Genes are contained in a complex of DNA and proteins (mostly histones) called chromatin, and its basic unit of structure is the nucleosome (Fig. 1.1). Each nucleosome is composed of an octamer of histone proteins and approximately 140 base pairs of DNA. Nucleosomes themselves are joined into clusters by binding of DNA existing between nucleosomes (linker DNA) with other histone proteins (H1 histones; Fig.1). Nucleosomes keep the DNA tightly coiled, such that it cannot be transcribed. In this inactive state, chromatin appears as beads of nucleosomes on a string of DNA and is referred to as heterochromatin. For transcription to occur, this DNA must be uncoiled from the beads. In this uncoiled state, chromatin is referred to as euchromatin.

Fig1. Drawing showing nucleosomes that form the basic unit of chromatin. Each nucleosome consists of an octamer of histone proteins and ap— proximately 140 base pairs of DNA. Nucleosomes are joined into clusters by linker DNA and other his— tone proteins.

Genes reside within the DNA strand and contain regions called exons, which can be translated into proteins, and introns, which are interspersed between exons and which are not transcribed into proteins (Fig.2). In addition to exons and introns, a typical gene includes the following: a promoter region that binds RNA

polymerase for the initiation of transcription; a transcription initiation site; a translation initiation site to designate the first amino acid in the protein; a translation termination codon; and a 3' untranslated region that includes a sequence (the poly A addition site) that assists with stabilizing the mRNA, allows it to exit the nucleus, and permits it to be translated into protein (Fig. 2). By convention, the 5’ and the 3’ regions of a gene are specified in relation to the RNA transcribed from the gene. Thus, DNA is transcribed from the 5’ to the 3’ end, and the promoter region is upstream from the transcription initiation site (Fig. 2). The promoter region, where the RNA polymerase binds, usually contains the sequence TATA, and this site is called the TATA box (Fig. 2). In order to bind to this site, however, the polymerase requires additional proteins called transcription factors (Fig. 3). Transcription factors also have a specific DNA-binding do main plus a transactivating domain that activates or inhibits transcription of the gene whose promoter or enhancer it has bound. In combi nation with other proteins, transcription factors activate gene expression by causing the DNA nucleosome complex to unwind, by releasing the polymerase so that it can transcribe the DNA template, and by preventing new nucleosomes from forming.

Fig2. Drawing of a “typical” gene showing the promoter region containing the TATA box; exons that contain DNA sequences that are translated into proteins; introns; the transcription initiation site; the translation initiation site that designates the code for the first amino acid in a protein; and the 3’ untranslated region that includes the poly A addition site that participates in stabilizing the mRNA, allows it to exit the nucleus, and permits its translation into a protein.

Fig3. Drawing showing binding of RNA polymerase II to the TATA box site of the promoter region of a gene. This binding requires a complex of proteins plus an additional protein called a transcription factor. Transcription factors have their own specific DNA—binding domain and function to regulate gene expression.

Enhancers are regulatory elements of DNA that activate utilization of promoters to control their efficiency and the rate of transcription from the promoter. Enhancers can reside anywhere along the DNA strand and do not have to reside close to a promoter. Like promoters, enhancers bind transcription factors (through the transcription factor’s transactivating domain) and are used to regulate the timing of a gene’s expression and its cell-specific location. For ex ample, separate enhancers in a gene can be used to direct the same gene to be expressed in different tissues. Hie PAX6 transcription factor, which participates in pancreas, eye, and neural tube development, contains three separate enhancers, each of which regulates the gene’s expression in the appropriate tissue. Enhancers act by altering chromatin to expose the promoter or by facilitating binding of the RNA polymerase. Sometimes, enhancers can inhibit transcription and are called silencers. This phenomenon allows a transcription factor to activate one gene while silencing another by binding to different enhancers. Thus, transcription factors themselves have a DNA-binding domain specific to a region of DNA plus a transactivating domain that binds to a promoter or an enhancer and activates or inhibits the gene regulated by these elements.

DNA Methylation Represses Transcription

 Methylation of cytosine bases in the promoter regions of genes represses transcription of those genes. Thus, some genes are silenced by this mechanism. For example, one of the X chromosomes in each cell of a female is inactivated (X chromosome inactivation) by this methylation mechanism. Similarly, genes in different types of cells are repressed by methylation, such that muscle cells make muscle proteins (their promoter DNA is mostly unmethylated) but not blood proteins (their DNA is highly methylated). In this manner, each cell can maintain its characteristic differentiated state. DNA methylation is also responsible for genomic imprinting in which only a gene inherited from the father or the mother is expressed, whereas the other gene is silenced. Approximately 40 to 60 human genes are imprinted, and their methylation patterns are established during spermatogenesis and oogenesis. Methylation silences DNA by inhibiting binding of transcription factors or by altering histone binding resulting in stabilization of nucleosomes and tightly coiled DNA that cannot be transcribed.

مواضيع ذات صلة

كيف نكشف عن هوية الشخص الجينية

طرق توسيم المجسات (labeling of probes) للكشف عن الجين الهدف

الـ PCR المتزامن الكمي (quantitative Real time PCR)

الـ PCR ذو البداية الحارة (hot start PCR)

Salt Effects on Protein-DNA Interactions

Structures of DNA-Binding Proteins

Secondary Structure Predictions

Calculation of Protein Tertiary Structure

RNA Heterogeneity

Nuclear Export of RNA

Regulation of RNA Processing: Capping, Splicing, and Polyadenylation

The Alpha Helix, Beta Sheet, and Beta Turn