The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expression
Name:
Article-PLoS_ONE-The_disequ-2011.pdf
Size:
999.1Kb
Format:
PDF
Description:
Article - Full Text
Name:
Supplement_1_-_PLoS_ONE-The_disequ-2011.pone.0023219.s001.pdf
Size:
16.44Kb
Format:
PDF
Description:
Supplemental File 1
Name:
Supplement_2_-_PLoS_ONE-The_disequ-2011.pone.0023219.s002.pdf
Size:
4.867Kb
Format:
PDF
Description:
Supplemental File 2
Name:
Supplement_3_-_PLoS_ONE-The_disequ-2011.pone.0023219.s003.pdf
Size:
945.3Kb
Format:
PDF
Description:
Supplemental File 3
Name:
Supplement_4_-_PLoS_ONE-The_disequ-2011.pone.0023219.s004.pdf
Size:
991.2Kb
Format:
PDF
Description:
Supplemental File 4
Name:
Supplement_5_-_PLoS_ONE-The_disequ-2011.pone.0023219.s005.doc
Size:
30Kb
Format:
Microsoft Word
Description:
Supplemental File 5
Name:
Supplement_6_-_PLoS_ONE-The_disequ-2011.pone.0023219.s006.xls
Size:
93Kb
Format:
Microsoft Excel
Description:
Supplemental File 6
Name:
Supplement_7_-_PLoS_ONE-The_disequ-2011.pone.0023219.s007.doc
Size:
31.5Kb
Format:
Microsoft Word
Description:
Supplemental File 7
Type
ArticleAuthors
Cui, Peng
Lin, Qiang
Zhang, Lingfang
Ding, Feng

Xin, Chengqi
Zhang, Daoyong
Sun, Fanglin
Hu, Songnian
Yu, Jun
KAUST Department
Biological and Environmental Sciences and Engineering (BESE) DivisionComputational Bioscience Research Center (CBRC)
Desert Agriculture Initiative
Date
2011-08-19Permanent link to this record
http://hdl.handle.net/10754/325293
Metadata
Show full item recordAbstract
To further understand the relationship between nucleosome-space occupancy (NO) and global transcriptional activity in mammals, we acquired a set of genome-wide nucleosome distribution and transcriptome data from the mouse cerebrum and testis based on ChIP (H3)-seq and RNA-seq, respectively. We identified a nearly consistent NO patterns among three mouse tissues-cerebrum, testis, and ESCs-and found, through clustering analysis for transcriptional activation, that the NO variations among chromosomes are closely associated with distinct expression levels between house-keeping (HK) genes and tissue-specific (TS) genes. Both TS and HK genes form clusters albeit the obvious majority. This feature implies that NO patterns, i.e. nucleosome binding and clustering, are coupled with gene clustering that may be functionally and evolutionarily conserved in regulating gene expression among different cell types. © 2011 Cui et al.Citation
Cui P, Lin Q, Zhang L, Ding F, Xin C, et al. (2011) The Disequilibrium of Nucleosomes Distribution along Chromosomes Plays a Functional and Evolutionarily Role in Regulating Gene Expression. PLoS ONE 6: e23219. doi:10.1371/journal.pone.0023219.Publisher
Public Library of Science (PLoS)Journal
PLoS ONEPubMed ID
21886783PubMed Central ID
PMC3158759ae974a485f413a2113503eed53cd6c53
10.1371/journal.pone.0023219
Scopus Count
Related articles
- A novel mechanism of epigenetic regulation: nucleosome-space occupancy.
- Authors: Cui P, Zhang L, Lin Q, Ding F, Xin C, Fang X, Hu S, Yu J
- Issue date: 2010 Jan 1
- Identification and analysis of house-keeping and tissue-specific genes based on RNA-seq data sets across 15 mouse tissues.
- Authors: Zeng J, Liu S, Zhao Y, Tan X, Aljohi HA, Liu W, Hu S
- Issue date: 2016 Jan 15
- Insights into distinct regulatory modes of nucleosome positioning.
- Authors: Dai Z, Dai X, Xiang Q, Feng J, Deng Y, Wang J
- Issue date: 2009 Dec 14
- Genome-wide transcriptome mapping analysis identifies organ-specific gene expression patterns along human chromosomes.
- Authors: Yamashita T, Honda M, Takatori H, Nishino R, Hoshino N, Kaneko S
- Issue date: 2004 Nov
- Two strategies for gene regulation by promoter nucleosomes.
- Authors: Tirosh I, Barkai N
- Issue date: 2008 Jul
Related items
Showing items related by title, author, creator and subject.
-
Arabidopsis SUMO protease ASP1 positively regulates flowering time partially through regulating FLC stabilityKong, Xiangxiong; Luo, Xi; Qu, Gao Ping; Liu, Peng; Jin, Jing Bo (Journal of Integrative Plant Biology, Wiley, 2017-01-10) [Article]The initiation of flowering is tightly regulated by the endogenous and environment signals, which is crucial for the reproductive success of flowering plants. It is well known that autonomous and vernalization pathways repress transcription of FLOWERING LOCUS C (FLC), a focal floral repressor, but how its protein stability is regulated remains largely unknown. Here, we found that mutations in a novel Arabidopsis SUMO protease 1 (ASP1) resulted in a strong late-flowering phenotype under long-days, but to a lesser extent under short-days. ASP1 localizes in the nucleus and exhibited a SUMO protease activity in vitro and in vivo. The conserved Cys-577 in ASP1 is critical for its enzymatic activity, as well as its physiological function in the regulation of flowering time. Genetic and gene expression analyses demonstrated that ASP1 promotes transcription of positive regulators of flowering, such as FT, SOC1 and FD, and may function in both CO-dependent photoperiod pathway and FLC-dependent pathways. Although the transcription level of FLC was not affected in the loss-of-function asp1 mutant, the protein stability of FLC was increased in the asp1 mutant. Taken together, this study identified a novel bona fide SUMO protease, ASP1, which positively regulates transition to flowering at least partly by repressing FLC protein stability.
-
Targeted genome regulation via synthetic programmable transcriptional regulatorsPiatek, Agnieszka Anna; Mahfouz, Magdy M. (Critical Reviews in Biotechnology, Informa UK Limited, 2016-04-19) [Article]Regulation of gene transcription controls cellular functions and coordinates responses to developmental, physiological and environmental cues. Precise and efficient molecular tools are needed to characterize the functions of single and multiple genes in linear and interacting pathways in a native context. Modular DNA-binding domains from zinc fingers (ZFs) and transcriptional activator-like proteins (TALE) are amenable to bioengineering to bind DNA target sequences of interest. As a result, ZF and TALE proteins were used to develop synthetic programmable transcription factors. However, these systems are limited by the requirement to re-engineer proteins for each new target sequence. The clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR associated 9 (Cas9) genome editing tool was recently repurposed for targeted transcriptional regulation by inactivation of the nuclease activity of Cas9. Due to the facile engineering, simplicity, precision and amenability to library construction, the CRISPR/Cas9 system is poised to revolutionize the functional genomics field across diverse eukaryotic species. In this review, we discuss the development of synthetic customizable transcriptional regulators and provide insights into their current and potential applications, with special emphasis on plant systems, in characterization of gene functions, elucidation of molecular mechanisms and their biotechnological applications. © 2016 Informa UK Limited, trading as Taylor & Francis Group
-
Conformational Regulation of the Essential Epigenetic Regulator UHRF1Pantoja Angles, Aarón (2018-05) [Thesis]
Advisor: Fischle, Wolfgang
Committee members: Adamo, Antonio; Mahfouz, Magdy M.; Jaremko, LukaszUHRF1 is an essential epigenetic regulator implicated in the maintenance of DNA methylation. While its functional state has been suggested to be allosterically regulated by phosphatidylinositol 5-phosphate and dependent on purification conditions and tags coupled to the protein, the expression system might have a broader impact on UHRF1s interaction properties. We hypothesized that the translation kinetics defined by the expression host has an impact on the folding process of the protein, which ultimately affects its structure and function. To test this idea, the cDNA of UHRF1 was recoded in order to generate optimized and harmonized sequences that were expected to alter the overall translation speed. Both proteins were expressed in Escherichia coli BL21-DE3 and their interaction profiles with H3K9me3 and unmodified H3 peptides were determined by microscale thermophoresis assays. The dissociation constants were compared by ttests in order to evaluate a possible change in the interaction properties of the optimized and harmonized proteins, compared to non-optimized UHRF1 expressed in E. coli BL21-DE3. While no difference was found for the interaction of optimized UHRF1 with the H3K9me3 peptide, a significant difference was found for its interaction with the unmodified H3 peptide. Moreover, both the interactions of harmonized UHRF1 with H3K9me3 and unmodified H3 peptides were determined to change. For this reason, we concluded that translation kinetics dependent on the expression system impacts the functional state of UHRF1. To further study this phenomenon, we expressed the consensus sequence of UHRF1 in Escherichia coli BL21-Codon Plus-(DE3)-RIL, a bacterial strain that is enriched with arginine, isoleucine, and leucine tRNA isoacceptors. Differences in its interaction profile with histone peptides were found when compared with UHRF1 expressed in Escherichia coli BL21-DE3. Since the major difference between these strains is the abundance of tRNAs, we obtained further findings that support our initial hypothesis. Additionally, the interaction profiles from the consensus UHRF1 protein were determined in the presence of PI5P to get an insight into how this phosphoinositide might impact the final structure and function of UHRF1. MST measurements and limited proteolysis assays led us to the idea of a partially open conformation for the UHRF1 expressed in E. coli BL21-DE3 and E.coli Codon Plus-(DE3)-RIL.