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Genes & Development

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https://www.readbyqxmd.com/read/28794186/hfq-links-translation-repression-to-stress-induced-mutagenesis-in-e-coli
#1
Jiandong Chen, Susan Gottesman
Mismatch repair (MMR) is a conserved mechanism exploited by cells to correct DNA replication errors both in growing cells and under nongrowing conditions. Hfq (host factor for RNA bacteriophage Qβ replication), a bacterial Lsm family RNA-binding protein, chaperones RNA-RNA interactions between regulatory small RNAs (sRNAs) and target messenger RNAs (mRNAs), leading to alterations of mRNA translation and/or stability. Hfq has been reported to post-transcriptionally repress the DNA MMR gene mutS in stationary phase, possibly limiting MMR to allow increased mutagenesis...
August 9, 2017: Genes & Development
https://www.readbyqxmd.com/read/28794185/id-genes-are-essential-for-early-heart-formation
#2
Thomas J Cunningham, Michael S Yu, Wesley L McKeithan, Sean Spiering, Florent Carrette, Chun-Teng Huang, Paul J Bushway, Matthew Tierney, Sonia Albini, Mauro Giacca, Miguel Mano, Pier Lorenzo Puri, Alessandra Sacco, Pilar Ruiz-Lozano, Jean-Francois Riou, Muriel Umbhauer, Gregg Duester, Mark Mercola, Alexandre R Colas
Deciphering the fundamental mechanisms controlling cardiac specification is critical for our understanding of how heart formation is initiated during embryonic development and for applying stem cell biology to regenerative medicine and disease modeling. Using systematic and unbiased functional screening approaches, we discovered that the Id family of helix-loop-helix proteins is both necessary and sufficient to direct cardiac mesoderm formation in frog embryos and human embryonic stem cells. Mechanistically, Id proteins specify cardiac cell fate by repressing two inhibitors of cardiogenic mesoderm formation-Tcf3 and Foxa2-and activating inducers Evx1, Grrp1, and Mesp1...
August 9, 2017: Genes & Development
https://www.readbyqxmd.com/read/28794184/post-transcriptional-regulation-of-mouse-neurogenesis-by-pumilio-proteins
#3
Meng Zhang, Dong Chen, Jing Xia, Wenqi Han, Xiekui Cui, Nils Neuenkirchen, Gretchen Hermes, Nenad Sestan, Haifan Lin
Despite extensive studies on mammalian neurogenesis, its post-transcriptional regulation remains under-explored. Here we report that neural-specific inactivation of two murine post-transcriptional regulators, Pumilio 1 (Pum1) and Pum2, severely reduced the number of neural stem cells (NSCs) in the postnatal dentate gyrus (DG), drastically increased perinatal apoptosis, altered DG cell composition, and impaired learning and memory. Consistently, the mutant DG neurospheres generated fewer NSCs with defects in proliferation, survival, and differentiation, supporting a major role of Pum1 and Pum2 in hippocampal neurogenesis and function...
August 9, 2017: Genes & Development
https://www.readbyqxmd.com/read/28790158/lung-tumors-with-distinct-p53-mutations-respond-similarly-to-p53-targeted-therapy-but-exhibit-genotype-specific-statin-sensitivity
#4
Frances K Turrell, Emma M Kerr, Meiling Gao, Hannah Thorpe, Gary J Doherty, Jake Cridge, David Shorthouse, Alyson Speed, Shamith Samarajiwa, Benjamin A Hall, Meryl Griffiths, Carla P Martins
Lung adenocarcinoma accounts for ∼40% of lung cancers, the leading cause of cancer-related death worldwide, and current therapies provide only limited survival benefit. Approximately half of lung adenocarcinomas harbor mutations in TP53 (p53), making these mutants appealing targets for lung cancer therapy. As mutant p53 remains untargetable, mutant p53-dependent phenotypes represent alternative targeting opportunities, but the prevalence and therapeutic relevance of such effects (gain of function and dominant-negative activity) in lung adenocarcinoma are unclear...
August 8, 2017: Genes & Development
https://www.readbyqxmd.com/read/28790157/sirt7-and-the-dead-box-helicase-ddx21-cooperate-to-resolve-genomic-r-loops-and-safeguard-genome-stability
#5
Chenlin Song, Agnes Hotz-Wagenblatt, Renate Voit, Ingrid Grummt
R loops are three-stranded nucleic acid structures consisting of an RNA:DNA heteroduplex and a "looped-out" nontemplate strand. As aberrant formation and persistence of R loops block transcription elongation and cause DNA damage, mechanisms that resolve R loops are essential for genome stability. Here we show that the DEAD (Asp-Glu-Ala-Asp)-box RNA helicase DDX21 efficiently unwinds R loops and that depletion of DDX21 leads to accumulation of cellular R loops and DNA damage. Significantly, the activity of DDX21 is regulated by acetylation...
August 8, 2017: Genes & Development
https://www.readbyqxmd.com/read/28779009/dach1-stimulates-shear-stress-guided-endothelial-cell-migration-and-coronary-artery-growth-through-the-cxcl12-cxcr4-signaling-axis
#6
Andrew H Chang, Brian C Raftrey, Gaetano D'Amato, Vinay N Surya, Aruna Poduri, Heidi I Chen, Andrew B Goldstone, Joseph Woo, Gerald G Fuller, Alexander R Dunn, Kristy Red-Horse
Sufficient blood flow to tissues relies on arterial blood vessels, but the mechanisms regulating their development are poorly understood. Many arteries, including coronary arteries of the heart, form through remodeling of an immature vascular plexus in a process triggered and shaped by blood flow. However, little is known about how cues from fluid shear stress are translated into responses that pattern artery development. Here, we show that mice lacking endothelial Dach1 had small coronary arteries, decreased endothelial cell polarization, and reduced expression of the chemokine Cxcl12 Under shear stress in culture, Dach1 overexpression stimulated endothelial cell polarization and migration against flow, which was reversed upon CXCL12/CXCR4 inhibition...
August 4, 2017: Genes & Development
https://www.readbyqxmd.com/read/28747430/ferredoxin-reductase-is-critical-for-p53-dependent-tumor-suppression-via-iron-regulatory-protein-2
#7
Yanhong Zhang, Yingjuan Qian, Jin Zhang, Wensheng Yan, Yong-Sam Jung, Mingyi Chen, Eric Huang, Kent Lloyd, Yuyou Duan, Jian Wang, Gang Liu, Xinbin Chen
Ferredoxin reductase (FDXR), a target of p53, modulates p53-dependent apoptosis and is necessary for steroidogenesis and biogenesis of iron-sulfur clusters. To determine the biological function of FDXR, we generated a Fdxr-deficient mouse model and found that loss of Fdxr led to embryonic lethality potentially due to iron overload in developing embryos. Interestingly, mice heterozygous in Fdxr had a short life span and were prone to spontaneous tumors and liver abnormalities, including steatosis, hepatitis, and hepatocellular carcinoma...
July 26, 2017: Genes & Development
https://www.readbyqxmd.com/read/28747429/the-hepatic-circadian-clock-fine-tunes-the-lipogenic-response-to-feeding-through-ror%C3%AE-%C3%AE
#8
Yuxiang Zhang, Romeo Papazyan, Manashree Damle, Bin Fang, Jennifer Jager, Dan Feng, Lindsey C Peed, Dongyin Guan, Zheng Sun, Mitchell A Lazar
Liver lipid metabolism is under intricate temporal control by both the circadian clock and feeding. The interplay between these two mechanisms is not clear. Here we show that liver-specific depletion of nuclear receptors RORα and RORγ, key components of the molecular circadian clock, up-regulate expression of lipogenic genes only under fed conditions at Zeitgeber time 22 (ZT22) but not under fasting conditions at ZT22 or ad libitum conditions at ZT10. RORα/γ controls circadian expression of Insig2, which keeps feeding-induced SREBP1c activation under check...
July 26, 2017: Genes & Development
https://www.readbyqxmd.com/read/28743695/ectopic-application-of-the-repressive-histone-modification-h3k9me2-establishes-post-zygotic-reproductive-isolation-in-arabidopsis-thaliana
#9
Hua Jiang, Jordi Moreno-Romero, Juan Santos-González, Geert De Jaeger, Kris Gevaert, Eveline Van De Slijke, Claudia Köhler
Hybrid seed lethality as a consequence of interspecies or interploidy hybridizations is a major mechanism of reproductive isolation in plants. This mechanism is manifested in the endosperm, a dosage-sensitive tissue supporting embryo growth. Deregulated expression of imprinted genes such as ADMETOS (ADM) underpin the interploidy hybridization barrier in Arabidopsis thaliana; however, the mechanisms of their action remained unknown. In this study, we show that ADM interacts with the AT hook domain protein AHL10 and the SET domain-containing SU(VAR)3-9 homolog SUVH9 and ectopically recruits the heterochromatic mark H3K9me2 to AT-rich transposable elements (TEs), causing deregulated expression of neighboring genes...
July 25, 2017: Genes & Development
https://www.readbyqxmd.com/read/28733371/an-mtr4-zfc3h1-complex-facilitates-turnover-of-unstable-nuclear-rnas-to-prevent-their-cytoplasmic-transport-and-global-translational-repression
#10
Koichi Ogami, Patricia Richard, Yaqiong Chen, Mainul Hoque, Wencheng Li, James J Moresco, John R Yates, Bin Tian, James L Manley
Many long noncoding RNAs (lncRNAs) are unstable and rapidly degraded in the nucleus by the nuclear exosome. An exosome adaptor complex called NEXT (nuclear exosome targeting) functions to facilitate turnover of some of these lncRNAs. Here we show that knockdown of one NEXT subunit, Mtr4, but neither of the other two subunits, resulted in accumulation of two types of lncRNAs: prematurely terminated RNAs (ptRNAs) and upstream antisense RNAs (uaRNAs). This suggested a NEXT-independent Mtr4 function, and, consistent with this, we isolated a distinct complex containing Mtr4 and the zinc finger protein ZFC3H1...
July 21, 2017: Genes & Development
https://www.readbyqxmd.com/read/28724615/glioblastoma-cellular-cross-talk-converges-on-nf-%C3%AE%C2%BAb-to-attenuate-egfr-inhibitor-sensitivity
#11
Ciro Zanca, Genaro R Villa, Jorge A Benitez, Amy Haseley Thorne, Tomoyuki Koga, Matteo D'Antonio, Shiro Ikegami, Jianhui Ma, Antonia D Boyer, Afsheen Banisadr, Nathan M Jameson, Alison D Parisian, Olesja V Eliseeva, Gabriela F Barnabe, Feng Liu, Sihan Wu, Huijun Yang, Jill Wykosky, Kelly A Frazer, Vladislav V Verkhusha, Maria G Isaguliants, William A Weiss, Timothy C Gahman, Andrew K Shiau, Clark C Chen, Paul S Mischel, Webster K Cavenee, Frank B Furnari
In glioblastoma (GBM), heterogeneous expression of amplified and mutated epidermal growth factor receptor (EGFR) presents a substantial challenge for the effective use of EGFR-directed therapeutics. Here we demonstrate that heterogeneous expression of the wild-type receptor and its constitutively active mutant form, EGFRvIII, limits sensitivity to these therapies through an interclonal communication mechanism mediated by interleukin-6 (IL-6) cytokine secreted from EGFRvIII-positive tumor cells. IL-6 activates a NF-κB signaling axis in a paracrine and autocrine manner, leading to bromodomain protein 4 (BRD4)-dependent expression of the prosurvival protein survivin (BIRC5) and attenuation of sensitivity to EGFR tyrosine kinase inhibitors (TKIs)...
July 19, 2017: Genes & Development
https://www.readbyqxmd.com/read/28724614/nuclear-mtor-acts-as-a-transcriptional-integrator-of-the-androgen-signaling-pathway-in-prostate-cancer
#12
Étienne Audet-Walsh, Catherine R Dufour, Tracey Yee, Fatima Z Zouanat, Ming Yan, Georges Kalloghlian, Mathieu Vernier, Maxime Caron, Guillaume Bourque, Eleonora Scarlata, Lucie Hamel, Fadi Brimo, Armen G Aprikian, Jacques Lapointe, Simone Chevalier, Vincent Giguère
Androgen receptor (AR) signaling reprograms cellular metabolism to support prostate cancer (PCa) growth and survival. Another key regulator of cellular metabolism is mTOR, a kinase found in diverse protein complexes and cellular localizations, including the nucleus. However, whether nuclear mTOR plays a role in PCa progression and participates in direct transcriptional cross-talk with the AR is unknown. Here, via the intersection of gene expression, genomic, and metabolic studies, we reveal the existence of a nuclear mTOR-AR transcriptional axis integral to the metabolic rewiring of PCa cells...
July 19, 2017: Genes & Development
https://www.readbyqxmd.com/read/28808066/maternal-mrnas-with-distinct-3-utrs-define-the-temporal-pattern-of-ccnb1-synthesis-during-mouse-oocyte-meiotic-maturation
#13
Ye Yang, Cai-Rong Yang, Seung Jin Han, Enrico Maria Daldello, Ara Cho, Joao P Sousa Martins, Guoliang Xia, Marco Conti
The final stages of female gamete maturation occur in the virtual absence of transcription, with gene expression driven by a program of selective unmasking, translation, and degradation of maternal mRNAs. Here we demonstrate that the timing of Ccnb1 mRNA translation in mouse oocytes is dependent on the presence of transcripts with different 3' untranslated regions (UTRs). This 3' UTR heterogeneity directs distinct temporal patterns of translational activation or repression. Inclusion or exclusion of cis-acting elements is responsible for these divergent regulations...
July 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28808065/the-punctilious-rna-polymerase-ii-core-promoter
#14
REVIEW
Long Vo Ngoc, Yuan-Liang Wang, George A Kassavetis, James T Kadonaga
The signals that direct the initiation of transcription ultimately converge at the core promoter, which is the gateway to transcription. Here we provide an overview of the RNA polymerase II core promoter in bilateria (bilaterally symmetric animals). The core promoter is diverse in terms of its composition and function yet is also punctilious, as it acts with strict rules and precision. We additionally describe an expanded view of the core promoter that comprises the classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure...
July 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28765161/the-interplay-between-epigenetic-changes-and-the-p53-protein-in-stem-cells
#15
REVIEW
Arnold J Levine, Shelley L Berger
Epigenetic programs regulate the development and maintenance of organisms over a lifetime. These programs are carried out through chemical modifications of DNA and proteins such as histones and transcription factors. These epigenetic modifications are less stable than genetic alterations and even reversible under a variety of circumstances, such as developmental changes, regeneration of tissues, cell divisions, aging, and pathological conditions observed in many cancers. The p53 protein not only enforces the stability of the genome by the prevention of genetic alterations in cells but also plays a role in regulating the epigenetic changes that can occur in cells...
June 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28765160/genome-integrity-and-disease-prevention-in-the-nervous-system
#16
REVIEW
Peter J McKinnon
Multiple DNA repair pathways maintain genome stability and ensure that DNA remains essentially unchanged over the life of a cell. Various human diseases occur if DNA repair is compromised, and most of these impact the nervous system, in some cases exclusively. However, it is often unclear what specific endogenous damage underpins disease pathology. Generally, the types of causative DNA damage are associated with replication, transcription, or oxidative metabolism; other direct sources of endogenous lesions may arise from aberrant topoisomerase activity or ribonucleotide incorporation into DNA...
June 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28765159/the-power-of-the-few
#17
REVIEW
Ran Chen, Yuan Pan, David H Gutmann
Converging evidence from numerous laboratories has revealed that malignant brain cancers are complex ecological systems composed of distinct cellular and acellular elements that collectively dictate glioblastoma biology. Our understanding of the individual contributions of each of these components is vital to the design of effective therapies against these cancers. In this issue of Genes & Development, Zanca and colleagues (pp. 1212-1227) demonstrate that one subpopulation of glioblastoma cells expressing a mutant epidermal growth factor receptor (EGFRvIII) is responsible for the survival of non-EGFRvIII-expressing tumor cells as well as for evading molecularly targeted therapy...
June 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28717046/from-structure-to-mechanism-understanding-initiation-of-dna-replication
#18
REVIEW
Alberto Riera, Marta Barbon, Yasunori Noguchi, L Maximilian Reuter, Sarah Schneider, Christian Speck
DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork. Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. We focus on the minichromosome maintenance (MCM2-7) proteins, which form the core of the eukaryotic replication fork, as this complex undergoes major structural rearrangements in order to engage with DNA, regulate its DNA-unwinding activity, and maintain genome stability...
June 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28717045/multitasking-by-polycomb-response-elements
#19
Elizabeth S Jaensch, Sharmistha Kundu, Robert E Kingston
Development requires the expression of master regulatory genes necessary to specify a cell lineage. Equally significant is the stable and heritable silencing of master regulators that would specify alternative lineages. This regulated gene silencing is carried out by Polycomb group (PcG) proteins, which must be correctly recruited only to the subset of their target loci that requires lineage-specific silencing. A recent study by Erceg and colleagues (pp. 590-602) expands on a key aspect of that targeting: The same DNA elements that recruit PcG complexes to a repressed locus also encode transcriptional enhancers that function in different lineages where that locus must be expressed...
June 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28717044/congenital-myotonic-dystrophy-an-rna-mediated-disease-across-a-developmental-continuum
#20
REVIEW
Sujatha Jagannathan, Robert K Bradley
Thomas and colleagues (pp. 1122-1133) demonstrate severe dysregulation of developmentally regulated alternative splicing and polyadenylation in congenital myotonic dystrophy (CDM). In doing so, they also highlight the importance of these post-transcriptional processes during normal fetal muscle development. Finally, they generate and characterize a mouse model of CDM that lacks all three Muscleblind-like proteins.
June 1, 2017: Genes & Development
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