scholarly journals Seed-Specific Gene MOTHER of FT and TFL1（MFT） Involved in Embryogenesis, Hormones and Stress Responses in Dimocarpus longan Lour.

2018 ◽  
Vol 19 (8) ◽  
pp. 2403 ◽  
Author(s):  
Yukun Chen ◽  
Xiaoping Xu ◽  
Xiaohui Chen ◽  
Yan Chen ◽  
Zihao Zhang ◽  
...  
Keyword(s):  
Seed Germination ◽  
Stress Responses ◽  
Zygotic Embryo ◽  
Promoter Sequence ◽  
Bioinformatic Analysis ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Zygotic Embryogenesis ◽  
Dimocarpus Longan ◽  
Maturation Stages

Mother of FT and TFL1 (MFT) belongs to phosphatidylethanolamine-binding protein (PEBP) family, which plays an important role in flowering time regulation, seed development, and germination. To gain insight into the molecular function of DlMFT in Dimocarpus longan Lour., we isolated DlMFT and its promoter sequence from longan embryogenic callus (EC). Bioinformatic analysis indicated that the promoter contained multiphytohormones and light responsive regulatory elements. Subcellular localization showed that the given the DlMFT signal localized in the nucleus, expression profiling implied that DlMFT showed significant upregulation during somatic embryogenesis (SE) and zygotic embryogenesis (ZE), and particular highly expressed in late or maturation stages. The accumulation of DlMFT was mainly detected in mature fruit and seed, while it was undetected in abortive seeds, and notably decreased during seed germination. DlMFT responded differentially to exogenous hormones in longan EC. Auxins, salicylic acid (SA) and methyl jasmonate (MeJa) suppressed its expression, however, abscisic acid (ABA), brassinosteroids (BR) showed the opposite function. Meanwhile, DlMFT differentially responded to various abiotic stresses. Our study revealed that DlMFT might be a key regulator of longan somatic and zygotic embryo development, and in seed germination, it is involved in complex plant hormones and abiotic stress signaling pathways.

scholarly journals Participation of the yeast activator Abf1 in meiosis-specific expression of the HOP1 gene.

1996 ◽  
Vol 16 (6) ◽  
pp. 2777-2786 ◽  
Author(s):  
V Gailus-Durner ◽  
J Xie ◽  
C Chintamaneni ◽  
A K Vershon
Keyword(s):  
Transcriptional Activation ◽  
Mutational Analysis ◽  
Consensus Sequence ◽  
Promoter Sequence ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Specific Expression ◽  
Autonomously Replicating Sequence

The meiosis-specific gene HOP1, which encodes a component of the synaptonemal complex, is controlled through two regulatory elements, UASH and URS1H. Sites similar to URS1H have been identified in the promoter region of virtually every early meiosis-specific gene, as well as in many promoters of nonmeiotic genes, and it has been shown that the proteins that bind to this site function to regulate meiotic and nonmeiotic transcription. Sites similar to the UASH site have been found in a number of meiotic and nonmeiotic genes as well. Since it has been shown that UASH functions as an activator site in vegetative haploid cells, it seemed likely that the factors binding to this site regulate both meiotic and nonmeiotic transcription. We purified the factor binding to the UASH element of the HOP1 promoter. Sequence analysis identified the protein as Abf1 (autonomously replicating sequence-binding factor 1), a multifunctional protein involved in DNA replication, silencing, and transcriptional regulation. We show by mutational analysis of the UASH site, that positions outside of the proposed UASH consensus sequence (TNTGN[A/T]GT) are required for DNA binding in vitro and transcriptional activation in vivo. A new UASH consensus sequence derived from this mutational analysis closely matches a consensus Abf1 binding site. We also show that an Abf1 site from a nonmeiotic gene can replace the function of the UASH site in the HOP1 promoter. Taken together, these results show that Abf1 functions to regulate meiotic gene expression.

scholarly journals Systematic analysis of NAC transcription factors in Gossypium barbadense uncovers their roles in response to Verticillium wilt

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7995 ◽  
Author(s):  
Zhanji Liu ◽  
Mingchuan Fu ◽  
Hao Li ◽  
Yizhen Chen ◽  
Liguo Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Verticillium Wilt ◽  
Stress Responses ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Hormone Regulation ◽  
Genome Wide ◽  
A Genome

As one of the largest plant-specific gene families, the NAC transcription factor gene family plays important roles in various plant physiological processes that are related to plant development, hormone signaling, and biotic and abiotic stresses. However, systematic investigation of the NAC gene family in sea-island cotton (Gossypium babardense L.) has not been reported, to date. The recent release of the complete genome sequence of sea-island cotton allowed us to perform systematic analyses of G. babardense NAC GbNAC) genes. In this study, we performed a genome-wide survey and identified 270 GbNAC genes in the sea-island cotton genome. Genome mapping analysis showed that GbNAC genes were unevenly distributed on 26 chromosomes. Through phylogenetic analyses of GbNACs along with their Arabidopsis counterparts, these proteins were divided into 10 groups (I–X), and each contained a different number of GbNACs with a similar gene structure and conserved motifs. One hundred and fifty-four duplicated gene pairs were identified, and almost all of them exhibited strong purifying selection during evolution. In addition, various cis-acting regulatory elements in GbNAC genes were found to be related to major hormones, defense and stress responses. Notably, transcriptome data analyses unveiled the expression profiles of 62 GbNAC genes under Verticillium wilt (VW) stress. Furthermore, the expression profiles of 15 GbNAC genes tested by quantitative real-time PCR (qPCR) demonstrated that they were sensitive to methyl jasmonate (MeJA) and salicylic acid (SA) treatments and that they could be involved in pathogen-related hormone regulation. Taken together, the genome-wide identification and expression profiling pave new avenues for systematic functional analysis of GbNAC candidates, which may be useful for improving cotton defense against VW.

scholarly journals Genome-Wide Profiling and Phylogenetic Analysis of the SWEET Sugar Transporter Gene Family in Walnut and Their Lack of Responsiveness to Xanthomonas arboricola pv. juglandis Infection

2020 ◽  
Vol 21 (4) ◽  
pp. 1251 ◽  
Author(s):  
Shijiao Jiang ◽  
Bipin Balan ◽  
Renata de A. B. Assis ◽  
Cintia H. D. Sagawa ◽  
Xueqin Wan ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Juglans Regia ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Transcription Activator ◽  
Sugar Transporters ◽  
Transporter Family ◽  
Xanthomonas Arboricola

Following photosynthesis, sucrose is translocated to sink organs, where it provides the primary source of carbon and energy to sustain plant growth and development. Sugar transporters from the SWEET (sugar will eventually be exported transporter) family are rate-limiting factors that mediate sucrose transport across concentration gradients, sustain yields, and participate in reproductive development, plant senescence, stress responses, as well as support plant–pathogen interaction, the focus of this study. We identified 25 SWEET genes in the walnut genome and distinguished each by its individual gene structure and pattern of expression in different walnut tissues. Their chromosomal locations, cis-acting motifs within their 5′ regulatory elements, and phylogenetic relationship patterns provided the first comprehensive analysis of the SWEET gene family of sugar transporters in walnut. This family is divided into four clades, the analysis of which suggests duplication and expansion of the SWEET gene family in Juglans regia. In addition, tissue-specific gene expression signatures suggest diverse possible functions for JrSWEET genes. Although these are commonly used by pathogens to harness sugar products from their plant hosts, little was known about their role during Xanthomonas arboricola pv. juglandis (Xaj) infection. We monitored the expression profiles of the JrSWEET genes in different tissues of “Chandler” walnuts when challenged with pathogen Xaj417 and concluded that SWEET-mediated sugar translocation from the host is not a trigger for walnut blight disease development. This may be directly related to the absence of type III secretion system-dependent transcription activator-like effectors (TALEs) in Xaj417, which suggests different strategies are employed by this pathogen to promote susceptibility to this major aboveground disease of walnuts.

scholarly journals Arabidopsis thaliana Myb59 Gene Is Involved in the Response to Heterodera schachtii Infestation, and Its Overexpression Disturbs Regular Development of Nematode-Induced Syncytia

2021 ◽  
Vol 22 (12) ◽  
pp. 6450
Author(s):  
Anita Wiśniewska ◽  
Kamila Wojszko ◽  
Elżbieta Różańska ◽  
Klaudia Lenarczyk ◽  
Karol Kuczerski ◽  
...  
Keyword(s):  
Cell Metabolism ◽  
Gene Promoter ◽  
Promoter Sequence ◽  
Regulatory Elements ◽  
Heterodera Schachtii ◽  
Myb Transcription Factor ◽  
Parasitic Nematodes ◽  
Regulatory Sequences ◽  
Gene Encoding ◽  
Constitutive Overexpression

Transcription factors are proteins that directly bind to regulatory sequences of genes to modulate and adjust plants’ responses to different stimuli including biotic and abiotic stresses. Sedentary plant parasitic nematodes, such as beet cyst nematode, Heterodera schachtii, have developed molecular tools to reprogram plant cell metabolism via the sophisticated manipulation of genes expression, to allow root invasion and the induction of a sequence of structural and physiological changes in plant tissues, leading to the formation of permanent feeding sites composed of modified plant cells (commonly called a syncytium). Here, we report on the AtMYB59 gene encoding putative MYB transcription factor that is downregulated in syncytia, as confirmed by RT-PCR and a promoter pMyb59::GUS activity assays. The constitutive overexpression of AtMYB59 led to the reduction in A. thaliana susceptibility, as indicated by decreased numbers of developed females, and to the disturbed development of nematode-induced syncytia. In contrast, mutant lines with a silenced expression of AtMYB59 were more susceptible to this parasite. The involvement of ABA in the modulation of AtMYB59 gene transcription appears feasible by several ABA-responsive cis regulatory elements, which were identified in silico in the gene promoter sequence, and experimental assays showed the induction of AtMYB59 transcription after ABA treatment. Based on these results, we suggest that AtMYB59 plays an important role in the successful parasitism of H. schachtii on A. thaliana roots.

scholarly journals Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhiwei Chen ◽  
Longhua Zhou ◽  
Panpan Jiang ◽  
Ruiju Lu ◽  
Nigel G. Halford ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Gene Family ◽  
Stress Responses ◽  
Phylogenetic Analyses ◽  
Regulatory Elements ◽  
Gene Promoters ◽  
Related Protein ◽  
Rna Seq ◽  
Response Elements ◽  
Genome Data

Abstract Background Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies, SnRK1, SnRK2 and SnRK3, of which SnRK2 and SnRK3 are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study, we describe the SnRK gene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environments. Results The barley HvSnRK gene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to the HvSnRK1 subfamily, 10 to HvSnRK2 and 34 to HvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50 SnRK genes in rice (four OsSnRK1, 11 OsSnRK2 and 35 OsSnRK3) and 39 in Arabidopsis (three AtSnRK1, 10 AtSnRK2 and 26 AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis showed that many of the HvSnRK genes responded to ABA, some positively, some negatively and some with complex time-dependent responses. Conclusions The barley HvSnRK gene family is large, comprising 50 members, subdivided into HvSnRK1 (6 members), HvSnRK2 (10 members) and HvSnRK3 (34 members), showing differential positive and negative responses to ABA.

scholarly journals The regulatory genome of the malaria vector Anopheles gambiae: integrating chromatin accessibility and gene expression

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
José L Ruiz ◽  
Lisa C Ranford-Cartwright ◽  
Elena Gómez-Díaz
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Anopheles Gambiae ◽  
Mosquito Control ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Malaria Vectors ◽  
Specific Gene ◽  
Mosquito Vector ◽  
Human Malaria

Abstract Anopheles gambiae mosquitoes are primary human malaria vectors, but we know very little about their mechanisms of transcriptional regulation. We profiled chromatin accessibility by the assay for transposase-accessible chromatin by sequencing (ATAC-seq) in laboratory-reared A. gambiae mosquitoes experimentally infected with the human malaria parasite Plasmodium falciparum. By integrating ATAC-seq, RNA-seq and ChIP-seq data, we showed a positive correlation between accessibility at promoters and introns, gene expression and active histone marks. By comparing expression and chromatin structure patterns in different tissues, we were able to infer cis-regulatory elements controlling tissue-specific gene expression and to predict the in vivo binding sites of relevant transcription factors. The ATAC-seq assay also allowed the precise mapping of active regulatory regions, including novel transcription start sites and enhancers that were annotated to mosquito immune-related genes. Not only is this study important for advancing our understanding of mechanisms of transcriptional regulation in the mosquito vector of human malaria, but the information we produced also has great potential for developing new mosquito-control and anti-malaria strategies.

A Global Vista of the Epigenomic State of the Mouse Submandibular Gland

2021 ◽  
pp. 002203452110120
Author(s):  
C. Gluck ◽  
S. Min ◽  
A. Oyelakin ◽  
M. Che ◽  
E. Horeth ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Submandibular Salivary Gland ◽  
Data Sets ◽  
Control Mechanisms ◽  
Chromatin Immunoprecipitation Sequencing

The parotid, submandibular, and sublingual glands represent a trio of oral secretory glands whose primary function is to produce saliva, facilitate digestion of food, provide protection against microbes, and maintain oral health. While recent studies have begun to shed light on the global gene expression patterns and profiles of salivary glands, particularly those of mice, relatively little is known about the location and identity of transcriptional control elements. Here we have established the epigenomic landscape of the mouse submandibular salivary gland (SMG) by performing chromatin immunoprecipitation sequencing experiments for 4 key histone marks. Our analysis of the comprehensive SMG data sets and comparisons with those from other adult organs have identified critical enhancers and super-enhancers of the mouse SMG. By further integrating these findings with complementary RNA-sequencing based gene expression data, we have unearthed a number of molecular regulators such as members of the Fox family of transcription factors that are enriched and likely to be functionally relevant for SMG biology. Overall, our studies provide a powerful atlas of cis-regulatory elements that can be leveraged for better understanding the transcriptional control mechanisms of the mouse SMG, discovery of novel genetic switches, and modulating tissue-specific gene expression in a targeted fashion.

scholarly journals Mitogen-Activated Protein Kinase Expression Profiling Revealed Its Role in Regulating Stress Responses in Potato (Solanum tuberosum)

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1371
Author(s):  
Madiha Zaynab ◽  
Athar Hussain ◽  
Yasir Sharif ◽  
Mahpara Fatima ◽  
Mateen Sajid ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Protein Kinase ◽  
Stress Responses ◽  
Expression Profiling ◽  
Regulatory Elements ◽  
Mitogen Activated Protein Kinase ◽  
High Expression ◽  
Primary Data ◽  
A Genome ◽  
Mitogen Activated Protein

Mitogen-activated protein kinase (MAPK) cascades are the universal signal transduction networks that regulate cell growth and development, hormone signaling, and other environmental stresses. However, their essential contribution to plant tolerance is very little known in the potato (Solanum tuberosum) plant. The current study carried out a genome-wide study of StMAPK and provided a deep insight using bioinformatics tools. In addition, the relative expression of StMAPKs was also assessed in different plant tissues. The similarity search results identified a total of 22 StMAPK genes in the potato genome. The sequence alignment also showed conserved motif TEY/TDY in most StMAPKs with conserved docking LHDXXEP sites. The phylogenetic analysis divided all 22 StMAPK genes into five groups, i.e., A, B, C, D, and E, showing some common structural motifs. In addition, most of the StMAPKs were found in a cluster form at the terminal of chromosomes. The promoter analysis predicted several stress-responsive Cis-acting regulatory elements in StMAPK genes. Gene duplication under selection pressure also indicated several purifying and positive selections in StMAPK genes. In potato, StMAPK2, StMAPK6, and StMAPK19 showed a high expression in response to heat stress. Under ABA and IAA treatment, the expression of the total 20 StMAPK genes revealed that ABA and IAA played an essential role in this defense process. The expression profiling and real-time qPCR (RT-qPCR) exhibited their high expression in roots and stems compared to leaves. These results deliver primary data for functional analysis and provide reference data for other important crops.

scholarly journals Genome-wide analysis and expression profile of the bZIP gene family in poplar

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kai Zhao ◽  
Song Chen ◽  
Wenjing Yao ◽  
Zihan Cheng ◽  
Boru Zhou ◽  
...  
Keyword(s):  
Salt Stress ◽  
Systems Biology ◽  
Gene Family ◽  
Stress Responses ◽  
Metal Ion ◽  
Gene Networks ◽  
Expression Patterns ◽  
Gene Set Enrichment Analysis ◽  
Specific Gene ◽  
Biological Processes

Abstract Background The bZIP gene family, which is widely present in plants, participates in varied biological processes including growth and development and stress responses. How do the genes regulate such biological processes? Systems biology is powerful for mechanistic understanding of gene functions. However, such studies have not yet been reported in poplar. Results In this study, we identified 86 poplar bZIP transcription factors and described their conserved domains. According to the results of phylogenetic tree, we divided these members into 12 groups with specific gene structures and motif compositions. The corresponding genes that harbor a large number of segmental duplication events are unevenly distributed on the 17 poplar chromosomes. In addition, we further examined collinearity between these genes and the related genes from six other species. Evidence from transcriptomic data indicated that the bZIP genes in poplar displayed different expression patterns in roots, stems, and leaves. Furthermore, we identified 45 bZIP genes that respond to salt stress in the three tissues. We performed co-expression analysis on the representative genes, followed by gene set enrichment analysis. The results demonstrated that tissue differentially expressed genes, especially the co-expressing genes, are mainly involved in secondary metabolic and secondary metabolite biosynthetic processes. However, salt stress responsive genes and their co-expressing genes mainly participate in the regulation of metal ion transport, and methionine biosynthetic. Conclusions Using comparative genomics and systems biology approaches, we, for the first time, systematically explore the structures and functions of the bZIP gene family in poplar. It appears that the bZIP gene family plays significant roles in regulation of poplar development and growth and salt stress responses through differential gene networks or biological processes. These findings provide the foundation for genetic breeding by engineering target regulators and corresponding gene networks into poplar lines.

scholarly journals Comprehensive analysis of single cell ATAC-seq data with SnapATAC

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Rongxin Fang ◽  
Sebastian Preissl ◽  
Yang Li ◽  
Xiaomeng Hou ◽  
Jacinta Lucero ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Cellular Heterogeneity ◽  
Specific Gene ◽  
Open Chromatin ◽  
Cell Type ◽  
Process Data ◽  
Cell Type Specific

AbstractIdentification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. Single cell analysis of accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volume of data pose unique computational challenges. Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states. Using the Nyström method, SnapATAC can process data from up to a million cells. Furthermore, SnapATAC incorporates existing tools into a comprehensive package for analyzing single cell ATAC-seq dataset. As demonstration of its utility, SnapATAC is applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex. The analysis reveals ~370,000 candidate regulatory elements in 31 distinct cell populations in this brain region and inferred candidate cell-type specific transcriptional regulators.

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