Matrix Attachment Regions Allow DNA Looping

Both in bacteria and in eukaryotes, the DNA is arranged in giant loops attached at intervals to the chromosomal scaffold (see Ch. 4). In bacteria the loops consist of about 40 kbp of DNA, whereas the eukaryotic loops are somewhat longer, about 60 kbp.

During interphase, a filamentous web of proteins, the nuclear matrix, appears just on the inside of the nuclear membrane. DNA is attached to the proteins of the matrix by sites known as matrix attachment regions, or MARs. Because the same DNA sites are used for attachment to the chromosomal scaffold during replication as for attachment to the nuclear matrix during interphase, they are sometimes also called SARs (scaffold attachment regions).

These MAR/SAR sites are 200-1000 bp long and AT-rich (70% AT) but otherwise share no obvious consensus. DNA with multiple runs of A's is inherently bent (see Ch. 4) and the nuclear proteins that bind the MAR sites recognize the bent DNA rather than a specific sequence. Topoisomerase II recognition sites are often found next to MAR sites, implying that the supercoiling of each giant loop is adjusted independently. Enhancers and other regulatory elements are often associated with MAR sites, and, at least in some cases, chromatin remodeling (see below) starts from a MAR site and affects the whole of the chromatin loop (Fig. 10.06).

In transgenic animals and plants, the efficient expression of the transgene is helped by making sure that it lies between two MAR sites. This region of chromatin is then more likely to be opened up for transcription.

matrix attachment region (MAR) Site on eukaryotic DNA that binds to proteins of the nuclear matrix or of the chromosomal scaffold—same as SAR sites nuclear matrix A mesh of filamentous proteins found on the inside of the nuclear membrane and used in anchoring DNA scaffold attachment region (SAR) Site on eukaryotic DNA that binds to proteins of the chromosomal scaffold or of the nuclear matrix—same as MAR sites

Negative Regulation of Transcription Occurs in Eukaryotes 269

DNA Octomer CAAT CAAT Octomer TATA ->- Startpoint

FIGURE 10.07 Blocking the CAAT Box in Sea Urchins

A) Several elements must bind the appropriate transcription factors before transcription occurs.

B) Transcription can be prevented if CAAT displacement protein (CDP) binds to the site that CAAT-binding factor (CTF) normally fills. This prevents assembly of the transcription apparatus and so stops gene expression.

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