A destabilized DNA conformation associated with tightly bound nuclear proteins in active genes of rat myoblast

Chromatin domains and prediction of MAR sequences

Polynuceosomes are constrained into loops or domains and are insulated from the effects of chromatin structure and torsional strain from flanking domains by the cross-complexation of matrix-attached regions (MARs) and matrix proteins. MARs or SARs have an average size of 500 bp, are spaced about every 30 kb, and are control elements maintaining independent realms of gene activity. A fraction of MARs may cohabit with core origin replication (ORIs) and another fraction might cohabit with transcriptional enhancers. DNA replication, transcription, repair, splicing, and recombination seem to take place on the nuclear matrix. Classical AT-rich MARs have been proposed to anchor the core enhancers and core origins complexed with low abundancy transcription factors to the nuclear matrix via the cooperative binding to MARs of abundant classical matrix proteins (topoisomerase II, histone H1, lamins, SP120, ARBP, SATB1); this creates a unique nuclear microenvironment rich in regulatory proteins able to sustain transcription, replication, repair, and recombination. Theoretical searches and experimental data strongly support a model of activation of MARs and ORIs by transcription factors. A set of 21 characteristics are deduced or proposed for MAR/ORI sequences including their enrichment in inverted repeats, AT tracts, DNA unwinding elements, replication initiator protein sites, homooligonucleotide repeats (i.e., AAA, TTT, CCC), curved DNA, DNase I-hypersensitive sites, nucleosome-free stretches, polypurine stretches, and motifs with a potential for left-handed and triplex structures. We are establishing Banks of ORI and MAR sequences and have undertaken a large project of sequencing a large number of MARs in an effort to determine classes of DNA sequences in these regulatory elements and to understand their role at the origins of replication and transcriptional enhancers.

Nature of DNA sequences at the attachment regions of genes to the nuclear matrix

Matrix-attached regions (MARs) have been demonstrated to nest origins of replication and transcriptional enhancers. A set of 13 rules is proposed aimed at facilitating the classification of a DNA sequence as a matrix attachment region.(ABSTRACT TRUNCATED AT 250 WORDS)

Complexes of nuclear matrix DNA with proteins tightly bound to DNA contain a specific small-size RNA of a novel type

Analysis of DNA-protein structures composed of nuclear matrix attached DNA and the most tightly bound proteins was performed. Although the previously described non-histone proteins (1) were present the buoyant density of the complex was the same as that of pure DNA. RNA inaccessible to RNase in 0.4 M NaCl but digestible in low ionic strength buffer was detected. This RNA is not a nascent one. It turned out to be homogeneous and represent a novel type of small nuclear RNA. Partial sequence of this RNA is presented.

The distribution of tightly bound proteins along the DNA chain reflects the type of cell differentiation

Distribution of proteins tightly bound to DNA (TBP) along the DNA chain was found to depend on the cell lineage. DNA sequences coding for alpha globin genes are preferentially represented in the TBP-associated DNA fractions isolated from erythroid cells (erythroblasts, mature erythrocytes, differentiated and non-differentiated Friend erythroleukemia cells), but not from cultured fibroblast cells. In transcriptionally active nuclei, complexes of TBP interact with the nuclear matrix, while in mature erythrocytes this interaction disappears.

Thiol proteins in chromatin

Total half-cystine residues in proteins of pig liver chromatin have been measured. About half of them are present in the reduced state. Thiol groups of non-histone chromatin proteins, which amount to about 40 nmol/mg of protein, are preferentially located in chromatin fragments which are more easily solubilised either by DNAse I or by DNAse II. The data obtained are compatible with an involvement of SH and SS groups in chromatin structure and function.

Distribution of tissue-specific tightly bound non-histone proteins in the first level of repeating chromatin structures

Non-histone proteins, tightly bound to DNA, have been extracted from whole chromatin and core particles prepared from pig liver or kidney. We have investigated by bidimensional slab gel electrophoresis the distribution of this protein class in the first level of repeating structure of chromatin. Our results reveal that non-histone proteins tightly bound to DNA are a heterogeneous protein class. Some of them, particularly in the core particles, appear to be essentially the same in both tissues, though having differences in their isoelectric point, which may be attributed to postsynthetic modifications. We have calculated that this protein class is associated to only 10% of nucleosomes, these nucleosomes having, on the average, one protein molecule for each core DNA. The tissue-specific proteins have high molecular mass (ranging from 135 kDa to 70 kDa in liver, over 135 kDa in kidney) and, in kidney, a more basic isoelectric point. These proteins are mainly located outside the core particles; they could be situated in the spacer regions and/or be involved in determining higher levels of chromatin organization.

Alpha actin gene exist in an active structural configuration in the proliferating myoblasts as well as in differentiated myotubes of the L6 line

Single-stranded DNA (ssDNA) mainly consisting of transcription sites was probed with cDNA actin clones for studying the expression of actin specific genes during myogenesis in the L6 line of rat myogenic cells. As compared with total nuclear DNA, ssDNA from myoblasts and myotubes was found greatly enriched in sequences complementary to both muscular and non muscular actin sequences. In contrast, ssDNA from spleen, hepatocytes or hepatoma cells was found enriched only in sequences complementary to non muscle actin cDNA. Actin specific sequences accumulated in the ssDNA fraction are almost entirely derived from the coding DNA strand. The DNAase I sensitivity of the actin genes sequences in myogenic and non myogenic cells correlated the data obtained with the ssDNA fraction. It is concluded that the muscle specific actin genes is either transcriptionally active or at least exist in an active configuration in the proliferating myoblasts as well as in the terminally differentiated myotubes.