Articles written in Journal of Biosciences
Volume 36 Issue 3 August 2011 pp 461-469 Articles
The special AT-rich DNA-binding protein 1 (SATB1) is a matrix attachment region (MAR)-binding protein that acts as a global repressor via recruitment of CtBP1:HDAC1-containing co-repressors to its binding targets. The N-terminal PSD95/Dlg-A/ZO-1 (PDZ)-like domain of SATB1 mediates interactions with several chromatin proteins. In the present study, we set out to address whether the PDZ-domain-mediated interactions of SATB1 are critical for its
Volume 40 Issue 5 December 2015 pp 891-907 Articles
The Asian elephant
Volume 43 Issue 1 March 2018 pp 155-171 Review
Protein scaffolds as essential backbones for organization of supramolecular signalling complexes are a recurrent theme inseveral model systems. Scaffold proteins preferentially employ linear peptide binding motifs for recruiting their interactionpartners. PDZ domains are one of the more commonly encountered peptide binding domains in several proteins includingthose involved in scaffolding functions. This domain is known for its promiscuity both in terms of ligand selection, mode ofinteraction with its ligands as well as its association with other protein interaction domains. PDZ domains are subject toseveral means of regulations by virtue of their functional diversity. Additionally, the PDZ domains are refractive to theeffect of mutations and maintain their three-dimensional architecture under extreme mutational load. The biochemical andbiophysical basis for this selectivity as well as promiscuity has been investigated and reviewed extensively. The presentreview focuses on the plasticity inherent in PDZ domains and its implications for modular organization as well as evolutionof cellular signalling pathways in higher eukaryotes.
Volume 45 All articles Published: 8 January 2020 Article ID 0001 Editorial
Volume 45 All articles Published: 20 January 2020 Article ID 0008 Article
Multicellular organisms have evolved sophisticated mechanisms for responding to various developmental,environmental and physical stimuli by regulating transcription. The correlation of distribution of RNAPolymerase II (RNA Pol II) with transcription is well established in higher metazoans, however genome-wideinformation about its distribution in early metazoans, such as Hydra, is virtually absent. To gain insights intoRNA Pol II-mediated transcription and chromatin organization in Hydra, we performed chromatin immunoprecipitation(ChIP)-coupled high-throughput sequencing (ChIP-seq) for RNA Pol II and Histone H3. Strikingly,we found that Hydra RNA Pol II is uniformly distributed across the entire gene body, as opposed to itscounterparts in bilaterians such as human and mouse. Furthermore, correlation with transcriptome datarevealed that the levels of RNA Pol II correlate with the magnitude of gene expression. Strikingly, thecharacteristic peak of RNA Pol II pause typically observed in bilaterians at the transcription start sites (TSSs)was not observed in Hydra. The RNA Pol II traversing ratio in Hydra was found to be intermediate to yeastand bilaterians. The search for factors involved in RNA Pol II pause revealed that RNA Pol II pausingmachinery was most likely acquired first in Cnidaria. However, only a small subset of genes exhibited thepromoter proximal RNP Pol II pause. Interestingly, the nucleosome occupancy is highest over the subset ofpaused genes as compared to total Hydra genes, which is another indication of paused RNA Pol II at thesegenes. Thus, this study provides evidence for the molecular basis of RNA Pol II pause early during theevolution of multicellular organisms.
Volume 45, 2020
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