BIOMAT Database Logo BIOMAT Database Logo

Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. 2012

Tali Raveh-Sadka, and Michal Levo, and Uri Shabi, and Boaz Shany, and Leeat Keren, and Maya Lotan-Pompan, and Danny Zeevi, and Eilon Sharon, and Adina Weinberger, and Eran Segal
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.

Understanding how precise control of gene expression is specified within regulatory DNA sequences is a key challenge with far-reaching implications. Many studies have focused on the regulatory role of transcription factor-binding sites. Here, we explore the transcriptional effects of different elements, nucleosome-disfavoring sequences and, specifically, poly(dA:dT) tracts that are highly prevalent in eukaryotic promoters. By measuring promoter activity for a large-scale promoter library, designed with systematic manipulations to the properties and spatial arrangement of poly(dA:dT) tracts, we show that these tracts significantly and causally affect transcription. We show that manipulating these elements offers a general genetic mechanism, applicable to promoters regulated by different transcription factors, for tuning expression in a predictable manner, with resolution that can be even finer than that attained by altering transcription factor sites. Overall, our results advance the understanding of the regulatory code and suggest a potential mechanism by which promoters yielding prespecified expression patterns can be designed.

UI MeSH Term Description Entries
D008969 Molecular Sequence Data Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D009707 Nucleosomes The repeating structural units of chromatin, each consisting of approximately 200 base pairs of DNA wound around a protein core. This core is composed of the histones H2A, H2B, H3, and H4. Dinucleosomes,Polynucleosomes,Dinucleosome,Nucleosome,Polynucleosome
D011401 Promoter Regions, Genetic DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes. rRNA Promoter,Early Promoters, Genetic,Late Promoters, Genetic,Middle Promoters, Genetic,Promoter Regions,Promoter, Genetic,Promotor Regions,Promotor, Genetic,Pseudopromoter, Genetic,Early Promoter, Genetic,Genetic Late Promoter,Genetic Middle Promoters,Genetic Promoter,Genetic Promoter Region,Genetic Promoter Regions,Genetic Promoters,Genetic Promotor,Genetic Promotors,Genetic Pseudopromoter,Genetic Pseudopromoters,Late Promoter, Genetic,Middle Promoter, Genetic,Promoter Region,Promoter Region, Genetic,Promoter, Genetic Early,Promoter, rRNA,Promoters, Genetic,Promoters, Genetic Middle,Promoters, rRNA,Promotor Region,Promotors, Genetic,Pseudopromoters, Genetic,Region, Genetic Promoter,Region, Promoter,Region, Promotor,Regions, Genetic Promoter,Regions, Promoter,Regions, Promotor,rRNA Promoters
D004271 DNA, Fungal Deoxyribonucleic acid that makes up the genetic material of fungi. Fungal DNA
D005800 Genes, Fungal The functional hereditary units of FUNGI. Fungal Genes,Fungal Gene,Gene, Fungal
D001483 Base Sequence The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D001665 Binding Sites The parts of a macromolecule that directly participate in its specific combination with another molecule. Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D014157 Transcription Factors Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process. Transcription Factor,Factor, Transcription,Factors, Transcription
D014158 Transcription, Genetic The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION. Genetic Transcription
D015003 Yeasts A general term for single-celled rounded fungi that reproduce by budding. Brewers' and bakers' yeasts are SACCHAROMYCES CEREVISIAE; therapeutic dried yeast is YEAST, DRIED. Yeast

Related Publications

Tali Raveh-Sadka, and Michal Levo, and Uri Shabi, and Boaz Shany, and Leeat Keren, and Maya Lotan-Pompan, and Danny Zeevi, and Eilon Sharon, and Adina Weinberger, and Eran Segal
Tuning gene expression with nucleosome-disfavoring sequences.
June 2012, Nature genetics,
Tali Raveh-Sadka, and Michal Levo, and Uri Shabi, and Boaz Shany, and Leeat Keren, and Maya Lotan-Pompan, and Danny Zeevi, and Eilon Sharon, and Adina Weinberger, and Eran Segal
Effects of triplet repeat sequences on nucleosome positioning and gene expression in yeast minichromosomes.
January 2002, Nucleic acids research. Supplement (2001),
Tali Raveh-Sadka, and Michal Levo, and Uri Shabi, and Boaz Shany, and Leeat Keren, and Maya Lotan-Pompan, and Danny Zeevi, and Eilon Sharon, and Adina Weinberger, and Eran Segal
Multiple conformational states of riboswitches fine-tune gene regulation.
February 2015, Current opinion in structural biology,
Tali Raveh-Sadka, and Michal Levo, and Uri Shabi, and Boaz Shany, and Leeat Keren, and Maya Lotan-Pompan, and Danny Zeevi, and Eilon Sharon, and Adina Weinberger, and Eran Segal
The Nucleosome Remodeling and Deacetylation Complex Modulates Chromatin Structure at Sites of Active Transcription to Fine-Tune Gene Expression.
July 2018, Molecular cell,
Tali Raveh-Sadka, and Michal Levo, and Uri Shabi, and Boaz Shany, and Leeat Keren, and Maya Lotan-Pompan, and Danny Zeevi, and Eilon Sharon, and Adina Weinberger, and Eran Segal
Fine-tuning of noise in gene expression with nucleosome remodeling.
June 2018, APL bioengineering,
Tali Raveh-Sadka, and Michal Levo, and Uri Shabi, and Boaz Shany, and Leeat Keren, and Maya Lotan-Pompan, and Danny Zeevi, and Eilon Sharon, and Adina Weinberger, and Eran Segal
Intrinsic variability of gene expression encoded in nucleosome positioning sequences.
April 2009, Nature genetics,
Tali Raveh-Sadka, and Michal Levo, and Uri Shabi, and Boaz Shany, and Leeat Keren, and Maya Lotan-Pompan, and Danny Zeevi, and Eilon Sharon, and Adina Weinberger, and Eran Segal
Yeast Synthetic Terminators: Fine Regulation of Strength through Linker Sequences.
September 2019, Chembiochem : a European journal of chemical biology,
Tali Raveh-Sadka, and Michal Levo, and Uri Shabi, and Boaz Shany, and Leeat Keren, and Maya Lotan-Pompan, and Danny Zeevi, and Eilon Sharon, and Adina Weinberger, and Eran Segal
Codon Bias as a Means to Fine-Tune Gene Expression.
July 2015, Molecular cell,
Tali Raveh-Sadka, and Michal Levo, and Uri Shabi, and Boaz Shany, and Leeat Keren, and Maya Lotan-Pompan, and Danny Zeevi, and Eilon Sharon, and Adina Weinberger, and Eran Segal
Nucleosome destabilization in the epigenetic regulation of gene expression.
January 2008, Nature reviews. Genetics,
Tali Raveh-Sadka, and Michal Levo, and Uri Shabi, and Boaz Shany, and Leeat Keren, and Maya Lotan-Pompan, and Danny Zeevi, and Eilon Sharon, and Adina Weinberger, and Eran Segal
Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast.
November 1999, Nature,
Copied contents to your clipboard!