Uncovering the interplay between DNA sequence preferences of transcription factors and nucleosomes

DNA-protein interaction: identification, prediction and data analysis

Life in living organisms is dependent on specific and purposeful interaction between other molecules. Such purposeful interactions make the various processes inside the cells and the bodies of living organisms possible. DNA-protein interactions, among all the types of interactions between different molecules, are of considerable importance. Currently, with the development of numerous experimental techniques, diverse methods are convenient for recognition and investigating such interactions. While the traditional experimental techniques to identify DNA-protein complexes are time-consuming and are unsuitable for genome-scale studies, the current high throughput approaches are more efficient in determining such interaction at a large-scale, but they are clearly too costly to be practice for daily applications. Hence, according to the availability of much information related to different biological sequences and clearing different dimensions of conditions in which such interactions are formed, with the developments related to the computer, mathematics, and statistics motivate scientists to develop bioinformatics tools for prediction the interaction site(s). Until now, there has been much progress in this field. In this review, the factors and conditions governing the interaction and the laboratory techniques for examining such interactions are addressed. In addition, developed bioinformatics tools are introduced and compared for this reason and, in the end, several suggestions are offered for the promotion of such tools in prediction with much more precision.

Application of MNase-Seq in the Global Mapping of Nucleosome Positioning in Plants

The precise positioning of nucleosomes along the underlying DNA is critical for a variety of biological processes, especially in regulating transcription. The interplay between nucleosomes and transcription factors for accessing the underlying DNA sequences is one of the key determinants that affect transcriptional regulation. Moreover, nucleosomes with various packing statuses confer distinct functions in regulating gene expressions in response to various internal or external signals. Therefore, global mapping of nucleosome positions is one informative way to elucidate the relationship between patterns of nucleosome positioning/occupancy and transcriptional regulations. MNase digestion coupled with high-throughput sequencing (MNase-seq) has been utilized widely for global mapping of nucleosome positioning in eukaryotes that have a sequenced genome. We have developed a robust MNase-seq procedure in plants. It mainly includes plant nuclei isolation, treatment of purified nuclei with MNase, gel recovery of MNase-trimmed mononucleosomal DNA with an approximate size of 150 bp, MNase-seq library preparation followed by Illumina sequencing, and data analysis. MNase-seq has already been successfully applied to identify genome-wide nucleosome positioning in model plants, rice, and Arabidopsis thaliana.

Gene expression and promoter characterization of heat-shock protein 90B gene (HSP90B) in the model unicellular green alga Chlamydomonas reinhardtii

Molecular chaperones or heat shock proteins are a large protein family with important functions in every cellular organism. Among all types of the heat shock proteins, information on the ER-localized HSP90 protein (HSP90B) and its encoding gene is relatively scarce in the literature, especially in photosynthetic organisms. In this study, expression profiles as well as promoter sequence of the HSP90B gene were investigated in the model green alga Chlamydomonas reinhardtii. We have found that HSP90B is strongly induced by heat and ER stresses, while other short-term exposure to abiotic stresses, such as salinity, dark-to-light transition or light stress does not appear to affect the expression. Promoter truncation analysis as well as chromatin immunoprecipitation using the antibodies recognizing histone H3 and acetylated histone H3, revealed a putative core constitutive promoter sequence between -1 to -253 bp from the transcription start site. Our results also suggested that the nucleotides upstream of the core promoter may contain repressive elements such as putative repressor binding site(s).

Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis

Temperature influences the distribution, range, and phenology of plants. The key transcriptional activators of heat shock response in eukaryotes, the heat shock factors (HSFs), have undergone large-scale gene amplification in plants. While HSFs are central in heat stress responses, their role in the response to ambient temperature changes is less well understood. We show here that the warm ambient temperature transcriptome is dependent upon the HSFA1 clade of Arabidopsis HSFs, which cause a rapid and dynamic eviction of H2A.Z nucleosomes at target genes. A transcriptional cascade results in the activation of multiple downstream stress-responsive transcription factors, triggering large-scale changes to the transcriptome in response to elevated temperature. H2A.Z nucleosomes are enriched at temperature-responsive genes at non-inducible temperature, and thus likely confer inducibility of gene expression and higher responsive dynamics. We propose that the antagonistic effects of H2A.Z and HSF1 provide a mechanism to activate gene expression rapidly and precisely in response to temperature, while preventing leaky transcription in the absence of an activation signal.

"Hit-and-run": Transcription factors get caught in the act

A key challenge for understanding transcriptional regulation is being able to measure transcription factor (TF)-DNA binding events with sufficient spatial and temporal resolution; that is, when and where TFs occupy their cognate sites. A recent study by Para et al. has highlighted the dynamics underlying the activation of gene expression by a master regulator TF. This study provides concrete evidence for a long-standing hypothesis in biology, the "hit-and-run" mechanism, which was first proposed decades ago. That is, gene expression is dynamically controlled by a TF that transiently binds and activates a target gene, which might stay in a transcriptionally active state after the initial binding event has ended. Importantly, the experimental procedure introduced, TARGET, provides a useful way for identifying multiple target genes transiently bound by their regulators, which can be used in conjunction with other well-established methods to improve our understanding of transcriptional regulatory dynamics.