scholarly journals Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

2020 ◽  
Author(s):  
zhonghua tu ◽  
Yufang Shen ◽  
Shaoying Wen ◽  
Huanhuan Liu ◽  
Lingmin Wei ◽  
...  
Keyword(s):  
Shoot Apex ◽  
Expression Profiles ◽  
Plant Defence ◽  
Pathway Enrichment Analysis ◽  
Specific Gene ◽  
Mads Box ◽  
Mads Box Genes ◽  
Vegetative Organs ◽  
Tissue Specific ◽  
Liriodendron Chinense

Abstract Background Liriodendron chinense (Hemsl.) Sarg. is an economically and ecologically important deciduous tree species that has been studied for many years. Although the complete L. chinense genome has been sequenced, the gene co-expression modules and tissue-specific genes of L. chinense remain unknown. Results Here, we used the bracts, petals, sepals, stamens, pistils, leaves, and the shoot apex of L. chinense as materials and analysed their gene co-expression modules and tissue-specific genes via hybrid sequencing. We identified 3,032 DEGs between the floral and vegetative tissues and 2,126 tissue-specific genes. By using WGCNA analysis, we identified 13 gene co-expression modules, and KEGG pathway enrichment analysis revealed that tissue-specific genes and genes from different modules were enriched in different pathways. Genes associated with plant defence were highly expressed in the bracts, genes participating in plant hormone signal transduction were highly expressed in the shoot apex, and genes participating in photosynthesis were highly expressed in the leaves, petals and sepals. Moreover, we identified 10 MIKC-type MADS-box genes that were classified as member of the AP3/PI, SVP, SEP, AG/SHP/STK, AGL12, SOC1 and TM8 subfamily. Phylogenetic analysis showed that the expression profiles of these ten genes were consistent with those reported in Arabidopsis and Populus , indicating that these genes are highly conserved evolutionarily and related to floral and vegetative tissue development. The small number of MIKC-type MADS-box genes in L. chinense was probably owing to its incomplete genome annotation. Conclusions In this work, we provided a reference transcriptome for L. chinense research by using hybrid sequencing. We identified 2,126 tissue-specific genes and 3,032 DEGs that contributed greatly to the functional differences between vegetative organs and floral organs. By using WGCNA analysis, 13 gene co-expression modules and 52 hub genes from six co-expression modules of interest were identified. Moreover, we identified 10 MIKC-type MADS-box genes that might be related to the development and growth regulation of floral and vegetative organs. These findings will improve our understanding of gene co-expression, tissue specific genes and flower development model of L. chinense .

scholarly journals A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhonghua Tu ◽  
Yufang Shen ◽  
Shaoying Wen ◽  
Huanhuan Liu ◽  
Lingmin Wei ◽  
...  
Keyword(s):  
Shoot Apex ◽  
Alternative Polyadenylation ◽  
Deciduous Tree ◽  
Specific Gene ◽  
Hub Genes ◽  
Tissue Specific ◽  
Liriodendron Chinense ◽  
The One ◽  
Tissue Characteristics

Liriodendron chinense is an economically and ecologically important deciduous tree species. Although the reference genome has been revealed, alternative polyadenylation (APA), transcription factors (TFs), long non-coding RNAs (lncRNAs), and co-expression networks of tissue-specific genes remain incompletely annotated. In this study, we used the bracts, petals, sepals, stamens, pistils, leaves, and shoot apex of L. chinense as materials for hybrid sequencing. On the one hand, we improved the annotation of the genome. We detected 13,139 novel genes, 7,527 lncRNAs, 1,791 TFs, and 6,721 genes with APA sites. On the other hand, we found that tissue-specific genes play a significant role in maintaining tissue characteristics. In total, 2,040 tissue-specific genes were identified, among which 9.2% of tissue-specific genes were affected by APA, and 1,809 tissue-specific genes were represented in seven specific co-expression modules. We also found that bract-specific hub genes were associated plant defense, leaf-specific hub genes were involved in energy metabolism. Moreover, we also found that a stamen-specific hub TF Lchi25777 may be involved in the determination of stamen identity, and a shoot-apex-specific hub TF Lchi05072 may participate in maintaining meristem characteristic. Our study provides a landscape of APA, lncRNAs, TFs, and tissue-specific gene co-expression networks in L. chinense that will improve genome annotation, strengthen our understanding of transcriptome complexity, and drive further research into the regulatory mechanisms of tissue-specific genes.

scholarly journals Trimethylated H3K27, and Di- and Trimethylated H3K4 Proteomic Profiling Distinguishes Acute Lymphoid Leukemia (ALL) from Acute Myeloid Leukemia (AML) and Associates with Overall Survival and Tyrosine Kinase Inhibitor Sensitivity in Adult ALL

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1460-1460
Author(s):  
Anneke D. van Dijk ◽  
Fieke W Hoff ◽  
Yihua Qiu ◽  
Mary Figueroa ◽  
Joya Chandra ◽  
...  
Keyword(s):  
Tyrosine Kinase ◽  
Histone Methylation ◽  
Research Funding ◽  
Expression Profiles ◽  
Methylation Status ◽  
Unsupervised Clustering ◽  
Response To Therapy ◽  
Pathway Enrichment Analysis ◽  
Specific Gene ◽  
Repressive Mark

Background: Lineage-specific gene transcription signatures between AML and ALL are recognized, but post-translational phenotype-specific protein expression profiles remain undefined. We hypothesized that functional proteomic patterns vary between AML and ALL and that the activity state of cells correlates with response to therapy within subgroups, complementing cytogenetic and molecular data. Methods: Reverse phase protein arrays (RPPA) were generated using bone marrow (BM) and peripheral blood (PB) samples from newly diagnosed B-ALL (n=114), T-ALL (n=14), and AML (n=241) adult patients admitted at the MD Anderson Cancer Center. RPPA allowed simultaneous expression measurement of 229 highly validated protein antibodies including 3 Histone 3 (H3) post-translational methylation regulatory modifications; H3K4Me2, H3K4Me3 and H3K27Me3. Results: Unsupervised clustering of histone modification protein expressions distinguished AML from ALL in freshly prepared lysates from BM (n=241) and PB (n=127) as well as when BM and PB samples were combined (fig. 1A). The ALL-enriched cluster was dominated by high H3K27Me3. Elevated H3K27Me3 levels were found in the BM derived leukemic blasts compared to PB blasts in ALL (P < 0.001), but not AML (P = 0.35). Trimethylation of the repressive mark H3K27 is catalyzed by the polycomb group protein Ezh2. Oncogenic gain-of-functions of Ezh2 are seen in patients with lymphoid malignancies and others have shown that mutated Ezh2 increased H3K27Me3 in B-cells which associated with tumorigenesis. H3K27Me3 and Ezh2 antibody expressions were highly correlated in another RPPA of ALL and AML we created (R2=0.49, P < 0.001). Profiling of methylation marks using unsupervised clustering in ALL divided patients in 2 clusters that correlated with survival (fig. 1B-C, P = 0.02). Cluster 1 (C1) with higher H3K27Me3, H3K4Me2 and H3K4Me3 was associated with better outcome. In ALL, Ph+ historically associated with poor prognosis but outcomes have improved substantially with the use of tyrosine kinase inhibitors (TKI). In our cohort, 11/26 Ph+ ALL patients were treated with TKIs and it is notable that sensitivity to TKIs correlated with cluster membership; all C1 patients (high degree of methylation) were alive after 7 years of follow-up in contrast to none of the TKI-treated Ph+ ALL patients in cluster 2 (C2, low degree of methylation) (fig. 1D, P = 0.01). Recently, TKI resistance in Ph+ ALL has been proposed to associate with smoking due to altered DNA methylation patterns caused by chemical components of cigarette smoke. Retrospectively, we identified that 2 of 11 TKI treated patients were smokers. Both had membership in C2, were resistant against TKIs and died after 1 year. Thus, 2 out of 3 resistant TKI treated Ph+ ALL were smokers compared to none of the 8 responders. We then aimed to identify proteins that are potentially downregulated by increased expression of the repressive mark H3K27Me3. Pathway enrichment analysis of 59 significant negatively correlated proteins with H3K27Me3 revealed that these are involved in tyrosine kinase activity and resistance, including Jak/STAT and PI3K/Akt signaling pathways. If these pathways are less activated in patients with high H3K27Me3, then this can partially explain the increased sensitivity to TKIs in this subgroup. Clinically, no differences were found in age, BM and PB blast counts between TKI-treated C1 and C2 patients to provide an explanation for the higher death rate in C2. Conclusion: ALL and AML share some pathophysiology and the identification of differences in the functional activity of cells may contribute to a better understanding of the etiology of both diseases. Here we report that high H3K27Me3 protein levels in BM and PB distinguish ALL from AML and are related to TKI sensitivity in Ph+ ALL. Histone methylation status defines a group of Ph+ ALL patients that does not benefit from the addition of TKI therapy. The idea that smoking alters the epigenetic machinery in TKI resistant Ph+ ALL has been proposed and warrants further investigation. Fig. 1 A) Heatmap showing histone methylation levels in BM and PB from AML and ALL patients. B) Heatmap showing histone methylation levels in ALL BM and PB. Unsupervised clustering divided samples into 2 clusters. C) ALL patients in C1 survived longer than patients in C2 (P = 0.02). D) Increased long-term sensitivity for TKI therapy in C1 Ph+ ALL patients compared to C2 (100 vs. 0%, P = 0.01). Figure.1 Disclosures Jabbour: AbbVie: Consultancy, Research Funding; Pfizer: Consultancy, Research Funding; Cyclacel LTD: Research Funding; Adaptive: Consultancy, Research Funding; Takeda: Consultancy, Research Funding; BMS: Consultancy, Research Funding; Amgen: Consultancy, Research Funding.

scholarly journals A Computational Method for Classifying Different Human Tissues with Quantitatively Tissue-Specific Expressed Genes

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 449 ◽  
Author(s):  
JiaRui Li ◽  
Lei Chen ◽  
Yu-Hang Zhang ◽  
XiangYin Kong ◽  
Tao Huang ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Expression Patterns ◽  
Machine Learning Algorithms ◽  
Computational Method ◽  
Support Vector ◽  
Specific Gene ◽  
Human Tissues ◽  
Tissue Development ◽  
Tissue Specific ◽  
And Function

Tissue-specific gene expression has long been recognized as a crucial key for understanding tissue development and function. Efforts have been made in the past decade to identify tissue-specific expression profiles, such as the Human Proteome Atlas and FANTOM5. However, these studies mainly focused on “qualitatively tissue-specific expressed genes” which are highly enriched in one or a group of tissues but paid less attention to “quantitatively tissue-specific expressed genes”, which are expressed in all or most tissues but with differential expression levels. In this study, we applied machine learning algorithms to build a computational method for identifying “quantitatively tissue-specific expressed genes” capable of distinguishing 25 human tissues from their expression patterns. Our results uncovered the expression of 432 genes as optimal features for tissue classification, which were obtained with a Matthews Correlation Coefficient (MCC) of more than 0.99 yielded by a support vector machine (SVM). This constructed model was superior to the SVM model using tissue enriched genes and yielded MCC of 0.985 on an independent test dataset, indicating its good generalization ability. These 432 genes were proven to be widely expressed in multiple tissues and a literature review of the top 23 genes found that most of them support their discriminating powers. As a complement to previous studies, our discovery of these quantitatively tissue-specific genes provides insights into the detailed understanding of tissue development and function.

Floral MADS-box Genes in Trioecious Papaya: Characterization of AG and AP1 Subfamily Genes Revealed a Sex-type-specific Gene

2007 ◽  
Vol 1 (2) ◽  
pp. 97-107 ◽  
Author(s):  
Qingyi Yu ◽  
Denise Steiger ◽  
Elena M. Kramer ◽  
Paul H. Moore ◽  
Ray Ming
Keyword(s):  
Specific Gene ◽  
Mads Box ◽  
Mads Box Genes ◽  
Sex Type

scholarly journals Genome-wide identification and characterization of the MADS-box gene family in Salix suchowensis

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8019 ◽  
Author(s):  
Yanshu Qu ◽  
Changwei Bi ◽  
Bing He ◽  
Ning Ye ◽  
Tongming Yin ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Evolutionary Analysis ◽  
Mads Box ◽  
Mads Box Genes ◽  
Floral Organogenesis ◽  
Functional Studies ◽  
Genome Wide ◽  
Development Processes ◽  
Mads Box Gene

MADS-box genes encode transcription factors that participate in various plant growth and development processes, particularly floral organogenesis. To date, MADS-box genes have been reported in many species, the completion of the sequence of the willow genome provides us with the opportunity to conduct a comprehensive analysis of the willow MADS-box gene family. Here, we identified 60 willow MADS-box genes using bioinformatics-based methods and classified them into 22 M-type (11 Mα, seven Mβ and four Mγ) and 38 MIKC-type (32 MIKCc and six MIKC*) genes based on a phylogenetic analysis. Fifty-six of the 60 SsMADS genes were randomly distributed on 19 putative willow chromosomes. By combining gene structure analysis with evolutionary analysis, we found that the MIKC-type genes were more conserved and played a more important role in willow growth. Further study showed that the MIKC* type was a transition between the M-type and MIKC-type. Additionally, the number of MADS-box genes in gymnosperms was notably lower than that in angiosperms. Finally, the expression profiles of these willow MADS-box genes were analysed in five different tissues (root, stem, leave, bud and bark) and validated by RT-qPCR experiments. This study is the first genome-wide analysis of the willow MADS-box gene family, and the results establish a basis for further functional studies of willow MADS-box genes and serve as a reference for related studies of other woody plants.

scholarly journals Expression profiling of MADS-box gene family revealed its role in vegetative development and stem ripening in S. spontaneum

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mahpara Fatima ◽  
Xiaodan Zhang ◽  
Jishan Lin ◽  
Ping Zhou ◽  
Dong Zhou ◽  
...  
Keyword(s):  
Tandem Duplication ◽  
Expression Profiles ◽  
Structural Diversity ◽  
Pcr Analysis ◽  
Type I ◽  
Mads Box ◽  
Mads Box Genes ◽  
Vegetative Development ◽  
Mads Box Gene ◽  
Identification And Characterization

AbstractSugarcane is the most important sugar and biofuel crop. MADS-box genes encode transcription factors that are involved in developmental control and signal transduction in plants. Systematic analyses of MADS-box genes have been reported in many plant species, but its identification and characterization were not possible until a reference genome of autotetraploid wild type sugarcane specie, Saccharum spontaneum is available recently. We identified 182 MADS-box sequences in the S. spontaneum genome, which were annotated into 63 genes, including 6 (9.5%) genes with four alleles, 21 (33.3%) with three, 29 (46%) with two, 7 (11.1%) with one allele. Paralogs (tandem duplication and disperse duplicated) were also identified and characterized. These MADS-box genes were divided into two groups; Type-I (21 Mα, 4 Mβ, 4 Mγ) and Type-II (32 MIKCc, 2 MIKC*) through phylogenetic analysis with orthologs in Arabidopsis and sorghum. Structural diversity and distribution of motifs were studied in detail. Chromosomal localizations revealed that S. spontaneum MADS-box genes were randomly distributed across eight homologous chromosome groups. The expression profiles of these MADS-box genes were analyzed in leaves, roots, stem sections and after hormones treatment. Important alleles based on promoter analysis and expression variations were dissected. qRT-PCR analysis was performed to verify the expression pattern of pivotal S. spontaneum MADS-box genes and suggested that flower timing genes (SOC1 and SVP) may regulate vegetative development.

scholarly journals GeneTIER: prioritization of candidate disease genes using tissue-specific gene expression profiles

2015 ◽  
Vol 31 (16) ◽  
pp. 2728-2735 ◽  
Author(s):  
Agne Antanaviciute ◽  
Catherine Daly ◽  
Laura A. Crinnion ◽  
Alexander F. Markham ◽  
Christopher M. Watson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Specific Gene ◽  
Disease Genes ◽  
Tissue Specific ◽  
Tissue Specific Gene ◽  
Specific Gene Expression

scholarly journals Genome-wide identification of MIKC-type genes related to stamen and gynoecium development in Liriodendron

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Huanhuan Liu ◽  
Lichun Yang ◽  
Zhonghua Tu ◽  
Shenghua Zhu ◽  
Chengge Zhang ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Expression Profiles ◽  
Reproductive Organs ◽  
Mads Box ◽  
Interspecies Difference ◽  
Mads Box Genes ◽  
Relict Species ◽  
Floral Organogenesis ◽  
New Genes ◽  
Genome Wide

AbstractThe organogenesis and development of reproductive organs, i.e., stamen and gynoecium, are important floral characteristics that are closely related to pollinators and reproductive fitness. As a genus from Magnoliaceae, Liriodendron has only two relict species: L. chinense and L. tulipifera. Despite the similar flower shapes of these species, their natural seed-setting rates differ significantly, implying interspecies difference in floral organogenesis and development. MADS-box genes, which participate in floral organogenesis and development, remain unexplored in Liriodendron. Here, to explore the interspecies difference in floral organogenesis and development and identify MADS-box genes in Liriodendron, we examined the stamen and gynoecium primordia of the two Liriodendron species by scanning electron microscopy combined with paraffin sectioning, and then collected two types of primordia for RNA-seq. A total of 12 libraries were constructed and 42,268 genes were identified, including 35,269 reference genes and 6,999 new genes. Monoterpenoid biosynthesis was enriched in L. tulipifera. Genome-wide analysis of 32 MADS-box genes was conducted, including phylogenetic trees, exon/intron structures, and conserved motif distributions. Twenty-six genes were anchored on 17 scaffolds, and six new genes had no location information. The expression profiles of MIKC-type genes via RT-qPCR acrossing six stamen and gynoecium developmental stages indicates that the PI-like, AG/STK-like, SEP-like, and SVP-like genes may contribute to the species-specific differentiation of the organogenesis and development of reproductive organs in Liriodendron. Our findings laid the groundwork for the future exploration of the mechanism underlying on the interspecific differences in reproductive organ development and fitness in Liriodendron.

scholarly journals The pineapple MADS-box gene family and the evolution of early monocot flower

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Juan Hu ◽  
Xiaojun Chang ◽  
Ying Zhang ◽  
Xianxian Yu ◽  
Yuan Qin ◽  
...  
Keyword(s):  
Fruit Development ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Ananas Comosus ◽  
Specific Gene ◽  
Type I ◽  
Mads Box ◽  
Specific Expression ◽  
Floral Organs ◽  
Species Specific

AbstractUnlike the flower of the model monocot rice, which has diverged greatly from the ancestral monocot flower, the pineapple (Ananas comosus) flower is more typical of monocot flowers. Here, we identified 43 pineapple genes containing MADS-box domains, including 11 type I and 32 type II genes. RNA-seq expression data generated from five pineapple floral organs (sepals, petals, stamens, pistils, and ovules) and quantitative real-time PCR revealed tissue-specific expression patterns for some genes. We found that AcAGL6 and AcFUL1 were mainly expressed in sepals and petals, suggesting their involvement in the regulation of these floral organs. A pineapple ‘ABCDE’ model was proposed based on the phylogenetic analysis and expression patterns of MADS-box genes. Unlike rice and orchid with frequent species-specific gene duplication and subsequent expression divergence, the composition and expression of the ABCDE genes were conserved in pineapple. We also found that AcSEP1/3, AcAG, AcAGL11a/b/c, and AcFUL1 were highly expressed at different stages of fruit development and have similar expression profiles, implicating these genes’ role in fruit development and ripening processes. We propose that the pineapple flower can be used as a model for studying the ancestral form of monocot flowers to investigate their development and evolutionary history.

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