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A Bird

Publications and source records attributed to A Bird.

124 records · Page 7Linked to original sources
PubMed1985

A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA.

About 1% of the mouse genome is cleaved by Hpa II to give a discrete fraction on gels. The nonmethylated fraction is present in all tested tissues, including sperm, and contains Hpa II sites at about 15 times their frequency in bulk DNA. About 80% of the fraction is composed of sequences that occur once or a few times per genome; the remainder is largely rDNA. Unlike bulk DNA, the fraction is not deficient in CpG, and this may be directly due to the lack of methylation. Genomic mapping of three nonribosomal fragments showed that they are part of islands of DNA within which nonmethylated Hpa II and Hha I sites are highly concentrated. We estimate about 30,000 islands per haploid genome and discuss evidence that many may be associated with genes.

Animals↗
PubMed1983

The origin of the rRNA precursor from Xenopus borealis, analysed in vivo and in vitro.

We have determined the origin of the major transcript of Xenopus borealis rDNA by the use of an SI nuclease protection assay. The DNA surrounding the origin of this transcript was sequenced, and the region upstream of the origin was shown to have strong sequence homology with that region from X.laevis rDNA. We have also demonstrated faithful transcription from this origin using cloned X.borealis rDNA in an extract derived from X. laevis culture cells. This in vitro transcription was insensitive to 100 micrograms/ml alpha-amanatin, suggesting that it was mediated by RNA polymerase 1.

Animals↗
PubMed1983

DNaseI-hypersensitive sites at promoter-like sequences in the spacer of Xenopus laevis and Xenopus borealis ribosomal DNA.

We have detected a DNAseI hypersensitive site in the ribosomal DNA spacer of Xenopus laevis and Xenopus borealis. The site is present in blood and embryonic nuclei of each species. In interspecies hybrids, however, the site is absent in unexpressed borealis rDNA, but is present normally in expressed laevis rDNA. Hypersensitive sites are located well upstream (over lkb) of the pre-ribosomal RNA promoter. Sequencing of the hypersensitive region in borealis rDNA, however, shows extensive homology with the promoter sequence, and with the hypersensitive region in X. laevis. Of two promoter-like duplications in each spacer, only the most upstream copy is associated with hypersensitivity to DNAaseI. Unlike DNAaseI, Endo R. MspI digests the rDNA of laevis blood nuclei at a domain extending downstream from the hypersensitive site to near the 40S promoter. Since the organisation of conserved sequence elements within this "proximal domain" is similar in three Xenopus species whose spacers have otherwise evolved rapidly, we conclude that this domain plays an important role in rDNA function.

Animals↗
PubMed1982

DNAase I sensitivity and methylation of active versus inactive rRNA genes in xenopus species hybrids.

We studied the chromatin structure and methylation of ribosomal RNA genes (rDNA) in hybrids between Xenopus laevis and Xenopus borealis. S1-nuclease protection experiments showed that 97%-98% of the rRNA precursor in hybrid tadpoles was of the X. laevis type. Preferential expression of the laevis rDNA was correlated with its hypersensitivity to DNAase I compared to borealis rDNA. Borealis and laevis rDNAs gave equivalent methylation patterns, however. The results show that hypomethylated sites in the nontranscribed spacer are not sufficient to ensure DNAase I hypersensitivity or transcription of the borealis rDNA. Also, heavy methylation of the transcribed region of laevis rDNA is compatible with its hypersensitivity to DNAase I. The absence of coupling between hypomethylation and DNAase I sensitivity argues against the view that the methylation pattern directly triggers the active chromatin structure, though it does not exclude a less intimate relationship between transcription and DNA hypomethylation. Examination of borealis sperm rDNA showed that hypomethylated sites were present at the same spacer locations as in somatic cells. This contrasts with X. laevis, where hypomethylated sites are detectable in the spacer of somatic rDNA, but not in sperm. Thus the loss of spacer methylation that is seen in early development of X. laevis does not occur in X. borealis.

Animals↗
PubMed1981

Loss of rDNA methylation accompanies the onset of ribosomal gene activity in early development of X. laevis.

The rRNA genes of Xenopus blood cells are heavily methylated, but there are two regions in the spacer that frequently contain unmethylated CpG. The undermethylated regions coincide with two regions containing a 60 nucleotide tandemly repeated sequence, and they are present in all somatic tissues that we have tested. Sperm rDNA, by contrast, is fully methylated at these sites in the spacer, and indirect evidence suggests that this may also be the case in oocytes. Loss of methyl groups occurs progressively over the first 20 hr of development, the same period in which embryonic rRNA synthesis initiates and increases in rate.

Age Factors↗
PubMedDate not supplied

Transcription in oocytes of highly methylated rDNA from Xenopus laevis sperm.

The genes for ribosomal RNA exist as multiple copies in the genome. Each repeated unit comprises a region that codes for the 40S rRNA precursor, and a spacer region of uncertain function (Fig. 1a). In Xenopus laevis there are about 1,000 copies of the dinucleotide sequence C-G in each repeat unit, and of these about 250 can be tested for the presence of 5-methylcytosine using restriction endonucleases. Most of the detectable C-Gs are heavily methylated, but in somatic cells unmethylated C-Gs occur in a 60 base pair (bp) sequence (NTS-60) that is repeated in the spacer. In contrast, the spacer of sperm rDNA is heavily methylated at these and all other testable C-Gs. Loss of methylation at NTS-60 takes place during the first day of embryonic development, near the time when rDNA transcription begins. In an attempt to assess the significance of this developmental change in methylation, we have isolated sperm rDNA and investigated whether it can be transcribed in oocytes. We have found that sperm rDNA is transcribed as efficiently as cloned rDNA, although no loss of methylation was detectable. Direct sequencing of sperm rDNA showed that all 19 C-GS in the promoter are highly methylated. Thus, in the case of rDNA injected into oocytes, loss of methylation is unnecessary for effective transcription.

Animals↗