Amino acid substitution matrices from protein blocks.
Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used...
The Blocks database--a system for protein classification.
Pietrokovski, S, Henikoff, J G, Henikoff, S
The Blocks Database contains multiple alignments of conserved regions in protein families. The database can be searched by e-mail and World Wide Web(WWW) servers (http://blocks.fhcrc.org/help) to...
Recent enhancements to the Blocks Database servers.
Henikoff, J G, Pietrokovski, S, Henikoff, S
The Blocks Database contains multiple alignments of conserved regions in protein families which can be searched by e-mail (blocks@blocks.fhcrc.org) and World Wide Web (http://blocks.fhcrc.org/ )...
Superior performance in protein homology detection with the Blocks Database servers.
Henikoff, S, Pietrokovski, S, Henikoff, J G
The Blocks Database World Wide Web (http://www.blocks.fhcrc.org ) and Email (blocks@blocks.fhcrc.org) servers provide tools for the detection and analysis of protein homology based on alignment...
Rose, T M, Schultz, E R, Henikoff, J G, Pietrokovski, S, McCallum, C M, Henikoff, S
We describe a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region and...
New features of the Blocks Database servers.
Henikoff, J G, Henikoff, S, Pietrokovski, S
Blocks are ungapped multiple sequence alignments representing conserved protein regions, and the Blocks Database consists of blocks from documented protein families. World Wide Web (http://www....
Coco, W M, Rothmel, R K, Henikoff, S, Chakrabarty, A M
The 3-chlorocatechol operon clcABD is central to the biodegradative pathway of 3-chlorobenzoate. The clcR regulatory gene, which activates the clcABD operon, was cloned from the region immediately...
Viale, A M, Kobayashi, H, Akazawa, T, Henikoff, S
An open reading frame, rbcR, was identified 226 bp upstream of rbcAB, i.e., the ribulose 1,5-bisphosphate carboxylase genes expressed in the phototrophic purple bacterium Chromatium vinosum. Several...
A large family of bacterial activator proteins.
Henikoff, S, Haughn, G W, Calvo, J M, Wallace, J C
At least nine different bacterial proteins belong to the LysR family. The gene sequence for one of these proteins is presented here. Six others (Escherichia coli LysR, IlvY, CysB; Salmonella...
Position-effect variegation in Drosophila is the variable inactivation of a gene that occurs when it is juxtaposed to heterochromatic regions of chromosomes. The brown gene, required for pteridine...
Multiple purine pathway enzyme activities are encoded at a single genetic locus in Drosophila.
Henikoff, S, Keene, M A, Sloan, J S, Bleskan, J, Hards, R, Patterson, D
The Drosophila melanogaster Gart locus, known from previous work to encode the enzyme activity phosphoribosylglycinamide formyltransferase (GART), specifies two alternatively processed mRNAs and two...
Two Drosophila melanogaster mutations block successive steps of de novo purine synthesis.
Henikoff, S, Nash, D, Hards, R, Bleskan, J, Woolford, J F, Naguib, F, ...
Drosophila melanogaster purine auxotrophs ade2(1) and ade3(1) have been characterized biochemically. The ade2(1) strain is deficient in the fourth step of the de novo purine synthetic pathway...
We have determined the complete DNA sequence of a segment derived from Drosophila melanogaster that complements a yeast adenine-8 (ade8) mutation. This sequence, in conjunction with transcriptional...
A novel method has been developed for determining the location of RNA termini and intron-exon boundaries using genomic clones. RNA is hybridized to a single-stranded M13 phage derivative of the...
Automated assembly of protein blocks for database searching.
A system is described for finding and assembling the most highly conserved regions of related proteins for database searching. First, an automated version of Smith's algorithm for finding motifs is...
A simple method is described for generating nested deletions from any fixed point in a cloned inset. Starting with a single-stranded phagemid template, T4 DNA polymerase is used to extend an annealed...
Detection of protein similarities using nucleotide sequence databases.
A simple procedure is described for finding similarities between proteins using nucleotide sequence databases. The approach is illustrated by several examples of previously unknown correspondences...
A moveable 5' splice site in adenine phosphoribosyltransferase genes of Drosophila species.
In two distantly related Drosophila species, the use of alternate 5' splice sites to process an intron in pre-mRNA from homologous adenine phosphoribosyltransferase (APRT)-encoding genes led to RNAs...
Dreesen, T D, Johnson, D H, Henikoff, S
The brown gene of Drosophila melanogaster is required for deposition of pteridine pigments in the compound eye and other tissues. We isolated a ca. 150-kilobase region including brown by...
Sequences responsible for transcription termination on a gene segment in Saccharomyces cerevisiae.
We have mapped a signal sequence for mRNA 3'-end formation in Saccharomyces cerevisiae by using a Drosophila melanogaster DNA segment that complements a yeast adenine-8 mutation. That the 3' end of...
Localization of RNA from heat-induced polysomes at puff sites in Drosophila melanogaster.
McKenzie, S L, Henikoff, S, Meselson, M
Heat treatment of D. melanogaster tissue culture cells causes drastic changes in the pattern of protein synthesis and the size distribution of polysomes. Like the heat shock puffs on polytene...
Somatic Instability of a Drosophila Chromosome
A mitotically unstable chromosome, detectable because of mosaic expression of marker genes, was generated by X-ray mutagenesis in Drosophila. Nondisjunction of this chromosome is evident in mitotic...
Modification of the Drosophila Heterochromatic Mutation Brown(dominant) by Linkage Alterations
Talbert, P. B., LeCiel, CDS., Henikoff, S.
The variegating mutation brown(Dominant) (bw(D)) of Drosophila melanogaster is associated with an insertion of heterochromatin into chromosome arm 2R at 59E, the site of the bw gene. Mutagenesis...
Conservation of Brown Gene Trans-Inactivation in Drosophila
Martin-Morris, L. E., Henikoff, S.
The mechanism underlying trans-inactivation associated with dominant position effect variegation (PEV) of the Drosophila melanogaster brown gene has been addressed by a comparison with its D. virilis...
Distance and Pairing Effects on the Brown(dominant) Heterochromatic Element in Drosophila
Henikoff, S., Jackson, J. M., Talbert, P. B.
We examined the behavior of the brown(Dominant) (bw(D)) heterochromatic insertion moved to different locations relative to centric heterochromatin. Effects were measured as the degree of silencing of...
The classical phenomenon of position-effect variegation (PEV) is the mosaic expression that occurs when a chromosomal rearrangement moves a euchromatic gene near heterochromatin. A striking feature...
Heterochromatic Trans-Inactivation of Drosophila White Transgenes
Martin-Morris, L. E., Csink, A. K., Dorer, D. R., Talbert, P. B., Henikoff, S.
Position effect variegation of most Drosophila melanogaster genes, including the white eye pigment gene, is recessive. We find that this is not always the case for white transgenes. Three examples...
Transgene Repeat Arrays Interact with Distant Heterochromatin and Cause Silencing in Cis and Trans
Tandem repeats of Drosophila transgenes can cause heterochromatic variegation for transgene expression in a copy-number and orientation-dependent manner. Here, we demonstrate different ways in which...
In Drosophila melanogaster, heterochromatin-induced silencing or position-effect variegation (PEV) of a reporter gene has provided insights into the properties of heterochromatin. Class I modifiers...
Chromodomains are thought to mediate protein-protein interactions between chromatin components. We have detected a chromodomain embedded within the catalytic region of a predicted Arabidopsis DNA...
We describe the precise positioning of a reporter gene within heterochromatin where it may be silenced. A transposition of the 59E-60A region into pericentric heterochromatin ensnares distal 59E-60A...
In Drosophila, heterochromatin causes mosaic silencing of euchromatic genes brought next to it by chromosomal rearrangements. Silencing has been observed to "spread": genes closer to the...
Adaptive evolution of Cid, a centromere-specific histone in Drosophila.
Centromeric DNA is generally composed of large blocks of tandem satellite repeats that change rapidly due to loss of old arrays and expansion of new repeat classes. This extreme heterogeneity of...
High-Throughput Screening for Induced Point Mutations
Colbert, T., Till, B. J., Tompa, R., Reynolds, S., Steine, M. N., Yeung, A. T., ...
Amino acid substitution matrices from protein blocks.
Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used...
The Blocks database--a system for protein classification.
Pietrokovski, S, Henikoff, J G, Henikoff, S
The Blocks Database contains multiple alignments of conserved regions in protein families. The database can be searched by e-mail and World Wide Web(WWW) servers (http://blocks.fhcrc.org/help) to...
Recent enhancements to the Blocks Database servers.
Henikoff, J G, Pietrokovski, S, Henikoff, S
The Blocks Database contains multiple alignments of conserved regions in protein families which can be searched by e-mail (blocks@blocks.fhcrc.org) and World Wide Web (http://blocks.fhcrc.org/ )...
Superior performance in protein homology detection with the Blocks Database servers.
Henikoff, S, Pietrokovski, S, Henikoff, J G
The Blocks Database World Wide Web (http://www.blocks.fhcrc.org ) and Email (blocks@blocks.fhcrc.org) servers provide tools for the detection and analysis of protein homology based on alignment...
Rose, T M, Schultz, E R, Henikoff, J G, Pietrokovski, S, McCallum, C M, Henikoff, S
We describe a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region and...
New features of the Blocks Database servers.
Henikoff, J G, Henikoff, S, Pietrokovski, S
Blocks are ungapped multiple sequence alignments representing conserved protein regions, and the Blocks Database consists of blocks from documented protein families. World Wide Web (http://www....
Coco, W M, Rothmel, R K, Henikoff, S, Chakrabarty, A M
The 3-chlorocatechol operon clcABD is central to the biodegradative pathway of 3-chlorobenzoate. The clcR regulatory gene, which activates the clcABD operon, was cloned from the region immediately...
Viale, A M, Kobayashi, H, Akazawa, T, Henikoff, S
An open reading frame, rbcR, was identified 226 bp upstream of rbcAB, i.e., the ribulose 1,5-bisphosphate carboxylase genes expressed in the phototrophic purple bacterium Chromatium vinosum. Several...
A large family of bacterial activator proteins.
Henikoff, S, Haughn, G W, Calvo, J M, Wallace, J C
At least nine different bacterial proteins belong to the LysR family. The gene sequence for one of these proteins is presented here. Six others (Escherichia coli LysR, IlvY, CysB; Salmonella...
Position-effect variegation in Drosophila is the variable inactivation of a gene that occurs when it is juxtaposed to heterochromatic regions of chromosomes. The brown gene, required for pteridine...
Multiple purine pathway enzyme activities are encoded at a single genetic locus in Drosophila.
Henikoff, S, Keene, M A, Sloan, J S, Bleskan, J, Hards, R, Patterson, D
The Drosophila melanogaster Gart locus, known from previous work to encode the enzyme activity phosphoribosylglycinamide formyltransferase (GART), specifies two alternatively processed mRNAs and two...
Two Drosophila melanogaster mutations block successive steps of de novo purine synthesis.
Henikoff, S, Nash, D, Hards, R, Bleskan, J, Woolford, J F, Naguib, F, ...
Drosophila melanogaster purine auxotrophs ade2(1) and ade3(1) have been characterized biochemically. The ade2(1) strain is deficient in the fourth step of the de novo purine synthetic pathway...
We have determined the complete DNA sequence of a segment derived from Drosophila melanogaster that complements a yeast adenine-8 (ade8) mutation. This sequence, in conjunction with transcriptional...
A novel method has been developed for determining the location of RNA termini and intron-exon boundaries using genomic clones. RNA is hybridized to a single-stranded M13 phage derivative of the...
Automated assembly of protein blocks for database searching.
A system is described for finding and assembling the most highly conserved regions of related proteins for database searching. First, an automated version of Smith's algorithm for finding motifs is...
A simple method is described for generating nested deletions from any fixed point in a cloned inset. Starting with a single-stranded phagemid template, T4 DNA polymerase is used to extend an annealed...
Detection of protein similarities using nucleotide sequence databases.
A simple procedure is described for finding similarities between proteins using nucleotide sequence databases. The approach is illustrated by several examples of previously unknown correspondences...
A moveable 5' splice site in adenine phosphoribosyltransferase genes of Drosophila species.
In two distantly related Drosophila species, the use of alternate 5' splice sites to process an intron in pre-mRNA from homologous adenine phosphoribosyltransferase (APRT)-encoding genes led to RNAs...
Dreesen, T D, Johnson, D H, Henikoff, S
The brown gene of Drosophila melanogaster is required for deposition of pteridine pigments in the compound eye and other tissues. We isolated a ca. 150-kilobase region including brown by...
Sequences responsible for transcription termination on a gene segment in Saccharomyces cerevisiae.
We have mapped a signal sequence for mRNA 3'-end formation in Saccharomyces cerevisiae by using a Drosophila melanogaster DNA segment that complements a yeast adenine-8 mutation. That the 3' end of...
Localization of RNA from heat-induced polysomes at puff sites in Drosophila melanogaster.
McKenzie, S L, Henikoff, S, Meselson, M
Heat treatment of D. melanogaster tissue culture cells causes drastic changes in the pattern of protein synthesis and the size distribution of polysomes. Like the heat shock puffs on polytene...
Somatic Instability of a Drosophila Chromosome
A mitotically unstable chromosome, detectable because of mosaic expression of marker genes, was generated by X-ray mutagenesis in Drosophila. Nondisjunction of this chromosome is evident in mitotic...
Modification of the Drosophila Heterochromatic Mutation Brown(dominant) by Linkage Alterations
Talbert, P. B., LeCiel, CDS., Henikoff, S.
The variegating mutation brown(Dominant) (bw(D)) of Drosophila melanogaster is associated with an insertion of heterochromatin into chromosome arm 2R at 59E, the site of the bw gene. Mutagenesis...
Conservation of Brown Gene Trans-Inactivation in Drosophila
Martin-Morris, L. E., Henikoff, S.
The mechanism underlying trans-inactivation associated with dominant position effect variegation (PEV) of the Drosophila melanogaster brown gene has been addressed by a comparison with its D. virilis...
Distance and Pairing Effects on the Brown(dominant) Heterochromatic Element in Drosophila
Henikoff, S., Jackson, J. M., Talbert, P. B.
We examined the behavior of the brown(Dominant) (bw(D)) heterochromatic insertion moved to different locations relative to centric heterochromatin. Effects were measured as the degree of silencing of...
The classical phenomenon of position-effect variegation (PEV) is the mosaic expression that occurs when a chromosomal rearrangement moves a euchromatic gene near heterochromatin. A striking feature...
Heterochromatic Trans-Inactivation of Drosophila White Transgenes
Martin-Morris, L. E., Csink, A. K., Dorer, D. R., Talbert, P. B., Henikoff, S.
Position effect variegation of most Drosophila melanogaster genes, including the white eye pigment gene, is recessive. We find that this is not always the case for white transgenes. Three examples...
Transgene Repeat Arrays Interact with Distant Heterochromatin and Cause Silencing in Cis and Trans
Tandem repeats of Drosophila transgenes can cause heterochromatic variegation for transgene expression in a copy-number and orientation-dependent manner. Here, we demonstrate different ways in which...
In Drosophila melanogaster, heterochromatin-induced silencing or position-effect variegation (PEV) of a reporter gene has provided insights into the properties of heterochromatin. Class I modifiers...
Chromodomains are thought to mediate protein-protein interactions between chromatin components. We have detected a chromodomain embedded within the catalytic region of a predicted Arabidopsis DNA...
We describe the precise positioning of a reporter gene within heterochromatin where it may be silenced. A transposition of the 59E-60A region into pericentric heterochromatin ensnares distal 59E-60A...
In Drosophila, heterochromatin causes mosaic silencing of euchromatic genes brought next to it by chromosomal rearrangements. Silencing has been observed to "spread": genes closer to the...
Adaptive evolution of Cid, a centromere-specific histone in Drosophila.
Centromeric DNA is generally composed of large blocks of tandem satellite repeats that change rapidly due to loss of old arrays and expansion of new repeat classes. This extreme heterogeneity of...
High-Throughput Screening for Induced Point Mutations
Colbert, T., Till, B. J., Tompa, R., Reynolds, S., Steine, M. N., Yeung, A. T., ...
Embedding strategies for effective use of information from multiple sequence alignments.
We describe a new strategy for utilizing multiple sequence alignment information to detect distant relationships in searches of sequence databases. A single sequence representing a protein family is...