scholarly journals RNA-Seq analysis of differential gene expression in Betula luminifera xylem during the early stages of tension wood formation

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5427 ◽  
Author(s):  
Miaomiao Cai ◽  
Huahong Huang ◽  
Fei Ni ◽  
Zaikang Tong ◽  
Erpei Lin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Tension Wood ◽  
Molecular Mechanisms ◽  
Southern China ◽  
Lignin Biosynthesis ◽  
Wood Formation ◽  
Cellulose Synthesis ◽  
Early Stages ◽  
Transcriptional Changes ◽  
Betula Luminifera

Background Betula luminifera H. Winkler, which is widely distributed in southern China, is an economically important broadleaf tree species. However, little genomic information of B. luminifera is available, and little is known about the molecular mechanisms of wood formation in this species. Meanwhile, few efforts have focused on investigating the early transcriptional changes during tension wood formation in woody plants. Results A reference transcriptome dataset was first generated containing 45,700 Unigenes, and 35,135 (76.9%) Unigenes were annotated by a BLAST similarity search against four public databases. Then, based on an anatomical investigation, the global gene expression changes during the early stages of tension wood formation were analyzed. Gene expression profiling showed that a total of 13,273 Unigenes were differentially regulated during the early stages of tension wood formation. Most genes involved in cellulose and lignin biosynthesis were highlighted to reveal their biological importance in tension wood formation. In addition, the transcription levels of many genes involved in the auxin response pathway were significantly changed during the early stages of tension wood formation. Furthermore, 18 TFs co-expressed with key enzymes of cellulose synthesis were identified. Conclusions Our results revealed the transcriptional changes associated with TW formation and identified potential key genes in the regulation of this process. These results will help to dissect the molecular mechanism of wood formation and provide key candidate genes for marker-assisted selection in B. luminifera.

scholarly journals Cloning and Functional Analysis of Lignin Biosynthesis Genes Cf4CL and CfCCoAOMT in Cryptomeria fortunei

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 619 ◽  
Author(s):  
Zhenhao Guo ◽  
Hui Hua ◽  
Jin Xu ◽  
Jiaxing Mo ◽  
Hui Zhao ◽  
...  
Keyword(s):  
Gene Editing ◽  
Bioinformatics Analysis ◽  
Southern China ◽  
Lignin Biosynthesis ◽  
Wood Formation ◽  
Primary Component ◽  
Vascular Cambium ◽  
Timber Species ◽  
Wood Production ◽  
Lignin Synthesis

Cryptomeria fortunei, also known as the Chinese cedar, is an important timber species in southern China. The primary component of its woody tissues is lignin, mainly present in secondary cell walls. Therefore, continuous lignin synthesis is crucial for wood formation. In this study, we aimed to discover key genes involved in lignin synthesis expressed in the vascular cambium of C. fortunei. Through transcriptome sequencing, we detected expression of two genes, 4CL and CCoAOMT, known to be homologous to enzymes involved in the lignin synthesis pathway. We studied the function of these genes through bioinformatics analysis, cloning, vascular cambium expression analysis, and transgenic cross-species functional validation studies. Our results show that Cf4CL and CfCCoAOMT do indeed function in the pathway of lignin synthesis and likely perform this function in C. fortunei. They are prime candidates for future (gene-editing) studies aimed at optimizing C. fortunei wood production.

Gene expression profiling reveals underlying molecular mechanisms of the early stages of tamoxifen-induced rat hepatocarcinogenesis☆

2007 ◽  
Vol 225 (1) ◽  
pp. 61-69 ◽  
Author(s):  
Igor P. Pogribny ◽  
Tetyana V. Bagnyukova ◽  
Volodymyr P. Tryndyak ◽  
Levan Muskhelishvili ◽  
Rocio Rodriguez-Juarez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Molecular Mechanisms ◽  
Early Stages

scholarly journals Transcriptional signatures throughout development: the effects of mouse embryo manipulation in vitro

Reproduction ◽  
2017 ◽  
Vol 153 (1) ◽  
pp. 107-122 ◽  
Author(s):  
Sky K Feuer ◽  
Xiaowei Liu ◽  
Annemarie Donjacour ◽  
Rhodel Simbulan ◽  
Emin Maltepe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Preimplantation Embryo ◽  
Environmental Exposures ◽  
Developmental Time ◽  
Transcriptional Responses ◽  
Transcriptional Changes ◽  
Specific Impact

Stressful environmental exposures incurred early in development can affect postnatal metabolic health and susceptibility to non-communicable diseases in adulthood, although the molecular mechanisms by which this occurs have yet to be elucidated. Here, we use a mouse model to investigate how assortedin vitroexposures restricted exclusively to the preimplantation period affect transcription both acutely in embryos and long term in subsequent offspring adult tissues, to determine if reliable transcriptional markers ofin vitrostress are present at specific developmental time points and throughout development. Eachin vitrofertilization or embryo culture environment led to a specific and unique blastocyst transcriptional profile, but we identified a common 18-gene and 9-pathway signature of preimplantation embryo manipulation that was present in allin vitroembryos irrespective of culture condition or method of fertilization. This fingerprint did not persist throughout development, and there was no clear transcriptional cohesion between adult IVF offspring tissues or compared to their preceding embryos, indicating a tissue-specific impact ofin vitrostress on gene expression. However, the transcriptional changes present in each IVF tissue were targeted by the same upstream transcriptional regulators, which provide insight as to how acute transcriptional responses to stressful environmental exposures might be preserved throughout development to influence adult gene expression.

scholarly journals Transcriptome analysis of immature xylem in Chinese fir at different developmental phases

2016 ◽  
Author(s):  
Yunxing Zhang ◽  
Xiaojiao Han ◽  
Jian Sang ◽  
Xuelian he ◽  
Mingying Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Transcriptome Sequencing ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Southern China ◽  
Wood Formation ◽  
Chinese Fir ◽  
Nac Transcription Factors ◽  
Transcriptome Variation ◽  
Developmental Phases

Background: Chinese fir [Cunninghamia lanceolata (Lamb .) Hook.], is one of the most important native tree species for timber production in southern China. An understanding of overall fast growing stage, stem growth stage and senescence stage cambium transcriptome variation is lacking. We used transcriptome sequencing to identify the repertoire of genes expressed during development of xylem tissue in Chinese fir, aiming to delineate the molecular mechanisms of wood formation. Results: We carried out transcriptome sequencing at three different cultivation ages (7Y, 15Y and 21Y) generating 68.71 million reads (13.88 Gbp). A total of 140,486 unigenes with a mean size of 568.64 base pairs (bp) were obtained via de novo assembly. Of these, 27,427 unigenes (19.52%) were further annotated by comparison to public protein databases. A total of 5,331 (3.79%) unigenes were mapped into 118 pathways by searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Differentially expressed genes (DEG) analysis identified 3, 16 and 5,899 DEGs from the comparison of 7Y vs. 15Y, 7Y vs. 21Y and 15Y vs. 21Y, respectively, in the immature xylem tissues, including 2,638 significantly up-regulated and 3,280 significantly down-regulated genes. Besides, five NAC transcription factors, 190 MYB transcription factors, and 34 WRKY transcription factors were identified respectively from Chinese fir transcriptome. Conclusion: Our results revealed the active transcriptional pathways and identified the DEGs at different cultivation phases of Chinese fir wood formation. This transcriptome dataset will aid in understanding and carrying out future studies on the molecular basis of Chinese fir wood formation and contribute to future artificial production and applications.

scholarly journals Expression of three phenylpropanoid pathway genes in Scots pine (Pinus sylvestris L.) in open-pollinated families with differing relative wood densities during early and late wood formation

2015 ◽  
Vol 64 (1-6) ◽  
pp. 148-159 ◽  
Author(s):  
K. Kanberga-Silina ◽  
A. Jansons ◽  
Dainis Rungis
Keyword(s):  
Gene Expression ◽  
Wood Density ◽  
Scots Pine ◽  
Lignin Content ◽  
Lignin Biosynthesis ◽  
Wood Formation ◽  
Phenylpropanoid Pathway ◽  
Structural Development ◽  
Late Wood ◽  
Forestry Production

Abstract Wood volume and quality are the most important aspects of commercial forestry production, and studies of wood formation are important in order to increase the value and efficiency of forestry production. The phenylpropanoid pathway produces various compounds with diverse functions both for plant defence against biotic and abiotic stress as well as structural development. One of the main roles is monolignol production for lignin biosynthesis, which is a crucial aspect of wood formation. For this study three candidate genes involved in lignin biosynthesis were selected: phenylalanine ammonialyase (PAL1), cinnamyl alcohol dehydrogenase (CAD) and cinnamoyl-CoA reductase (CCR). Candidate gene expression was analysed in selected individuals with high and low wood density from open-pollinated Scots pine families during early wood (EW) and late wood (LW) formation and correlation between expression of these genes, total lignin content, and wood density was determined. Wood density values for analysed trees were similar within tree families but differed significantly between families with high and low wood density (p=1,06E-20). Wood density was slightly negatively correlated with lignin content (r=-0.36, p=0.038), but only in individuals in the high density wood group. In trees with low wood density, expression of the CAD gene was significantly lower in late wood formation compared to early wood (p=0.00179). In trees with high wood density, expression of the PAL1 gene was five times higher during early wood formation compared to late wood formation. A positive correlation was detected between PAL1 and CCR gene expression during early wood formation (r=0.804) and late wood formation (r=0.466).

scholarly journals PmMYB4, a Transcriptional Activator from Pinus massoniana, Regulates Secondary Cell Wall Formation and Lignin Biosynthesis

Forests ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1618
Author(s):  
Sheng Yao ◽  
Peizhen Chen ◽  
Ye Yu ◽  
Mengyang Zhang ◽  
Dengbao Wang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Secondary Cell Wall ◽  
Paper Industry ◽  
Lignin Biosynthesis ◽  
Pinus Massoniana ◽  
Wood Formation ◽  
Genetically Engineered ◽  
Cellulose Synthesis ◽  
Masson Pine ◽  
Reading Frame

Wood formation originates in the biosynthesis of lignin and further leads to secondary cell wall (SCW) biosynthesis in woody plants. Masson pine (Pinus massoniana Lamb) is an economically important industrial timber tree, and its wood yield affects the stable development of the paper industry. However, the regulatory mechanisms of SCW formation in Masson pine are still unclear. In this study, we characterized PmMYB4, which is a Pinus massoniana MYB gene involved in SCW biosynthesis. The open reading frame (ORF) of PmMYB4 was 1473 bp, which encoded a 490 aa protein and contained two distinctive R2 and R3 MYB domains. It was shown to be a transcription factor, with the highest expression in semi-lignified stems. We overexpressed PmMYB4 in tobacco. The results indicated that PmMYB4 overexpression increased lignin deposition, SCW thickness, and the expression of genes involved in SCW formation. Further analysis indicated that PmMYB4 bound to AC-box motifs and might directly activate the promoters of genes (PmPAL and PmCCoAOMT) involved in SCW biosynthesis. In addition, PmMYB4-OE(over expression) transgenic lines had higher lignin and cellulose contents and gene expression than control plants, indicating that PmMYB4 regulates SCW mainly by targeting lignin biosynthetic genes. In summary, this study illustrated the MYB-induced SCW mechanism in Masson pine and will facilitate enhanced lignin and cellulose synthesis in genetically engineered trees.

scholarly journals The interdependence of gene-regulatory elements and the 3D genome

2018 ◽  
Vol 218 (1) ◽  
pp. 12-26 ◽  
Author(s):  
Marit W. Vermunt ◽  
Di Zhang ◽  
Gerd A. Blobel
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Regulatory Elements ◽  
3D Genome ◽  
Gene Positioning ◽  
Transcriptional Changes ◽  
Gene Regulatory Elements ◽  
Chromatin Folding ◽  
Gene Regulatory ◽  
Relationship Of

Imaging studies, high-resolution chromatin conformation maps, and genome-wide occupancy data of architectural proteins have revealed that genome topology is tightly intertwined with gene expression. Cross-talk between gene-regulatory elements is often organized within insulated neighborhoods, and regulatory cues that induce transcriptional changes can reshape chromatin folding patterns and gene positioning within the nucleus. The cause–consequence relationship of genome architecture and gene expression is intricate, and its molecular mechanisms are under intense investigation. Here, we review the interdependency of transcription and genome organization with emphasis on enhancer–promoter contacts in gene regulation.

scholarly journals Transcriptomic Profiling of Cryptomeria fortunei Hooibrenk Vascular Cambium Identifies Candidate Genes Involved in Phenylpropanoid Metabolism

Forests ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 766
Author(s):  
Junjie Yang ◽  
Zhenhao Guo ◽  
Yingting Zhang ◽  
Jiaxing Mo ◽  
Jiebing Cui ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Southern China ◽  
Expression Profiles ◽  
Wood Formation ◽  
Differentially Expressed ◽  
Myb Transcription Factor ◽  
Growth Stages ◽  
Phenylpropanoid Metabolism ◽  
Protein Database ◽  
Cambial Zone

Cryptomeria fortunei Hooibrenk (Chinese cedar) is a coniferous tree from southern China that has an important function in landscaping and timber production. Lignin is one of the key components of secondary cell walls, which have a crucial role in conducting water and providing mechanical support for the upward growth of plants. It is mainly biosynthesized via the phenylpropanoid metabolic pathway, of which the molecular mechanism remains so far unresolved in C. fortunei. In order to obtain further insight into this pathway, we performed transcriptome sequencing of the C. fortunei cambial zone at 5 successive growth stages. We generated 78,673 unigenes from transcriptome data, of which 45,214 (57.47%) were successfully annotated in the non-redundant protein database (NR). A total of 8975 unigenes were identified to be significantly differentially expressed between Sample_B and Sample_A after analyzing their expression profiles. Of the differentially expressed genes (DEGs), 6817 (75.96%) and 2158 (24.04%) were up- and down-regulated, respectively. 83 DEGs were involved in phenylpropanoid metabolism, 37 DEGs that encoded v-Myb avian myeloblastosis viral oncogene homolog (MYB) transcription factor (TF), and many candidates that encoded lignin synthesizing enzymes. These findings contribute to understanding the expression pattern of C. fortunei cambial zone transcriptome. Furthermore, our results provide additional insight towards understanding the molecular mechanisms of wood formation in C. fortunei.

scholarly journals Age-related changes of gene expression in the neocortex: Preliminary data on RNA-Seq of the transcriptome in three functionally distinct cortical areas

2012 ◽  
Vol 24 (4) ◽  
pp. 1427-1442 ◽  
Author(s):  
Oksana Yu. Naumova ◽  
Dean Palejev ◽  
Natalia V. Vlasova ◽  
Maria Lee ◽  
Sergei Yu. Rychkov ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Rna Seq ◽  
Signaling Systems ◽  
Cortical Areas ◽  
Age Related ◽  
Transcriptional Changes ◽  
Atypical Development ◽  
The Brain ◽  
Age Related Changes

AbstractThe study of gene expression (i.e., the study of the transcriptome) in different cells and tissues allows us to understand the molecular mechanisms of their differentiation, development and functioning. In this article, we describe some studies of gene-expression profiling for the purposes of understanding developmental (age-related) changes in the brain using different technologies (e.g., DNA-Microarray) and the new and increasingly popular RNA-Seq. We focus on advancements in studies of gene expression in the human brain, which have provided data on the structure and age-related variability of the transcriptome in the brain. We present data on RNA-Seq of the transcriptome in three distinct areas of the neocortex from different ages: mature and elderly individuals. We report that most age-related transcriptional changes affect cellular signaling systems, and, as a result, the transmission of nerve impulses. In general, the results demonstrate the high potential of RNA-Seq for the study of distinctive features of gene expression among cortical areas and the changes in expression through normal and atypical development of the central nervous system.

scholarly journals Analysis of transcriptional changes associated with pubertal development

2021 ◽  
Author(s):  
Justyna Resztak ◽  
Jane Choe ◽  
Julong Wei ◽  
Rachel Bruinsma ◽  
Russell Houpt ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Pubertal Development ◽  
Genetic Effect ◽  
Age At Menarche ◽  
Immune Gene ◽  
Study Approach ◽  
Transcriptional Changes ◽  
Immune Changes ◽  
Short Time

Puberty is an important developmental period marked by hormonal, metabolic and immune changes, which have been implicated in predisposition to immune diseases later in life. Yet, little is known about the gene expression changes in immune cells that occur during pubertal development. In a longitudinal cohort of 251 children we assessed pubertal development and leukocyte gene expression. We identified largely overlapping gene expression changes in boys and girls for thousands of genes over a short time period. For 108 genes we detected gene expression changes associated with pubertal development. Substantial transcriptional changes were detected between pre- and post-menarcheal girls, which suggested a shift from predominantly innate to adaptive immunity as girls sexually matured. We identified genetic effects on gene expression that dynamically change during pubertal development for IGKV1-27 and PGAP1 in males, DSC1 and TRBV30 in females. We discovered that menarche is associated with a change in sign of a genetic effect on the expression of the asthma-associated gene FLOT2. Using a Transcriptome-Wide Association Study approach, we discovered that in girls, gene expression changes during puberty are associated with age at menarche. For example, expression of the endometrial cancer risk gene EEFSEC increases as girls become older, suggesting a link between age at menarche, transcriptional changes happening during puberty and poor health outcomes. These findings shed light on immune gene expression processes accompanying puberty and can advance the understanding of the molecular mechanisms through which pubertal development relates to immune diseases later in life.

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