NHP6B / YBR089C-A Overview
- Standard Name
- NHP6B 1
- Systematic Name
- YBR089C-A
- SGD ID
- SGD:S000002157
- Aliases
- YBR090C-A
- Feature Type
- ORF , Verified
- Description
- High-mobility group (HMG) protein; binds to and remodels nucleosomes; involved in recruiting FACT and other chromatin remodelling complexes to the chromosomes; functionally redundant with Nhp6Ap; required for transcriptional initiation fidelity of some tRNA genes; homologous to mammalian HMGB1 and HMGB2; NHP6B has a paralog, NHP6A, that arose from the whole genome duplication 2 4 5 6 7 8 9
- Name Description
- Non-Histone Protein 3
- Paralog
- NHP6A 9
- Comparative Info
-
Sequence
The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C. Download DNA or protein sequence, view genomic context and coordinates. Click "Sequence Details" to view all sequence information for this locus, including that for other strains.
- Summary
- NHP6B has a paralog, NHP6A, that arose from the whole genome duplication
Analyze Sequence
S288C only
BLASTN | BLASTP | Design Primers | Restriction Fragment Map | Restriction Fragment Sizes | Six-Frame Translation
S288C vs. other species
BLASTN vs. fungi | BLASTP at NCBI | BLASTP vs. fungi
S288C vs. other strains
Protein
Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein.
- Length (a.a.)
- 99
- Mol. Weight (Da)
- 11485.2
- Isoelectric Point
- 10.54
- Median Abundance (molecules/cell)
- 7847 +/- 2432
- Half-life (hr)
- 7.7
Alleles
Curated mutant alleles for the specified gene, listed alphabetically. Click on the allele name to open the allele page. Click "SGD search" to view all alleles in search results.
View all NHP6B alleles in SGD search
Gene Ontology
GO Annotations consist of four mandatory components: a gene product, a term from one of the three Gene Ontology (GO) controlled vocabularies (Molecular Function, Biological Process, and Cellular Component), a reference, and an evidence code. SGD has manually curated and high-throughput GO Annotations, both derived from the literature, as well as computational, or predicted, annotations. Click "Gene Ontology Details" to view all GO information and evidence for this locus as well as biological processes it shares with other genes.
- Summary
- DNA and nucleosome-binding protein involved in chromatin remodeling, assembly of the RNA polymerase II and III pre-initiation complexes, and maintenance of transcriptional fidelity; localizes in the nucleus
View computational annotations
Molecular Function
- Manually Curated
- enables DNA binding, bending (IDA)
- enables sequence-specific DNA binding (HDA)
Biological Process
- Manually Curated
- involved in chromatin remodeling (IGI)
- involved in maintenance of transcriptional fidelity during transcription elongation by RNA polymerase III (IDA)
- involved in RNA polymerase III preinitiation complex assembly (IDA, IGI)
- involved in transcription by RNA polymerase II (IGI)
Phenotype
Phenotype annotations for a gene are curated single mutant phenotypes that require an observable (e.g., "cell shape"), a qualifier (e.g., "abnormal"), a mutant type (e.g., null), strain background, and a reference. In addition, annotations are classified as classical genetics or high-throughput (e.g., large scale survey, systematic mutation set). Whenever possible, allele information and additional details are provided. Click "Phenotype Details" to view all phenotype annotations and evidence for this locus as well as phenotypes it shares with other genes.
Classical Genetics
- null
- overexpression
Interaction
Interaction annotations are curated by BioGRID and include physical or genetic interactions observed between at least two genes. An interaction annotation is composed of the interaction type, name of the interactor, assay type (e.g., Two-Hybrid), annotation type (e.g., manual or high-throughput), and a reference, as well as other experimental details. Click "Interaction Details" to view all interaction annotations and evidence for this locus, including an interaction visualization.
- Summary
- The nhp6b null mutant is viable; the null mutant of paralog nhp6a is viable; the nhp6b nhp6a double mutant displays a synthetic growth defect.
215 total interactions for 166 unique genes
Physical Interactions
- Affinity Capture-MS: 31
- Affinity Capture-RNA: 4
- Biochemical Activity: 1
- Co-localization: 1
- Co-purification: 1
- PCA: 35
- Reconstituted Complex: 17
Genetic Interactions
- Dosage Lethality: 4
- Dosage Rescue: 6
- Negative Genetic: 55
- Phenotypic Enhancement: 4
- Phenotypic Suppression: 3
- Positive Genetic: 17
- Synthetic Growth Defect: 18
- Synthetic Lethality: 14
- Synthetic Rescue: 4
Regulation
The number of putative Regulators (genes that regulate it) and Targets (genes it regulates) for the given locus, based on experimental evidence. This evidence includes data generated through high-throughput techniques. Click "Regulation Details" to view all regulation annotations, shared GO enrichment among regulation Targets, and a regulator/target diagram for the locus.
- Summary
- NHP6A and NHP6B encode paralogous High Mobility Group (HMG) B domain-containing transcription factors that are involved in the modulation of chromatin structure. The Nhp6A and Nhp6B proteins differ at their N-termini, but over the 90 amino acid core region are 96% similar. Nhp6p contains a single HMGB domain that binds DNA in the minor groove and a basic N-terminal extension that wraps around DNA to contact the major groove, enabling Nhp6p to bind DNA as a monomer in a sequence-nonspecific manner, and bend DNA sharply. Nhp6p affects a range of processes linked to appropriate regulation of transcription through maintenance of normal chromatin structure. Nhp6p functions in the formation of preinitiation complexes at RNA polymerase II promoters, and also promotes RNA polymerase III transcription, as well as facilitating the activity of chromatin modifying complexes. Nhp6p localization in the vicinity of transcription start sites parallels that of nucleosomes. Expression of NHP6 genes is regulated by the concentration of Nhp6 protein or RNA, as overexpression of Nhp6p results in a dramatic decrease in NHP6 expression, and is toxic to cells.
Expression
Expression data are derived from records contained in the Gene Expression Omnibus (GEO), and are first log2 transformed and normalized. Referenced datasets may contain one or more condition(s), and as a result there may be a greater number of conditions than datasets represented in a single clickable histogram bar. The histogram division at 0.0 separates the down-regulated (green) conditions and datasets from those that are up-regulated (red). Click "Expression Details" to view all expression annotations and details for this locus, including a visualization of genes that share a similar expression pattern.
Summary Paragraph
A summary of the locus, written by SGD Biocurators following a thorough review of the literature. Links to gene names and curated GO terms are included within the Summary Paragraphs.
Last Updated: 2010-03-30
Literature
All manually curated literature for the specified gene, organized into topics according to their relevance to the gene (Primary Literature, Additional Literature, or Review). Click "Literature Details" to view all literature information for this locus, including shared literature between genes.