The root appears to be the most relevant organ for breeding drought stress tolerance.However, our knowledge about temporal and spatial regulation of drought-associated genes in the root remains fragmented, especially ...The root appears to be the most relevant organ for breeding drought stress tolerance.However, our knowledge about temporal and spatial regulation of drought-associated genes in the root remains fragmented, especially in crop plants. We performed a meta-analysis of expression divergence of essential drought-inducible genes and analyzed their association with cis-elements in model crops and major cereal crops. Our analysis of42 selected drought-inducible genes revealed that these are expressed primarily in roots,followed by shoot, leaf, and inflorescence tissues, especially in wheat. Quantitative real-time RT-PCR analysis confirmed higher expression of TaDREB2 and TaAQP7 in roots,correlated with extensive rooting and drought-stress tolerance in wheat. A promoter scan up to 2 kb upstream of the translation start site using phylogenetic footprinting revealed708 transcription factor binding sites, including drought response elements(DREs), auxin response elements(Aux REs), MYCREs/MYBREs, ABAREs, and ERD1 in 19 selected genes.Interestingly, these elements were organized into clusters of overlapping transcription factor binding sites known as homotypic clusters(HCTs), which modulate drought physiology in plants. Taken together, these results revealed the expression preeminence of major drought-inducible genes in the root, suggesting its crucial role in drought adaptation. The occurrence of HCTs in drought-inducible genes highlights the putative evolutionary modifications of crop plants in developing drought adaptation. We propose that these DNA motifs can be used as molecular markers for breeding drought-resilient cultivars, particularly in the cereal crops.展开更多
The cis-acting regulatory elements, e.g., promoters and ribosome binding sites （RBSs） with various desired properties, are building blocks widely used in synthetic biology for fine tuning gene expression. In the las...The cis-acting regulatory elements, e.g., promoters and ribosome binding sites （RBSs） with various desired properties, are building blocks widely used in synthetic biology for fine tuning gene expression. In the last decade, acquisition of a controllable regulatory element from a random library has been established and applied to control the protein expression and metabolic flux in different chassis cells. However, more rational strategies are still urgently needed to improve the efficiency and reduce the laborious screening and multifaceted characterizations. Building precise computational models that can predict the activity of regulatory elements and quantitatively design elements with desired strength have been demonstrated tremendous potentiality. Here, recent progress on construction of cis- acting regulatory element library and the quantitative predicting models for design of such elements are reviewed and discussed in detail.展开更多
Divergence of gene expression and alter native splicing is a crucial driving force in the evolution of species;to date, however the molecular mechanism remains unclear. Hybrids of closely related species provide a sui...Divergence of gene expression and alter native splicing is a crucial driving force in the evolution of species;to date, however the molecular mechanism remains unclear. Hybrids of closely related species provide a suitable model to analyze allele-specific expressi on (ASE) and allele-specific alter native splicing (ASS). Analysis of ASE and ASS can uncover the differences in cis-regulatory elements between closely related species, while eliminating interferenee of trans-regulatory elements. Here, we provide a detailed characterization of ASE and ASS from 19 and 10 transcriptome datasets across five tissues from reciprocal-cross hybrids of horsex don key (mule/hi nny) and cattlexyak (dzo), respectively. Results showed that 4.8%-8.7% and 10.8%-16.7% of genes exhibited ASE and ASS, respectively. Notably, IncRNAs and pseudogenes were more likely to show ASE than protein-coding genes. In addition, genes showing ASE and ASS in mule/hinny were found to be involved in the regulation of muscle strength, whereas those of dzo were involved in high-altitude adaptati on. In con clusi on, our study dem on strated that explorati on of genes showing ASE and ASS in hybrids of closely related species is feasible for species evolution research.展开更多
A genetic association between single nucleotide polymorphisms (SNPs) and pulmonary hypertension syndrome (PHS) was established in a commercial population of broiler chickens. The associated SNPs were found in the NOS3...A genetic association between single nucleotide polymorphisms (SNPs) and pulmonary hypertension syndrome (PHS) was established in a commercial population of broiler chickens. The associated SNPs were found in the NOS3 and HIF1α genes (LOD > 6;p NOS3 gene interfere with its trans-activation and transcriptional activation activities under natural hypobaric hypoxia conditions and are located in a consensus sequence that is called the hypoxia response element (HRE). SNPs located in the HIF1α gene could act as alternative cryptic splicing sites in intron six, which may stimulate non-sense mediated early decay (NMD) of the primary transcript. A fragment of intron 3 of the EDN1 gene was also evaluated, but the polymorphisms found were not associated with PHS (lod 0.001). However, further studies on the regulatory transcription sequences of EDN1 are recommended. The findings of this study indicate that intronic sequences should be included when searching for polymorphisms that produce physiological changes. Introns have transcriptional regulatory sequences or post-transcriptional control signals, which are known as cis- and trans-activation regulatory elements and are able to alter the physiological processes of hypoxia adaptation when modified. Based on these findings, it can be concluded that the inheritance pattern of PHS is autosomal overdominant and has deleterious effects that are characterized by higher penetrance in heterozygous than in homozygous animals, which prevent broiler chickens from being able to adapt to high altitudes.展开更多
The cis-regulatory elements of promoters regulate temporal and spatial expression of genes. DNA inethylation, histone methylation and histone acetylation are the main types of epigenetic modifications, which play impo...The cis-regulatory elements of promoters regulate temporal and spatial expression of genes. DNA inethylation, histone methylation and histone acetylation are the main types of epigenetic modifications, which play important roles in plant growth and development. DNA methylation could seilenco transposons, affect gene imprinting and gene expression. In this study, we found that granule bound starch synthase 1 （GBSSI） gene is expressed specifically in wheat endosperm rath- er than in the embryo. We also analyzed the cis-elements within this promoter region and found some seed-specific elements. In order to confirm the tissue specifici- ty, we cloned 4k bp sequences upstream of GBSS1 gene to link to vector with GUS and this construct was transferred to tobacco by Agrobacterium mediated transfor- marion. The results showed that wheat GBSS1 promoter mediated the seed-specific expression of GUS gene, hut not mediated expression in embryo. In addition, we found that GBSSI promoter is methylated in wheat embryo and de-methylated in wheat endosperm. Our study might provide the molecular basis for specific expres- sion of GBSSI gene.展开更多
Development and ripening of tomato fruit are precisely controlled by transcriptional regulation, which de- pends on the orchestrated accessibility of regulatory proteins to promoters and other c/s-regulatory DNA eleme...Development and ripening of tomato fruit are precisely controlled by transcriptional regulation, which de- pends on the orchestrated accessibility of regulatory proteins to promoters and other c/s-regulatory DNA elements. This accessibility and its effect on gene expression play a major role in defining the develop- mental process. To understand the regulatory mechanism and functional elements modulating morpholog- ical and anatomical changes during fruit development, we generated genome-wide high-resolution maps of DNase I hypersensitive sites （DHSs） from the fruit tissues of the tomato cultivar ＂Moneymaker＂ at 20 days post anthesis as well as break stage. By exploring variation of DHSs across fruit development stages, we pinpointed the most likely hypersensitive sites related to development-specific genes. By detecting binding motifs on DHSs of these development-specific genes or genes in the ascorbic acid biosynthetic pathway, we revealed the common regulatory elements contributing to coordinating gene transcription of plant ripening and specialized metabolic pathways. Our results contribute to a better understanding of the regulatory dynamics of genes involved in tomato fruit development and ripening.展开更多
The control of gene expression by transcriptional regulators and other types of functional y relevant DNA transactions such as chromatin remodeling and replication underlie a vast spectrum of biological processes in a...The control of gene expression by transcriptional regulators and other types of functional y relevant DNA transactions such as chromatin remodeling and replication underlie a vast spectrum of biological processes in al organisms. DNA transactions require the control ed interaction of proteins with DNA sequence motifs which are often located in nucleosome-depleted regions （NDRs） of the chromatin. Formaldehyde-assisted isolation of regulatory elements （FAIRE） has been established as an easy-to-implement method for the isolation of NDRs from a number of eukaryotic organisms, and it has been successful y employed for the discovery of new regulatory segments in genomic DNA from, for example, yeast, Drosophila, and humans. Until today, however, FAIRE has only rarely been employed in plant research and currently no detailed FAIRE protocol for plants has been published. Here, we provide a step-by-step FAIRE protocol for NDR discovery in Arabidopsis thaliana. We demonstrate that NDRs isolated from plant chromatin are readily amenable to quantitative polymerase chain reaction and next-generation sequencing. Only minor modification of the FAIRE protocol wil be needed to adapt it to other plants, thus facilitating the global inventory of regulatory regions across species.展开更多
基金supported by German–Pakistani Research Cooperation(grant no.56453308)via German Academic Exchange Service(DAAD)to build German–Pakistani research and academic exchange and partnerships
文摘The root appears to be the most relevant organ for breeding drought stress tolerance.However, our knowledge about temporal and spatial regulation of drought-associated genes in the root remains fragmented, especially in crop plants. We performed a meta-analysis of expression divergence of essential drought-inducible genes and analyzed their association with cis-elements in model crops and major cereal crops. Our analysis of42 selected drought-inducible genes revealed that these are expressed primarily in roots,followed by shoot, leaf, and inflorescence tissues, especially in wheat. Quantitative real-time RT-PCR analysis confirmed higher expression of TaDREB2 and TaAQP7 in roots,correlated with extensive rooting and drought-stress tolerance in wheat. A promoter scan up to 2 kb upstream of the translation start site using phylogenetic footprinting revealed708 transcription factor binding sites, including drought response elements(DREs), auxin response elements(Aux REs), MYCREs/MYBREs, ABAREs, and ERD1 in 19 selected genes.Interestingly, these elements were organized into clusters of overlapping transcription factor binding sites known as homotypic clusters(HCTs), which modulate drought physiology in plants. Taken together, these results revealed the expression preeminence of major drought-inducible genes in the root, suggesting its crucial role in drought adaptation. The occurrence of HCTs in drought-inducible genes highlights the putative evolutionary modifications of crop plants in developing drought adaptation. We propose that these DNA motifs can be used as molecular markers for breeding drought-resilient cultivars, particularly in the cereal crops.
基金This work was supported by the National Basic Research Program of China （973 Program, grant No. 2012CB721104）, the National High Technology Research and Development Program （863 Program, grant No. 2012AA02A701）, the National Natural Science Foundation of China （grant Nos. 31170101 and 31301017）, and the Natural Science Foundation of Guangdong Province, China （grant No. 2015A030310317）.
文摘The cis-acting regulatory elements, e.g., promoters and ribosome binding sites （RBSs） with various desired properties, are building blocks widely used in synthetic biology for fine tuning gene expression. In the last decade, acquisition of a controllable regulatory element from a random library has been established and applied to control the protein expression and metabolic flux in different chassis cells. However, more rational strategies are still urgently needed to improve the efficiency and reduce the laborious screening and multifaceted characterizations. Building precise computational models that can predict the activity of regulatory elements and quantitatively design elements with desired strength have been demonstrated tremendous potentiality. Here, recent progress on construction of cis- acting regulatory element library and the quantitative predicting models for design of such elements are reviewed and discussed in detail.
基金supported by grants from the National Natural Science Foundation of China(31572381)National Thousand Youth Talents Plan of the International Science and Technology Cooperation Project of China(2013DFA31420)Science and Technology Innovation Capability Promotion Program of the Science and Technology Department of Qinghai Province(2015-ZJ-712)
文摘Divergence of gene expression and alter native splicing is a crucial driving force in the evolution of species;to date, however the molecular mechanism remains unclear. Hybrids of closely related species provide a suitable model to analyze allele-specific expressi on (ASE) and allele-specific alter native splicing (ASS). Analysis of ASE and ASS can uncover the differences in cis-regulatory elements between closely related species, while eliminating interferenee of trans-regulatory elements. Here, we provide a detailed characterization of ASE and ASS from 19 and 10 transcriptome datasets across five tissues from reciprocal-cross hybrids of horsex don key (mule/hi nny) and cattlexyak (dzo), respectively. Results showed that 4.8%-8.7% and 10.8%-16.7% of genes exhibited ASE and ASS, respectively. Notably, IncRNAs and pseudogenes were more likely to show ASE than protein-coding genes. In addition, genes showing ASE and ASS in mule/hinny were found to be involved in the regulation of muscle strength, whereas those of dzo were involved in high-altitude adaptati on. In con clusi on, our study dem on strated that explorati on of genes showing ASE and ASS in hybrids of closely related species is feasible for species evolution research.
文摘A genetic association between single nucleotide polymorphisms (SNPs) and pulmonary hypertension syndrome (PHS) was established in a commercial population of broiler chickens. The associated SNPs were found in the NOS3 and HIF1α genes (LOD > 6;p NOS3 gene interfere with its trans-activation and transcriptional activation activities under natural hypobaric hypoxia conditions and are located in a consensus sequence that is called the hypoxia response element (HRE). SNPs located in the HIF1α gene could act as alternative cryptic splicing sites in intron six, which may stimulate non-sense mediated early decay (NMD) of the primary transcript. A fragment of intron 3 of the EDN1 gene was also evaluated, but the polymorphisms found were not associated with PHS (lod 0.001). However, further studies on the regulatory transcription sequences of EDN1 are recommended. The findings of this study indicate that intronic sequences should be included when searching for polymorphisms that produce physiological changes. Introns have transcriptional regulatory sequences or post-transcriptional control signals, which are known as cis- and trans-activation regulatory elements and are able to alter the physiological processes of hypoxia adaptation when modified. Based on these findings, it can be concluded that the inheritance pattern of PHS is autosomal overdominant and has deleterious effects that are characterized by higher penetrance in heterozygous than in homozygous animals, which prevent broiler chickens from being able to adapt to high altitudes.
基金Supported by Agricultural Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences(CXGC2016D01)
文摘The cis-regulatory elements of promoters regulate temporal and spatial expression of genes. DNA inethylation, histone methylation and histone acetylation are the main types of epigenetic modifications, which play important roles in plant growth and development. DNA methylation could seilenco transposons, affect gene imprinting and gene expression. In this study, we found that granule bound starch synthase 1 （GBSSI） gene is expressed specifically in wheat endosperm rath- er than in the embryo. We also analyzed the cis-elements within this promoter region and found some seed-specific elements. In order to confirm the tissue specifici- ty, we cloned 4k bp sequences upstream of GBSS1 gene to link to vector with GUS and this construct was transferred to tobacco by Agrobacterium mediated transfor- marion. The results showed that wheat GBSS1 promoter mediated the seed-specific expression of GUS gene, hut not mediated expression in embryo. In addition, we found that GBSSI promoter is methylated in wheat embryo and de-methylated in wheat endosperm. Our study might provide the molecular basis for specific expres- sion of GBSSI gene.
文摘Development and ripening of tomato fruit are precisely controlled by transcriptional regulation, which de- pends on the orchestrated accessibility of regulatory proteins to promoters and other c/s-regulatory DNA elements. This accessibility and its effect on gene expression play a major role in defining the develop- mental process. To understand the regulatory mechanism and functional elements modulating morpholog- ical and anatomical changes during fruit development, we generated genome-wide high-resolution maps of DNase I hypersensitive sites （DHSs） from the fruit tissues of the tomato cultivar ＂Moneymaker＂ at 20 days post anthesis as well as break stage. By exploring variation of DHSs across fruit development stages, we pinpointed the most likely hypersensitive sites related to development-specific genes. By detecting binding motifs on DHSs of these development-specific genes or genes in the ascorbic acid biosynthetic pathway, we revealed the common regulatory elements contributing to coordinating gene transcription of plant ripening and specialized metabolic pathways. Our results contribute to a better understanding of the regulatory dynamics of genes involved in tomato fruit development and ripening.
文摘The control of gene expression by transcriptional regulators and other types of functional y relevant DNA transactions such as chromatin remodeling and replication underlie a vast spectrum of biological processes in al organisms. DNA transactions require the control ed interaction of proteins with DNA sequence motifs which are often located in nucleosome-depleted regions （NDRs） of the chromatin. Formaldehyde-assisted isolation of regulatory elements （FAIRE） has been established as an easy-to-implement method for the isolation of NDRs from a number of eukaryotic organisms, and it has been successful y employed for the discovery of new regulatory segments in genomic DNA from, for example, yeast, Drosophila, and humans. Until today, however, FAIRE has only rarely been employed in plant research and currently no detailed FAIRE protocol for plants has been published. Here, we provide a step-by-step FAIRE protocol for NDR discovery in Arabidopsis thaliana. We demonstrate that NDRs isolated from plant chromatin are readily amenable to quantitative polymerase chain reaction and next-generation sequencing. Only minor modification of the FAIRE protocol wil be needed to adapt it to other plants, thus facilitating the global inventory of regulatory regions across species.
