Psoralen-crosslinking of DNA as a probe for the structure of active nucleolar chromatin

Sogo, José M.; Ness, Penelope J.; Widmer, Rosa M.; Parish, Roger W.; Koller, Th.

doi:10.1016/0022-2836(84)90318-8

Cited by 126 publications

(90 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In previous studies it was shown that chloroquine binds only to DNA, not proteins, and at low binding ratios it does not significantly alter the bending and torsional stiffness of the DNA [15,16]. Within the chromatin, chloroquine was shown to bind essentially entirely to the linker DNA [9][10][11] without any noticeable disassembly of nucleosome core particles [9][10][11]. At concentrations up to 10 mg/ml limited-time chloroquine treatment is not cytotoxic for cells [8,9], and in relatively low concentrations its effects on chromatin are limited, presumably by its intercalatory action [91.…”

Section: Resultsmentioning

confidence: 96%

Alterations in the internucleosomal DNA helical twist in chromatin of human erythroleukemia cells in vivo influences the chromatin higher‐order folding

Krajewski

1995

FEBS Letters

View full text Add to dashboard Cite

~.bstract In the present study chloroquine diphosphate, a DNA intercalating drug, was used to alter the internucleosomal DNA helical twist in chromatin of living mammalian cells. The intercalative binding of ehloroquine effectively unwinds the DNA double helix and its binding is restricted to nucleosomal linker regions without noticeable disruption of nuclensomes. The results pre~ented here imply that the alterations in the rotation angle between the adjacent nucleosomes in chromatin of eukaryotic cells in vivo significantly influences the way the chain of nucleosomes folds in higher-order chromatin structures, as evidenced by spe4fie alterations in nuclease susceptibility of chromatin.

show abstract

Section: Resultsmentioning

confidence: 96%

Alterations in the internucleosomal DNA helical twist in chromatin of human erythroleukemia cells in vivo influences the chromatin higher‐order folding

Krajewski

1995

FEBS Letters

View full text Add to dashboard Cite

show abstract

“…Only a subset of rRNA genes is actively transcribed during interphase (Shaw et al, 1995), even in yeast with comparatively few rRNA genes (Dammann et al, 1993), and heavily transcribed cistrons are not organized in nucleosomal structures (e.g., Sogo et al, 1984; Conconi et al, 1992; Dammann et al, 1993). Apparently, transcriptional activity within nucleoli is upregulated by increased activity of already active cistrons that are free of nucleosomes (reflected by "Christmas tree"-like structures of nascent transcripts in electron microscopic images; Miller and Beatty, 1969) rather than by activation of …”

Section: H4 Is More Strongly Acetylated At the Nor During Mitosis Whmentioning

confidence: 99%

“…Transcriptionally active rDNA genes were shown to be devoid of nucleosomes (Sogo et al, 1984;Conconi et al, 1989Conconi et al, , 1992Dammann et al, 1993), but the presence of histones within the nucleolus and their degree of acetylation during the course of interphase is still an open question (Derenzini et al, 1985;Thiry and Muller, 1989;González-Melendi et al, 1998).…”

Section: Introductionmentioning

confidence: 99%

“…Deposition-related acetylation of lysines 5 and 12 of H4, that is, incorporation of these acetylated isoforms into newly replicated chromatin, appears to be a highly conserved phenomenon (Sobel et al, 1995). Moreover, Idei et al (1996) reported different histone H4 acetylation patterns of plant interphase nuclei; however, they were unable to relate the different patterns with either defined cell cycle stages or specific chromatin domains (except for the nucleolus).Transcriptionally active rDNA genes were shown to be devoid of nucleosomes (Sogo et al, 1984; Conconi et al, 1989 Conconi et al, , 1992 Dammann et al, 1993), but the presence of histones within the nucleolus and their degree of acetylation during the course of interphase is still an open question (Derenzini et al, 1985;Thiry and Muller, 1989;González-Melendi et al, 1998).To learn whether the extent of acetylation at all acetylatable positions of the core histones H3 and H4 remains constant along the cell cycle for specific chromatin domains (nucleolus organizers, euchromatin, and two fractions of heterochromatin of the field bean), we developed a new approach. After immunodetection of histone isoforms on isolated meristematic nuclei sorted on the basis of their DNA content into G1, early S, mid-S, late S, and G2 fractions, defined chromatin domains of individual chromosomes are identified by fluorescence in situ hybridization (FISH) with specific probes.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Histone H4 Acetylation of Euchromatin and Heterochromatin Is Cell Cycle Dependent and Correlated with Replication Rather Than with Transcription

Jasencakova¹,

Meister²,

et al. 2000

View full text Add to dashboard Cite

Reversible acetylation of nucleosomal histones H3 and H4 generally is believed to be correlated with potential transcriptional activity of eukaryotic chromatin domains. Here, we report that the extent of H4 acetylation within euchromatin and heterochromatic domains is linked with DNA replication rather than with transcriptional activity, whereas H3 acetylation remains fairly constant throughout the cell cycle. Compared with euchromatin, plant nucleolus organizers were more strongly acetylated at H4 during mitosis but less acetylated during S phase, when the nucleolus appeared to be (at least transiently) devoid of nucleosomes. Deposition-related acetylation of lysines 5 and 12 of H4 seems to be conserved in animals and plants and extended to K16 in plants. A possibly species-specific above-average acetylation at lysines 9/18 and 14 of H3 appeared in 4 ,6-diamidino-2-phenylindole (DAPI)-stained heterochromatin fractions. These results were obtained by combining immunodetection of all acetylatable isoforms of H3 and H4 on mitotic chromosomes and nuclei in G1, early S, mid-S, late S, and G2 phases of the field bean with identification of specific chromatin domains by fluorescence in situ hybridization or DAPI staining. In addition, the histone acetylation patterns of distinct domains were compared with their replication and transcription patterns. INTRODUCTIONThe histone proteins H2A, H2B, H3, and H4 form octamers that constitute the nucleosome core particles in all eukaryotes. Their N-terminal tails are subject to post-translational modifications such as acetylation, phosphorylation, methylation, ubiquitination, glycosylation, and ADP ribosylation (reviewed in Smith et al., 1995;Spencer and Davie, 1999).The reversible acetylation of N-terminal lysine residues at positions 5, 8, 12, and 16 of H4 and 9, 14, 18, and 23 of H3 mediates decondensation of the nucleosome structure (Loidl, 1988(Loidl, , 1994Garcia-Ramirez et al., 1995), alters histone-DNA interactions (Hong et al., 1993), and facilitates access and binding of transcription factors to genes transcribed by RNA polymerases II or III (Lee et al., 1993;Vettese-Dadey et al., 1996).A correlation between histone acetylation and potential transcriptional activity, initially proposed by Allfrey et al. (1964), has been proved in several cases (reviewed in Csordas, 1990;Turner, 1991Turner, , 1993Loidl, 1994;Grunstein, 1997;Struhl, 1998). According to one attractive recent hypothesis, histone modifications may constitute a concerted code to "specify unique downstream functions" (Strahl and Allis, 2000;Turner, 2000).After indirect immunolabeling with antibodies raised against acetylated isoforms of histone H4 (Turner and Fellows, 1989;, mammalian metaphase chromosomes show intense acetylation of euchromatic R-bands and less intense acetylation of constitutive and facultative heterochromatin (Jeppesen and Turner, 1993). The patterns of histone H4 acetylation described for plant chromosomes (Houben et al., 1996Belyaev et al., 1997;Vyskot et al., 1999) also reveal a below...

show abstract

“…Nucleosome folding is also able to affect TMP binding to DNA (18) (19). Several DNase I hypersensitive sites have been mapped over the flanking regions of the ␤-globin genes (2).…”

Section: Discussionmentioning

confidence: 99%

In Vivo Binding of Trimethylpsoralen Detects DNA Structural Alterations Associated with Transcribing Regions in the Human β-Globin Cluster

Jiménez-Ruı́z

Zhang

Shen

1995

Journal of Biological Chemistry

View full text Add to dashboard Cite

In order to increase our knowledge about the mechanisms that regulate expression of human ␤-like globin genes, we have used a novel technique to analyze the chromatin structure in living cells. This approach allowed us to detect specific DNA regions in vivo where nucleosome folding or unconstrained DNA supercoiling in erythroid cells differs from that in non-erythroid cells. In this method, we use 4,5,8-trimethylpsoralen (TMP) as a probe capable of detecting altered chromatin conformations. Our results show that TMP binds to DNA with a higher affinity over the regions in the locus that are actively expressed, including both the promoter and the transcribed region. This higher affinity detected when comparing erythroid cells with non-erythroid cells does not extend to other regions inside the ␤-globin cluster. Our data suggest that the observed effect is likely due to nucleosome displacement. Alternatively, it could result from localized DNA supercoiling, but not from widespread torsional stress across the entire ␤-like globin locus as hypothesized previously.Human ␤-globin cluster is located in chromosome 11 and contains six genes expressed only in erythroid cells at different developmental stages. The pattern of expression of these genes during development is precisely regulated: ⑀-gene is expressed during the early stages of embryo development, the ␥-genes ( A ␥ and G ␥) are expressed during the fetal stages, and the product of the ␤-gene is the most prominent form in adults. A sequence located 5 to 15 kb 1 upstream from the embryonic ⑀-globin gene plays an essential role on both the tissue-specific and the developmental specific expression of the ␤-globin cluster. This sequence has been named locus control region (LCR) and contains four DNase I-hypersensitive sites: 5ЈHS-1, 5ЈHS-2, 5ЈHS-3, and 5ЈHS-4. Chromatin structure analysis on the human ␤-globin cluster has revealed that the entire locus is preferentially sensitive to DNase I in erythroid cells (1-4). However, natural deletions that eliminate the LCR elements, such as that occurring in Hispanics (␥␦␤) 0 -thalassemia, prevent tissue-specific changes in chromatin structure and render the ␤-globin locus resistant to DNase I (5). On the other hand, there are evidences indicating that some LCR elements are able to exert their effect only when integrated into the genome or at least when they are folded into chromatin (6 -8). According to these results, there is reason to believe that the LCR elements may regulate ␤-globin locus expression through alterations on the chromatin structure within the locus.In the present work we use a novel technique to compare chromatin structure in vivo in the ␤-globin locus in K562 cells and HeLa cells. Our approach is based on the original technique described by Cook et al. (9), where 4,5Ј,8-trimethylpsoralen (TMP) is used as a probe for altered chromatin conformations. Variations on nucleosome folding or unconstrained DNA supercoiling affect the rate of TMP binding to DNA. Our results show that TMP cross-links DNA more effici...

show abstract

Psoralen-crosslinking of DNA as a probe for the structure of active nucleolar chromatin

Cited by 126 publications

References 46 publications

Alterations in the internucleosomal DNA helical twist in chromatin of human erythroleukemia cells in vivo influences the chromatin higher‐order folding

Alterations in the internucleosomal DNA helical twist in chromatin of human erythroleukemia cells in vivo influences the chromatin higher‐order folding

Histone H4 Acetylation of Euchromatin and Heterochromatin Is Cell Cycle Dependent and Correlated with Replication Rather Than with Transcription

In Vivo Binding of Trimethylpsoralen Detects DNA Structural Alterations Associated with Transcribing Regions in the Human β-Globin Cluster

Contact Info

Product

Resources

About