scholarly journals Transcriptomic Time-Series Analyses of Gene Expression Profile During Zygotic Embryo Development in Picea mongolica

2021 ◽  
Vol 12 ◽  
Author(s):  
Jia Yan ◽  
Ha buer ◽  
Ya ping Wang ◽  
Gegen zhula ◽  
Yu´e Bai
Keyword(s):  
Gene Expression ◽  
Embryo Development ◽  
Transcriptional Activation ◽  
Large Scale ◽  
Zygotic Embryo ◽  
Early Stage ◽  
Zygotic Embryos ◽  
Zygotic Embryogenesis ◽  
Mature Embryos ◽  
Picea Mongolica

Zygotic embryogenesis is a critical process during seed development in gymnosperms. However, knowledge on the genome-wide transcriptional activation that guides this process in conifers is limited, especially in Picea mongolica. This tree species is endemic to semiarid habitats of Inner Mongolia in China. To extend what is known about the molecular events underpinning its zygotic embryogenesis, comparative transcriptomic analyses of gene expression in zygotic embryos were performed by RNA sequencing in P. mongolica. Our results showed that most changes in transcript levels occurred in the early embryonic pattering determination and formation of mature embryos. Transcripts related to embryogenic competence, cell division pattern, hormones, and stress response genes were identified during embryogenesis. Auxin is essential for early embryo patterning and pre-cotyledon embryonic formation. However, ABA is a major regulator of embryo maturation. Moreover, we found that methylation-related gene expression is associated with activation of early-stage embryos, late embryogenesis abundant proteins, and storage/energy-related genes with late and mature embryos. Furthermore, network analysis revealed stage-specific and multistage gene expression clusters during embryogenesis. WOX, MYB, AP2, and HLH transcription factors seem more relevant to embryogenesis in different stages. Our results provide large-scale and comprehensive transcriptome data for embryo development in P. mongolica. These data will lay a foundation for the protection and utilization of P. mongolica resources.

scholarly journals Genome-wide profiling of transcribed enhancers during macrophage activation

2017 ◽  
Author(s):  
Elena Denisenko ◽  
Reto Guler ◽  
Musa Mhlanga ◽  
Harukazu Suzuki ◽  
Frank Brombacher ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Activation ◽  
Large Scale ◽  
Transcriptional Control ◽  
Macrophage Activation ◽  
Transcriptional Responses ◽  
Protein Coding ◽  
Genome Wide ◽  
Ifn Γ ◽  
Cap Analysis

AbstractMacrophages are sentinel cells essential for tissue homeostasis and host defence. Owing to their plasticity, macrophages acquire a range of functional phenotypes in response to microenvironmental stimuli, of which M(IFN-γ) and M(IL-4/IL-13) are well-known for their opposing pro- and anti-inflammatory roles. Enhancers have emerged as regulatory DNA elements crucial for transcriptional activation of gene expression. Using cap analysis of gene expression and epigenetic data, we identify on large-scale transcribed enhancers in mouse macrophages, their time kinetics and target protein-coding genes. We observe an increase in target gene expression, concomitant with increasing numbers of associated enhancers and find that genes associated to many enhancers show a shift towards stronger enrichment for macrophage-specific biological processes. We infer enhancers that drive transcriptional responses of genes upon M(IFN-γ) and M(IL-4/IL-13) macrophage activation and demonstrate stimuli-specificity of regulatory associations. Finally, we show that enhancer regions are enriched for binding sites of inflammation-related transcription factors, suggesting a link between stimuli response and enhancer transcriptional control. Our study provides new insights into genome-wide enhancer-mediated transcriptional control of macrophage genes, including those implicated in macrophage activation, and offers a detailed genome-wide catalogue to further elucidate enhancer regulation in macrophages.

scholarly journals Identifikasi homolog TcAGL-15 untuk penanda embriogenesis tanaman kakao melalui pendekatan bioinformatika Identification of TcAGL-15 homolog in the embryogenic culture from the zygotic embryo explant

2016 ◽  
Vol 74 (2) ◽  
Author(s):  
Oktaviany Ferry TRIASTANTO ◽  
Muhammad JUSUF ◽  
Djoko SANTOSO
Keyword(s):  
Gene Expression ◽  
Zygotic Embryo ◽  
Regulatory Gene ◽  
Low Frequency ◽  
Zygotic Embryos ◽  
Rt Pcr ◽  
Specific Primers ◽  
Process Understanding ◽  
Differential Pattern

Summary One of the major problems encountered in micropropagation of cacao through tissue culture is very low frequency of embryo formation. Embryogenesis is believed to have key regulatory gene determining the process. Understanding such gene may help to solve problems in the regeneration process. One of the genes reported to involve in the embryogenesis is AGAMOUS-like 15 (AGL-15). This gene has an important role in the regulation of early embryogenesis in several plants. This experiment aimed to identify AGL-15 homolog in cacao through bioinformatics approach. The first step of this experiment is to identify the AGL-15 homolog using hetero-logous primers from DNA genomic isolated from leaves of cacao plants. The sequence of the AGL-15 fragment was used in designing specific primers for longer AGL-15 fragment. These primers were then used to identify AGL-15 gene using total RNA isolated from cultured zygotic embryos. Differential pattern of AGL-15 gene expression was observed in zygotic embryos cultured for five weeks. AGL-15 heterologous primers designed from several plants could be used to identify cacao AGL-15 homolog. The putative cacao AGL-15 gene could be identified from zygotic embryos. The differential pattern of the AGL-15 gene expression is a strong indication that AGL-15 can be used as an embryogenesis marker in cacao plants.Ringkasan Salah satu kendala perbanyakan kakao melalui kultur jaringan adalah sulitnya embriogenesis, yang diduga melibatkan satu atau lebih gen kunci yang menentukan proses tersebut. Keberhasilan mengidentifikasi gen-gen kunci akan membantu menyelesaikan masalah dalam regenerasi embrio kakao. Salah satu gen yang diduga terlibat dalam proses ini adalah AGAMOUS-like 15 (AGL-15). Gen ini berperan pada regulasi selama masa awal perkembangan embrio beberapa tanaman. Penelitian ini bertujuan untuk mengidentifikasi homolog AGL-15 pada kakao melalui pen-dekatan bioinformatika dan RT-PCR. Pene-litian diawali dengan identifikasi homolog AGL-15 dari DNA genomik daun kakao meng-gunakan primer heterologus. Sekuen fragmen homolog AGL-15 yang diperoleh, kemudian digunakan untuk merancang primer spesifik AGL-15 yang berukuran lebih panjang. Primer ini selanjutnya digunakan untuk meng-identifikasi gen AGL-15 dari RNA total embrio zigotik. Pengamatan pola pita gen AGL-15 dilakukan pada kultur in vitro embrio zigotik yang berumur lima minggu. Primer hetero-logus gen AGL-15 yang berasal dari berbagai tanaman, mampu mengidentifikasi keberadaan homolog  gen  tersebut  pada  tanaman   kakao. Fragmen homolog AGL-15 putatif tanaman kakao teridentifikasi pada tingkat RNA embrio. Dengan adanya pola diferensial dari ekspresi gen AGL-15 hingga lima minggu pertama perkembangan embrio, ada indikasi kuat bahwa fragmen homolog AGL-15 dapat menjadi penanda embriogenesis pada tanaman kakao.

scholarly journals Identifikasi homolog TcAGL-15 untuk penanda embriogenesis tanaman kakao melalui pendekatan bioinformatika Identification of TcAGL-15 homolog in the embryogenic culture from the zygotic embryo explant

2016 ◽  
Vol 74 (2) ◽  
Author(s):  
Oktaviany Ferry TRIASTANTO ◽  
Muhammad JUSUF ◽  
Djoko SANTOSO
Keyword(s):  
Gene Expression ◽  
Zygotic Embryo ◽  
Regulatory Gene ◽  
Low Frequency ◽  
Zygotic Embryos ◽  
Rt Pcr ◽  
Specific Primers ◽  
Process Understanding ◽  
Differential Pattern

Summary One of the major problems encountered in micropropagation of cacao through tissue culture is very low frequency of embryo formation. Embryogenesis is believed to have key regulatory gene determining the process. Understanding such gene may help to solve problems in the regeneration process. One of the genes reported to involve in the embryogenesis is AGAMOUS-like 15 (AGL-15). This gene has an important role in the regulation of early embryogenesis in several plants. This experiment aimed to identify AGL-15 homolog in cacao through bioinformatics approach. The first step of this experiment is to identify the AGL-15 homolog using hetero-logous primers from DNA genomic isolated from leaves of cacao plants. The sequence of the AGL-15 fragment was used in designing specific primers for longer AGL-15 fragment. These primers were then used to identify AGL-15 gene using total RNA isolated from cultured zygotic embryos. Differential pattern of AGL-15 gene expression was observed in zygotic embryos cultured for five weeks. AGL-15 heterologous primers designed from several plants could be used to identify cacao AGL-15 homolog. The putative cacao AGL-15 gene could be identified from zygotic embryos. The differential pattern of the AGL-15 gene expression is a strong indication that AGL-15 can be used as an embryogenesis marker in cacao plants.Ringkasan Salah satu kendala perbanyakan kakao melalui kultur jaringan adalah sulitnya embriogenesis, yang diduga melibatkan satu atau lebih gen kunci yang menentukan proses tersebut. Keberhasilan mengidentifikasi gen-gen kunci akan membantu menyelesaikan masalah dalam regenerasi embrio kakao. Salah satu gen yang diduga terlibat dalam proses ini adalah AGAMOUS-like 15 (AGL-15). Gen ini berperan pada regulasi selama masa awal perkembangan embrio beberapa tanaman. Penelitian ini bertujuan untuk mengidentifikasi homolog AGL-15 pada kakao melalui pen-dekatan bioinformatika dan RT-PCR. Pene-litian diawali dengan identifikasi homolog AGL-15 dari DNA genomik daun kakao meng-gunakan primer heterologus. Sekuen fragmen homolog AGL-15 yang diperoleh, kemudian digunakan untuk merancang primer spesifik AGL-15 yang berukuran lebih panjang. Primer ini selanjutnya digunakan untuk meng-identifikasi gen AGL-15 dari RNA total embrio zigotik. Pengamatan pola pita gen AGL-15 dilakukan pada kultur in vitro embrio zigotik yang berumur lima minggu. Primer hetero-logus gen AGL-15 yang berasal dari berbagai tanaman, mampu mengidentifikasi keberadaan homolog  gen  tersebut  pada  tanaman   kakao. Fragmen homolog AGL-15 putatif tanaman kakao teridentifikasi pada tingkat RNA embrio. Dengan adanya pola diferensial dari ekspresi gen AGL-15 hingga lima minggu pertama perkembangan embrio, ada indikasi kuat bahwa fragmen homolog AGL-15 dapat menjadi penanda embriogenesis pada tanaman kakao.

scholarly journals GENE EXPRESSION IN PECAN SOMATIC EMBRYOS

HortScience ◽  
1991 ◽  
Vol 26 (6) ◽  
pp. 726A-726 ◽  
Author(s):  
Amnon Levi ◽  
Hazel Y. Wetzstein ◽  
Glen A. Galau
Keyword(s):  
Gene Expression ◽  
Somatic Embryos ◽  
Zygotic Embryo ◽  
Germination Rate ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Zygotic Embryos ◽  
Embryo Germination ◽  
Coordinate Gene Expression ◽  
Somatic Embryogenic

Repetitive somatic embryogenic lines of pecan (Carya illinoensis) were obtained and subcultured on basal WPM, following a one week induction of zygotic embryo tissue on modified WPM with 6 mg/L NAA. Gene expression of somatic embryos has been studied and compared with that occurring in zygotic embryos. Somatic embryos simultaneously expressed mRNA classes that are specific to each of the zygotic embryo cotyledon (Cot), maturation (Mat), and post abscission stages (Late embryogenesis, Lea). Somatic embryos exhibiting such multiple, nonregulated gene expression patterns have a low germination rate. Treatments found to enhance embryo germination (cold and desiccation) may be effective in part, by modifying gene expression patterns. Some of the Cot and Mat mRNA classes decreased following such treatments, while Lea mRNAs were not effected. Cold and desiccation treatments appear to coordinate gene expression in pecan somatic embryos, which might be associated with embryo germination.

scholarly journals The effect of respiratory gases and incubation temperature on early stage embryonic development in sea turtles

2020 ◽  
Author(s):  
David Terrington Booth ◽  
Alexander Archibald-Binge ◽  
Colin James Limpus
Keyword(s):  
Carbon Dioxide ◽  
Embryonic Development ◽  
Embryo Development ◽  
Incubation Temperature ◽  
Early Stage ◽  
Sea Turtle ◽  
Low Oxygen ◽  
Prolonged Incubation ◽  
Mature Embryos ◽  
Stage Embryo

AbstractSea turtle embryos at high density nesting beaches experience relative high rates of early stage embryo death. One hypothesis to explain this high dead rate is that there is an increased probability that newly constructed nests are located close to maturing clutches whose metabolising embryos cause low oxygen levels, high carbon dioxide levels, and high temperatures. Although these altered environmental conditions are well tolerated by mature embryos, early stage embryos may not be as tolerant leading to an increase in their mortality. To test this hypothesis, we incubated newly laid sea turtle eggs for a week over a range of temperatures in different combinations of oxygen and carbon dioxide concentrations and assessed embryo development and death rates. We found that gas mixtures of decreased oxygen and increased carbon dioxide, similar to those found in natural sea turtle nest containing mature embryos, slowed embryonic development but did not influence embryo mortality of early stage embryos. In contrast, high incubation temperature not only decreased embryo development rate, but prolonged incubation at 34°C was fatal.

scholarly journals Endogenous Retroviruses Function as Gene Expression Regulatory Elements During Mammalian Pre-implantation Embryo Development

2019 ◽  
Vol 20 (3) ◽  
pp. 790 ◽  
Author(s):  
Bo Fu ◽  
Hong Ma ◽  
Di Liu
Keyword(s):  
Gene Expression ◽  
Embryo Development ◽  
Transcriptional Activation ◽  
Nuclear Transfer ◽  
Regulatory Elements ◽  
Endogenous Retroviruses ◽  
Maternal Control ◽  
Close Relationship ◽  
Genome Activation ◽  
Zygotic Genome

Pre-implantation embryo development encompasses several key developmental events, especially the activation of zygotic genome activation (ZGA)-related genes. Endogenous retroviruses (ERVs), which are regarded as “deleterious genomic parasites”, were previously considered to be “junk DNA”. However, it is now known that ERVs, with limited conservatism across species, mediate conserved developmental processes (e.g., ZGA). Transcriptional activation of ERVs occurs during the transition from maternal control to zygotic genome control, signifying ZGA. ERVs are versatile participants in rewiring gene expression networks during epigenetic reprogramming. Particularly, a subtle balance exists between ERV activation and ERV repression in host–virus interplay, which leads to stage-specific ERV expression during pre-implantation embryo development. A large portion of somatic cell nuclear transfer (SCNT) embryos display developmental arrest and ZGA failure during pre-implantation embryo development. Furthermore, because of the close relationship between ERV activation and ZGA, exploring the regulatory mechanism underlying ERV activation may also shed more light on the enigma of SCNT embryo development in model animals.

Initiation of embryogenic cultures and somatic embryo development in loblolly pine (Pinustaeda)

1990 ◽  
Vol 20 (6) ◽  
pp. 810-817 ◽  
Author(s):  
M. R. Becwar ◽  
R. Nagmani ◽  
S. R. Wann
Keyword(s):  
Somatic Embryo ◽  
Embryo Development ◽  
Loblolly Pine ◽  
Somatic Embryos ◽  
Zygotic Embryo ◽  
Basal Medium ◽  
Embryogenic Tissue ◽  
Zygotic Embryos ◽  
Embryogenic Cultures ◽  
Somatic Embryo Development

Immature zygotic embryo explants (isolated or with intact megagametophytes) from 10 loblolly pine (Pinustaeda L.) clones (7-34, 7-56, 11-9, 11-16, 11-25, 10-1003, 10-1007, 10-1011, 10-1018, and 10-1019) were surveyed for their potential to form embryogenic tissue from the suspensor region of zygotic embryos. After over 14 000 explants were cultured, embryogenic cultures were initiated from explants of 8 of the 10 clones; only explants from clones 11-25 and 10-1019 were not responsive. Embryogenic tissue was initiated from zygotic embryos with intact megagametophytes on MSG basal medium with no exogenous plant growth regulators or with 2–5 mg/L 2,4-dichlorophenoxy acetic acid (2,4-D) and 0–1 mg/L N6-benzyladenine (BA). The highest initiation frequency (5%) was obtained from isolated zygotic embryos of clone 7-34 less than 0.5 mm in length just prior to cotyledon primordia development on DCR basal medium with 3 mg/L 2,4-D and 0.5 mg/L BA. Two types of embryogenic cultures were maintained on medium with 2,4-D and BA: (i) those that contained pre-embryonal masses of cells interspersed with unaggregated suspensorlike cells, but which rarely contained well-formed somatic embryos, and (ii) those that frequently contained well-formed somatic embryos. Somatic embryo development from both types of cultures progressed to a precotyledonary stage on medium with 2.6 mg/L abscisic acid.

Somatic embryogenesis for plant production of Abies lasiocarpa

2005 ◽  
Vol 35 (5) ◽  
pp. 1053-1060 ◽  
Author(s):  
Harald Kvaalen ◽  
Ola Gram Daehlen ◽  
Anne Tove Rognstad ◽  
Borgny Grønstad ◽  
Ulrika Egertsdotter
Keyword(s):  
Somatic Embryogenesis ◽  
New Media ◽  
Culture Medium ◽  
Culture Media ◽  
Zygotic Embryo ◽  
Plant Production ◽  
Zygotic Embryos ◽  
Abies Lasiocarpa ◽  
Subalpine Fir ◽  
Mature Embryos

Seeds of Abies lasiocarpa (Hook.) Nutt. (subalpine fir) were dissected, and the different parts were analyzed for elemental composition. The data were used to design a novel growth medium for initiation of somatic embryogenesis. Embryogenic cultures were initiated from immature zygotic embryos from six open-pollinated families of A. lasiocarpa on three different media. The frequency of initiation was the highest in early to mid-July when the zygotic embryo explants were ca. 0.8 mm long. Thereafter the response declined rapidly. The culture media did not significantly affect the initiation frequencies, but the subsequent growth and culture survival was dependent on the culture medium. On the Schenk Hildebrandt medium, many cultures ceased to grow and died. Several of the decaying cultures were rescued after transfer to one of the new media. Proliferating cultures could be stimulated to produce mature embryos. Of 2510 mature somatic embryos, 212 (8.4%) converted to plants, and 35 plants have grown over two periods.

154 Exposure of bulls to heat stress had deleterious effects on embryo development

2019 ◽  
Vol 31 (1) ◽  
pp. 202
Author(s):  
N. Llamas Luceño ◽  
M. Van Poucke ◽  
M. Batlle Perez ◽  
K. J. Szymanska ◽  
D. Angrimani ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Embryo Development ◽  
Sperm Morphology ◽  
Early Stage ◽  
Sperm Quality ◽  
Advanced Stage ◽  
Cell Ratio ◽  
Frozen Semen ◽  
Significant Difference

Concerns about global climate change reducing animal fertility are arising. Therefore, our objective was to determine the effects of increased environmental temperature on Holstein bulls and its effects on sperm quality and embryo development. Frozen semen samples were obtained from 6 bulls exposed to natural heat stress (HS) in August 2016, compared with a lower temperature (control) in March 2016 (temperature-humidity index of up to 74.5 and 40.6, respectively). We evaluated sperm morphology, embryo development, gene expression, inner cell mass/trophectoderm ratio (ICM/TE), and apoptosis cell ratio of Day-8 blastocysts. Sperm morphology was evaluated using eosin/nigrosin staining. Blastocysts were produced by routine in vitro methods (Wydooghe et al. 2014 Reprod. Fertil. Dev.). Cleavage rates were determined 48h after insemination, and blastocyst rates were determined on Days 7 and 8. Expression of NANOG, SOX2, POU5F1, DNMT (1, 3a, 3b), HSP (A1a, A2, A8, 10, 60, 90), HSF1, IFNT2, H19, SNRPN, IGF2, IGF2R, MEST, PHLDA2, MEG3, MEG9, PEG10 and PLAGL1 were analysed. Total RNA was extracted from Day-8 blastocysts for gene expression analysis using RNeasy Micro Kit (Qiagen, Valencia, CA, USA). Reverse transcription and qPCR were performed with iScript (BioRad, Hercules, CA, USA) and SsoAdvanced™ Universal SYBR® Green Supermix (BioRad) in a CFX Connect system (BioRad). Blastocysts were differentially stained (Wydooghe et al. 2011 Anal. Biochem.) and analysed using a Leica TCS-SP8×confocal microscope (Leica Microsystems, Wetzlar, Germany). Data analyses included a GLM procedure and paired-samples Student’s t test (P ≤ 0.05). A normal distribution was verified with a UNIVARIATE procedure and Shapiro-Wilk test. A Wilcoxon signed rank test was used to analyse qPCR data. Detached heads (P=0.006) and coiled tails (P=0.018) were significantly lower in the HS group (4.9 and 0.2%, respectively) compared with the control (5.5 and 0.5%). Moreover, proximal droplets (P=0.051) were lower in the HS group (0.7%) compared with the control (1.3%). Remarkably, cleavage and blastocyst rates at Days 7 and 8 were significantly higher in control (78.4, 19.6 and 29.5%, respectively) compared with HS (75, 14.5 and 23.2%). Early and normal blastocysts were grouped as early stage, whereas expanded, hatching and hatched blastocysts were grouped as advanced stage. There was a significant reduction in the HS group of early stage blastocysts on Day 7 and of advanced stage blastocysts on Days 7 and 8. However, in Day-8 blastocysts, there was no significant difference in gene expression for any target gene. Moreover, there were no significant differences in total number of cells or apoptosis cell ratio in blastocysts. However, the ICM/TE ratio was significantly higher (P=0.021) in control (0.7) compared with HS (0.56). Sperm samples collected in August had reduced fertility compared with those obtained in March. Although fewer sperm abnormalities were present in HS, based on decreased blastocyst rates and ICM/TE ratio in embryos produced with HS semen, we inferred that molecular mechanisms for advanced blastocyst development were affected. However, those mechanisms did not involve our target genes. This work was funded by the European Union, Horizon 2020 Marie Sklodowska-Curie Action, REPBIOTECH 675526.

scholarly journals The embryonic transcriptome of Arabidopsis thaliana

2018 ◽  
Author(s):  
Falko Hofmann ◽  
Michael A. Schon ◽  
Michael D. Nodine
Keyword(s):  
Arabidopsis Thaliana ◽  
Somatic Embryos ◽  
Developmental Stages ◽  
Zygotic Embryo ◽  
Low Cost ◽  
Superior Performance ◽  
Zygotic Embryos ◽  
Zygotic Embryogenesis ◽  
Biological Processes

AbstractCellular differentiation is associated with changes in transcript populations. Accurate quantification of transcriptomes during development can thus provide global insights into differentiation processes including the fundamental specification and differentiation events operating during plant embryogenesis. However, multiple technical challenges have limited the ability to obtain high quality early embryonic transcriptomes, namely the low amount of RNA obtainable and contamination from surrounding endosperm and seed-coat tissues. We compared the performance of three low-input mRNA sequencing (mRNA-seq) library preparation kits on 0.1 to 5 nanograms (ng) of total RNA isolated from Arabidopsis thaliana (Arabidopsis) embryos and identified a low-cost method with superior performance. This mRNA-seq method was then used to profile the transcriptomes of Arabidopsis embryos across eight developmental stages. By comprehensively comparing embryonic and post-embryonic transcriptomes, we found that embryonic transcriptomes do not resemble any other plant tissue we analyzed. Moreover, transcriptome clustering analyses revealed the presence of four distinct phases of embryogenesis which are enriched in specific biological processes. We also compared zygotic embryo transcriptomes with publicly available somatic embryo transcriptomes. Strikingly, we found little resemblance between zygotic embryos and somatic embryos derived from late-staged zygotic embryos suggesting that the molecular basis of somatic and zygotic embryogenesis are distinct from each other. In addition to the biological insights gained from our systematic characterization of the Arabidopsis embryonic transcriptome, we provide a data-rich resource for the community to explore.Key MessageArabidopsis embryos possess unique transcriptomes relative to other plant tissues including somatic embryos, and can be partitioned into four transcriptional phases with characteristic biological processes.

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