scholarly journals Subcellular dynamics studies reveal how tissue-specific distribution patterns of iron are established in developing wheat grains

2021 ◽  
Author(s):  
Sadia Sheraz ◽  
Yongfang Wan ◽  
Eudri Venter ◽  
Shailender K Verma ◽  
Qing Xiong ◽  
...  
Keyword(s):  
Iron Homeostasis ◽  
Distribution Patterns ◽  
Cell Types ◽  
Specific Gene ◽  
Tissue Specific ◽  
Iron Trafficking ◽  
Specific Distribution ◽  
Novel Approach ◽  
In Transit ◽  
Different Cell Types

AbstractUnderstanding iron trafficking in plants is key to enhancing the nutritional quality of crops. Due to the difficulty of imaging iron in transit, little is known about iron translocation and distribution in developing seeds. A novel approach, combining 57Fe isotope labelling and NanoSIMS, was used to visualize iron translocation dynamics at the subcellular level in wheat grain, Triticum aestivum L. We were able to track the main route of iron from maternal tissues to the embryo through different cell types. Further evidence for this route was provided by genetically diverting iron into storage vacuoles, as confirmed by histological staining and TEM-EDS. Virtually all iron was found in intracellular bodies, indicating symplastic rather than apoplastic transport. Aleurone cells contained a new type of iron body, highly enriched in 57Fe, and most likely represents iron-nicotianamine being delivered to phytate globoids. Correlation with tissue-specific gene expression provides an updated model of iron homeostasis in cereal grains with relevance for future biofortification efforts.

scholarly journals Effect of Copper On Bioconcentration of Benzotriazole Ultraviolet Stabilizers (BUVSs) in Common Carp (Cyprinus Carpio)

2021 ◽  
Author(s):  
Dandan Zhao ◽  
Tadiyose Girma Bekele ◽  
Hongxia Zhao
Keyword(s):  
Common Carp ◽  
Distribution Patterns ◽  
Ecological Effect ◽  
Tissue Specific ◽  
Treatment Groups ◽  
Specific Distribution ◽  
Muscle Tissues ◽  
Effect Of Copper ◽  
Depuration Rate ◽  
Kinetics Of

Abstract Benzotriazole ultraviolet stabilizers (BUVSs) have received increasing attention due to their widespread usage, ubiquitous detection and their adverse ecological effect. However, information about the bioaccumulation potential of BUVSs and their joint exposure with heavy metals remains scarce. In this study, we investigated the bioaccumulation kinetics of 6 frequently reported BUVSs in common carp under different Cu concentration for 48 d, and their tissue-specific distribution patterns (liver, kidney, gill, and muscle tissues) were also evaluated. The bioconcentration factors (BCFs) and half-lives (t1/2) in the tissues ranged from 5.73 (UV-PS) to 1076 (UV-327), and 2.19 (UV-PS) to 31.5 (UV-320) days, respectively. The tissue-specific concentration and BCF values followed the order of liver > kidney > gill > muscle with or without Cu exposure. An increase in BCF with rising Cu concentration was observed, which is caused by the decreased depuration rate (k2) in more than half of treatment groups. These results indicated that BUVSs accumulated in fish and provides important insight into the risk assessment of this group of chemicals.

scholarly journals Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans

Genetics ◽  
2020 ◽  
Vol 216 (4) ◽  
pp. 931-945 ◽  
Author(s):  
Georgina Gómez-Saldivar ◽  
Jaime Osuna-Luque ◽  
Jennifer I. Semple ◽  
Dominique A. Glauser ◽  
Sophie Jarriault ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Rna Polymerase ◽  
Cell Types ◽  
Neuroendocrine Cells ◽  
Cell Physiology ◽  
Specific Gene ◽  
Cell Content ◽  
Tissue Specific ◽  
C Elegans ◽  
Active Transcription

Differential gene expression across cell types underlies development and cell physiology in multicellular organisms. Caenorhabditis elegans is a powerful, extensively used model to address these biological questions. A remaining bottleneck relates to the difficulty to obtain comprehensive tissue-specific gene transcription data, since available methods are still challenging to execute and/or require large worm populations. Here, we introduce the RNA Polymerase DamID (RAPID) approach, in which the Dam methyltransferase is fused to a ubiquitous RNA polymerase subunit to create transcriptional footprints via methyl marks on the DNA of transcribed genes. To validate the method, we determined the polymerase footprints in whole animals, in sorted embryonic blastomeres and in different tissues from intact young adults by driving tissue-specific Dam fusion expression. We obtained meaningful transcriptional footprints in line with RNA-sequencing (RNA-seq) studies in whole animals or specific tissues. To challenge the sensitivity of RAPID and demonstrate its utility to determine novel tissue-specific transcriptional profiles, we determined the transcriptional footprints of the pair of XXX neuroendocrine cells, representing 0.2% of the somatic cell content of the animals. We identified 3901 candidate genes with putatively active transcription in XXX cells, including the few previously known markers for these cells. Using transcriptional reporters for a subset of new hits, we confirmed that the majority of them were expressed in XXX cells and identified novel XXX-specific markers. Taken together, our work establishes RAPID as a valid method for the determination of RNA polymerase footprints in specific tissues of C. elegans without the need for cell sorting or RNA tagging.

scholarly journals Global Analysis of Cell Type-Specific Gene Expression

2003 ◽  
Vol 4 (2) ◽  
pp. 208-215 ◽  
Author(s):  
David W. Galbraith
Keyword(s):  
Gene Expression ◽  
Fluorescent Protein ◽  
Global Analysis ◽  
Expression Patterns ◽  
Three Dimensional ◽  
Global Gene Expression ◽  
Cell Types ◽  
Reasonable Assumption ◽  
Specific Gene ◽  
Different Cell Types

The tissues and organs of multicellular eukaryotes are frequently observed to comprise complex three-dimensional interspersions of different cell types. It is a reasonable assumption that different global patterns of gene expression are found within these different cell types. This review outlines general experimental strategies designed to characterize these global gene expression patterns, based on a combination of methods of transgenic fluorescent protein (FP) expression and targeting, of flow cytometry and sorting and of high-throughput gene expression analysis.

Parenteral vs. oral iron: influence on hepcidin signaling pathways through analysis of Hfe/Tfr2-null mice

2014 ◽  
Vol 306 (2) ◽  
pp. G132-G139 ◽  
Author(s):  
Cameron J. McDonald ◽  
Daniel F. Wallace ◽  
Lesa Ostini ◽  
V. Nathan Subramaniam
Keyword(s):  
Iron Homeostasis ◽  
Regulatory System ◽  
Cell Types ◽  
Deficiency Anemia ◽  
Systematic Analysis ◽  
Cellular Iron ◽  
Morphogenetic Protein ◽  
Smad Signaling Pathway ◽  
Associated Proteins ◽  
Different Cell Types

Treatment for iron deficiency anemia can involve iron supplementation via dietary or parenteral routes that result in different cellular iron distributions. The effect of the administered iron on the iron regulatory system and hepcidin in the liver has not been well studied. Hepcidin, the liver-expressed central iron-regulatory peptide, is itself regulated through the bone morphogenetic protein (BMP)/SMAD signaling pathway. Specifically, Bmp6 expression is upregulated in response to iron and induces hepcidin through phosphorylation of Smad1/5/8. The hemochromatosis-associated proteins Hfe and transferrin receptor 2 (Tfr2) are known upstream regulators of hepcidin, although their precise roles are still unclear. To investigate the mechanisms of this regulation and the roles of the Hfe and Tfr2, we subjected wild-type, Hfe−/−, Tfr2−/−, and Hfe−/−/ Tfr2−/− mice to iron loading via dietary or parenteral routes. Systematic analysis demonstrated that Tfr2 is required for effective upregulation of Bmp6 in response to hepatocyte iron, but not nonparenchymal iron. Hfe is not required for Bmp6 upregulation, regardless of iron localization, but rather, is required for efficient downstream transmission of the regulatory signal. Our results demonstrate that Hfe and Tfr2 play separate roles in the regulatory responses to iron compartmentalized in different cell types and further elucidates the regulatory mechanisms controlling iron homeostasis.

Detection of genes with tissue-specific expression patterns using Akaike’s information criterion procedure

2003 ◽  
Vol 12 (3) ◽  
pp. 251-259 ◽  
Author(s):  
Koji Kadota ◽  
Shin-Ichiro Nishimura ◽  
Hidemasa Bono ◽  
Shugo Nakamura ◽  
Yoshihide Hayashizaki ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Information Criterion ◽  
Cell Types ◽  
Specific Gene ◽  
Akaike's Information Criterion ◽  
Expression Array ◽  
Specific Expression ◽  
Tissue Specific ◽  
Significance Level ◽  
Akaike’S Information Criterion

We applied a method based on Akaike’s information criterion (AIC) to detect genes whose expression profile is considerably different in some tissue(s) than in others. Such observations are detected as outliers, and the method we used was originally developed to detect outliers. The main advantage of the method is that objective decisions are possible because the procedure is independent of a significance level. We applied the method to 48 expression ratios corresponding to various tissues in each of 14,610 clones obtained from the RIKEN Expression Array Database (READ; http://read.gsc.riken.go.jp ). As a result, for several tissues (e.g., muscle, heart, and tongue tissues that contain similar cell types) we objectively obtained specific clones without any “thresholding.” Our study demonstrates the feasibility of the method for detecting tissue-specific gene expression patterns.

scholarly journals Expression profiling of antisense transcripts on DNA arrays

2007 ◽  
Vol 28 (3) ◽  
pp. 294-300 ◽  
Author(s):  
Andreas Werner ◽  
Gabriele Schmutzler ◽  
Mark Carlile ◽  
Colin G. Miles ◽  
Heiko Peters
Keyword(s):  
Large Scale ◽  
Expression Patterns ◽  
Distribution Patterns ◽  
Mouse Kidney ◽  
Dna Arrays ◽  
Antisense Transcripts ◽  
Specific Expression ◽  
Tissue Specific ◽  
Antisense Rnas ◽  
Specific Distribution

The majority of mouse genes are estimated to undergo bidirectional transcription; however, their tissue-specific distribution patterns and physiological significance are largely unknown. This is in part due to the lack of methodology to routinely assess the expression of natural antisense transcripts (NATs) on a large scale. Here we tested whether commercial DNA arrays can be used to monitor antisense transcription in mouse kidney and brain. We took advantage of the reversely annotated oligonucleotides on the U74 mouse genome array from Affymetrix that hybridize to NATs overlapping with the sense transcript in the area of the probe set. In RNA samples from mouse kidney and brain, 11.9% and 10.1%, respectively, of 5,652 potential NATs returned positive and about half of the antisense RNAs were detected in both tissues, which was similar to the fraction of sense transcripts expressed in both tissues. Notably, we found that the majority of NATs are related to the sense transcriptome since corresponding sense transcripts were detected for 92.5% (kidney) and 74.5% (brain) of the detected antisense RNAs. Antisense RNA transcription was confirmed by real-time PCR and included additional RNA samples from heart, thymus, and liver. The randomly selected transcripts showed tissue specific expression patterns and varying sense/antisense ratios. The results indicate that antisense transcriptomes are tissue specific, and although pairing of sense/antisense transcripts are known to result in rapid degradation, our data provide proof of principle that the sensitivity of commercial DNA arrays is sufficient to assess NATs in total RNA of whole organs.

scholarly journals Human USP18 is regulated by miRNAs via the 3’UTR, a sequence duplicated in lincRNA genes residing in chr22q11.21

2020 ◽  
Author(s):  
Erminia Rubino ◽  
Melania Cruciani ◽  
Nicolas Tchitchek ◽  
Anna Le Tortorec ◽  
Antoine D. Rolland ◽  
...  
Keyword(s):  
Cell Types ◽  
Type I ◽  
Rna Seq ◽  
Specific Expression ◽  
Tissue Specific ◽  
Specific Expression Pattern ◽  
Post Transcriptional Regulation ◽  
Different Cell Types ◽  
Fine Tune ◽  
Feedback Regulator

ABSTRACTUbiquitin-specific peptidase 18 (USP18) acts as gatekeeper of type I interferon (IFN) responses by binding to the IFN receptor subunit IFNAR2 and preventing activation of the downstream JAK/STAT pathway. In any given cell type, the level of USP18 is a key determinant of the output of interferon-stimulated transcripts. How the baseline level of USP18 is finely tuned in different cell types remains ill defined. Here we explored post-transcriptional regulation of USP18 by microRNAs (miRNAs) and identified four miRNAs (miR-24-3p, miR-191-5p, miR-423-5p and miR-532-3p) that efficiently target USP18 through binding to the 3’UTR. Among these, three miRNAs are particularly enriched in circulating monocytes which exhibit low baseline USP18. Intriguingly, the USP18 3’UTR sequence is duplicated in human and chimpanzee genomes. In human, we found several copies of the 3’UTR that are embedded in long intergenic non-coding (linc) RNA genes residing in chr22q11.21 and exhibiting a tissue-specific expression pattern. Interestingly, one of these lincRNAs (here named linc-UR-B1) is uniquely and highly expressed in testis. RNA-seq data analyses from testicular cell subsets revealed a positive correlation between linc-UR-B1 and USP18 expression in spermatocytes and spermatids. Overall, our findings uncover a set of miRNAs and lincRNAs, which may be part of a network evolved to fine-tune baseline USP18, particularly in cell types where IFN responsiveness needs to be tightly controlled.SIGNIFICANT STATEMENTUSP18 is a non-redundant negative feedback regulator of type I IFN signaling and a key determinant of cell responsiveness to IFN. How baseline USP18 is set in different human cell types is ill defined. We identified three microRNAs that restrain USP18 level notably in primary monocytes through binding the 3’UTR. We found several copies of the USP18 3’UTR embedded in long intergenic non-coding (linc) RNAs which reside in a complex region of human chromosome 22. These lincRNAs are expressed in a tissue-specific manner. We describe one lincRNA expressed only in testis, and most notably in germ cells. Correlative analyses suggest that microRNAs and lincRNAs may form a network controlling baseline USP18 and IFN responsiveness.

scholarly journals Subcellular dynamics studies of iron reveal how tissue‐specific distribution patterns are established in developing wheat grains

2021 ◽  
Author(s):  
Sadia Sheraz ◽  
Yongfang Wan ◽  
Eudri Venter ◽  
Shailender K Verma ◽  
Qing Xiong ◽  
...  
Keyword(s):  
Distribution Patterns ◽  
Tissue Specific ◽  
Wheat Grains ◽  
Specific Distribution

scholarly journals An Eye in the Replication Stress Response: Lessons From Tissue-Specific Studies in vivo

2021 ◽  
Vol 9 ◽  
Author(s):  
Gabriel E. Matos-Rodrigues ◽  
Rodrigo A. P. Martins
Keyword(s):  
Stress Response ◽  
Progenitor Cells ◽  
Eye Development ◽  
Replication Stress ◽  
Cell Types ◽  
Tissue Specific ◽  
Ocular Manifestations ◽  
Molecular Machinery ◽  
Different Cell Types

Several inherited human syndromes that severely affect organogenesis and other developmental processes are caused by mutations in replication stress response (RSR) genes. Although the molecular machinery of RSR is conserved, disease-causing mutations in RSR-genes may have distinct tissue-specific outcomes, indicating that progenitor cells may differ in their responses to RSR inactivation. Therefore, understanding how different cell types respond to replication stress is crucial to uncover the mechanisms of RSR-related human syndromes. Here, we review the ocular manifestations in RSR-related human syndromes and summarize recent findings investigating the mechanisms of RSR during eye development in vivo. We highlight a remarkable heterogeneity of progenitor cells responses to RSR inactivation and discuss its implications for RSR-related human syndromes.

scholarly journals Quantifying the Tissue-Specific Regulatory Information within Enhancer DNA Sequences

2021 ◽  
Author(s):  
Philipp Benner ◽  
Martin Vingron
Keyword(s):  
Dna Sequences ◽  
Cell Types ◽  
Cell Type ◽  
Regulate Gene Expression ◽  
Tissue Specific ◽  
Sequence Patterns ◽  
Cell Type Specific ◽  
Specific Regulation ◽  
Different Cell Types ◽  
Regulatory Landscape

AbstractRecent efforts to measure epigenetic marks across a wide variety of different cell types and tissues provide insights into the cell type-specific regulatory landscape. We use this data to study if there exists a correlate of epigenetic signals in the DNA sequence of enhancers and explore with computational methods to what degree such sequence patterns can be used to predict cell type-specific regulatory activity. By constructing classifiers that predict in which tissues enhancers are active, we are able to identify sequence features that might be recognized by the cell in order to regulate gene expression. While classification performances vary greatly between tissues, we show examples where our classifiers correctly predict tissue specific regulation from sequence alone. We also show that many of the informative patterns indeed harbor transcription factor footprints.

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