1: Mol Cell Biol. 2005 Apr;25(7):2632-43. TATA-binding protein (TBP)-like factor (TLF) is a functional regulator of transcription: reciprocal regulation of the neurofibromatosis type 1 and c-fos genes by TLF/TRF2 and TBP. Chong JA, Moran MM, Teichmann M, Kaczmarek JS, Roeder R, Clapham DE. Department of Cardiology, Children's Hospital, Enders 1309, 320 Longwood Ave., Boston, MA 02115, USA. The lack of direct targets for TATA-binding protein (TBP)-like factors (TLFs) confounds the understanding of their role in gene expression. Here we report that human TLF (also called TBP-related factor 2 [TRF2]) activates a number of different genes, including the neurofibromatosis type 1 (NF1) gene. The overexpression of TLF increases the amount of NF1 mRNA in cells. In vivo, TLF binds to and upregulates transcription from a fragment of the NF1 promoter. In vitro, purified TLF-TFIIA binds directly to the same NF1 promoter fragment that is required for TLF responsiveness in cells. Furthermore, targeted deletion of TLF in mice reduces NF1 levels. In contrast, TLF inhibits transcription driven by a fragment from the TATA-containing c-fos promoter by sequestering TFIIA. TBP affects the NF1 and c-fos promoters in a manner reciprocal to that of TLF, stimulating the c-fos promoter and inhibiting NF1 transcription. We conclude that TLF is a functional regulator of transcription with targets distinct from those of TBP. PMID: 15767669 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 2: Hepatol Res. 2003 Jul;26(3):199-208. DNA alterations during multi-step development of human hepatocellular carcinomas revealed by laser capture microdissection. Nagai H, Emi M, Terada Y, Baba M, Shimizu M, Konishi N, Kaneko S, Kobayashi K, Yumoto Y, Ghazizadeh M, Kawanami O, Matsubara K. Department of Molecular Biology, Institute of Gerontology, Nippon Medical School, 1-396, Kosugi-cho, Nakahara-ku, 211-0063, Kawasaki, Japan In order to clarify early molecular events involved in liver carcinogenesis, we analyzed 53 liver-cirrhosis nodules (LCNs) from five patients and 13 micro-hepatocellular carcinoma (HCC) nodules from one patient and looked for alterations of microsatellites in genomic DNA after carefully preparing the tissue samples by laser-capture microdissection (LCM). Allelotyping was done with 20 markers corresponding to anonymous microsatellites and 13 corresponding to tumor suppressor genes (TSGs) that had shown significant alterations in HCCs. We detected both loss of heterozygosity (LOH) and microsatellite shifts (MS). Overall, 24 of 53 (47%) of LCNs showed LOH with any of the informative markers used in the study, reflecting that proportion of LCNs with clonal growth. The fractional allelic loss (FAL) index, an indication of total genomic complexity, was not significantly different between LCN and micro-HCC nodules, but their profiles of alteration were different. These profiles were classified into three groups: (1) LCN profile-allelic loss at chromosomal arms 1q and 14q, TBP and BRCA1; (2) HCC profile-LOH at 4q, 6q, 7q, 17p, NF1, IGFIIr and p53 in micro-HCC nodules; these changes in early lesions were identical to those seen in mature HCCs; (3) Common profile-LOH at NF1 and 6q, including IGFIIr, common to both LCN and HCC. No LCN showed LOH at p53 and Rb, loci that are generally altered in HCCs. However, 12 intra-tumoral nodules examined had lost p53 in all informative cases, although the loss of Rb was a late event. These results suggest that early genomic profiles confined to LCNs, and additional profiles that can be observed when liver tissue undergoes malignant transformation, support a model of multi-step development of HCC. PMID: 12850692 [PubMed - as supplied by publisher] --------------------------------------------------------------- 3: Biochem Biophys Res Commun. 1997 Sep 29;238(3):744-7. Identification of the transcriptional repression domain of nuclear factor 1-A. Osada S, Ikeda T, Xu M, Nishihara T, Imagawa M. Laboratory of Environmental Biochemistry, School of Pharmaceutical Sciences, Osaka University, Suita, Japan. We previously showed that nuclear factor 1-A (NF1-A) binds to the silencer elements in the glutathione transferase P (GST-P) gene, and the carboxy terminal region of NF1-A represses the transcription activity of human metallothionein IIA (hMTIIA) promoter. In this study, we identified a repression region which is divided into two 100 amino acid domains (RD1 and RD2). RD1 increased the repression activity of RD2 to the hMTIIA promoter activity. The NF1-A repression domain inhibited the promoter activities of not only the hMTIIA gene but also those of the GST-P and CCAAT/enhancer binding protein delta genes. RD1 and RD2 had abundant serine and glycine residues, and proline and serine residues, respectively. Whereas some repression domains identified previously are enriched with alanine, proline, or serine, and are associated with the general transcription factors, the NF1-A repression domains did not interact with transcription factor IIB, TATA-binding protein (TBP), or TBP-associated factors in vitro. PMID: 9325160 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 4: Nucleic Acids Res. 1996 Nov 1;24(21):4349-55. The translational placement of nucleosome cores in vitro determines the access of the transacting factor suGF1 to DNA. Patterton HG, Hapgood J. Department of Biochemistry, University of Cape Town, South Africa. The sea urchin G-string binding factor (suGF1) is one of several proteins that bind sequence-specifically to oligo(dGxdC) motifs, frequently present upstream of eukaryotic genes. In this study we investigate the interaction of suGF1, purified to near homogeneity, with its oligo(dGxdC) binding site in a reconstituted nucleosome core in vitro. We show that the in vitro reconstitution of a 214 bp fragment containing a suGF1 binding site results in the appearance of five distinct nucleosome core species. These species contain the histone octamer in an identical rotational setting but in different translational frames. The resulting different nucleosomal locations of the suGF1 binding site in the five core species are shown to modulate the ability of suGF1 to bind to nucleosomal DNA, even though the rotational setting of the DNA in the nucleosome cores maximally exposes the suGF1 binding site. We propose that a direct protein-protein steric clash between suGF1 and the histone octamer is the most likely determinant in modulating the binding of suGF1 to its nucleosomally wrapped binding site. This result suggests that in vivo suGF1, like TBP, NF1 and heat shock factor, may require a complementary nucleosome disrupting activity or that suGF1 binds to free nascent replicated DNA prior to nucleosome deposition. PMID: 8932393 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 5: Nucleic Acids Res. 1994 Jun 11;22(11):1966-73. The upstream activator CTF/NF1 and RNA polymerase II share a common element involved in transcriptional activation. Xiao H, Lis JT, Xiao H, Greenblatt J, Friesen JD. Department of Genetics, Hospital for Sick Children, Toronto, Ontario, Canada. The carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II consists of tandem repeats of a heptapeptide with the consensus YSPTSPS. It has been shown that the heptapeptide repeat interacts directly with the general transcription factor TFIID. We report here that the CTD activates transcription when fused to the DNA-binding domain of GAL4. More importantly, we find that the proline-rich transcriptional activation domain of the CCAAT-box-binding factor CTF/NF1 contains a sequence with striking similarity to the heptapeptide repeats of the CTD. We show that this CTD-like motif is essential for the transcriptional activator function of the proline-rich domain of CTF/NF1. Deletion of and point mutations in this CTD-like motif abolish the transcriptional activator function of the proline-rich domain, while natural CTD repeats from RNA polymerase II are fully functional in place of the CTD-like motif. We further show that the proline-rich activation domain of CTF/NF1 interacts directly with the TATA-box-binding protein (TBP), and that a mutation in the CTD-like motif that abolishes transcriptional activation reduces the affinity of the proline-rich domain for TBP. These results demonstrate that a class of proline-rich activator proteins and RNA polymerase II possess a common structural and functional component which can interact with the same target in the general transcription machinery. We discuss the implications of these results for the mechanisms of transcriptional activation in eucaryotes. PMID: 8029001 [PubMed - indexed for MEDLINE] ---------------------------------------------------------------