We have isolated and analyzed human CTCF cDNA clones and show here that the ubiquitously expressed 11-zinc-finger factor CTCF is an exceptionally highly conserved protein displaying 93% identity between avian and human amino acid sequences. It binds specifically to regulatory sequences in the promoter-proximal regions of chicken, mouse, and human c-myc oncogenes. CTCF contains two transcription repressor domains transferable to a heterologous DNA binding domain. One CTCF binding site, conserved in mouse and human c-myc genes, is found immediately downstream of the major P2 promoter at a sequence which maps precisely within the region of RNA polymerase II pausing and release. Gel shift assays of nuclear extracts from mouse and human cells show that CTCF is the predominant factor binding to this sequence. Mutational analysis of the P2-proximal CTCF binding site and transient-cotransfection experiments demonstrate that CTCF is a transcriptional repressor of the human c-myc gene. Although there is 100% sequence identity in the DNA binding domains of the avian and human CTCF proteins, the regulatory sequences recognized by CTCF in chicken and human c-myc promoters are clearly diverged. Mutating the contact nucleotides confirms that CTCF binding to the human c-myc P2 promoter requires a number of unique contact DNA bases that are absent in the chicken c-myc CTCF binding site. Moreover, proteolytic-protection assays indicate that several more CTCF Zn fingers are involved in contacting the human CTCF binding site than the chicken site. Gel shift assays utilizing successively deleted Zn finger domains indicate that CTCF Zn fingers 2 to 7 are involved in binding to the chicken c-myc promoter, while fingers 3 to 11 mediate CTCF binding to the human promoter. This flexibility in Zn finger usage reveals CTCF to be a unique "multivalent" transcriptional factor and provides the first feasible explanation of how certain homologous genes (i.e., c-myc) of different vertebrate species are regulated by the same factor and maintain similar expression patterns despite significant promoter sequence divergence.

A new group of chromatin-associated proteins having a high content of acidic and basic amino acids have been isolated from the 0.35 M NaC1-extractable proteins from calf thymus.This new group, designated "high-mobility group" proteins have been partially separated and some interesting new proteins identified. One such protein contains over 55O/, acidic and basic amino acids.The major group of chromatin proteins, the histones, have received a great deal of attention over the past ten years [I]. Methods have been developed for their isolation in a pure form, and the complete amino acid sequence of all but one of the fractions is known. Since they appear to be non-specific gene repressors [2], possibly acting by causing some conformational change in the DNA which restricts transcription in a very non-specific manner, attention has turned to the so-called "acidic proteins" of chromatin in an attempt to find more specific interactions with DNA, which may have some relevance to specific gene derepression [3]. Work in this field has been generally unsuccessful since these proteins, once removed from the chromatin complex, seem to aggregate easily and are difficult to keep in solution.We have shown previously [5] that most of the non-histone proteins can be removed from calf thymus chromatin by extracting with 0.35 M NaCl and we have suggested that some of these were contaminants picked up from the cytoplasm during the preparative procedures. A recent paper [5] has indicated that this contamination is very small and our recent results agree with this but also indicate that those cytoplasmic contaminants which are present are in the low mobility group of proteins as determined by polyacrylamide gel electrophoresis [6]. This being so, we decided to separate the high and low mobility groups of proteins of the 0.35 M NaCl extract, quite arbitrarily, by precipitation with trichloroacetic acid. We found that once separated from the low mobility group of proteins, the high mobility group was easy to work with and quite soluble in dilute acids. It constitutes an easily defined group of chromatin proteins which, as far as we are aware, has not been described previously by other laboratories. This paper gives a preparative method for these proteins and an initial partial separation and characterisation. EXPERIMENTAL PROCEDURE AND RESULTS Polyacrylamide-Gel ElectrophoresisThe method used was that developed for the histones by Johns [ 7 ] with the modifications described by Dick and Johns [S]. The non-histone proteins were, however, dissolved in and applied to the gel in 0.1 N HCl, 9 M urea instead of the sample solvent described. The method for applying two samples to one gel for more exact comparative electrophoresis has also been described previously [9]. Preparation of Calf -Thymus ChromatinCalf thymus was obtained immediately after slaughter of the animal and frozen in solid CO, until required. It was then thawed and freed from membranes and connective tissue and minced using a domestic mincer. All subsequent operations were ...

Individuals with permanent neonatal diabetes mellitus usually present within the first three months of life and require insulin treatment. We recently identified a locus on chromosome 10p13-p12.1 involved in permanent neonatal diabetes mellitus associated with pancreatic and cerebellar agenesis in a genome-wide linkage search of a consanguineous Pakistani family. Here we report the further linkage analysis of this family and a second family of Northern European descent segregating an identical phenotype. Positional cloning identified the mutations 705insG and C886T in the gene PTF1A, encoding pancreas transcription factor 1alpha, as disease-causing sequence changes. Both mutations cause truncation of the expressed PTF1A protein C-terminal to the basic-helix-loop-helix domain. Reporter-gene studies using a minimal PTF1A deletion mutant indicate that the deleted region defines a new domain that is crucial for the function of this protein. PTF1A is known to have a role in mammalian pancreatic development, and the clinical phenotype of the affected individuals implicated the protein as a key regulator of cerebellar neurogenesis. The essential role of PTF1A in normal cerebellar development was confirmed by detailed neuropathological analysis of Ptf1a(-/-) mice.

Gene duplication followed by adaptive evolution is one of the primary forces for the emergence of new gene function. Here we describe the recent proliferation, transposition and selection of a 20-kilobase (kb) duplicated segment throughout 15 Mb of the short arm of human chromosome 16. The dispersal of this segment was accompanied by considerable variation in chromosomal-map location and copy number among hominoid species. In humans, we identified a gene family (morpheus) within the duplicated segment. Comparison of putative protein-encoding exons revealed the most extreme case of positive selection among hominoids. The major episode of enhanced amino-acid replacement occurred after the separation of human and great-ape lineages from the orangutan. Positive selection continued to alter amino-acid composition after the divergence of human and chimpanzee lineages. The rapidity and bias for amino-acid-altering nucleotide changes suggest adaptive evolution of the morpheus gene family during the emergence of humans and African apes. Moreover, some genes emerge and evolve very rapidly, generating copies that bear little similarity to their ancestral precursors. Consequently, a small fraction of human genes may not possess discernible orthologues within the genomes of model organisms.

The t(X;18)(p11.2;q11.2) chromosomal translocation commonly found in synovial sarcomas fuses the SYT gene on chromosome 18 to either of two similar genes, SSX1 or SSX2, on the X chromosome. The SYT protein appears to act as a transcriptional co-activator and the SSX proteins as co-repressors. Here we have investigated the functional domains of the proteins. The SYT protein has a novel conserved 54 amino acid domain at the N-terminus of the protein (the SNH domain) which is found in proteins from a wide variety of species, and a C-terminal domain, rich in glutamine, proline, glycine and tyrosine (the QPGY domain), which contains the transcriptional activator sequences. Deletion of the SNH domain results in a more active transcriptional activator, suggesting that this domain acts as an inhibitor of the activation domain. The C-terminal SSX domain present in SYT-SSX translocation protein contributes a transcriptional repressor domain to the protein. Thus, the fusion protein has transcriptional activating and repressing domains. We demonstrate that the human homologue of the SNF2/Brahama protein BRM co-localizes with SYT and SYT-SSX in nuclear speckles, and also interacts with SYT and SYT-SSX proteins in vitro. This interaction may provide an explanation of how the SYT protein activates gene transcription.