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Developmental transcriptome

Xiaomu Wei, M Nieves Calvo-Vidal, Siwei Chen, Gang Wu, Maria V Revuelta, Jian Sun, Jinghui Zhang, Michael F Walsh, Kim E Nichols, Vijai Joseph, Carrie Snyder, Celine M Vachon, James D McKay, Shu-Ping Wang, David S Jayabalan, Lauren M Jacobs, Dina Becirovic, Rosalie G Waller, Mykyta Artomov, Agnes Viale, Jayeshkumar Patel, Jude M Phillip, Selina Chen-Kiang, Karen Curtin, Mohamed Salama, Djordje Atanackovic, Ruben Niesvizky, Ola Landgren, Susan L Slager, Lucy A Godley, Jane Churpek, Judy E Garber, Kenneth C Anderson, Mark J Daly, Robert G Roeder, Charles Dumontet, Henry T Lynch, Charles G Mullighan, Nicola J Camp, Kenneth Offit, Robert J Klein, Haiyuan Yu, Leandro Cerchietti, Steven M Lipkin
Given the frequent and largely incurable occurrence of multiple myeloma (MM), identification of germline genetic mutations that predispose cells to MM may provide insight into disease etiology and the developmental mechanisms of its cell of origin, the plasma cell. Here we identified familial and early-onset MM kindreds with truncating mutations in lysine-specific demethylase 1 (LSD1/KDM1A), an epigenetic transcriptional repressor that primarily demethylates histone H3 on lysine 4 and regulates hematopoietic stem cell self-renewal...
March 20, 2018: Cancer Research
Xin-Xin Yu, Wei-Lin Qiu, Liu Yang, Lin-Chen Li, Yu-Wei Zhang, Cheng-Ran Xu
Pancreatic endocrine lineages are derived from pancreatic progenitors that undergo a cell fate transition requiring a switch from low to high Ngn3 expression. However, the underlying chromatin regulatory mechanisms are unclear. Here, we performed epigenomic analysis of gene regulatory loci featuring histone marks in cells with low or high level of Ngn3 expression. In combination with transcriptomic analysis, we discovered that in Ngn3-high cells, the removal of H3K27me3 was associated with the activation of key transcription factors and the establishment of primed and active enhancers...
March 20, 2018: Development
Xiaolong Li, Shutian Tao, Shuwei Wei, Meiling Ming, Xiaosan Huang, Shaoling Zhang, Jun Wu
BACKGROUND: In plants, ERF genes participate in a variety of regulatory pathways, such as plant growth and biotic and/or abiotic stress responses. Although the genome of Chinese white pear ('Dangshansuli') has been released, knowledge regarding the ERF family in pear, such as gene functions, evolutionary history and expression patterns, remains limited. RESULTS: In our study, a total of 155 members of ERF families were identified in pear (Pyrus bretschneideri). The Ka and Ks values suggested that whole-genome duplication (WGD) and dispersed duplication have effectively contributed to the expansion of the pear ERF family...
March 20, 2018: BMC Plant Biology
Ying Han, Yangmin Zheng, Jingpu Zhang, Changqin Hu
Most third- and fourth-generation cephalosporins, such as cefotaxime, cefmenoxime, cefepime, and cefpirome, contain an aminothiazoyl ring at the C-7 position. Drug impurity, which may be produced either during synthesis or upon degradation, can induce adverse effects. Various reports have indicated that neurotoxicity is a side effect of cephalosporin. In this study, we developed methods for assessing the free-swimming activities and behaviors in zebrafish larvae in response to continuous darkness and stimulation of light-to-dark photoperiod transition by chemical treatments...
2018: Frontiers in Pharmacology
Daniel Pensold, Geraldine Zimmer
The correct establishment of inhibitory circuits is crucial for cortical functionality and defects during the development of γ-aminobutyric acid-expressing cortical interneurons contribute to the pathophysiology of psychiatric disorders. A critical developmental step is the migration of cortical interneurons from their site of origin within the subpallium to the cerebral cortex, orchestrated by intrinsic and extrinsic signals. In addition to genetic networks, epigenetic mechanisms such as DNA methylation by DNA methyltransferases (DNMTs) are suggested to drive stage-specific gene expression underlying developmental processes...
2018: Journal of Experimental Neuroscience
Alexander B Rosenberg, Charles M Roco, Richard A Muscat, Anna Kuchina, Paul Sample, Zizhen Yao, Lucas Gray, David J Peeler, Sumit Mukherjee, Wei Chen, Suzie H Pun, Drew L Sellers, Bosiljka Tasic, Georg Seelig
To facilitate scalable profiling of single cells, we developed split-pool ligation-based transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq is compatible with fixed cells or nuclei, allows efficient sample multiplexing and requires no customized equipment. We used SPLiT-seq to analyze 156,049 single-nucleus transcriptomes from postnatal day 2 and 11 mouse brains and spinal cords. Over 100 cell types were identified, with gene expression patterns corresponding to cellular function, regional specificity, and stage of differentiation...
March 15, 2018: Science
Ji Dong, Yuqiong Hu, Xiaoying Fan, Xinglong Wu, Yunuo Mao, Boqiang Hu, Hongshan Guo, Lu Wen, Fuchou Tang
BACKGROUND: Organogenesis is crucial for proper organ formation during mammalian embryonic development. However, the similarities and shared features between different organs and the cellular heterogeneity during this process at single-cell resolution remain elusive. RESULTS: We perform single-cell RNA sequencing analysis of 1916 individual cells from eight organs and tissues of E9.5 to E11.5 mouse embryos, namely, the forebrain, hindbrain, skin, heart, somite, lung, liver, and intestine...
March 14, 2018: Genome Biology
Suijuan Zhong, Shu Zhang, Xiaoying Fan, Qian Wu, Liying Yan, Ji Dong, Haofeng Zhang, Long Li, Le Sun, Na Pan, Xiaohui Xu, Fuchou Tang, Jun Zhang, Jie Qiao, Xiaoqun Wang
The mammalian prefrontal cortex comprises a set of highly specialized brain areas containing billions of cells and serves as the centre of the highest-order cognitive functions, such as memory, cognitive ability, decision-making and social behaviour. Although neural circuits are formed in the late stages of human embryonic development and even after birth, diverse classes of functional cells are generated and migrate to the appropriate locations earlier in development. Dysfunction of the prefrontal cortex contributes to cognitive deficits and the majority of neurodevelopmental disorders; there is therefore a need for detailed knowledge of the development of the prefrontal cortex...
March 14, 2018: Nature
Tiandong Che, Diyan Li, Long Jin, Yuhua Fu, Yingkai Liu, Pengliang Liu, Yixin Wang, Qianzi Tang, Jideng Ma, Xun Wang, Anan Jiang, Xuewei Li, Mingzhou Li
Genome-wide transcriptomic studies in humans and mice have become extensive and mature. However, a comprehensive and systematic understanding of protein-coding genes and long non-coding RNAs (lncRNAs) expressed during pig spleen development has not been achieved. LncRNAs are known to participate in regulatory networks for an array of biological processes. Here, we constructed 18 RNA libraries from developing fetal pig spleen (55 days before birth), postnatal pig spleens (0, 30, 180 days and 2 years after birth), and the samples from the 2-year-old Wild Boar...
2018: PloS One
Diego Hojsgaard
Polyploid genomes evolve and follow a series of dynamic transfigurations along with adaptation and speciation. The initial formation of a new polyploid individual within a diploid population usually involves a triploid bridge, a two-step mechanism of cell fusions between ubiquitous (reduced) and rare (unreduced) gametes. The primary fusion event creates an intermediate triploid individual with unbalanced genome sets, a situation of genomic-shock characterized by gene expression dysregulation, high dosage sensitivity, disturbed cell divisions, and physiological and reproductive attributes drastically altered...
2018: Frontiers in Plant Science
Jun You, Yanyan Wang, Yujuan Zhang, Komivi Dossa, Donghua Li, Rong Zhou, Linhai Wang, Xiurong Zhang
Sesame (Sesamum indicum L.) is an important oilseed crop. However, multiple abiotic stresses severely affect sesame growth and production. Raffinose family oligosaccharides (RFOs), such as raffinose and stachyose, play an important role in desiccation tolerance of plants and developing seeds. In the present study, three types of key enzymes, galactinol synthase (GolS), raffinose synthase (RafS) and stachyose synthase (StaS), responsible for the biosynthesis of RFOs were identified at the genome-wide scale in sesame...
March 12, 2018: Scientific Reports
Sébastien Bélanger, Suzanne Marchand, Pierre-Étienne Jacques, Blake Meyers, François Belzile
In barley, it is possible to induce embryogenesis in the haploid and uninucleate microspore to obtain a diploid plant that is perfectly homozygous. To change developmental fates in this fashion, microspores need to engage in cellular de-differentiation, interrupting the pollen formation, and restore totipotency prior to engaging in embryogenesis. In this work, we used the barley cultivar Gobernadora to characterize the transcriptome of microspores prior to (day 0) and immediately after (days 2 and 5) the application of a stress pretreatment...
March 12, 2018: G3: Genes—Genomes—Genetics
Alessandro Vannozzi, Darren Chern Jan Wong, Janine Höll, Ibrahim Hmmam, José Tomás Matus, Jochen Bogs, Tobias Ziegler, Ian Dry, Gianni Barcaccia, Margherita Lucchin
Stilbene synthase (STS) is the key enzyme leading to the biosynthesis of resveratrol. Recently we reported two R2R3-MYB transcription factors (TFs) that regulate the stilbene biosynthetic pathway in grapevine: VviMYB14 and VviMYB15. These genes strongly co-express with STSs under a range of stress and developmental conditions, in agreement with the specific activation of STS promoters by these TFs. Genome-wide gene co-expression analysis using two separate transcriptome compendia based on microarray and RNA-Seq data revealed that WRKY TFs were the top TF family correlated with STS genes...
February 26, 2018: Plant & Cell Physiology
T Porseryd, N Reyhanian Caspillo, K Volkova, L Elabbas, T Källman, P Dinnétz, P-E Olsson, I Porsch-Hällström
17α-Ethinylestradiol (EE2 ) is a ubiquitous aquatic contaminant shown to decrease fish fertility at low concentrations, especially in fish exposed during development. The mechanisms of the decreased fertility are not fully understood. In this study, we perform transcriptome analysis by RNA sequencing of testes from zebrafish with previously reported lowered fertility due to exposure to low concentrations of EE2 during development. Fish were exposed to 1.2 and 1.6 ng/L (measured concentration; nominal concentrations 3 and 10 ng/L) of EE2 from fertilization to 80 days of age, followed by 82 days of remediation in clean water...
March 8, 2018: General and Comparative Endocrinology
Orlando Contreras-López, Tomás C Moyano, Daniela C Soto, Rodrigo A Gutiérrez
The rapid increase in the availability of transcriptomics data generated by RNA sequencing represents both a challenge and an opportunity for biologists without bioinformatics training. The challenge is handling, integrating, and interpreting these data sets. The opportunity is to use this information to generate testable hypothesis to understand molecular mechanisms controlling gene expression and biological processes (Fig. 1). A successful strategy to generate tractable hypotheses from transcriptomics data has been to build undirected network graphs based on patterns of gene co-expression...
2018: Methods in Molecular Biology
Khurram Bashir, Sultana Rasheed, Akihiro Matsui, Kei Iida, Maho Tanaka, Motoaki Seki
Numerous experiments have been performed in Arabidopsis to monitor changes in gene expression that occur in response to a variety of abiotic and biotic stresses, different growth conditions, and at various developmental stages. In addition, gene expression patterns have also been characterized among wild-type and mutant genotypes. Despite these numerous reports, transcriptional changes occurring in roots of soil-grown plants subjected to a progressive drought stress have remained undocumented. To fill this gap, we established a system that allows one to establish water-deficit conditions and to collect root and shoot samples with minimal damage to the root system...
2018: Methods in Molecular Biology
Violaine Herrbach, Fabienne Maillet, Sandra Bensmihen
Almost all legume plants have the capacity to form two types of root organs: lateral roots and nodules (that will host rhizobia that fix nitrogen). Transcriptomic analyses are useful to understand both the similarities and differences between nodule and LR formation and to compare the LR developmental programs used by Arabidopsis and model legumes such as Medicago truncatula. However, in M. truncatula as in Arabidopsis, root cells "committed" to LR formation programs are scattered along the primary root and localized in the inner most layers of the root...
2018: Methods in Molecular Biology
Stefan A Rensing
500Ma ago the terrestrial habitat was a barren, unwelcoming place for species other than, for example, bacteria or fungi. Most probably, filamentous freshwater algae adapted to aerial conditions and eventually conquered land. Adaptation to a severely different habitat apparently included sturdy cell walls enabling an erect body plan as well as protection against abiotic stresses such as ultraviolet radiation, drought and varying temperature. To thrive on land, plants probably required more elaborate signaling pathways to react to diverse environmental conditions, and phytohormones to control developmental programs...
March 8, 2018: Current Opinion in Plant Biology
Lei Liu, Yuanyuan Fu, Fang Zhu, Changkao Mu, Ronghua Li, Weiwei Song, Ce Shi, Yangfang Ye, Chunlin Wang
The swimming crab (Portunus trituberculatus) is among the most economically important seawater crustacean species in Asia. Despite its commercial importance and being well-studied status, genomic and transcriptomic data are scarce for this crab species. In the present study, limb bud tissue was collected at different developmental stages post amputation for transcriptomic analysis. Illumina RNA-sequencing was applied to characterise the limb regeneration transcriptome and identify the most characteristic genes...
March 7, 2018: Gene
Jiaxuan Guo, Shufang Wang, XiaoYang Yu, Rui Dong, Yuzhong Li, Xurong Mei, Yuanyue Shen
Polyamines (PAs) participate in many plant growth and developmental processes, including fruit ripening. However, it is not clear whether PAs play a role in the ripening of strawberry (Fragaria ananassa), a model non-climacteric plant. Here, we found that the content of the PA spermine (Spm) increased more sharply after the onset of fruit coloration than did that of the PAs putrescine (Put) or spermidine (Spd). Spm dominance in ripe fruit resulted from abundant transcripts of a strawberry S-adenosyl-L-methionine decarboxylase gene (FaSAMDC), which encodes an enzyme that generates a residue needed for PA biosynthesis...
March 9, 2018: Plant Physiology
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