Regulatory elements in the upstream region of metallothionein gene in tilapia species

Tilapia is a hardy fish which can survive in water bodies polluted with heavy metals. Metal resistance is conferred by higher expression of metallothionein gene (mt) in many organisms. Level, time and tissue-specificity of gene expression is regulated through transcription factor binding sites (TFBS) which may be present in the upstream, downstream, or even in the introns of a gene. So, as a candidate regulatory region, the 5’upstream sequence of mt gene in three tilapia species, Oreochromis aureus, O. niloticus and O. mossambicus was studied. The targeted region was PCR-amplified and then sequenced using a pair of custom-designed primer. A total of only 2.7% variation was found in the sequenced genomic region among the three species. Metal-related TFBS were predicted from these sequences. A total of twenty eight TFBS were found in O. aureus and twenty nine in O. mossambicus and O. niloticus. The number of metalrelated TFBS predicted in the targeted sequence was significantly higher compared to that found in randomly selected other genomic regions of same size from O. niloticus genome. Thus, the results suggest the presence of putative regulatory elements in the targeted upstream region which might have important role in the regulation of mt gene function. Dhaka Univ. J. Biol. Sci. 30(1): 95-103, 2021 (January)

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Differential methylation tests of regulatory regions

Statistical Applications in Genetics and Molecular Biology ◽

10.1515/sagmb-2015-0037 ◽

2016 ◽

Vol 15 (3) ◽

Cited By ~ 3

Author(s):

Duchwan Ryu ◽

Hongyan Xu ◽

Varghese George ◽

Shaoyong Su ◽

Xiaoling Wang ◽

...

Keyword(s):

Regulatory Region ◽

Regulatory Elements ◽

Genomic Region ◽

Differential Methylation ◽

Lymphocytic Leukemia ◽

Smoothing Methods ◽

Sample Data ◽

The Gift ◽

Average Profile ◽

Genomic Regions

AbstractDifferential methylation of regulatory elements is critical in epigenetic researches and can be statistically tested. We developed a new statistical test, the generalized integrated functional test (GIFT), that tests for regional differences in methylation based on the methylation percent at each CpG site within a genomic region. The GIFT uses estimated subject-specific profiles with smoothing methods, specifically wavelet smoothing, and calculates an ANOVA-like test to compare the average profile of groups. In this way, possibly correlated CpG sites within the regulatory region are compared all together. Simulations and analyses of data obtained from patients with chronic lymphocytic leukemia indicate that GIFT has good statistical properties and is able to identify promising genomic regions. Further, GIFT is likely to work with multiple different types of experiments since different smoothing methods can be used to estimate the profiles of data without noise. Matlab code for GIFT and sample data are available at

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Transvection at the End of the Truncated Chromosome in Drosophila melanogaster

Genetics ◽

10.1093/genetics/163.4.1375 ◽

2003 ◽

Vol 163 (4) ◽

pp. 1375-1387

Author(s):

Mikhail Savitsky ◽

Tatyana Kahn ◽

Ekaterina Pomerantseva ◽

Pavel Georgiev

Keyword(s):

Drosophila Melanogaster ◽

Homologous Chromosome ◽

Regulatory Region ◽

Proximal Region ◽

The Other ◽

Upstream Region ◽

Upstream Sequence ◽

Transcription Start ◽

Promoter Proximal Region

Abstract The phenomenon of transvection is well known for the Drosophila yellow locus. Thus enhancers of a promoterless yellow locus in one homologous chromosome can activate the yellow promoter in the other chromosome where the enhancers are inactive or deleted. In this report, we examined the requirements for trans-activation of the yellow promoter at the end of the deficient chromosome. A number of truncated chromosomes ending in different areas of the yellow regulatory region were examined in combination with the promoterless y alleles. We found that trans-activation of the yellow promoter at the end of a deficient chromosome required ∼6 kb of an additional upstream sequence. The nature of upstream sequences affected the strength of transvection: addition of gypsy sequences induced stronger trans-activation than addition of HeT-A or yellow sequences. Only the promoter proximal region (within -158 bp of the yellow transcription start) was essential for trans-activation; i.e., transvection did not require extensive homology in the yellow upstream region. Finally, the yellow enhancers located on the two pairing chromosomes could cooperatively activate one yellow promoter.

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Cloning and Functional characterization of seed-specific LEC1A promoter from peanut (Arachis hypogaea L.)

10.1101/2020.11.13.381327 ◽

2020 ◽

Author(s):

Guiying Tang ◽

Pingli Xu ◽

Pengxiang Li ◽

Jieqiong Zhu ◽

Guangxia Chen ◽

...

Keyword(s):

Transcriptional Start Site ◽

Functional Characterization ◽

Regulatory Region ◽

Regulatory Elements ◽

Histochemical Staining ◽

Expression Vectors ◽

Upstream Sequence ◽

Functional Region ◽

Chromosomal Walking ◽

Storage Reserve

AbstractLEAFY COTYLEDON1 (LEC1) is a HAP3 subunit of CCAAT-binding transcription factor, which controls several aspects of embryo and postembryo development, including embryo morphogenesis, storage reserve accumulation and skotomorphogenesis. Herein, using the method of chromosomal walking, a 2707bp upstream sequence from the ATG initiation codon site of AhLEC1A which is a homolog of Arabidopsis LEC1 was isolated in peanut. Its transcriptional start site confirmed by 5’ RACE was located at 82 nt from 5’ upstream of ATG. The bioinformatics analysis revealed that there existed many tissue-specific elements and light responsive motifs in its promoter. To identify the functional region of the AhLEC1A promoter, seven plant expression vectors expressing the GUS (β-glucuronidase) gene, driven by 5’ terminal series deleted fragments of AhLEC1A promoter, were constructed and transformed into Arabidopsis. Results of GUS histochemical staining showed that the regulatory region containing 82bp of 5’ UTR and 2228bp promoter could facilitate GUS to express preferentially in the embryos at different development periods of Arabidopsis. Taken together, it was inferred that the expression of AhLEC1A during seed development of peanut might be controlled positively by several seed-specific regulatory elements, as well as negatively by some other regulatory elements inhibiting its expression in other organs. Moreover, the GUS expression pattern of transgenic seedlings in darkness and in light was relevant to the light-responsive elements scattered in AhLEC1A promoter segment, implying that these light-responsive elements harbored in the AhLEC1A promoter regulate skotomorphogenesis of peanut seeds, and AhLEC1A expression was inhibited after the germinated seedlings were transferred from darkness to light.

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Repeated divergent selection on pigmentation genes in a rapid finch radiation driven by sexual selection

10.1101/075713 ◽

2016 ◽

Cited By ~ 1

Author(s):

Leonardo Campagna ◽

Márcio Repenning ◽

Luis Fabio Silveira ◽

Carla Suertegaray Fontana ◽

Pablo L Tubaro ◽

...

Keyword(s):

Biological Diversity ◽

Phenotypic Diversity ◽

Regulatory Region ◽

Bird Species ◽

Regulatory Elements ◽

Divergent Selection ◽

Sexually Selected Traits ◽

Conserved Genes ◽

Selected Traits ◽

Genomic Regions

ABSTRACTThe search for molecular targets of selection is leading to a better understanding of how evolution shapes biological diversity. Instances of recent and rapid speciation are suitable for associating phenotypes with their causal genotypes, because gene flow may homogenize areas of the genome that are not under divergent selection. Locating differentiated genomic regions among taxa allows us to test associations between the genes in these regions and their contributions to phenotypic diversity. Here we study a rapid radiation of nine sympatric bird species known as southern capuchino seedeaters, which are strikingly differentiated in sexually selected characters of male plumage and song. We sequenced the genomes of 72 individuals representing a diverse set of species and associated phenotypes to search for differentiated genomic regions. We asked what genes are harbored in divergent regions and to what extent has selection on the same targets shaped phenotypic diversity across different lineages. Capuchinos show differences in a small proportion of their genomes, yet selection has acted independently on the same targets during the groups’ radiation. Many divergence peaks contain genes involved in the melanogenesis pathway, with the strongest signal originating from a regulatory region upstream of the gene coding for the Agouti-signaling protein. Across all divergence peaks, the most differentiated areas are similarly likely regulatory. Our findings are consistent with selection acting on the same genomic regions in different lineages to shape the evolution of cis-regulatory elements, which control how more conserved genes are expressed and thereby generate diversity in sexually selected traits.

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Cloning and functional characterization of seed-specific LEC1A promoter from peanut (Arachis hypogaea L.)

PLoS ONE ◽

10.1371/journal.pone.0242949 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0242949

Author(s):

Guiying Tang ◽

Pingli Xu ◽

Pengxiang Li ◽

Jieqiong Zhu ◽

Guangxia Chen ◽

...

Keyword(s):

Transcriptional Start Site ◽

Functional Characterization ◽

Regulatory Region ◽

Regulatory Elements ◽

Histochemical Staining ◽

Expression Vectors ◽

Upstream Sequence ◽

Functional Region ◽

Chromosomal Walking ◽

Storage Reserve

LEAFY COTYLEDON1 (LEC1) is a HAP3 subunit of CCAAT-binding transcription factor, which controls several aspects of embryo and postembryo development, including embryo morphogenesis, storage reserve accumulation and skotomorphogenesis. Herein, using the method of chromosomal walking, a 2707bp upstream sequence from the ATG initiation codon site of AhLEC1A which is a homolog of Arabidopsis LEC1 was isolated in peanut. Its transcriptional start site confirmed by 5’ RACE was located at 82 nt from 5’ upstream of ATG. The bioinformatics analysis revealed that there existed many tissue-specific elements and light responsive motifs in its promoter. To identify the functional region of the AhLEC1A promoter, seven plant expression vectors expressing the GUS (β-glucuronidase) gene, driven by 5’ terminal series deleted fragments of AhLEC1A promoter, were constructed and transformed into Arabidopsis. Results of GUS histochemical staining showed that the regulatory region containing 82bp of 5’ UTR and 2228bp promoter could facilitate GUS to express preferentially in the embryos at different development periods of Arabidopsis. Taken together, it was inferred that the expression of AhLEC1A during seed development of peanut might be controlled positively by several seed-specific regulatory elements, as well as negatively by some other regulatory elements inhibiting its expression in other organs. Moreover, the GUS expression pattern of transgenic seedlings in darkness and in light was relevant to the light-responsive elements scattered in AhLEC1A promoter segment, implying that these light-responsive elements harbored in the AhLEC1A promoter regulate skotomorphogenesis of peanut seeds, and AhLEC1A expression was inhibited after the germinated seedlings were transferred from darkness to light.

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Involvement of AP-2 in regulation of the R-FABP gene in the developing chick retina.

Molecular and Cellular Biology ◽

10.1128/mcb.17.10.5935 ◽

1997 ◽

Vol 17 (10) ◽

pp. 5935-5945 ◽

Cited By ~ 16

Author(s):

D A Bisgrove ◽

E A Monckton ◽

R Godbout

Keyword(s):

Binding Site ◽

Retinal Development ◽

Regulatory Elements ◽

Dnase I ◽

Upstream Region ◽

Upstream Sequence ◽

Dna Transfection ◽

Fatty Acid Binding ◽

Chick Retina ◽

Fabp Gene

Little is known regarding the molecular pathways that underlie the retinal maturation process. We are studying the regulation of the retinal fatty-acid-binding protein (R-FABP) gene, highly expressed in retinal precursor cells, to identify DNA regulatory elements and transcriptional factors involved in retinal development. Although the upstream sequence of the R-FABP gene is extremely GC rich, CpG methylation in this region is not implicated in the regulation of this gene because the 5' flanking DNA remains unmethylated with tissue differentiation when there is a dramatic decrease in R-FABP transcript levels. Using a combination of DNase I hypersensitivity experiments, gel shift assays, and DNase I footprinting, we have found three sites of DNA-protein interaction within 205 bp of 5' flanking DNA in the undifferentiated retina and four sites in the differentiated retina. DNA transfection analysis indicates that the first two footprints located within 150 bp of 5' flanking DNA are required for high levels of transcription in primary undifferentiated retinal cultures. The first footprint includes a putative TATA box and Spl binding sites while the second footprint contains a consensus AP-2 DNA binding site. Supershift experiments using antibodies to AP-2 and methylation interference experiments indicate that an AP-2-like transcription factor present in both late-proliferative-stage retina and differentiated retina binds to the upstream region of the R-FABP gene. A combination of data including the expression profile of AP-2 during retinal development and DNA transfection analysis using constructs mutated at critical residues within the AP-2 binding site suggests that AP-2 is a repressor of R-FABP transcription.

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The genetic architecture of fruit colour in strawberry (Fragaria × ananassa) uncovers the predominant contribution of the F. vesca subgenome to anthocyanins and reveals underlying genetic variations

10.1101/2020.06.25.171496 ◽

2020 ◽

Author(s):

Marc Labadie ◽

Guillaume Vallin ◽

Aurélie Petit ◽

Ludwig Ring ◽

Thomas Hoffmann ◽

...

Keyword(s):

Regulatory Region ◽

Snp Array ◽

Water Soluble ◽

Upstream Region ◽

Binding Motif ◽

Fragaria Ananassa ◽

Fruit Colour ◽

Total Anthocyanins ◽

Resolution Mapping ◽

Genomic Regions

AbstractFruit colour, which is central to the sensorial and nutritional quality of the fruit, is a major breeding target in cultivated strawberry (Fragaria × ananassa). Red fruit colour is caused by the accumulation of anthocyanins, which are water-soluble flavonoids. Here, using pseudo F1 progeny derived from the cv. ‘Capitola’ and the advanced line ‘CF1116’ and taking advantage of the available high density SNP array, we delineated fruit flavonoids mQTLs (13 compounds: anthocyanin, flavonols and flavan-3-ols) and colour-related QTLs (total anthocyanins and fruit colour) to narrow genomic regions corresponding to specific subgenomes of the cultivated strawberry. Findings showed that the overwhelming majority of the anthocyanin mQTLs and other colour-related QTLs are specific to F. vesca subgenome but that other subgenomes also contribute to colour variations. We then focused on two major homoeo-mQTLs for pelargonidin-3-glucoside (PgGs) localized on both male and female maps on linkage group LG3a (F. vesca subgenome). Combined high-resolution mapping of PgGs mQTLs and colour QTLs, transcriptome analysis of selected progeny individuals and whole genome sequencing of the parents led to the identification of several INDELS in the cis-regulatory region of a MYB102-like ODORANT gene and of the deletion of a putative MADS box binding motif in the 5’UTR upstream region of an anthocyanidin reductase (ANR) gene, which likely underlie significant colour variations in strawberry fruit. The implications of these findings are important for the functional analysis and genetic engineering of colour-related genes and for the breeding by Marker-Assisted-Selection of new strawberry varieties with improved colour and health-benefits.

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H19 and Igf2 monoallelic expression is regulated in two distinct ways by a shared cis acting regulatory region upstream of H19

Genes & Development ◽

10.1101/gad.14.10.1186 ◽

2000 ◽

Vol 14 (10) ◽

pp. 1186-1195 ◽

Cited By ~ 2

Author(s):

Madhulika Srivastava ◽

Sandra Hsieh ◽

Alexander Grinberg ◽

Lisa Williams-Simons ◽

Sing-Ping Huang ◽

...

Keyword(s):

Promoter Region ◽

Regulatory Region ◽

Regulatory Elements ◽

Upstream Region ◽

Monoallelic Expression ◽

Direct Role ◽

Specific Expression ◽

Cis Acting ◽

Allele Specific ◽

Mammalian System

H19 and Igf2 are expressed in a monoallelic fashion from the maternal and paternal chromosomes, respectively. A region upstream of H19 has been shown to regulate such imprinted expression of both genes in cis. We have taken advantage of aloxP/cre recombinase-based strategy to delete this region in mice in a conditional manner to determine the temporal requirement of the upstream region in initiating and maintaining the imprinted expression of H19 and Igf2. Analysis of allele-specific expression of H19 and Igf2 and DNA methylation at the H19 promoter demonstrates that this region controls the monoallelic expression of the two genes in different ways, suggesting that it harbors two functionally distinct regulatory elements. Continued presence of the region is required to silence maternal Igf2 in accordance with its proposed role as an insulator. However, it does not have a direct role in keeping the paternal H19 promoter silenced. Instead, on the paternal chromosome, the upstream element mediates epigenetic modifications of the H19 promoter region during development, leading to transcriptional silencing of H19. Thereafter, its presence is redundant for preventing transcription. Presently, this temporal requirement of the silencing element appears to be a unique cisactivity in the mammalian system. However, it is likely that othercis-acting elements, positive and negative, have the ability to effect stable changes in the chromatin structure and are not constantly required to give signals to the transcriptional machinery.

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Comparative Genomic Analysis of Acinetobacter oleivorans DR1 To Determine Strain-Specific Genomic Regions and Gentisate Biodegradation

Applied and Environmental Microbiology ◽

10.1128/aem.05231-11 ◽

2011 ◽

Vol 77 (20) ◽

pp. 7418-7424 ◽

Cited By ~ 20

Author(s):

Jaejoon Jung ◽

Eugene L. Madsen ◽

Che Ok Jeon ◽

Woojun Park

Keyword(s):

Metabolic Pathways ◽

Genomic Analysis ◽

Metal Resistance ◽

Genomic Region ◽

Open Reading Frames ◽

Comparative Genomic ◽

Content Type ◽

Large Size ◽

Genomic Regions ◽

Reading Frames

ABSTRACTThe comparative genomics ofAcinetobacter oleivoransDR1 assayed withA. baylyiADP1,A. calcoaceticusPHEA-2, andA. baumanniiATCC 17978 revealed that the incorporation of phage-related genomic regions and the absence of transposable elements have contributed to the large size (4.15 Mb) of the DR1 genome. A horizontally transferred genomic region and a higher proportion of transcriptional regulator- and signal peptide-coding genes were identified as characteristics of the DR1 genome. Incomplete glucose metabolism, metabolic pathways of aromatic compounds, biofilm formation, antibiotics and metal resistance, and natural competence genes were conserved in four compared genomes. Interestingly, only strain DR1 possesses gentisate 1,2-dioxygenase (nagI) and grows on gentisate, whereas other species cannot. Expression of thenagIgene was upregulated during gentisate utilization, and four downstream open reading frames (ORFs) were cotranscribed, supporting the notion that gentisate metabolism is a unique characteristic of strain DR1. The genomic analysis of strain DR1 provides additional insights into the function, ecology, and evolution ofAcinetobacterspecies.

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Transcriptional Regulation of AQP-8, a Caenorhabditis elegans Aquaporin Exclusively Expressed in the Excretory System, by the POU Homeobox Transcription Factor CEH-6

Journal of Biological Chemistry ◽

10.1074/jbc.m703305200 ◽

2007 ◽

Vol 282 (38) ◽

pp. 28074-28086 ◽

Cited By ~ 22

Author(s):

Allan K. Mah ◽

Kristin R. Armstrong ◽

Derek S. Chew ◽

Jeffrey S. Chu ◽

Domena K. Tu ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Regulatory Networks ◽

Regulatory Region ◽

Regulatory Elements ◽

Upstream Sequence ◽

Consensus Binding Site ◽

Mobility Shift ◽

C Elegans ◽

Octamer Motif ◽

Excretory Cell

Due to the ever changing environmental conditions in soil, regulation of osmotic homeostasis in the soil-dwelling nematode Caenorhabditis elegans is critical. AQP-8 is a C. elegans aquaporin that is expressed in the excretory cell, a renal equivalent tissue, where the protein participates in maintaining water balance. To better understand the regulation of AQP-8, we undertook a promoter analysis to identify the aqp-8 cis-regulatory elements. Using progressive 5′ deletions of upstream sequence, we have mapped an essential regulatory region to roughly 300 bp upstream of the translational start site of aqp-8. Analysis of this region revealed a sequence corresponding to a known DNA functional element (octamer motif), which interacts with POU homeobox transcription factors. Phylogenetic footprinting showed that this site is perfectly conserved in four nematode species. The octamer site's function was further confirmed by deletion analyses, mutagenesis, functional studies, and electrophoretic mobility shift assays. Of the three POU homeobox proteins encoded in the C. elegans genome, CEH-6 is the only member that is expressed in the excretory cell. We show that expression of AQP-8 is regulated by CEH-6 by performing RNA interference experiments. CEH-6's mammalian ortholog, Brn1, is expressed both in the kidney and the central nervous system and binds to the same octamer consensus binding site to drive gene expression. These parallels in transcriptional control between Brn1 and CEH-6 suggest that C. elegans may well be an appropriate model for determining gene-regulatory networks in the developing vertebrate kidney.

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