Chromatin Structure, DNA Sequences and Replication Proteins: Searching for the Principles of Eukaryotic Chromosome Replication

1983 ◽  
pp. 203-233 ◽  
Author(s):  
Melvin L. DePamphilis ◽  
Michael E. Cusick ◽  
Ronald T. Hay ◽  
Cynthia Pritchard ◽  
Lois C. Tack ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Chromatin Structure ◽  
Chromosome Replication ◽  
Replication Proteins ◽  
Eukaryotic Chromosome

scholarly journals Chromosome replication in cell-free systems from Xenopus eggs

1987 ◽  
Vol 317 (1187) ◽  
pp. 483-494 ◽  
Keyword(s):  
Cell Cycle ◽  
Dna Sequences ◽  
Chromosome Replication ◽  
Nucleosome Assembly ◽  
Cloning And Sequencing ◽  
Eukaryotic Chromosome ◽  
Initiation Of Replication ◽  
Egg Extracts ◽  
Acidic Proteins

Cell-free systems from eggs of the frog Xenopus laevis are able to perform most of the acts of eukaryotic chromosome replication in vitro . This now includes the crucial regulatory step of initiation, which had only been achieved for viral systems previously. Purified DNA or nuclei are able to initiate and complete semiconservation replication in egg extracts in vitro (Blow & Laskey, Cell 47, 557-587 (1986)). Replication does not require specialized DNA sequences either in vitro or in microinjected eggs, but in both systems large templates replicate more efficiently than small templates. In some cases replication can re-initiate, excluding the possibility that replication is primed by preexisting primers in the template preparations. When nuclei are replicated in vitro , only one round of replication is observed in a single incubation resembling the single round of replication observed for purified DNA after micro-injection. The mechanism that prevents re-initiation of replication within a single cell cycle is discussed and certain models are eliminated. Nucleosome assembly from histones and DNA has also been studied in cell-free systems from Xenopus eggs. Fractionation has led to the identification of two acidic proteins called nucleoplasmin and N1, which bind histones and transfer them to DNA. The sequences of both proteins have been determined by cDNA cloning and sequencing. Both proteins are found as complexes with histones in eggs.

Serum stimulation of the c-fos enhancer induces reversible changes in c-fos chromatin structure

1990 ◽  
Vol 10 (3) ◽  
pp. 1126-1133
Author(s):  
J L Feng ◽  
B Villeponteau
Keyword(s):  
Growth Factors ◽  
Dna Sequences ◽  
Chromatin Structure ◽  
Transcriptional Activity ◽  
Dnase I ◽  
Enhancer Activity ◽  
Serum Stimulation ◽  
Fos Protein ◽  
Dnase I Sensitivity ◽  
Stimulation Of

Transcription of the proto-oncogene c-fos is known to be activated by growth factors in serum and subsequently repressed by the Fos protein. We show that generalized DNase I sensitivity of c-fos chromatin correlates closely with enhancer activity during induction, repression, and superinduction of the c-fos gene. Within 90 s of serum stimulation, proximal DNA sequences on both sides of the enhancer exhibit increased DNase I sensitivity. Within 5 min, elevated DNase I sensitivity spreads to chromatin at the distal 3' end of the c-fos gene. These results suggest that an open state of chromatin is propagated in both directions from the enhancer. The induced alterations in chromatin structure precede the increased transcriptional activity of the c-fos gene, suggesting that these changes in chromatin structure potentiate transcription.

scholarly journals Centromeric Transcription: A Conserved Swiss-Army Knife

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 911
Author(s):  
Ganesan Arunkumar ◽  
Daniël P. Melters
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Chromatin Structure ◽  
Repetitive Dna Sequences ◽  
Mitotic Spindles ◽  
Heterochromatin Formation ◽  
Protein Loading ◽  
Range Of Functions ◽  
Centromeric Protein ◽  
Essential Function

In most species, the centromere is comprised of repetitive DNA sequences, which rapidly evolve. Paradoxically, centromeres fulfill an essential function during mitosis, as they are the chromosomal sites wherein, through the kinetochore, the mitotic spindles bind. It is now generally accepted that centromeres are transcribed, and that such transcription is associated with a broad range of functions. More than a decade of work on this topic has shown that centromeric transcripts are found across the eukaryotic tree and associate with heterochromatin formation, chromatin structure, kinetochore structure, centromeric protein loading, and inner centromere signaling. In this review, we discuss the conservation of small and long non-coding centromeric RNAs, their associations with various centromeric functions, and their potential roles in disease.

scholarly journals Tumor mutational landscape is a record of the pre-malignant state

2019 ◽  
Author(s):  
Kirsten Kübler ◽  
Rosa Karlić ◽  
Nicholas J. Haradhvala ◽  
Kyungsik Ha ◽  
Jaegil Kim ◽  
...  
Keyword(s):  
Cancer Cell ◽  
Dna Sequences ◽  
Chromatin Structure ◽  
Somatic Mutations ◽  
Major Influence ◽  
Cell Of Origin ◽  
Regional Patterns ◽  
Cancer Subtypes ◽  
Mutational Landscape ◽  
Cancer Types

ABSTRACTChromatin structure has a major influence on the cell-specific density of somatic mutations along the cancer genome. Here, we present a pan-cancer study in which we searched for the putative cancer cell-of-origin of 2,550 whole genomes, representing 32 cancer types by matching their mutational landscape to the regional patterns of chromatin modifications ascertained in 104 normal tissue types. We found that, in almost all cancer types, the cell-of-origin can be predicted solely from their DNA sequences. Our analysis validated the hypothesis that high-grade serous ovarian cancer originates in the fallopian tube and identified distinct origins of breast cancer subtypes. We also demonstrated that the technique is equally capable of identifying the cell-of-origin for a series of 2,044 metastatic samples from 22 of the tumor types available as primaries. Moreover, cancer drivers, whether inherited or acquired, reside in active chromatin regions in the respective cell-of-origin. Taken together, our findings highlight that many somatic mutations accumulate while the chromatin structure of the cell-of-origin is maintained and that this historical record, captured in the DNA, can be used to identify the often elusive cancer cell-of-origin.

Chromatin structure of the HLA-DR alpha gene in different functional states of major histocompatibility complex class II gene expression

1987 ◽  
Vol 7 (5) ◽  
pp. 1967-1972
Author(s):  
B M Peterlin ◽  
K J Hardy ◽  
A S Larsen
Keyword(s):  
Dna Sequences ◽  
Chromatin Structure ◽  
Gene Promoter ◽  
Dnase I ◽  
Consensus Sequences ◽  
Histocompatibility Complex ◽  
Hla Dr ◽  
Hypersensitive Sites ◽  
Alpha Gene ◽  
Regulatory Loci

We utilized DNase I hypersensitivity mapping to study chromatin structure within the HLA-DR alpha gene. We found a single DNase I-hypersensitive site coinciding with the HLA-DR alpha gene promoter in all cells studied. Moreover, in cells that constitutively express HLA-DR, two additional DNase I-hypersensitive sites were observed. These lie within the first intron of the HLA-DR alpha gene and encompass DNA sequences that share homologies with regulatory loci of the immunoglobulin and immune response genes, as well as with core enhancer consensus sequences.

scholarly journals Chromatin structure of the HLA-DR alpha gene in different functional states of major histocompatibility complex class II gene expression.

1987 ◽  
Vol 7 (5) ◽  
pp. 1967-1972 ◽  
Author(s):  
B M Peterlin ◽  
K J Hardy ◽  
A S Larsen
Keyword(s):  
Dna Sequences ◽  
Chromatin Structure ◽  
Gene Promoter ◽  
Dnase I ◽  
Consensus Sequences ◽  
Histocompatibility Complex ◽  
Hla Dr ◽  
Hypersensitive Sites ◽  
Alpha Gene ◽  
Regulatory Loci

We utilized DNase I hypersensitivity mapping to study chromatin structure within the HLA-DR alpha gene. We found a single DNase I-hypersensitive site coinciding with the HLA-DR alpha gene promoter in all cells studied. Moreover, in cells that constitutively express HLA-DR, two additional DNase I-hypersensitive sites were observed. These lie within the first intron of the HLA-DR alpha gene and encompass DNA sequences that share homologies with regulatory loci of the immunoglobulin and immune response genes, as well as with core enhancer consensus sequences.

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