNA, with accompanying changes in chromatin structure, chromatin hierarchy and transcription. In most, but not ad cases, deacetylation correlates with the repressed state and acetylation correlates with the transcriptionady active state. 

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