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Gene regulatory networks

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https://www.readbyqxmd.com/read/29240875/the-expanding-roles-of-argonautes-rna-interference-splicing-and-beyond
#1
Xiaoxia Ma, Ziwei Zuo, Weishan Shao, Yongfeng Jin, Yijun Meng
Argonaute (AGO) protein family is highly conserved in eukaryotes and prokaryotes, reflecting its evolutionarily indispensible role in maintaining normal life cycle of the organisms. Small RNA-guided, AGO-dependent RNA interference (RNAi) is a well-studied pathway for gene expression regulation, which can be performed at transcriptional, posttranscriptional or translational level. In addition to RNAi, growing pieces of evidence point to a novel role of AGOs in pre-mRNA (messenger RNA precursor) splicing in animals...
December 11, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29239765/immune-responses-transcriptional-and-post-transcriptional-networks-pass-the-baton
#2
Johannes Lichti, Christian Gallus, Elke Glasmacher
Diverse gene regulatory mechanisms impact on immune homeostasis, and a new model now emerges as fundamental in light of recent genome-wide studies. In this picture, transcriptional networks drive functional changes during immune activation, whereas autoregulatory feedback loops of post-transcriptional programs ensure the original cell lineage identity and subsequent immune resolution.
November 24, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/29239721/natural-changes-in-light-interact-with-circadian-regulation-at-promoters-to-control-gene-expression-in-cyanobacteria
#3
Joseph Robert Piechura, Kapil Amarnath, Erin K O'Shea
The circadian clock interacts with other regulatory pathways to tune physiology to predictable daily changes and unexpected environmental fluctuations. However, the complexity of circadian clocks in higher organisms has prevented a clear understanding of how natural environmental conditions affect circadian clocks and their physiological outputs. Here, we dissect the interaction between circadian regulation and responses to fluctuating light in the cyanobacterium Synechococcus elongatus. We demonstrate that natural changes in light intensity substantially affect the expression of hundreds of circadian-clock-controlled genes, many of which are involved in key steps of metabolism...
December 14, 2017: ELife
https://www.readbyqxmd.com/read/29239106/er-stress-in-skeletal-muscle-remodeling-and-myopathies
#4
REVIEW
Dil Afroze, Ashok Kumar
Skeletal muscle is a highly plastic tissue in the human body that undergoes extensive adaptation in response to environmental cues, such as physical activity, metabolic perturbation, and disease conditions. The endoplasmic reticulum (ER) plays a pivotal role in protein folding and calcium homeostasis in many mammalian cell types including skeletal muscle. However, overload of misfolded or unfolded proteins in the ER lumen cause stress, which results in the activation of a signaling network called the unfolded protein response (UPR)...
December 14, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29238347/langerhans-cells-programmed-by-the-epidermis
#5
REVIEW
Kalum Clayton, Andres F Vallejo, James Davies, Sofia Sirvent, Marta E Polak
Langerhans cells (LCs) reside in the epidermis as a dense network of immune system sentinels. These cells determine the appropriate adaptive immune response (inflammation or tolerance) by interpreting the microenvironmental context in which they encounter foreign substances. In a normal physiological, "non-dangerous" situation, LCs coordinate a continuous state of immune tolerance, preventing unnecessary and harmful immune activation. Conversely, when they sense a danger signal, for example during infection or when the physical integrity of skin has been compromised as a result of a trauma, they instruct T lymphocytes of the adaptive immune system to mount efficient effector responses...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29237467/estimating-drivers-of-cell-state-transitions-using-gene-regulatory-network-models
#6
Daniel Schlauch, Kimberly Glass, Craig P Hersh, Edwin K Silverman, John Quackenbush
BACKGROUND: Specific cellular states are often associated with distinct gene expression patterns. These states are plastic, changing during development, or in the transition from health to disease. One relatively simple extension of this concept is to recognize that we can classify different cell-types by their active gene regulatory networks and that, consequently, transitions between cellular states can be modeled by changes in these underlying regulatory networks. RESULTS: Here we describe MONSTER, MOdeling Network State Transitions from Expression and Regulatory data, a regression-based method for inferring transcription factor drivers of cell state conditions at the gene regulatory network level...
December 13, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29237423/deciphering-the-genetic-regulation-of-peripheral-blood-transcriptome-in-pigs-through-expression-genome-wide-association-study-and-allele-specific-expression-analysis
#7
T Maroilley, G Lemonnier, J Lecardonnel, D Esquerré, Y Ramayo-Caldas, M J Mercat, C Rogel-Gaillard, J Estellé
BACKGROUND: Efforts to improve sustainability in livestock production systems have focused on two objectives: investigating the genetic control of immune function as it pertains to robustness and disease resistance, and finding predictive markers for use in breeding programs. In this context, the peripheral blood transcriptome represents an important source of biological information about an individual's health and immunological status, and has been proposed for use as an intermediate phenotype to measure immune capacity...
December 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29236054/genome-wide-profiling-of-small-rnas-and-degradome-revealed-conserved-regulations-of-mirnas-on-auxin-responsive-genes-during-fruit-enlargement-in-peaches
#8
Mengya Shi, Xiao Hu, Yu Wei, Xu Hou, Xue Yuan, Jun Liu, Yueping Liu
Auxin has long been known as a critical phytohormone that regulates fruit development in plants. However, due to the lack of an enlarged ovary wall in the model plants Arabidopsis and rice, the molecular regulatory mechanisms of fruit division and enlargement remain unclear. In this study, we performed small RNA sequencing and degradome sequencing analyses to systematically explore post-transcriptional regulation in the mesocarp at the hard core stage following treatment of the peach (Prunus persica L.) fruit with the synthetic auxin α-naphthylacetic acid (NAA)...
December 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29235467/in-situ-functional-dissection-of-rna-cis-regulatory-elements-by-multiplex-crispr-cas9-genome-engineering
#9
Qianxin Wu, Quentin R V Ferry, Toni A Baeumler, Yale S Michaels, Dimitrios M Vitsios, Omer Habib, Roland Arnold, Xiaowei Jiang, Stefano Maio, Bruno R Steinkraus, Marta Tapia, Paolo Piazza, Ni Xu, Georg A Holländer, Thomas A Milne, Jin-Soo Kim, Anton J Enright, Andrew R Bassett, Tudor A Fulga
RNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. Deciphering the prevalence and functional impact of this post-transcriptional control layer requires technologies for disrupting RREs without perturbing cellular homeostasis. Here we describe genome-engineering based evaluation of RNA regulatory element activity (GenERA), a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 platform for in situ high-content functional analysis of RREs...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29234348/diurnal-transcriptome-and-gene-network-represented-through-sparse-modeling-in-brachypodium-distachyon
#10
Satoru Koda, Yoshihiko Onda, Hidetoshi Matsui, Kotaro Takahagi, Yukiko Yamaguchi-Uehara, Minami Shimizu, Komaki Inoue, Takuhiro Yoshida, Tetsuya Sakurai, Hiroshi Honda, Shinto Eguchi, Ryuei Nishii, Keiichi Mochida
We report the comprehensive identification of periodic genes and their network inference, based on a gene co-expression analysis and an Auto-Regressive eXogenous (ARX) model with a group smoothly clipped absolute deviation (SCAD) method using a time-series transcriptome dataset in a model grass, Brachypodium distachyon. To reveal the diurnal changes in the transcriptome in B. distachyon, we performed RNA-seq analysis of its leaves sampled through a diurnal cycle of over 48 h at 4 h intervals using three biological replications, and identified 3,621 periodic genes through our wavelet analysis...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29234131/a-gene-expression-study-of-ornamental-fin-shape-in-neolamprologus-brichardi-an-african-cichlid-species
#11
Ehsan Pashay Ahi, Florian Richter, Kristina M Sefc
The diversity of fin morphology within and across fish taxa offers great, but still largely unexplored, opportunities to investigate the proximate mechanisms underlying fin shape variation. Relying on available genetic knowledge brought forth mainly by the comprehensive study of the zebrafish caudal fin, we explored candidate molecular mechanisms for the maintenance and formation of the conspicuously elongated filaments adorning the unpaired fins of the East African "princess cichlid" Neolamprologus brichardi...
December 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29233811/dissecting-the-roles-of-the-calcineurin-pathway-in-unisexual-reproduction-stress-responses-and-virulence-in-cryptococcus-deneoformans
#12
Ci Fu, Nicholas Donadio, Maria E Cardenas, Joseph Heitman
The Ca2+/calmodulin-dependent protein phosphatase calcineurin orchestrates sexual reproduction, stress responses, and virulence via branched downstream pathways in the opportunistic human fungal pathogen, Cryptococcus neoformans The calcineurin binding protein Cbp1, the calcineurin temperature suppressor Cts1, the calcineurin responsive zinc finger transcription factor Crz1, and the calcineurin targets Pbp1, Tif3, and Puf4 all function downstream of calcineurin to orchestrate distinct cellular processes. To elucidate how the calcineurin pathway regulatory network governs unisexual reproduction, stress responses, and virulence, we have analyzed the self-filamentous C...
December 12, 2017: Genetics
https://www.readbyqxmd.com/read/29231846/the-discrepant-and-similar-responses-of-genome-wide-transcriptional-profiles-between-drought-and-cold-stresses-in-cassava
#13
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/29229981/the-mating-type-locus-protein-mat1-2-1-of-trichoderma-reesei-interacts-with-xyr1-and-regulates-cellulase-gene-expression-in-response-to-light
#14
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/29229852/regulatory-networks-specifying-cortical-interneurons-from-human-embryonic-stem-cells-reveal-roles-for-chd2-in-interneuron-development
#15
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/29229750/profiling-of-accessible-chromatin-regions-across-multiple-plant-species-and-cell-types-reveals-common-gene-regulatory-principles-and-new-control-modules
#16
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/29229492/programming-morphogenesis-through-systems-and-synthetic-biology
#17
REVIEW
Jeremy J Velazquez, Emily Su, Patrick Cahan, Mo R Ebrahimkhani
Mammalian tissue development is an intricate, spatiotemporal process of self-organization that emerges from gene regulatory networks of differentiating stem cells. A major goal in stem cell biology is to gain a sufficient understanding of gene regulatory networks and cell-cell interactions to enable the reliable and robust engineering of morphogenesis. Here, we review advances in synthetic biology, single cell genomics, and multiscale modeling, which, when synthesized, provide a framework to achieve the ambitious goal of programming morphogenesis in complex tissues and organoids...
December 8, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/29227951/transcriptome-analysis-reveals-novel-genes-involved-in-anthocyanin-biosynthesis-in-the-flesh-of-peach
#18
Ke Cao, Tiyu Ding, Dongmin Mao, Gengrui Zhu, Weichao Fang, Changwen Chen, Xinwei Wang, Lirong Wang
Peach is an important deciduous fruit tree species. Anthocyanins play an important role in fruit color formation and, through linkage analysis, previous studies have identified and mapped the key genes regulating anthocyanins' accumulation to chromosomes 3 and 5 in two different germplasms. To understand the overall regulatory network of anthocyanins biosynthesis, genes co-expressed with these key genes were identified in the red-fleshed 'Tianjin Shui Mi' and white-fleshed 'Hakuho' germplasms. Analysis of their flesh anthocyanin contents revealed differences 15 days before maturation...
December 7, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29227558/rna-sequencing-identifies-gene-regulatory-networks-controlling-extracellular-matrix-synthesis-in-intervertebral-disk-tissues
#19
Scott M Riester, Yang Lin, Wei Wang, Lin Cong, Abdel-Moneim Mohamed Ali, Sun H Peck, Lachlan J Smith, Bradford L Currier, Michelle Clark, Paul Huddleston, William Krauss, Michael J Yaszemski, Mark E Morrey, Matthew P Abdel, Mohamad Bydon, Wenchun Qu, A Noelle Larson, Andre J van Wijnen, Ahmad Nassr
Degenerative disk disease of the spine is a major cause of back pain and disability. Optimization of regenerative medical therapies for degenerative disk disease requires a deep mechanistic understanding of the factors controlling the structural integrity of spinal tissues. In this investigation, we sought to identify candidate regulatory genes controlling extracellular matrix synthesis in spinal tissues. To achieve this goal we performed high throughput next generation RNA sequencing on 39 annulus fibrosus and 21 nucleus pulposus human tissue samples...
December 11, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/29224008/mirnas-mediate-gdnf-induced-proliferation-and-migration-of-glioma-cells
#20
Bao-Le Zhang, Fu-Lu Dong, Ting-Wen Guo, Xiao-He Gu, Lin-Yan Huang, Dian-Shuai Gao
BACKGROUND/AIMS: Glial cell line-derived neurotrophic factor (GDNF) is an important factor promoting invasive glioma growth. This study was performed to reveal a unique mechanism of glioma cell proliferation and migration. METHODS: Human U251 glioma cells were used to screen the optimal GDNF concentration and treatment time to stimulate proliferation and migration. MicroRNA (MiRNA) expression profiles were detected by microarray and confirmed by real-time polymerase chain reaction (PCR)...
December 8, 2017: Cellular Physiology and Biochemistry
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