scholarly journals The Mitochondrial Iron Regulated (MIR) gene is Oryza genus-specific and evolved before the speciation of major AA-genome lineages

2019 ◽  
Author(s):  
Ben-Hur Neves de Oliveira ◽  
Andriele Wairich ◽  
Andreia Carina Turchetto-Zolet ◽  
Janette Palma Fett ◽  
Felipe Klein Ricachenevsky
Keyword(s):  
De Novo ◽  
Regulatory Region ◽  
Fe Deficiency ◽  
Cultivated Rice ◽  
Orphan Gene ◽  
Evolutionary Pattern ◽  
Genomic Changes ◽  
Raffinose Synthase ◽  
Mitochondrial Iron ◽  
Aa Genome

AbstractRice (Oryza sativa L.) is both a model species and an economically relevant crop. The Oryza genus comprises 25 species, which constitute a genetic reservoir for cultivated rice breeding. Genomic data is available for several Oryza species, making it a good model for genetics and evolution within closely related species. The Mitochondrial Iron Regulated (MIR) gene was previously implicated in O. sativa Fe deficiency response, and was considered an orphan gene present only in rice. Here we show that MIR is also found in other Oryza species that belong to the AA genome group. We characterized the evolutionary pattern of MIR genes within the Oryza genus. Our data suggest that MIR originated de novo from non-coding sequences present only in AA genome species, but these sequences in turn are derived from an exon fragment of Raffinose Synthase genes, present in several groups of monocots. We also show that all species that have a putative functional MIR conserve their regulation by Fe deficiency, with the exception of Oryza barthii. In O. barthii, the MIR coding sequence was translocated to a different chromosomal position and separated from its regulatory region, which led to a lack of Fe deficiency responsiveness. Moreover, we show that MIR co-expression subnetwork cluster in O. sativa is responsive to Fe deficiency, evidencing the importance of the newly originated gene in Fe uptake. This work establishes that MIR is not an orphan gene as previously proposed, but a de novo originated gene within the Oryza genus. We also showed that MIR is undergoing genomic changes in at least one species (O. barthii), which can impact its role in Fe deficiency.

scholarly journals Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1465
Author(s):  
Ramon de Koning ◽  
Raphaël Kiekens ◽  
Mary Esther Muyoka Toili ◽  
Geert Angenon
Keyword(s):  
Common Bean ◽  
Seed Development ◽  
Expression Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Gene Families ◽  
Rna Seq ◽  
Raffinose Family Oligosaccharides ◽  
Specific Expression ◽  
Raffinose Synthase

Raffinose family oligosaccharides (RFO) play an important role in plants but are also considered to be antinutritional factors. A profound understanding of the galactinol and RFO biosynthetic gene families and the expression patterns of the individual genes is a prerequisite for the sustainable reduction of the RFO content in the seeds, without compromising normal plant development and functioning. In this paper, an overview of the annotation and genetic structure of all galactinol- and RFO biosynthesis genes is given for soybean and common bean. In common bean, three galactinol synthase genes, two raffinose synthase genes and one stachyose synthase gene were identified for the first time. To discover the expression patterns of these genes in different tissues, two expression atlases have been created through re-analysis of publicly available RNA-seq data. De novo expression analysis through an RNA-seq study during seed development of three varieties of common bean gave more insight into the expression patterns of these genes during the seed development. The results of the expression analysis suggest that different classes of galactinol- and RFO synthase genes have tissue-specific expression patterns in soybean and common bean. With the obtained knowledge, important galactinol- and RFO synthase genes that specifically play a key role in the accumulation of RFOs in the seeds are identified. These candidate genes may play a pivotal role in reducing the RFO content in the seeds of important legumes which could improve the nutritional quality of these beans and would solve the discomforts associated with their consumption.

scholarly journals Accelerated molecular breeding of novel cytoplasmic male sterility lines in rice using orfH79 or orf290 haplotypes

2020 ◽  
Author(s):  
Yanping Tan ◽  
Tong Chen ◽  
Ze Tian ◽  
Jiayang Li ◽  
Xuequn Liu ◽  
...  
Keyword(s):  
Cytoplasmic Male Sterility ◽  
Male Sterility ◽  
Higher Plants ◽  
Amino Acid Sequences ◽  
Cultivated Rice ◽  
Maintainer Line ◽  
Breeding Programs ◽  
Aa Genome ◽  
Allele Variation ◽  
Grain Security

Abstract The identification and development of new cytoplasmic male sterility (CMS) lines in higher plants is important for the preservation of grain security and the prevention of homogenization of hybrid rice. Molecular markers assisted selection (MAS) based on CMS-associated genes or mitochondrial-specific chimeric sequences are important for rapid and effective breeding of new CMS lines and hybrids. In our study, the distribution and allele variation of orfH79 and orf290 genes were characterized from 273 wild and cultivated rice in the AA genome species. Based on the alignment of nucleotide and amino acid sequences, four accessions with orfH79 and three accessions with orf290 were screened. Four novel CMS lines carrying orfH79 haplotypes and three novel CMS lines carrying orf290 haplotypes were then developed using multiple backcross generations with a maintainer line under MAS. The breeding process used in our study provides an efficient and feasible approach for selecting new CMS lines. CMS lines selected in our study are important for enriching rice germplasm resources and guaranteeing rice breeding programs.

scholarly journals Progressive methylation of POU5F1 regulatory regions during blastocyst development

Reproduction ◽  
2018 ◽  
Vol 156 (2) ◽  
pp. 145-161 ◽  
Author(s):  
E Canon ◽  
L Jouneau ◽  
T Blachère ◽  
N Peynot ◽  
N Daniel ◽  
...  
Keyword(s):  
De Novo ◽  
Regulatory Region ◽  
Upstream Region ◽  
Distal Enhancer ◽  
Blastocyst Development ◽  
Differentiated Cells ◽  
Rabbit Blastocyst ◽  
Highly Correlated ◽  
And Function

ThePOU5F1gene encodes one of the ‘core’ transcription factors necessary to establish and maintain pluripotency in mammals. Its function depends on its precise level of expression, so its transcription has to be tightly regulated. To date, few conserved functional elements have been identified in its 5′ regulatory region: a distal and a proximal enhancer, and a minimal promoter, epigenetic modifications of which interfere withPOU5F1expression and function inin vitro-derived cell lines. Also, its permanent inactivation in differentiated cells depends onde novomethylation of its promoter. However, little is known about the epigenetic regulation ofPOU5F1expression in the embryo itself. We used the rabbit blastocyst as a model to analyze the methylation dynamics of thePOU5F15′ upstream region, relative to its regulated expression in different compartments of the blastocyst over a 2-day period of development. We evidenced progressive methylation of the 5′ regulatory region and the first exon accompanying differentiation and the gradual repression ofPOU5F1. Methylation started in the early trophectoderm before complete transcriptional inactivation. Interestingly, the distal enhancer, which is known to be active in naïve pluripotent cells only, retained a very low level of methylation in primed pluripotent epiblasts and remained less methylated in differentiated compartments than the proximal enhancer. This detailed study identified CpGs with the greatest variations in methylation, as well as groups of CpGs showing a highly correlated behavior, during differentiation. Moreover, our findings evidenced few CpGs with very specific behavior during this period of development.

scholarly journals Segregation Distortion Observed in the Progeny of Crosses Between Oryza sativa and O. meridionalis Caused by Abortion During Seed Development

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 398
Author(s):  
Daiki Toyomoto ◽  
Masato Uemura ◽  
Satoru Taura ◽  
Tadashi Sato ◽  
Robert Henry ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Seed Development ◽  
Wild Rice ◽  
Lethal Gene ◽  
Chromosome 6 ◽  
Cultivated Rice ◽  
Substitution Lines ◽  
Putative Gene ◽  
Aa Genome ◽  
Recurrent Backcrossing

Wild rice relatives having the same AA genome as domesticated rice (Oryza sativa) comprise the primary gene pool for rice genetic improvement. Among them, O. meridionalis and O. rufipogon are found in the northern part of Australia. Three Australian wild rice strains, Jpn1 (O. rufipogon), Jpn2, and W1297 (O. meridionalis), and one cultivated rice cultivar Taichung 65 (T65) were used in this study. A recurrent backcrossing strategy was adopted to produce chromosomal segment substitution lines (CSSLs) carrying chromosomal segments from wild relatives and used for trait evaluation and genetic analysis. The segregation of the DNA marker RM136 locus on chromosome 6 was found to be highly distorted, and a recessive lethal gene causing abortion at the seed developmental stage was shown to be located between two DNA markers, KGC6_10.09 and KGC6_22.19 on chromosome 6 of W1297. We name this gene as SEED DEVELOPMENT 1 (gene symbol: SDV1). O. sativa is thought to share the functional dominant allele Sdv1-s (s for sativa), and O. meridionalis is thought to share the recessive abortive allele sdv1-m (m for meridionalis). Though carrying the sdv1-m allele, the O. meridionalis accessions can self-fertilize and bear seeds. We speculate that the SDV1 gene may have been duplicated before the divergence between O. meridionalis and the other AA genome Oryza species, and that O. meridionalis has lost the function of the SDV1 gene and has kept the function of another putative gene named SDV2.

scholarly journals Genetic Landscape of Mitochondrial Regulatory Region in Pediatric Acute Myeloid Leukemia: Changes from Diagnosis to Relapse

2019 ◽  
Vol 08 (04) ◽  
pp. 193-197
Author(s):  
Anudishi Tyagi ◽  
Raja Pramanik ◽  
Radhika Bakhshi ◽  
Sreenivas Vishnubhatla ◽  
Sameer Bakhshi
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
De Novo ◽  
Regulatory Region ◽  
Mt Dna ◽  
Pediatric Acute Myeloid Leukemia ◽  
Loop Region ◽  
Significant Difference ◽  
D Loop ◽  
Acute Myeloid

AbstractThis prospective study aimed to compare the pattern of mitochondrial deoxyribonucleic acid D-loop (mt-DNA D-loop) variations in 41 paired samples of de novo pediatric acute myeloid leukemia (AML) (baseline vs. relapse) patients by Sanger's sequencing. Mean mt-DNA D-loop variation was 10.1 at baseline as compared with 9.4 per patients at relapse. In our study, 28 (68.3%) patients showed change in number of variations from baseline to relapse, 11 (26.8%) patients showed increase, 17 (41.6%) patients showed decrease, and 7 (17.1%) patients who suffered a relapse had a gain at position T489C. No statistically significant difference was observed in the mutation profile of mt-DNA D-loop region from baseline to relapse in the evaluated population of pediatric AML.

Identification and function of phosphorylation in the glucose-regulated transcription factor ChREBP

2008 ◽  
Vol 411 (2) ◽  
pp. 261-270 ◽  
Author(s):  
Nikolas G. Tsatsos ◽  
Michael N. Davies ◽  
Brennon L. O'callaghan ◽  
Howard C. Towle
Keyword(s):  
Transcription Factor ◽  
High Glucose ◽  
Leucine Zipper ◽  
De Novo ◽  
Regulatory Region ◽  
De Novo Lipogenesis ◽  
Nuclear Accumulation ◽  
Helix Loop Helix ◽  
Genes Encoding ◽  
And Function

In the liver, induction of genes encoding enzymes involved in de novo lipogenesis occurs in response to increased glucose metabolism. ChREBP (carbohydrate-response-element-binding protein) is a basic helix–loop–helix/leucine zipper transcription factor that regulates expression of these genes. To evaluate the potential role of ChREBP phosphorylation in its regulation, we used MS to identify modified residues. In the present paper, we report the detection of multiple phosphorylation sites of ChREBP expressed in hepatocytes, several of which are only observed under high-glucose conditions. Mutation of each of these serine/threonine residues of ChREBP did not alter its ability to respond to glucose. However, mutation of five N-terminal phosphoacceptor sites resulted in a major decrease in activity under high-glucose conditions. These phosphorylated residues are located within a region of ChREBP (amino acids 1–197) that is critical for glucose regulation. Mutation of Ser56 within this region to an aspartate residue resulted in increased nuclear accumulation and activity under high-glucose conditions. Together, these data suggest that ChREBP activity is regulated by complex multisite phosphorylation patterns involving its N-terminal regulatory region.

scholarly journals Targeting of De Novo DNA Methylation Throughout the Oct-4 Gene Regulatory Region in Differentiating Embryonic Stem Cells

PLoS ONE ◽  
2010 ◽  
Vol 5 (4) ◽  
pp. e9937 ◽  
Author(s):  
Rodoniki Athanasiadou ◽  
Dina de Sousa ◽  
Kevin Myant ◽  
Cara Merusi ◽  
Irina Stancheva ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Stem Cells ◽  
Embryonic Stem Cells ◽  
De Novo ◽  
Regulatory Region ◽  
Embryonic Stem ◽  
Gene Regulatory

scholarly journals A novel disease mechanism leading to the expression of a disallowed gene in the pancreatic beta-cell identified by non-coding, regulatory mutations controlling HK1

2021 ◽  
Author(s):  
Matthew N. Wakeling ◽  
Nick D. L. Owens ◽  
Jessica R. Hopkinson ◽  
Matthew B. Johnson ◽  
Jayne A.L. Houghton ◽  
...  
Keyword(s):  
Beta Cell ◽  
Pancreatic Beta Cells ◽  
De Novo ◽  
Regulatory Element ◽  
Pancreatic Beta Cell ◽  
Regulatory Region ◽  
Protein Product ◽  
Congenital Hyperinsulinism ◽  
Disease Mechanism ◽  
Regulatory Mutations

AbstractGene expression is tightly regulated with many genes exhibiting cell-specific silencing when their protein product would disrupt normal cellular function. This silencing is largely controlled by non-coding elements and their disruption might cause human disease. We performed gene-agnostic screening of the non-coding regions to discover new molecular causes of congenital hyperinsulinism. This identified 14 non-coding de novo mutations affecting a 42bp conserved region encompassed by a regulatory element in intron 2 of Hexokinase 1 (HK1), a pancreatic beta-cell disallowed gene. We demonstrated that these mutations resulted in expression of HK1 in the pancreatic beta-cells causing inappropriate insulin secretion and congenital hyperinsulinism. These mutations identify a regulatory region critical for cell-specific silencing. Importantly, this has revealed a new disease mechanism for non-coding mutations that cause inappropriate expression of a disallowed gene.

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