Genomic transcriptional activity and the structure of chromatin

Reeves, Raymond; Jones, Alma H.

doi:10.1038/260495a0

Cited by 75 publications

(44 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Micrococcal nuclease digestion patterns ofX. laevis ribosomal chromatin in different cell types have always been consistent with the presence of a considerable fraction of nucleosomes in the coding regions (38,39,46), which in the light of our results can be interpreted as being released from the transcriptionally inactive sequences present within the mixed population.…”

Section: Resultsmentioning

confidence: 56%

Different chromatin structures along the spacers flanking active and inactive Xenopus rRNA genes.

Lucchini¹,

Sogo²

1992

Mol. Cell. Biol.

View full text Add to dashboard Cite

The accessibility of DNA in chromatin to psoralen was assayed to compare the chromatin structure of the rRNA coding and spacer regions of the two related frog species Xenopus laevis and Xenopus borealis. Isolated nuclei from tissue culture cells were photoreacted with psoralen, and the extent of cross-linking in the different rDNA regions was analyzed by using a gel retardation assay. In both species, restriction fragments from the coding regions showed two distinct extents of cross-linking, indicating the presence of two types of chromatin, one that contains nucleosomes and represents the inactive gene copies, and the other one which is more cross-linked and corresponds to the transcribed genes. A similar cross-linking pattern was obtained with restriction fragments from the enhancer region. Analysis of fragments including these sequences and the upstream portions of the genes suggests that active genes are preceded by nonnucleosomal enhancer regions. The spacer regions flanking the 3' end of the genes gave different results in the two frog species. In X. borealis, all these sequences are packaged in nucleosomes, whereas in X. laevis a distinct fraction, presumably those flanking the active genes, show a heterogeneous chromatin structure. This disturbed nucleosomal organization correlates with the presence of a weaker terminator at the 3' end of the X. laevis genes compared with those of X. borealis, which allows polymerases to transcribe into the downstream spacer.In the last few years, much progress has been achieved in identifying the different sequence elements located in the intergenic spacers that are involved in the regulation of the rRNA genes. Despite the fact that the DNA sequence of the ribosomal spacers has diverged very rapidly between different organisms, recent studies indicate a general consensus in the function as well as in the arrangement of transcriptional regulatory elements in almost all higher eukaryotes (for reviews, see references 35, 44, and 45). However, some exceptions seem to exist even among closely related species. The most striking difference resides in the function of the spacer elements close to the 3' end of the rRNA precursor coding regions in the two frog species Xenopus laevis and Xenopus borealis. In fact, a series of transcriptional analyses failed to detect a true termination site at the 3' end of the X. laevis rRNA genes (9, 18), whereas the related sites in X. borealis behave like efficient terminators (21) (sites T2, see Fig.

show abstract

Section: Resultsmentioning

confidence: 56%

Different chromatin structures along the spacers flanking active and inactive Xenopus rRNA genes.

Lucchini¹,

Sogo²

1992

Mol. Cell. Biol.

View full text Add to dashboard Cite

show abstract

“…The findings in various laboratories that transcriptional complexes and/or sequences complementary to transcriptional products can be recovered in the nucleosomal fraction obtained by nuclease digestions (for example, Lacy and Axel , 1975;Gottesfeld et al ., 1975;Garel and Axel, 1976;Mathis and Gorovsky , 1976;Kuo et aI. , 1976;Piper et aI., 1976;Reeves and Jones, 1976;Reeves, 1976Reeves, , 1977Brown et al ., 1977) are not contrad ictory to the conclusion that nucleosomal beads are absent in chromatin regions engaged in transcription. It has been shown that nucleosome-sized fragments are also obtained from digestion with micrococcal nuclease when chromatin is unfolded as , for example, in high urea concentrations (Jackson and Ghalkley, 1975; for related observations, see also Woodcock and Frado, 1977;Oudet, Spadafora, and Ghambon, 1977) .…”

Section: Discussionmentioning

confidence: 99%

Changes of nucleosome frequency in nucleolar and non-nucleolar chromatin as a function of transcription: an electron microscopic study

Scheer

1978

Cell

152

View full text Add to dashboard Cite

SummaryThe morphology of nucleolar and non-nucleolar (Iampbrush chromosome loops) chromatin was studied in the electron microscope during states of reduced transcriptional activity in amphibian oocytes (Xenopus laevis, Triturus alpestris, T. cristatus). Reduced transcriptional activity was observed in maturing stages of oocyte development and after treatment with an inhibitor, actinomycin D.Strands of nucleolar chromatin appear smooth and thin, and contain only few, if any, nucleosomal particles in the transcribed units. This is true whether they are densely or only sparsely covered with lateral ribonucleoprotein fibrils. This smooth and non-nucleosomal character is also predominant in the interspersed, apparently nontranscribed rDNA spacer regions. During inactivation, however, nucleolar chromatin frequently and progressively assumes a beaded appearance in extended fibril-free-that is, apparently nontranscribed -regions. I n either fUll-grown 00-cytes or late after drug treatment, most of the nucleolar chromatin is no longer smooth and thin, but rather shows a beaded configuration indistinguishable from inactive non -nucleolar chromatin. In many chromatin strands, transitions of fibril-associated regions of smooth character into beaded regions wihout lateral fibrils are seen.Similarly, in the non-nucleolar chromatin of the retracting lampbrush chromosome loops, reduced transcriptional activity is correlated with a change from smooth to beaded morphology. Here, however, beaded regions are also commonly found interspersed between the more or less distant bases of the lateral fibrils, the putative transcriptional complexes.I n both sorts of chromatin, detergents (in particular Sarkosyl) that remove most of the chromatin proteins including histones from the DNA axis but leave the RNA polymerases of the transcriptional complexes attached were used to discriminate between polymerases and nucleosomal particles. The results suggest that nucleosomes are absent in heavily transcribed chromatin regions but are reformed after inactivation. In contrast to the findings with inactivated nucleolar genes, in lampbrush chromosome loops the beaded nucleosomal configuration appears to be assumed also in regions within transcriptional units that, perhaps temporarily, are not involved in transcription.

show abstract

“…However, with the advent of massively parallel short-read DNA sequencing and its potential for single base-pair resolution, there has been a renaissance of interest in traditional methods for chromatin characterization, including the use of bisulfite sequencing for mapping DNA methylation [10] and the use of non-specific nucleases, including micrococcal nuclease (MNase) [11], deoxyribonuclease I (DNase I) [12] and exonuclease [13] (Table 1). Here, we focus on recently developed strategies for characterizing nucleosomes, TFs and chromatin-associated proteins at base-pair resolution, and we discuss prospects for full epigenome characterization.…”

Section: The Epigenomementioning

confidence: 99%