NORMAL GENOMIC

• Sawa S et al.
• The HAT2 gene, a member of the HD-Zip gene family, isolated as an auxininducible gene by DNA microarray screening, affects auxin response inArabidopsis.
• Plant J. 2002; 32: 1011-22
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• The plant hormone, auxin, regulates many aspects of growth anddevelopment. Despite its importance, the molecular mechanisms underlyingthe action of auxin are largely unknown. To gain a more comprehensiveunderstanding of the primary responses to auxin, we analyzed theexpression of genes in Arabidopsis seedlings treated with indole-3-aceticacid (IAA) for 15 min. We identified a single gene that is downregulatedearly, and 29 genes that are upregulated early. Several types of typicaltranscription factors are identified as early upregulated genes,suggesting that auxin signals are mediated by a master set of diversetranscriptional regulators. Of the genes that responded to auxin, theexpression of the homeobox gene, HAT2, was induced rapidly. Furthermore,we show that the expression of HAT2 is induced by auxin, but not by otherphytohormones. To analyze the function of HAT2 in the plant's response toauxin, we generated 35S::HAT2 transgenic plants. These produced longhypocotyls, epinastic cotyledons, long petioles, and small leaves, whichare characteristic of the phenotypes of the auxin-overproducing mutants,superroot1 (sur1) and superroot2 (sur2). On the other hand, 35S::HAT2plants showed reduced lateral root elongation, and reduced auxinsensitivity compared to wild-type plants. Together with the results of RNAblotting and biochemical analyses, these findings suggest that HAT2 playsopposite roles in the shoot and root tissues in regulating auxin-mediatedmorphogenesis.

• Cooke R, Raynal M, Laudie M, Delseny M
• Identification of members of gene families in Arabidopsis thaliana bycontig construction from partial cDNA sequences: 106 genes encoding 50cytoplasmic ribosomal proteins.
• Plant J. 1997; 11: 1127-40
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• Partial cDNA sequencing to obtain expressed sequence tags (ESTs) has ledto the identification of tags to about 8,000 of the estimated 20,000 geneson Arabidopsis thaliana. This figure represents four to five times thenumber of complete coding sequences from this organism available ininternational databases. In contrast to mammals, many proteins are encodedby multigene families in A. thaliana. Using ribosomal protein genefamilies as an example, it is possible to construct relatively longsequences from overlapping ESTs which are of sufficiently high quality tobe able to unambiguously identify tags to individual members of multigenefamilies, even when the sequences are highly conserved. A total of 106genes encoding 50 different cytoplasmic ribosomal protein types have beenidentified, most proteins being encoded by at least two and up to fourgenes. Coding sequences of members of individual gene families are almostalways very highly conserved and derived amino acid sequences are almost,if not completely, identical in the vast majority of cases. Sequencedivergence is observed in untranslated regions which allows the definitionof gene-specific probes. The method can be used to construct high-qualitytags to any protein.

• Prasad R et al.
• Leucine-zipper dimerization motif encoded by the AF17 gene fused to ALL-1(MLL) in acute leukemia.
• Proc Natl Acad Sci U S A. 1994; 91: 8107-11
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• Chromosome region 11q23 is involved in reciprocal chromosometranslocations associated with human acute leukemias. These aberrationsfuse the ALL-1 gene located at 11q23 to a series of partner genespositioned on a variety of human chromosomes. The fused genes encodechimeric proteins. Here we report the cloning and characterization of theALL-1 partner at 17q21, the AF17 gene. The AF17 gene encodes a protein of1093 amino acids, containing a leucine-zipper dimerization motif located3' of the fusion point and a cysteine-rich domain at the N terminus. Thelatter can be arranged in three zinc fingers and shows homology to adomain within the protein Br140 (peregrin). AF17 contains stretches ofamino acids previously associated with domains involved in transcriptionalrepression or activation. Based on features of AF17 and of the proteinsencoded by the other partner genes analyzed and in conjunction with otherrecent studies, we propose a model in which ALL-1 rearrangements result inloss of function of the gene. In this model, the partner polypeptide playsan accessory role either by repressing activity of the truncated ALL-1protein or by blocking the function of the normal protein presumablypresent in the leukemic cells.

• Lawler J, Duquette M, Urry L, McHenry K, Smith TF
• The evolution of the thrombospondin gene family.
• J Mol Evol. 1993; 36: 509-16
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• Thrombospondin-1 is an adhesive glycoprotein that is involved in cellularattachment, spreading, migration, and proliferation. To date, four geneshave been identified that encode for the members of the thrombospondingene family. These four genes are homologous to each other in the EGF-like(type 2) repeats, the calcium-binding (type 3) motifs, and theCOOH-terminal. The latter has been reported to be a cell-binding domain inthrombospondin-1. Phylogenetic trees have been constructed from themultisequence alignment of thrombospondin sequences from human, mouse,chicken, and frog. Two different algorithms generate comparable results interms of the topology and the branch lengths. The analysis indicates thatan early form of the thrombospondin gene duplicated about 925 millionyears ago. The gene duplication that produced the thrombospondin-1 and -2branches of the family is predicted to have occurred 583 million yearsago, whereas the gene duplication that produced the thrombospondin-3 and-4 branches of the family is predicted to have occurred 644 million yearsago. These results indicate that the members of the thrombospondin genefamily have existed throughout the evolution of the animal kingdom andthus probably participate in functions that are common to most of itsmembers.