Ethylene and 1-Methylcyclopropene Differentially Regulate Gene Expression during Onion Sprout Suppression

Abstract Plant heat shock transcription factors (HSFs) are involved in heat and other abiotic stress responses. However, their functions in salt tolerance are little known. In this study, we characterized the function of a HSF from Arabidopsis, AtHSFA7b, in salt tolerance. AtHSFA7b is a nuclear protein with transactivation activity. ChIP-seq combined with an RNA-seq assay indicated that AtHSFA7b preferentially binds to a novel cis-acting element, termed the E-box-like motif, to regulate gene expression; it also binds to the heat shock element motif. Under salt conditions, AtHSFA7b regulates its target genes to mediate serial physiological changes, including maintaining cellular ion homeostasis, reducing water loss rate, decreasing reactive oxygen species accumulation, and adjusting osmotic potential, which ultimately leads to improved salt tolerance. Additionally, most cellulose synthase-like (CSL) and cellulose synthase (CESA) family genes were inhibited by AtHSFA7b; some of them were randomly selected for salt tolerance characterization, and they were mainly found to negatively modulate salt tolerance. By contrast, some transcription factors (TFs) were induced by AtHSFA7b; among them, we randomly identified six TFs that positively regulate salt tolerance. Thus, AtHSFA7b serves as a transactivator that positively mediates salinity tolerance mainly through binding to the E-box-like motif to regulate gene expression.

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Genome‐wide chromatin occupancy of BRDT and gene expression analysis suggest transcriptional partners and specific epigenetic landscapes that regulate gene expression during spermatogenesis

Molecular Reproduction and Development ◽

10.1002/mrd.23449 ◽

2021 ◽

Author(s):

Yoon Ra Her ◽

Li Wang ◽

Iouri Chepelev ◽

Marcia Manterola ◽

Binyamin Berkovits ◽

...

Keyword(s):

Gene Expression ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Regulate Gene Expression ◽

Genome Wide ◽

Regulate Gene

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A First Step towards Learning which uORFs Regulate Gene Expression

Journal of Integrative Bioinformatics ◽

10.1515/jib-2006-31 ◽

2006 ◽

Vol 3 (2) ◽

pp. 109-122 ◽

Cited By ~ 1

Author(s):

◽

Christopher H. Bryant ◽

Graham J.L. Kemp ◽

Marija Cvijovic

Keyword(s):

Gene Expression ◽

Inductive Logic ◽

Preliminary Evidence ◽

Open Reading Frames ◽

Yeast Saccharomyces Cerevisiae ◽

Regulate Gene Expression ◽

Integrative System ◽

Upstream Open Reading Frames ◽

Reading Frames ◽

Regulate Gene

Summary We have taken a first step towards learning which upstream Open Reading Frames (uORFs) regulate gene expression (i.e., which uORFs are functional) in the yeast Saccharomyces cerevisiae. We do this by integrating data from several resources and combining a bioinformatics tool, ORF Finder, with a machine learning technique, inductive logic programming (ILP). Here, we report the challenge of using ILP as part of this integrative system, in order to automatically generate a model that identifies functional uORFs. Our method makes searching for novel functional uORFs more efficient than random sampling. An attempt has been made to predict novel functional uORFs using our method. Some preliminary evidence that our model may be biologically meaningful is presented.

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Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

Nature ◽

10.1038/nature06904 ◽

2008 ◽

Vol 453 (7194) ◽

pp. 534-538 ◽

Cited By ~ 705

Author(s):

Oliver H. Tam ◽

Alexei A. Aravin ◽

Paula Stein ◽

Angelique Girard ◽

Elizabeth P. Murchison ◽

...

Keyword(s):

Gene Expression ◽

Small Interfering Rnas ◽

Regulate Gene Expression ◽

Mouse Oocytes ◽

Regulate Gene

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The selective post-translational processing of transcription factor Nrf1 yields distinct isoforms that dictate its ability to differentially regulate gene expression

Scientific Reports ◽

10.1038/srep12983 ◽

2015 ◽

Vol 5 (1) ◽

Cited By ~ 32

Author(s):

Yiguo Zhang ◽

Shaojun Li ◽

Yuancai Xiang ◽

Lu Qiu ◽

Huakan Zhao ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Regulate Gene Expression ◽

Regulate Gene

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Regulation of Multiple Core Spliceosomal Proteins by Alternative Splicing-Coupled Nonsense-Mediated mRNA Decay

Molecular and Cellular Biology ◽

10.1128/mcb.00361-08 ◽

2008 ◽

Vol 28 (13) ◽

pp. 4320-4330 ◽

Cited By ~ 126

Author(s):

Arneet L. Saltzman ◽

Yoon Ki Kim ◽

Qun Pan ◽

Matthew M. Fagnani ◽

Lynne E. Maquat ◽

...

Keyword(s):

Gene Expression ◽

Alternative Splicing ◽

Mrna Decay ◽

Splice Variants ◽

Cellular Functions ◽

Regulate Gene Expression ◽

Premature Termination Codons ◽

Microarray Profiling ◽

Nonsense Mediated Mrna Decay ◽

Regulate Gene

ABSTRACT Alternative splicing (AS) can regulate gene expression by introducing premature termination codons (PTCs) into spliced mRNA that subsequently elicit transcript degradation by the nonsense-mediated mRNA decay (NMD) pathway. However, the range of cellular functions controlled by this process and the factors required are poorly understood. By quantitative AS microarray profiling, we find that there are significant overlaps among the sets of PTC-introducing AS events affected by individual knockdown of the three core human NMD factors, Up-Frameshift 1 (UPF1), UPF2, and UPF3X/B. However, the levels of some PTC-containing splice variants are less or not detectably affected by the knockdown of UPF2 and/or UPF3X, compared with the knockdown of UPF1. The intron sequences flanking the affected alternative exons are often highly conserved, suggesting important regulatory roles for these AS events. The corresponding genes represent diverse cellular functions, and surprisingly, many encode core spliceosomal proteins and assembly factors. We further show that conserved, PTC-introducing AS events are enriched in genes that encode core spliceosomal proteins. Where tested, altering the expression levels of these core spliceosomal components affects the regulation of PTC-containing splice variants from the corresponding genes. Together, our results show that AS-coupled NMD can have different UPF factor requirements and is likely to regulate many general components of the spliceosome. The results further implicate general spliceosomal components in AS regulation.

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