Inverted duplication of histone genes in chicken and disposition of regulatory sequences

Sw, Wang; Robins, Allan J.; D’Andrea, Richard J.; Wells, J. R. E.

doi:10.1093/nar/13.4.1369

Cited by 42 publications

(15 citation statements)

References 25 publications

(15 reference statements)

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“…Outside the duplicated region the sequences diverged considerably, that is, the boundaries of the duplication were well defined. A significant feature was that these precise boundaries were characterized by a 10-base-pair direct repeat at the H4 end and a 10-base-pair inverted repeat at the H2A end (30). These repeats were closely related and may represent the sites of recombination events which generated the symmetrical structure (Fig.…”

Section: Methodsmentioning

confidence: 99%

“…Histone genes are indicated at the top by arrows, and the clones derived from this region are indicated below them. The direction of transcription (5'--3') indicated by the horizontal arrows was determined by DNA sequencing (R. Sturm, L. S. Coles, and J. Powell, personal communication; 30). Clones ACH1Oa and XCH3d have been described previously (26).…”

Section: Methodsmentioning

confidence: 99%

“…The detailed restriction mapping of subclones containing individual gene clusters ( Fig. 2 and 3 DNA sequencing (30). In the clones in which restriction site symmetry was observed, clustered histone genes appeared as an inverted duplication centered around H3 genes.…”

Section: Methodsmentioning

confidence: 99%

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Chromosomal organization of chicken histone genes: preferred associations and inverted duplications.

D’Andrea¹,

Coles²,

Lesnikowski³

et al. 1985

Mol. Cell. Biol.

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We present a detailed picture of the disposition of core and HI histone genes in the chicken genome. Forty-two genes were located within four nonoverlapping regions totalling approximately 175 kilobases and covered by three cosmid clones and a number of A clones. The genes for the tissue-specific H5 histone and other variant histones were not found in these regions. The longest continuous region mapped was 67 kilobases and contained 21 histone genes in five dissimilar clusters. No long-range repeat was evident, but there were preferred associations, such as HI genes with paired, divergently transcribed H2A-H2B genes and H3-H4 associations. However, there were exceptions, and even when associations such as H1-H2A-H2B were maintained, the order of those genes within a cluster may not have been. Another feature was the presence of three (unrelated) clusters in which genes were symmetrically ordered around central H3 genes; in one such cluster, the boundaries of a duplicated H2A-H4 gene pair contained related repeat sequences. Despite the dispersed nature of chicken histone genes, the number of each type was approximately equal, being represented as follows: 6 Hi, 10 H2A, 8 H2B, 10 H3, and 8 H4.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Chromosomal organization of chicken histone genes: preferred associations and inverted duplications.

D’Andrea¹,

Coles²,

Lesnikowski³

et al. 1985

Mol. Cell. Biol.

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“…Of the 44 chicken H1 and core genes, 30 have been sequenced, and available nucleotide sequence data indicate that the H1, H2A, H2B, and H3 families, respectively, comprise at least six, two, four, and three different protein variants (3,(21)(22)(23)(24)(25)(26)(27)(28)(29). All of the eight H2B genes belong to two major histone gene clusters with a total length of about 140 kb 1 (24).…”

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confidence: 99%

Targeted Disruption of H2B-V Encoding a Particular H2B Histone Variant Causes Changes in Protein Patterns on Two-dimensional Polyacrylamide Gel Electrophoresis in the DT40 Chicken B Cell Line

Yasuda¹,

Takeda

Nakayama³

1995

Journal of Biological Chemistry

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The chicken H2B gene family comprises eight members (H2B-I to H2B-VIII), which are all located in two major histone gene clusters. All of them have been shown to encode four different protein variants (classes I to IV). In the DT40 chicken B cell line, the H2B-V gene, encoding the class III H2B variant, constituted about 10% of the total intracellular mRNA from all the H2B genes. To study the nature of this particular variant in vivo, we generated heterozygous (H2B-V, ؉/؊) and homozygous (H2B-V, ؊/؊) DT40 mutants by targeted integration. The remaining H2B genes were shown to be expressed more in these mutants than in the wild-type cell lines. The growth rate of DT40 cells was unchanged in the absence of the H2B-V gene. Two-dimensional polyacrylamide gel electrophoresis showed that the protein patterns were, on the whole, similar between the wildtype and homozygous cell lines. However, within this constant background, some cellular proteins disappeared or decreased quantitatively in the homozygous mutants, and several other proteins increased or newly appeared. These results suggest that the class III H2B variant participates negatively or positively in regulation of the expression of particular genes that encode the proteins that vary in DT40 cells. This type of regulation is possibly mediated through alterations in nucleosome structure over the restricted regions involving the putative genes of the DT40 genome.Chickens have fewer copies of the histone genes, ranging from six copies of the H1 gene to about ten copies of the core genes (H2A, H2B, H3, and H4) (1-3) than most higher eukaryotes, which possess large numbers of the genes of each histone subtype, ranging from several dozen to hundreds (4 -7). Recently, furthermore, compensation for disruption of particular histone genes has been shown in yeast and chickens (8 -15). Thus, in eukaryotes, this type of regulation, as well as the presence of multiple copies of the histone genes, should ensure that all the core histone subtypes remain in stoichiometric balance so that the chromatin structure is maintained precisely during cell proliferation.On the other hand, there are several protein variants for each histone subtype in many higher organisms (16 -20). Of the 44 chicken H1 and core genes, 30 have been sequenced, and available nucleotide sequence data indicate that the H1, H2A, H2B, and H3 families, respectively, comprise at least six, two, four, and three different protein variants (3,(21)(22)(23)(24)(25)(26)(27)(28)(29). All of the eight H2B genes belong to two major histone gene clusters with a total length of about 140 kb 1 (24). Five H2B genes (H2B-I, H2B-II, H2B-III, H2B-IV, and H2B-VI) encode the same amino acid sequence (class I), and that of H2B-VII differs from that of class I in three amino acid residues (Lys 31 3 Arg, Ser 32 3 Ala, Gly 60 3 Ser; class II) (24). H2B-V contains a single amino acid alteration (Lys 30 3 Arg; class III) (26), and the amino acid sequence of H2B-VIII is distinct from that of class I in two amino acid residues (Lys 30 3 A...

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“…Figure 6 (lane 1) shows that purified H4TF2 produced a single complex (a) with an oligonucleotide containing the cognate sequence of the human histone H4 gene pHu4A (19). This complex was specifically inhibited by oligonucleotides containing the homologous sequence or the corresponding regions of the chicken H4L (53) and HS genes but not by an HS oligonucleotide carrying a mutation of the relevant region (Fig. 6, lanes 2 to 5).…”

Section: Resultsmentioning

confidence: 97%

Transcription of the histone H5 gene is regulated by three differentiation-specific enhancers.

et al. 1993

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Histone H5, an early marker of the avian erythroid lineage, is expressed at low levels in early erythroid precursors and at higher levels in more mature cells. We show that the increase in H5 expression is due to transcriptional activation of the H5 gene following differentiation of precursor CFU(E). We have found and characterized two upstream enhancers, El (between -2233 and -1878 from the site of transcription initiation, +1) and E3 (between -1321 and -1163), and confirmed the presence of a downstream enhancer (C. D.Trainor, S. J. Stamler, and J. D. Engel, Nature [London] 328:827-830, 1987) E7 (between +846 and + 1181) which are responsible for the increase in H5 gene transcription. The enhancers had a weak effect in nondifferentiated CFU(E) but a strong effect when the cells were induced to differentiate. Cooperation among the three enhancers, however, was not required for HS gene activity in the differentiated cells. The enhancers contain binding sites for several ubiquitous and erythroid cell-specific nuclear proteins, including GATA-1, as demonstrated with GATA-1-specific antibodies. Although the GATA sites were required for enhancer function, the concentration of GATA-1, GATA-2, and GATA-3 decreased during cell differentiation, and overexpression of these factors had little effect on H5 transcription. Hence, the differentiation-specific effect of the enhancers is not mediated by changes in relative levels of the GATA factors. Functional analysis of the H5 promoter indicated that the requirement of several elements, including a GC box necessary for transcription enhancement, did not change during the early stages of CFU(E) differentiation. However, the UPE, a positive element in proliferating CFU(E) recognized by the transcription factor H4TF2, was dispensable in the differentiated cells. These results suggest that as the cells enter the final stages of differentiation, there is a reprogramming of the regulatory factors that control H5 transcription and that the enhancers rescue and increase the activity of the promoter.Vertebrate erythropoiesis is characterized by the expression of sets of tissue-specific genes which are temporally regulated during maturation of the committed precursors. The chicken histone H5 gene is an interesting marker by which to study how these processes are regulated, because it responds both to early and late differentiation cues during erythropoiesis. Contrary to late erythroid markers, including the adult globin chains and cell surface proteins (2), H5 is already present in the early precursor CFU(E) (3, 45), and its expression increases further with the onset of the expression of these late genes (1). Transcription run-on analysis of erythroid cells at different stages of maturation have also indicated that the activity of the H5 gene is lower in proliferating erythroid precursors than in more mature cells (1). Thus, H5 expression during maturation is predominantly regulated at the transcription level.In an attempt to understand the molecular mechanisms accounting for the t...

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Inverted duplication of histone genes in chicken and disposition of regulatory sequences

Cited by 42 publications

References 25 publications

Chromosomal organization of chicken histone genes: preferred associations and inverted duplications.

Chromosomal organization of chicken histone genes: preferred associations and inverted duplications.

Targeted Disruption of H2B-V Encoding a Particular H2B Histone Variant Causes Changes in Protein Patterns on Two-dimensional Polyacrylamide Gel Electrophoresis in the DT40 Chicken B Cell Line

Transcription of the histone H5 gene is regulated by three differentiation-specific enhancers.

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