Faculty Opinions recommendation of Close sequence comparisons are sufficient to identify human cis-regulatory elements.

Comparative genomic analysis was used to investigate the gene structure of the bli-4 locus from two relatedCaenorhabditis species, C. elegans and C. briggsae. In C. elegans, bli-4 is a complex gene encoding a member of the kex2/subtilisin-like family of proprotein convertases. Genomic sequence comparisons coupled with RT–PCR analysis identified five additional coding exons that had not been identified previously using standard recombinant DNA techniques. The C. briggsae gene was able to rescue both viable blistered and developmentally arrested mutants of C. elegans bli-4, demonstrating functional conservation. In addition, deletion analysis of conserved sequences outside of coding regions, combined with phenotypic rescue experiments, identified regulatory elements that alter the expression of the bli-4 gene. These results demonstrate the utility of genomic sequence comparisons of homologous genes in related species as an effective tool with which to dissect the functional information of complex genes.[The sequence for cosmid K0410 is available at GenBank (accession no. AFO 39719); fosmids G06P23 and G25K01 are available as online supplementary material atwww.genome.org.]

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Comparative Analysis of Glycosylated and Nonglycosylated Filarial Homologues of the 20-Kilodalton Retinol Binding Protein fromOnchocerca volvulus (Ov20)

Infection and Immunity ◽

10.1128/iai.67.12.6329-6334.1999 ◽

1999 ◽

Vol 67 (12) ◽

pp. 6329-6334 ◽

Cited By ~ 6

Author(s):

Niroshini Nirmalan ◽

N. J. V. Cordeiro ◽

Sabine L. Kläger ◽

Janette E. Bradley ◽

Judith E. Allen

Keyword(s):

Immune Responses ◽

Binding Protein ◽

Sequence Similarity ◽

Inbred Strains ◽

Retinol Binding Protein ◽

Biological Functions ◽

Sequence Comparisons ◽

Biological Investigation ◽

Acanthocheilonema Viteae ◽

Close Sequence

ABSTRACT Ov20 is a structurally novel 20-kDa retinol binding protein secreted by Onchocerca volvulus. Immunological and biological investigation of this protein has been hampered by the inability to maintain O. volvulus in a laboratory setting. In an effort to find a system more amenable to laboratory investigation, we have cloned, sequenced, and expressed cDNA encoding homologues of Ov20 from two closely related filarial species,Brugia malayi (Bm20) and Acanthocheilonema viteae (Av20). Sequence comparisons have highlighted differences in glycosylation of the homologues. We present here an analysis of mouse immune responses to Ov20, Bm20, and Av20. The results suggest a strong genetic restriction in response to native Bm20 that is overcome when recombinant, nonnative material is used. Reactivity of human filarial sera to the three recombinant proteins confirmed previous specificity studies with Ov20 but highlighted important differences in the reactivity patterns of the O. volvulus and B. malayi homologues that may be due to differences in glycosylation patterns. Ov20 is a dominant antigen in infected individuals, while Bm20 is not. The availability of the B. malayi homologue enabled us to use defined murine reagents and inbred strains for genetic analysis of responsiveness in a way that is not possible for Ov20. However, the close sequence similarity between Ov20 and Av20 suggests that the A. viteae model may be more suited to the investigation of the biological functions of Ov20.

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Novel member of the zinc finger superfamily: A C2-HC finger that recognizes a glia-specific gene.

Molecular and Cellular Biology ◽

10.1128/mcb.12.12.5632 ◽

1992 ◽

Vol 12 (12) ◽

pp. 5632-5639 ◽

Cited By ~ 85

Author(s):

J G Kim ◽

L D Hudson

Keyword(s):

Dna Binding ◽

Zinc Finger ◽

Chelating Agent ◽

Proteolipid Protein ◽

Polymerase Chain Reaction Analysis ◽

Regulatory Elements ◽

Binding Activity ◽

Order Structure ◽

Specific Gene ◽

Sequence Comparisons

A novel member of the zinc finger superfamily was cloned by virtue of its binding to cis-regulatory elements of a glia-specific gene, the myelin proteolipid protein (PLP) gene. Named MyTI (myelin transcription factor I), this gene is most highly transcribed in the developing nervous system, where expression precedes induction of its presumptive target, PLP. Low levels of MyTI transcripts can be detected in nonneural tissues only by polymerase chain reaction analysis. Zinc is a necessary cofactor for DNA binding of MyTI, as the zinc-chelating agent 1,10-orthophenanthroline eliminates binding activity. Zinc may stabilize the DNA-binding domain of MyTI by coordinating three cysteine and one histidine residue in a Cys-X5-Cys-X12-His-X4-Cys (C2-HC) arrangement. The MyTI protein has six fingers of the C2-HC class arranged in two widely separated clusters. These two domains of DNA binding can function independently and recognize the same DNA sequence, suggesting that MyTI may contribute to the higher-order structure of a target promoter by simultaneously binding both proximal and distal sites. The six fingers are highly conserved, suggesting that they arose from successive duplication events, while the linker regions diverge in size and sequence. Both amino acid sequence comparisons and secondary-structure predictions indicate that the C2-HC fingers of MyTI do not resemble the zinc-mediated loops of C2-H2 fingers, C2-C2 fingers, or Cx clusters. MyTI may therefore be the prototype of a new structural family of zinc-stabilized DNA binding proteins.

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Novel member of the zinc finger superfamily: A C2-HC finger that recognizes a glia-specific gene

Molecular and Cellular Biology ◽

10.1128/mcb.12.12.5632-5639.1992 ◽

1992 ◽

Vol 12 (12) ◽

pp. 5632-5639

Author(s):

J G Kim ◽

L D Hudson

Keyword(s):

Dna Binding ◽

Zinc Finger ◽

Chelating Agent ◽

Proteolipid Protein ◽

Polymerase Chain Reaction Analysis ◽

Regulatory Elements ◽

Binding Activity ◽

Order Structure ◽

Specific Gene ◽

Sequence Comparisons

A novel member of the zinc finger superfamily was cloned by virtue of its binding to cis-regulatory elements of a glia-specific gene, the myelin proteolipid protein (PLP) gene. Named MyTI (myelin transcription factor I), this gene is most highly transcribed in the developing nervous system, where expression precedes induction of its presumptive target, PLP. Low levels of MyTI transcripts can be detected in nonneural tissues only by polymerase chain reaction analysis. Zinc is a necessary cofactor for DNA binding of MyTI, as the zinc-chelating agent 1,10-orthophenanthroline eliminates binding activity. Zinc may stabilize the DNA-binding domain of MyTI by coordinating three cysteine and one histidine residue in a Cys-X5-Cys-X12-His-X4-Cys (C2-HC) arrangement. The MyTI protein has six fingers of the C2-HC class arranged in two widely separated clusters. These two domains of DNA binding can function independently and recognize the same DNA sequence, suggesting that MyTI may contribute to the higher-order structure of a target promoter by simultaneously binding both proximal and distal sites. The six fingers are highly conserved, suggesting that they arose from successive duplication events, while the linker regions diverge in size and sequence. Both amino acid sequence comparisons and secondary-structure predictions indicate that the C2-HC fingers of MyTI do not resemble the zinc-mediated loops of C2-H2 fingers, C2-C2 fingers, or Cx clusters. MyTI may therefore be the prototype of a new structural family of zinc-stabilized DNA binding proteins.

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Transcriptional Regulation of the SCL Locus: Identification of an Enhancer That Targets the Primitive Erythroid Lineage In Vivo

Molecular and Cellular Biology ◽

10.1128/mcb.25.12.5215-5225.2005 ◽

2005 ◽

Vol 25 (12) ◽

pp. 5215-5225 ◽

Cited By ~ 42

Author(s):

E. Delabesse ◽

S. Ogilvy ◽

M. A. Chapman ◽

S. G. Piltz ◽

B. Gottgens ◽

...

Keyword(s):

Transcriptional Regulation ◽

Cell Types ◽

Regulatory Elements ◽

Hematopoietic Cell ◽

Erythroid Cell ◽

Sequence Comparisons ◽

Helix Loop Helix ◽

Primitive Erythropoiesis

ABSTRACT The stem cell leukemia (SCL) gene, also known as TAL-1, encodes a basic helix-loop-helix protein that is essential for the formation of all hematopoietic lineages, including primitive erythropoiesis. Appropriate transcriptional regulation is essential for the biological functions of SCL, and we have previously identified five distinct enhancers which target different subdomains of the normal SCL expression pattern. However, it is not known whether these SCL enhancers also regulate neighboring genes within the SCL locus, and the erythroid expression of SCL remains unexplained. Here, we have quantitated transcripts from SCL and neighboring genes in multiple hematopoietic cell types. Our results show striking coexpression of SCL and its immediate downstream neighbor, MAP17, suggesting that they share regulatory elements. A systematic survey of histone H3 and H4 acetylation throughout the SCL locus in different hematopoietic cell types identified several peaks of histone acetylation between SIL and MAP17, all of which corresponded to previously characterized SCL enhancers or to the MAP17 promoter. Downstream of MAP17 (and 40 kb downstream of SCL exon 1a), an additional peak of acetylation was identified in hematopoietic cells and was found to correlate with expression of SCL but not other neighboring genes. This +40 region is conserved in human-dog-mouse-rat sequence comparisons, functions as an erythroid cell-restricted enhancer in vitro, and directs β-galactosidase expression to primitive, but not definitive, erythroblasts in transgenic mice. The SCL +40 enhancer provides a powerful tool for studying the molecular and cellular biology of the primitive erythroid lineage.

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Evolution of the autosomal chorion locus in Drosophila. I. General organization of the locus and sequence comparisons of genes s15 and s19 in evolutionary distant species.

Genetics ◽

10.1093/genetics/119.3.663 ◽

1988 ◽

Vol 119 (3) ◽

pp. 663-677

Author(s):

J C Martínez-Cruzado ◽

C Swimmer ◽

M G Fenerjian ◽

F C Kafatos

Keyword(s):

Drosophila Melanogaster ◽

Related Species ◽

Sequence Divergence ◽

Regulatory Elements ◽

Nucleotide Sequences ◽

Sequence Comparisons ◽

Extensive Sequence ◽

Chorion Genes ◽

General Organization

Abstract We have isolated clones corresponding to the autosomal chorion locus of Drosophila melanogaster, from two distantly (D. virilis and D. grimshawi) and one closely (D. subobscura) related species. In all the species the locus is unique within the genome and encompasses the same four chorion genes and an adjacent nonchorion gene, in the same order. In all species the locus specifically amplifies in the ovary, as in D. melanogaster. We present the nucleotide sequences of DNA segments that total 8.3 kb in length and include gene s15-1 from D. subobscura, D. virilis, and D. grimshawi as well as gene s19-1 from D. subobscura and D. grimshawi. They show clearly nonuniform rates of divergence, both within and outside the limits of the genes. Highlighted by a background of extensive sequence divergence elsewhere in the extragenic region, highly conserved elements are observed in the 5' flanking DNA and might represent regulatory elements.

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Hungarian small business tax and possibilities to minimize distortions from capital income taxation

Society and Economy ◽

10.1556/204.2015.37.s.6 ◽

2015 ◽

Vol 37 (s1) ◽

pp. 87-105

Author(s):

Benedek Nobilis ◽

András Svraka

Keyword(s):

Small Business ◽

Cash Flow ◽

Capital Accumulation ◽

Value Added ◽

Regulatory Elements ◽

Capital Income ◽

Potential Growth ◽

Elegant Method ◽

Business Tax ◽

Working Out

Governments throughout the EU and OECD countries rely on revenues raised on capital income. Albeit several arguments can be made for keeping these taxes, in their widespread form they hinder capital accumulation and significantly lower potential growth due to their savings and investment distorting nature. At the same time, the actual economic impact of tax types is largely influenced by their structure. An elegant method, which is also simple in its concept, for eliminating the economic distortions of profit taxes is cash-flow taxation which moves income taxes closer to the more growth-friendly value-added taxes. The small business tax, which was introduced in Hungary in 2013, was designed along these principles. In this paper we review the theoretical literature on cash-flow taxation and discuss the main regulatory elements of the small business tax, as well as the solutions elaborated for working out the challenges related to its implementation.

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