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https://www.readbyqxmd.com/read/29231846/the-discrepant-and-similar-responses-of-genome-wide-transcriptional-profiles-between-drought-and-cold-stresses-in-cassava
#1
Changying Zeng, Zehong Ding, Fang Zhou, Yufei Zhou, Ruiju Yang, Zi Yang, Wenquan Wang, Ming Peng
Background: Cassava, an important tropical crop, has remarkable drought tolerance, but is very sensitive to cold. The growth, development, and root productivity of cassava are all adversely affected under cold and drought. Methods: To profile the transcriptional response to cold and drought stresses, cassava seedlings were respectively subjected to 0, 6, 24, and 48 h of cold stress and 0, 4, 6, and 10 days of drought stress. Their folded leaves, fully extended leaves, and roots were respectively investigated using RNA-seq...
December 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29230213/transcription-factor-c-ebp-homologous-protein-in-health-and-diseases
#2
REVIEW
Yuan Yang, Lian Liu, Ishan Naik, Zachary Braunstein, Jixin Zhong, Boxu Ren
C/EBP homologous protein (CHOP), known also as DNA damage-inducible transcript 3 and as growth arrest and DNA damage-inducible protein 153 (GADD153), is induced in response to certain stressors. CHOP is universally acknowledged as a main conduit to endoplasmic reticulum stress-induced apoptosis. Ongoing research established the existence of CHOP-mediated apoptosis signaling networks, for which novel downstream targets are still being determined. However, there are studies that contradict this notion and assert that apoptosis is not the only mechanism by which CHOP plays in the development of pathologies...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29230020/snp-co-association-and-network-analyses-identify-e2f3-kdm5a-and-bach2-as-key-regulators-of-the-bovine-milk-fatty-acid-profile
#3
Sara Pegolo, Christos Dadousis, Núria Mach, Yuliaxis Ramayo-Caldas, Marcello Mele, Giuseppe Conte, Stefano Schiavon, Giovanni Bittante, Alessio Cecchinato
The fatty acid (FA) profile has a considerable impact on the nutritional and technological quality of milk and dairy products. The molecular mechanism underlying the regulation of fat metabolism in bovine mammary gland have been not completely elucidated. We conducted genome-wide association studies (GWAS) across 65 milk FAs and fat percentage in 1,152 Brown Swiss cows. In total, we identified 175 significant single nucleotide polymorphism (SNPs) spanning all chromosomes. Pathway analyses revealed that 12:0 was associated with the greatest number of overrepresented categories/pathways (e...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29229981/the-mating-type-locus-protein-mat1-2-1-of-trichoderma-reesei-interacts-with-xyr1-and-regulates-cellulase-gene-expression-in-response-to-light
#4
Fanglin Zheng, Yanli Cao, Lei Wang, Xinxing Lv, Xiangfeng Meng, Weixin Zhang, Guanjun Chen, Weifeng Liu
Cellulase production in the model cellulolytic fungus Trichoderma reesei is subject to a variety of environmental and physiological conditions involving an intricate regulatory network with multiple transcription factors. Here, we identified the mating type locus protein MAT1-2-1 as an interacting partner for the key transcriptional activator Xyr1 of T. reesei cellulase genes. Yeast two-hybrid and GST pulldown analyses revealed that MAT1-2-1 directly interacted with the putative transcription activation domain (AD, 767~940 aa) and the middle homology region (MHR2, 314~632 aa) of Xyr1...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29229866/allosteric-histidine-switch-for-regulation-of-intracellular-zinc-ii-fluctuation
#5
Rongfeng Zhu, Yanqun Song, Haiping Liu, Yufei Yang, Shenlin Wang, Chengqi Yi, Peng R Chen
Metalloregulators allosterically control transcriptional activity through metal binding-induced reorganization of ligand residues and/or hydrogen bonding networks, while the coordination atoms on the same ligand residues remain seldom changed. Here we show that the MarR-type zinc transcriptional regulator ZitR switches one of its histidine nitrogen atoms for zinc coordination during the allosteric control of DNA binding. The Zn(II)-coordination nitrogen on histidine 42 within ZitR's high-affinity zinc site (site 1) switches from Nε2 to Nδ1 upon Zn(II) binding to its low-affinity zinc site (site 2), which facilitates ZitR's conversion from the nonoptimal to the optimal DNA-binding conformation...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29229852/regulatory-networks-specifying-cortical-interneurons-from-human-embryonic-stem-cells-reveal-roles-for-chd2-in-interneuron-development
#6
Kesavan Meganathan, Emily M A Lewis, Paul Gontarz, Shaopeng Liu, Edouard G Stanley, Andrew G Elefanty, James E Huettner, Bo Zhang, Kristen L Kroll
Cortical interneurons (cINs) modulate excitatory neuronal activity by providing local inhibition. During fetal development, several cIN subtypes derive from the medial ganglionic eminence (MGE), a transient ventral telencephalic structure. While altered cIN development contributes to neurodevelopmental disorders, the inaccessibility of human fetal brain tissue during development has hampered efforts to define molecular networks controlling this process. Here, we modified protocols for directed differentiation of human embryonic stem cells, obtaining efficient, accelerated production of MGE-like progenitors and MGE-derived cIN subtypes with the expected electrophysiological properties...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29229825/network-analysis-identifies-chromosome-intermingling-regions-as-regulatory-hotspots-for-transcription
#7
Anastasiya Belyaeva, Saradha Venkatachalapathy, Mallika Nagarajan, G V Shivashankar, Caroline Uhler
The 3D structure of the genome plays a key role in regulatory control of the cell. Experimental methods such as high-throughput chromosome conformation capture (Hi-C) have been developed to probe the 3D structure of the genome. However, it remains a challenge to deduce from these data chromosome regions that are colocalized and coregulated. Here, we present an integrative approach that leverages 1D functional genomic features (e.g., epigenetic marks) with 3D interactions from Hi-C data to identify functional interchromosomal interactions...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29229750/profiling-of-accessible-chromatin-regions-across-multiple-plant-species-and-cell-types-reveals-common-gene-regulatory-principles-and-new-control-modules
#8
Kelsey A Maher, Marko Bajic, Kaisa Kajala, Mauricio Reynoso, Germain Pauluzzi, Donnelly West, Kristina Zumstein, Margaret Woodhouse, Kerry L Bubb, Michael W Dorrity, Christine Queitsch, Julia Bailey-Serres, Neelima Sinha, Siobhan M Brady, Roger Deal
The transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how many cis-regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the Assay for Transposase-Accessible Chromatin (ATAC-seq) in four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome...
December 11, 2017: Plant Cell
https://www.readbyqxmd.com/read/29228702/lncrna-and-mrna-profiling-during-activation-of-tilapia-macrophages-by-hsp70-and-streptococcus-agalactiae-antigen
#9
Honglin Luo, Huizan Yang, Yong Lin, Yongde Zhang, Chuanyan Pan, Pengfei Feng, Yanling Yu, Xiaohan Chen
Objectives: To investigate the lncRNA profiling during tilapia peritoneal macrophages (TPMs) activation and discuss the relationship between lncRNA and mRNA. Materials and Methods: RNA sequencing was used to investigate the lncRNA and mRNA profiles of TPMs activation following stimulation with Streptococcus agalactiae (Sa) antigen, heat shock protein 70 (HSP70) and HSP70+Sa. The expressions of lncRNA and mRNA were confirmed by qPCR. 356 lncRNA, 10173 mRNA and 1782 transcripts of uncertain coding potential (TUCP) were differentially expressed by pairwise comparison...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228601/genome-wide-analysis-of-circular-rnas-in-prenatal-and-postnatal-muscle-of-sheep
#10
Cunyuan Li, Xiaoyue Li, Yang Yao, Qiman Ma, Wei Ni, Xiangyu Zhang, Yang Cao, Wureli Hazi, Dawei Wang, Renzhe Quan, Xiaoxu Hou, Zhijin Liu, Qianqian Zhan, Li Liu, Mengdan Zhang, Shuting Yu, Shengwei Hu
Circular RNAs (circRNAs), a type of non-coding RNA with circular structure, were generated by back splicing and widely expressed in animals and plants. Recent studies have shown that circRNAs extensively participate in cell proliferation, cell differentiation, cell autophagy and other biological processes. However, the role and expression of circRNAs in the development and growth of muscle have not been studied in sheep. In our study, we first used RNA-seq to study the circRNAs in prenatal and postnatal longissimus dorsi muscle of sheep...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228146/identification-and-characterization-of-a-specific-13-mirna-expression-signature-during-follicle-activation-in-the-zebrafish-ovary
#11
Queenie Wing-Lei Wong, Ming-An Sun, Shuk-Wa Lau, Chirag Parsania, Shaolong Zhou, Silin Zhong, Wei Ge
Ovarian folliculogenesis is always of great interest in reproductive biology. However, the molecular mechanisms that control follicle development, particularly the early phase of follicle activation or recruitment, still remain poorly understood. In an attempt to decipher the gene networks and signaling pathways involved in such transition, we conducted a transcriptomic analysis (RNA-seq) on zebrafish primary growth (PG, stage I; inactive) and pre-vitellogenic (PV, stage II; activated) follicles. A total of 118 unique microRNAs (miRNAs) (11 down-regulated and 83 up-regulated during PG/PV transition) and 56711 unique messenger RNAs (mRNAs) (1839 down-regulated and 7243 up-regulated during PG/PV transition) were identified...
December 6, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/29228019/loci-and-pathways-associated-with-uterine-capacity-for-pregnancy-and-fertility-in-beef-cattle
#12
Mahesh Neupane, Thomas W Geary, Jennifer N Kiser, Gregory W Burns, Peter J Hansen, Thomas E Spencer, Holly L Neibergs
Infertility and subfertility negatively impact the economics and reproductive performance of cattle. Of note, significant pregnancy loss occurs in cattle during the first month of pregnancy, yet little is known about the genetic loci influencing pregnancy success and loss in cattle. To identify quantitative trait loci (QTL) with large effects associated with early pregnancy loss, Angus crossbred heifers were classified based on day 28 pregnancy outcomes to serial embryo transfer. A genome wide association analysis (GWAA) was conducted comparing 30 high fertility heifers with 100% success in establishing pregnancy to 55 subfertile heifers with 25% or less success...
2017: PloS One
https://www.readbyqxmd.com/read/29228002/comparative-cell-cycle-transcriptomics-reveals-synchronization-of-developmental-transcription-factor-networks-in-cancer-cells
#13
Johan Boström, Zuzana Sramkova, Alena Salašová, Helena Johard, Diana Mahdessian, Radek Fedr, Carolyn Marks, Jiřina Medalová, Karel Souček, Emma Lundberg, Sten Linnarsson, Vítězslav Bryja, Petra Sekyrova, Mikael Altun, Michael Andäng
The cell cycle coordinates core functions such as replication and cell division. However, cell-cycle-regulated transcription in the control of non-core functions, such as cell identity maintenance through specific transcription factors (TFs) and signalling pathways remains unclear. Here, we provide a resource consisting of mapped transcriptomes in unsynchronized HeLa and U2OS cancer cells sorted for cell cycle phase by Fucci reporter expression. We developed a novel algorithm for data analysis that enables efficient visualization and data comparisons and identified cell cycle synchronization of Notch signalling and TFs associated with development...
2017: PloS One
https://www.readbyqxmd.com/read/29227103/a-robust-molecular-network-motif-for-period-doubling-devices
#14
Christian Cuba Samaniego, Elisa Franco
Life is sustained by a variety of cyclic processes such as cell division, muscle contraction, and neuron firing. The periodic signals powering these processes often direct a variety of other downstream systems, which operate at different time scales and must have the capacity to divide or multiply the period of the master clock. Period modulation is also an important challenge in synthetic molecular systems, where slow and fast components may have to be coordinated simultaneously by a single oscillator whose frequency is often difficult to tune...
December 11, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29226156/micrornas-regulate-thymic-epithelium-in-age-related-thymic-involution-via-down-or-upregulation-of-transcription-factors
#15
REVIEW
Minwen Xu, Xiaoli Zhang, Ruiyun Hong, Dong-Ming Su, Liefeng Wang
Age-related thymic involution is primarily induced by defects in nonhematopoietic thymic epithelial cells (TECs). It is characterized by dysfunction of multiple transcription factors (TFs), such as p63 and FoxN1, and also involves other TEC-associated regulators, such as Aire. These TFs and regulators are controlled by complicated regulatory networks, in which microRNAs (miRNAs) act as a key player. miRNAs can either directly target the 3'-UTRs (untranslated regions) of the TFs to suppress TF expression or target TF inhibitors to reduce or increase TF inhibitor expression and thereby indirectly enhance or inhibit TF expression...
2017: Journal of Immunology Research
https://www.readbyqxmd.com/read/29226075/prediction-of-target-genes-for-mir-140-5p-in-pulmonary-arterial-hypertension-using-bioinformatics-methods
#16
Fangwei Li, Wenhua Shi, Yixin Wan, Qingting Wang, Wei Feng, Xin Yan, Jian Wang, Limin Chai, Qianqian Zhang, Manxiang Li
The expression of microRNA (miR)-140-5p is known to be reduced in both pulmonary arterial hypertension (PAH) patients and monocrotaline-induced PAH models in rat. Identification of target genes for miR-140-5p with bioinformatics analysis may reveal new pathways and connections in PAH. This study aimed to explore downstream target genes and relevant signaling pathways regulated by miR-140-5p to provide theoretical evidences for further researches on role of miR-140-5p in PAH. Multiple downstream target genes and upstream transcription factors (TFs) of miR-140-5p were predicted in the analysis...
December 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/29226034/constructing-a-comprehensive-gene-co-expression-based-interactome-in-bos-taurus
#17
Yan Chen, Yining Liu, Min Du, Wengang Zhang, Ling Xu, Xue Gao, Lupei Zhang, Huijiang Gao, Lingyang Xu, Junya Li, Min Zhao
Integrating genomic information into cattle breeding is an important approach to exploring genotype-phenotype relationships for complex traits related to diary and meat production. To assist with genomic-based selection, a reference map of interactome is needed to fully understand and identify the functional relevant genes. To this end, we constructed a co-expression analysis of 92 tissues and this represents the systematic exploration of gene-gene relationship in Bos taurus. By using robust WGCNA (Weighted Gene Correlation Network Analysis), we described the gene co-expression network of 5,000 protein-coding genes with majority variations in expression across 92 tissues...
2017: PeerJ
https://www.readbyqxmd.com/read/29224918/the-regulatory-network-behind-mhc-class-i-expression
#18
Marlieke L M Jongsma, Greta Guarda, Robbert M Spaapen
The MHC class I pathway, presenting endogenously derived peptides to T lymphocytes, is hijacked in many pathological conditions. This affects MHC class I levels and peptide presentation at the cell surface leading to immune escape of cancer cells or microbes. It is therefore important to identify the molecular mechanisms behind MHC class I expression, processing and antigen presentation. The identification of NLRC5 as regulator of MHC class I transcription was a huge step forward in understanding the transcriptional mechanism involved...
December 7, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/29224668/circadian-clock-gastrointestinal-peptide-interaction-in-peripheral-tissues-and-the-brain
#19
REVIEW
Dominic Landgraf, Anne-Marie Neumann, Henrik Oster
Food intake and sleep are two mutually exclusive behaviors and both are normally confined to opposing phases of the diurnal cycle. The temporal coordination of behavior and physiology along the 24-h day-night cycle is organized by a network of circadian clocks that orchestrate transcriptional programs controlling cellular physiology. Many of the peptide hormones of the gastrointestinal tract are not only secreted in a circadian fashion, they can also affect circadian clock function in peripheral metabolic tissues and the brain, thus providing metabolic feedback to metabolic and neurobehavioral circuits...
December 2017: Best Practice & Research. Clinical Endocrinology & Metabolism
https://www.readbyqxmd.com/read/29222761/coupling-fluxes-enzymes-and-regulation-in-genome-scale-metabolic-models
#20
Paul A Jensen
Genome-scale models have expanded beyond their metabolic origins. Multiple modeling frameworks are required to combine metabolism with enzymatic networks, transcription, translation, and regulation. Mathematical programming offers a powerful set of tools for tackling these "multi-modality" models, although special attention must be paid to the connections between modeling types. This chapter reviews common methods for combining metabolic and discrete logical models into a single mathematical programming framework...
2018: Methods in Molecular Biology
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