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Journal articles on the topic 'Convergent transcription'

Author: Grafiati

Published: 25 May 2024

Last updated: 31 July 2025

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1

Lin, Yunfu, Mei Leng, Ma Wan, and John H. Wilson. "Convergent Transcription through a Long CAG Tract Destabilizes Repeats and Induces Apoptosis." Molecular and Cellular Biology 30, no. 18 (2010): 4435–51. http://dx.doi.org/10.1128/mcb.00332-10.

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ABSTRACT Short repetitive sequences are common in the human genome, and many fall within transcription units. We have previously shown that transcription through CAG repeat tracts destabilizes them in a way that depends on transcription-coupled nucleotide excision repair and mismatch repair. Recent observations that antisense transcription accompanies sense transcription in many human genes led us to test the effects of antisense transcription on triplet repeat instability in human cells. Here, we report that simultaneous sense and antisense transcription (convergent transcription) initiated f

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2

Hobson, David J., Wu Wei, Lars M. Steinmetz, and Jesper Q. Svejstrup. "RNA Polymerase II Collision Interrupts Convergent Transcription." Molecular Cell 48, no. 3 (2012): 365–74. http://dx.doi.org/10.1016/j.molcel.2012.08.027.

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3

Gullerova, Monika, and Nick J. Proudfoot. "Convergent transcription induces transcriptional gene silencing in fission yeast and mammalian cells." Nature Structural & Molecular Biology 19, no. 11 (2012): 1193–201. http://dx.doi.org/10.1038/nsmb.2392.

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4

Inagaki, Soichi, Mayumi Takahashi, Kazuya Takashima, Satoyo Oya, and Tetsuji Kakutani. "Chromatin-based mechanisms to coordinate convergent overlapping transcription." Nature Plants 7, no. 3 (2021): 295–302. http://dx.doi.org/10.1038/s41477-021-00868-3.

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5

Eszterhas, Susan K., Eric E. Bouhassira, David I. K. Martin, and Steven Fiering. "Transcriptional Interference by Independently Regulated Genes Occurs in Any Relative Arrangement of the Genes and Is Influenced by Chromosomal Integration Position." Molecular and Cellular Biology 22, no. 2 (2002): 469–79. http://dx.doi.org/10.1128/mcb.22.2.469-479.2002.

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ABSTRACT Transcriptional interference is the influence, generally suppressive, of one active transcriptional unit on another unit linked in cis. Its wide occurrence in experimental systems suggests that it may also influence transcription in many loci, but little is known about its precise nature or underlying mechanisms. Here we report a study of the interaction of two nearly identical transcription units juxtaposed in various arrangements. Each reporter gene in the constructs has its own promoter and enhancer and a strong polyadenylation signal. We used recombinase-mediated cassette exchange

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6

Marinov, Georgi K., Alexandro E. Trevino, Tingting Xiang, Anshul Kundaje, Arthur R. Grossman, and William J. Greenleaf. "Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum." Nature Genetics 53, no. 5 (2021): 613–17. http://dx.doi.org/10.1038/s41588-021-00848-5.

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AbstractDinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state; are not packaged by histones; and contain genes organized into tandem gene arrays, with minimal transcriptional regulation. We analyze the three-dimensional genome of Breviolum minutum, and find large topological domains (dinoflagellate topologically associating domains, which we term ‘dinoTADs’) without chromatin loops, which are demarcated by convergent gene array boundaries. Transcriptional inhibition disrupts dinoTADs, implicating transcription-

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7

Dang, Yunkun, Liande Li, Wei Guo, Zhihong Xue, and Yi Liu. "Convergent Transcription Induces Dynamic DNA Methylation at disiRNA Loci." PLoS Genetics 9, no. 9 (2013): e1003761. http://dx.doi.org/10.1371/journal.pgen.1003761.

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8

Lin, William Y., Yunfu Lin, and John H. Wilson. "Convergent transcription through microsatellite repeat tracts induces cell death." Molecular Biology Reports 41, no. 9 (2014): 5627–34. http://dx.doi.org/10.1007/s11033-014-3432-y.

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9

El Houdaigui, Bilal, Raphaël Forquet, Thomas Hindré, et al. "Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling." Nucleic Acids Research 47, no. 11 (2019): 5648–57. http://dx.doi.org/10.1093/nar/gkz300.

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Abstract DNA supercoiling acts as a global transcriptional regulator in bacteria, that plays an important role in adapting their expression programme to environmental changes, but for which no quantitative or even qualitative regulatory model is available. Here, we focus on spatial supercoiling heterogeneities caused by the transcription process itself, which strongly contribute to this regulation mode. We propose a new mechanistic modeling of the transcription-supercoiling dynamical coupling along a genome, which allows simulating and quantitatively reproducing in vitro and in vivo transcript

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10

Calero-Nieto, Fernando J., Andrew G. Bert, and Peter N. Cockerill. "Transcription-dependent silencing of inducible convergent transgenes in transgenic mice." Epigenetics & Chromatin 3, no. 1 (2010): 3. http://dx.doi.org/10.1186/1756-8935-3-3.

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11

Chatterjee, A., C. M. Johnson, C. C. Shu, et al. "Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation." Proceedings of the National Academy of Sciences 108, no. 23 (2011): 9721–26. http://dx.doi.org/10.1073/pnas.1101569108.

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12

Tripathi, Shubham, Sumitabha Brahmachari, José N. Onuchic, and Herbert Levine. "DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases." Nucleic Acids Research 50, no. 3 (2021): 1269–79. http://dx.doi.org/10.1093/nar/gkab1252.

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Abstract Multiple RNA polymerases (RNAPs) transcribing a gene have been known to exhibit collective group behavior, causing the transcription elongation rate to increase with the rate of transcription initiation. Such behavior has long been believed to be driven by a physical interaction or ‘push’ between closely spaced RNAPs. However, recent studies have posited that RNAPs separated by longer distances may cooperate by modifying the DNA segment under transcription. Here, we present a theoretical model incorporating the mechanical coupling between RNAP translocation and the DNA torsional respo

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13

Iosue, Christine L., Anthony P. Gulotta, Kathleen B. Selhorst, et al. "A Novel cis Element Achieves the Same Solution as an Ancestral cis Element During Thiamine Starvation in Candida glabrata." G3: Genes|Genomes|Genetics 10, no. 1 (2019): 321–31. http://dx.doi.org/10.1534/g3.119.400897.

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Regulatory networks often converge on very similar cis sequences to drive transcriptional programs due to constraints on what transcription factors are present. To determine the role of constraint loss on cis element evolution, we examined the recent appearance of a thiamine starvation regulated promoter in Candida glabrata. This species lacks the ancestral transcription factor Thi2, but still has the transcription factor Pdc2, which regulates thiamine starvation genes, allowing us to determine the effect of constraint change on a new promoter. We identified two different cis elements in C. gl

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14

Giordano, Ennio, Rosaria Rendina, Ivana Peluso, and Maria Furia. "RNAi Triggered by Symmetrically Transcribed Transgenes in Drosophila melanogaster." Genetics 160, no. 2 (2002): 637–48. http://dx.doi.org/10.1093/genetics/160.2.637.

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Abstract Specific silencing of target genes can be induced in a variety of organisms by providing homologous double-stranded RNA molecules. In vivo, these molecules can be generated either by transcription of sequences having an inverted-repeat (IR) configuration or by simultaneous transcription of sense-antisense strands. Since IR constructs are difficult to prepare and can stimulate genomic rearrangements, we investigated the silencing potential of symmetrically transcribed sequences. We report that Drosophila transgenes whose sense-antisense transcription was driven by two convergent arrays

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15

Castilla-Earls, Anny, and Katrina Fulcher-Rood. "Convergent and Divergent Validity of the Grammaticality and Utterance Length Instrument." Journal of Speech, Language, and Hearing Research 61, no. 1 (2018): 120–29. http://dx.doi.org/10.1044/2017_jslhr-l-17-0152.

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Purpose This feasibility study examines the convergent and divergent validity of the Grammaticality and Utterance Length Instrument (GLi), a tool designed to assess the grammaticality and average utterance length of a child's prerecorded story retell. Method Three raters used the GLi to rate audio-recorded story retells from 100 English-speaking preschool children. To examine convergent validity, the results of the GLi were correlated with 2 language sample measures, mean length of utterance in words and percentage of grammatical utterances, and with the results of the Structured Photographic

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16

Meng, Fei-Long, Zhou Du, Alexander Federation, et al. "Convergent Transcription at Intragenic Super-Enhancers Targets AID-Initiated Genomic Instability." Cell 159, no. 7 (2014): 1538–48. http://dx.doi.org/10.1016/j.cell.2014.11.014.

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17

Pannunzio, Nicholas R., and Michael R. Lieber. "Dissecting the Roles of Divergent and Convergent Transcription in Chromosome Instability." Cell Reports 14, no. 5 (2016): 1025–31. http://dx.doi.org/10.1016/j.celrep.2015.12.098.

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18

Anderson, Kevin M., Meghan A. Collins, Ru Kong, et al. "Convergent molecular, cellular, and cortical neuroimaging signatures of major depressive disorder." Proceedings of the National Academy of Sciences 117, no. 40 (2020): 25138–49. http://dx.doi.org/10.1073/pnas.2008004117.

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Major depressive disorder emerges from the complex interactions of biological systems that span genes and molecules through cells, networks, and behavior. Establishing how neurobiological processes coalesce to contribute to depression requires a multiscale approach, encompassing measures of brain structure and function as well as genetic and cell-specific transcriptional data. Here, we examine anatomical (cortical thickness) and functional (functional variability, global brain connectivity) correlates of depression and negative affect across three population-imaging datasets: UK Biobank, Brain

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19

Kim, Dong Eun, Maria-Giuseppina Procopio, Soumitra Ghosh, et al. "Convergent roles of ATF3 and CSL in chromatin control of cancer-associated fibroblast activation." Journal of Experimental Medicine 214, no. 8 (2017): 2349–68. http://dx.doi.org/10.1084/jem.20170724.

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Cancer-associated fibroblasts (CAFs) are important for tumor initiation and promotion. CSL, a transcriptional repressor and Notch mediator, suppresses CAF activation. Like CSL, ATF3, a stress-responsive transcriptional repressor, is down-modulated in skin cancer stromal cells, and Atf3 knockout mice develop aggressive chemically induced skin tumors with enhanced CAF activation. Even at low basal levels, ATF3 converges with CSL in global chromatin control, binding to few genomic sites at a large distance from target genes. Consistent with this mode of regulation, deletion of one such site 2 Mb

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20

Tsaneva-Atanasova, Krasimira, Petros Mina, Christopher J. Caunt, Stephen P. Armstrong, and Craig A. McArdle. "Decoding GnRH neurohormone pulse frequency by convergent signalling modules." Journal of The Royal Society Interface 9, no. 66 (2011): 170–82. http://dx.doi.org/10.1098/rsif.2011.0215.

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Gonadotropin-releasing hormone (GnRH) mediates control of reproduction. It is secreted in pulses and acts via intracellular effectors to activate gonadotrophin secretion and gene expression. Sub-maximal GnRH pulse frequency can elicit maximal responses, yielding bell-shaped frequency–response curves characteristic of genuine frequency decoders. GnRH frequency decoding is therapeutically important (pulsatile GnRH can drive ovulation in assisted reproduction whereas sustained activation can treat breast and prostate cancers), but the mechanisms are unknown. Here, we consider the possibility that

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21

Xue, Peng, David Corbett, Marie Goldrick, Clare Naylor, and Ian S. Roberts. "Regulation of Expression of the Region 3 Promoter of the Escherichia coli K5 Capsule Gene Cluster Involves H-NS, SlyA, and a Large 5′ Untranslated Region." Journal of Bacteriology 191, no. 6 (2008): 1838–46. http://dx.doi.org/10.1128/jb.01388-08.

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ABSTRACT Escherichia coli group 2 capsule gene clusters are temperature regulated, being expressed at 37°C but not at 20°C. Expression is regulated at the level of transcription by two convergent promoters, PR1 and PR3. In this paper, we show that regulation of transcription from PR3 involves a number of novel features including H-NS, SlyA, and a large 741-bp 5′ untranslated region (UTR). H-NS represses transcription from PR3 at 20°C and binds both 5′ and 3′ of the transcription start site. The 3′ downstream regulatory element (DRE) was essential for temperature-dependent H-NS repression. At 3

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22

Lengronne, Armelle, Yuki Katou, Saori Mori, et al. "Cohesin relocation from sites of chromosomal loading to places of convergent transcription." Nature 430, no. 6999 (2004): 573–78. http://dx.doi.org/10.1038/nature02742.

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23

Mills, William T., Noor N. Nassar, Deepa Ravindra, Xinbei Li та Mollie K. Meffert. "Multi-Level Regulatory Interactions between NF-κB and the Pluripotency Factor Lin28". Cells 9, № 12 (2020): 2710. http://dx.doi.org/10.3390/cells9122710.

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An appreciation for the complex interactions between the NF-κB transcription factor and the Lin28 RNA binding protein/let-7 microRNA pathways has grown substantially over the past decade. Both the NF-κB and Lin28/let-7 pathways are master regulators impacting cell survival, growth and proliferation, and an understanding of how interfaces between these pathways participate in governing pluripotency, progenitor differentiation, and neuroplastic responses remains an emerging area of research. In this review, we provide a concise summary of the respective pathways and focus on the function of sign

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24

Hundley, Thomas R., Alasdair M. Gilfillan, Christine Tkaczyk, Marcus V. Andrade, Dean D. Metcalfe та Michael A. Beaven. "Kit and FcϵRI mediate unique and convergent signals for release of inflammatory mediators from human mast cells". Blood 104, № 8 (2004): 2410–17. http://dx.doi.org/10.1182/blood-2004-02-0631.

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Abstract In human mast cells, derived from CD34+ peripheral blood cells, we observed that Kit ligand (KL) failed to induce degranulation but acted in synergy with antigen to markedly enhance degranulation, levels of cytokine gene transcripts, and production of cytokines. Further examination revealed that antigen and KL activated common and unique signaling pathways to account for these varied responses. KL, unlike antigen, failed to activate protein kinase C but activated phospholipase Cγ and calcium mobilization and augmented these signals as well as degranulation when added together with ant

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25

Qiu, Yichun, and Claudia Köhler. "Mobility connects: transposable elements wire new transcriptional networks by transferring transcription factor binding motifs." Biochemical Society Transactions 48, no. 3 (2020): 1005–17. http://dx.doi.org/10.1042/bst20190937.

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Transposable elements (TEs) constitute major fractions of plant genomes. Their potential to be mobile provides them with the capacity to cause major genome rearrangements. Those effects are potentially deleterious and enforced the evolution of epigenetic suppressive mechanisms controlling TE activity. However, beyond their deleterious effects, TE insertions can be neutral or even advantageous for the host, leading to long-term retention of TEs in the host genome. Indeed, TEs are increasingly recognized as major drivers of evolutionary novelties by regulating the expression of nearby genes. TEs

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26

Fang, Zhiming, Zhongming Zhao, Valsamma Eapen, and Raymond A. Clarke. "siRNA Mediate RNA Interference Concordant with Early On-Target Transient Transcriptional Interference." Genes 12, no. 8 (2021): 1290. http://dx.doi.org/10.3390/genes12081290.

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Exogenous siRNAs are commonly used to regulate endogenous gene expression levels for gene function analysis, genotype–phenotype association studies and for gene therapy. Exogenous siRNAs can target mRNAs within the cytosol as well as nascent RNA transcripts within the nucleus, thus complicating siRNA targeting specificity. To highlight challenges in achieving siRNA target specificity, we targeted an overlapping gene set that we found associated with a familial form of multiple synostosis syndrome type 4 (SYSN4). In the affected family, we found that a previously unknown non-coding gene TOSPEAK

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27

Crampton, Neal, William A. Bonass, Jennifer Kirkham, Claudio Rivetti, and Neil H. Thomson. "Collision events between RNA polymerases in convergent transcription studied by atomic force microscopy." Nucleic Acids Research 34, no. 19 (2006): 5416–25. http://dx.doi.org/10.1093/nar/gkl668.

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28

Martínez-Calvillo, Santiago, Dan Nguyen, Kenneth Stuart, and Peter J. Myler. "Transcription Initiation and Termination on Leishmania major Chromosome 3." Eukaryotic Cell 3, no. 2 (2004): 506–17. http://dx.doi.org/10.1128/ec.3.2.506-517.2004.

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ABSTRACT Genome projects involving Leishmania and other trypanosomatids have revealed that most genes in these organisms are organized into large clusters of genes on the same DNA strand. We have previously shown that transcription of the entire Leishmania major Friedlin (LmjF) chromosome 1 (chr1) initiates bidirectionally between two divergent gene clusters. Here, we analyze transcription of LmjF chr3, which contains two convergent clusters of 67 and 30 genes, separated by a tRNA gene, with a single divergent protein-coding gene located close to the “left” telomere. Nuclear run-on analyses in

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29

Tsaneva-Atanasova, Krasimira, Christopher J. Caunt, Stephen P. Armstrong, Rebecca M. Perrett, and Craig A. McArdle. "Decoding neurohormone pulse frequency by convergent signalling modules." Biochemical Society Transactions 40, no. 1 (2012): 273–78. http://dx.doi.org/10.1042/bst20110645.

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GnRH (gonadotropin-releasing hormone) mediates control of reproduction. It is secreted in pulses and acts via intracellular effectors to activate gene expression. Submaximal GnRH pulse frequency can elicit maximal responses, yielding bell-shaped frequency–response curves characteristic of genuine frequency decoders. GnRH frequency decoding is therapeutically important (pulsatile GnRH can drive ovulation in assisted reproduction, whereas sustained activation can treat breast and prostate cancers), but the mechanisms are unknown. In the present paper, we review recent work in this area, placing

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30

Jaeger, Tina, and Christoph Mayer. "The Transcriptional Factors MurR and Catabolite Activator Protein Regulate N-Acetylmuramic Acid Catabolism in Escherichia coli." Journal of Bacteriology 190, no. 20 (2008): 6598–608. http://dx.doi.org/10.1128/jb.00642-08.

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ABSTRACT The MurNAc etherase MurQ of Escherichia coli is essential for the catabolism of the bacterial cell wall sugar N-acetylmuramic acid (MurNAc) obtained either from the environment or from the endogenous cell wall (i.e., recycling). High-level expression of murQ is required for growth on MurNAc as the sole source of carbon and energy, whereas constitutive low-level expression of murQ is sufficient for the recycling of peptidoglycan fragments continuously released from the cell wall during growth of the bacteria. Here we characterize for the first time the expression of murQ and its regula

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Zhang, Xinyan, Meixia Zhao, Donald R. McCarty, and Damon Lisch. "Transposable elements employ distinct integration strategies with respect to transcriptional landscapes in eukaryotic genomes." Nucleic Acids Research 48, no. 12 (2020): 6685–98. http://dx.doi.org/10.1093/nar/gkaa370.

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Abstract Transposable elements (TEs) are ubiquitous DNA segments capable of moving from one site to another within host genomes. The extant distributions of TEs in eukaryotic genomes have been shaped by both bona fide TE integration preferences in eukaryotic genomes and by selection following integration. Here, we compare TE target site distribution in host genomes using multiple de novo transposon insertion datasets in both plants and animals and compare them in the context of genome-wide transcriptional landscapes. We showcase two distinct types of transcription-associated TE targeting strat

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32

Blombach, Fabian, Tina Daviter, Daniel Fielden, Dina Grohmann, Katherine Smollett, and Finn Werner. "Archaeology of RNA polymerase: factor swapping during the transcription cycle." Biochemical Society Transactions 41, no. 1 (2013): 362–67. http://dx.doi.org/10.1042/bst20120274.

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All RNAPs (RNA polymerases) repeatedly make use of their DNA template by progressing through the transcription cycle multiple times. During transcription initiation and elongation, distinct sets of transcription factors associate with multisubunit RNAPs and modulate their nucleic-acid-binding and catalytic properties. Between the initiation and elongation phases of the cycle, the factors have to be exchanged by a largely unknown mechanism. We have shown that the binding sites for initiation and elongation factors are overlapping and that the binding of the factors to RNAP is mutually exclusive

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33

O’Donovan, Aoife, Bing Sun, Steve Cole, et al. "Transcriptional Control of Monocyte Gene Expression in Post-Traumatic Stress Disorder." Disease Markers 30, no. 2-3 (2011): 123–32. http://dx.doi.org/10.1155/2011/560572.

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Post-traumatic stress disorder (PTSD) confers an increased risk for disorders with an inflammatory etiology. PTSD-related dysregulation of the sympathetic nervous system (SNS) and hypothalamic-pituitary adrenal (HPA) axis and associated alterations in inflammatory activity may contribute to this increased risk. However, little is known about convergent SNS, HPA and inflammatory signaling at the level of the immune cell transcriptome in PTSD. To explore such signaling, we examined the prevalence of specific transcription factor binding motifs in the promoter regions of differentially expressed

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34

Sameshima, J. H., R. C. Wek, and G. W. Hatfield. "Overlapping Transcription and Termination of the Convergent ilvA and ilvY Genes of Escherichia coli." Journal of Biological Chemistry 264, no. 2 (1989): 1224–31. http://dx.doi.org/10.1016/s0021-9258(19)85075-5.

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35

Chatterjee, Nimrat, Yunfu Lin, and John H. Wilson. "Mismatch repair enhances convergent transcription-induced cell death at trinucleotide repeats by activating ATR." DNA Repair 42 (June 2016): 26–32. http://dx.doi.org/10.1016/j.dnarep.2016.03.016.

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36

Chu, Jeffrey SC, David L. Baillie, and Nansheng Chen. "Convergent evolution of RFX transcription factors and ciliary genes predated the origin of metazoans." BMC Evolutionary Biology 10, no. 1 (2010): 130. http://dx.doi.org/10.1186/1471-2148-10-130.

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37

Tran, Ngat T., Michael T. Laub, and Tung B. K. Le. "SMC Progressively Aligns Chromosomal Arms in Caulobacter crescentus but Is Antagonized by Convergent Transcription." Cell Reports 20, no. 9 (2017): 2057–71. http://dx.doi.org/10.1016/j.celrep.2017.08.026.

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38

Chen, Kok-Siong, Jonathan W. C. Lim, Linda J. Richards, and Jens Bunt. "The convergent roles of the nuclear factor I transcription factors in development and cancer." Cancer Letters 410 (December 2017): 124–38. http://dx.doi.org/10.1016/j.canlet.2017.09.015.

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39

Deeble, Paul D., Daniel J. Murphy, Sarah J. Parsons, and Michael E. Cox. "Interleukin-6- and Cyclic AMP-Mediated Signaling Potentiates Neuroendocrine Differentiation of LNCaP Prostate Tumor Cells." Molecular and Cellular Biology 21, no. 24 (2001): 8471–82. http://dx.doi.org/10.1128/mcb.21.24.8471-8482.2001.

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ABSTRACT Neuroendocrine (NE) differentiation in prostatic adenocarcinomas has been reported to be an early marker for development of androgen independence. Secretion of mitogenic peptides from nondividing NE cells is thought to contribute to a more aggressive disease by promoting the proliferation of surrounding tumor cells. We undertook studies to determine whether the prostate cancer cell line LNCaP could be induced to acquire NE characteristics by treatment with agents that are found in the complex environment in which progression of prostate cancer towards androgen independence occurs. We

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40

Arnone, James T., Jeffrey R. Arace, Anand R. Soorneedi, Teryn T. Citino, Tadashi L. Kamitaki, and Michael A. McAlear. "Dissecting thecisandtransElements That Regulate Adjacent-Gene Coregulation in Saccharomyces cerevisiae." Eukaryotic Cell 13, no. 6 (2014): 738–48. http://dx.doi.org/10.1128/ec.00317-13.

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ABSTRACTThe relative positions that genes occupy on their respective chromosomes can play a critical role in determining how they are regulated at the transcriptional level. For example, a significant fraction of the genes from a variety of coregulated gene sets, including the ribosomal protein (RP) and the rRNA and ribosome biogenesis (RRB) regulons, exist as immediate, adjacent gene pairs. These gene pairs occur in all possible divergent, tandem, and convergent orientations. Adjacent-gene pairing in these regulons is associated with a tighter transcriptional coregulation than is observed for

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41

García-Rubio, María L., and Andrés Aguilera. "Topological constraints impair RNA polymerase II transcription and causes instability of plasmid-borne convergent genes." Nucleic Acids Research 40, no. 3 (2011): 1050–64. http://dx.doi.org/10.1093/nar/gkr840.

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42

Georgieva, L., V. Moskvina, T. Peirce, et al. "Convergent evidence that oligodendrocyte lineage transcription factor 2 (OLIG2) and interacting genes influence susceptibility to schizophrenia." Proceedings of the National Academy of Sciences 103, no. 33 (2006): 12469–74. http://dx.doi.org/10.1073/pnas.0603029103.

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43

Schmitt, Rebecca E., Brandon C. Shell, Kristen M. Lee, et al. "Convergent Evidence From Humans and Drosophila melanogaster Implicates the Transcription Factor MEF2B / Mef2 in Alcohol Sensitivity." Alcoholism: Clinical and Experimental Research 43, no. 9 (2019): 1872–86. http://dx.doi.org/10.1111/acer.14138.

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44

Liu, Zheng, Shuangcheng Gao, Shumin Zhang, Shangjun Yang, and Ning Sun. "Complex structures of transgene rearrangement implicate novel mechanisms of RNA-directed DNA methylation and convergent transcription." Genes & Genomics 36, no. 1 (2013): 95–103. http://dx.doi.org/10.1007/s13258-013-0147-8.

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45

Howell, Michael, Gareth J. Inman, and Caroline S. Hill. "A novel Xenopus Smad-interacting forkhead transcription factor (XFast-3) cooperates with XFast-1 in regulating gastrulation movements." Development 129, no. 12 (2002): 2823–34. http://dx.doi.org/10.1242/dev.129.12.2823.

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In early Xenopus embryos, the prototypical XFast-1/Smad2/Smad4 complex ARF1 is induced at the Mix.2 ARE by activin overexpression. We have characterised ARF2, a related, but much more abundant, complex formed during gastrulation in response to endogenous TGFβ family members and we have identified a novel Fast family member, XFast-3, as its transcription factor component. Endogenous ARF2 efficiently competes out ARF1 at early gastrulation, due to the ability of XFast-3 to interact with activated Smads with much higher affinity than XFast-1. We demonstrate that ARF1 and ARF2 are activated by dis

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Wilinski, Daniel, Natascha Buter, Andrew D. Klocko, et al. "Recurrent rewiring and emergence of RNA regulatory networks." Proceedings of the National Academy of Sciences 114, no. 14 (2017): E2816—E2825. http://dx.doi.org/10.1073/pnas.1617777114.

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Alterations in regulatory networks contribute to evolutionary change. Transcriptional networks are reconfigured by changes in the binding specificity of transcription factors and their cognate sites. The evolution of RNA–protein regulatory networks is far less understood. The PUF (Pumilio and FBF) family of RNA regulatory proteins controls the translation, stability, and movements of hundreds of mRNAs in a single species. We probe the evolution of PUF–RNA networks by direct identification of the mRNAs bound to PUF proteins in budding and filamentous fungi and by computational analyses of ortho

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Pénzes, Judit J., Hanh T. Pham, Paul Chipman, et al. "Molecular biology and structure of a novel penaeid shrimp densovirus elucidate convergent parvoviral host capsid evolution." Proceedings of the National Academy of Sciences 117, no. 33 (2020): 20211–22. http://dx.doi.org/10.1073/pnas.2008191117.

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The giant tiger prawn (Penaeus monodon) is a decapod crustacean widely reared for human consumption. Currently, viruses of two distinct lineages of parvoviruses (PVs, familyParvoviridae; subfamilyHamaparvovirinae) infect penaeid shrimp. Here, a PV was isolated and cloned from VietnameseP. monodonspecimens, designatedPenaeus monodonmetallodensovirus (PmMDV). This is the first member of a third divergent lineage shown to infect penaeid decapods. PmMDV has a transcription strategy unique among invertebrate PVs, using extensive alternative splicing and incorporating transcription elements characte

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Takano, Hideaki, Saemi Obitsu, Teruhiko Beppu, and Kenji Ueda. "Light-Induced Carotenogenesis in Streptomyces coelicolor A3(2): Identification of an Extracytoplasmic Function Sigma Factor That Directs Photodependent Transcription of the Carotenoid Biosynthesis Gene Cluster." Journal of Bacteriology 187, no. 5 (2005): 1825–32. http://dx.doi.org/10.1128/jb.187.5.1825-1832.2005.

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ABSTRACT Carotenoids are produced by a variety of organisms, but the mechanisms that regulate gene expression leading to carotenoid biosynthesis have been characterized for only a few organisms. In this study, we found that Streptomyces coelicolor A3(2), a gram-positive filamentous bacterium, produces carotenoids under blue light induction. The carotenoid fraction isolated from the cell extract contained multiple compounds, including isorenieratene and β-carotene. The carotenoid biosynthesis gene cluster of S. coelicolor consists of two convergent operons, crtEIBV and crtYTU, as previously sho

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Маркелова, Н. Ю., and N. Yu Markelova. "REP-elements of the Escherichia coli Genome and Transcription Signals: Positional and Functional Analysis." Mathematical Biology and Bioinformatics 10, no. 1 (2015): 245–59. http://dx.doi.org/10.17537/2015.10.245.

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In the intergenic regions of the Escherichia coli genome there are 356 REP- elements, containing 1-12 repeated sequences with degenerated consensus. Their biological role is poorly understood, but multiplicity in the genome, preferential localization between convergent genes and ability to form hairpin structures have led to the assumption that REP-elements participate in the transcription termination and processes affecting stability of the corresponding RNAs. Though the direct experiments did not confirm the ability of the model REP-sequence to stop RNA synthesis leaving some ambiguity regar

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Minchiotti, G., and P. P. Di Nocera. "Convergent transcription initiates from oppositely oriented promoters within the 5' end regions of Drosophila melanogaster F elements." Molecular and Cellular Biology 11, no. 10 (1991): 5171–80. http://dx.doi.org/10.1128/mcb.11.10.5171-5180.1991.

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Drosophila melanogaster F elements are mobile, oligo(A)-terminated DNA sequences that likely propagate by the retrotranscription of RNA intermediates. Plasmids bearing DNA segments from the left-hand region of a full-length F element fused to the CAT gene were used as templates for transient expression assays in Drosophila Schneider II cultured cells. Protein and RNA analyses led to the identification of two promoters, Fin and Fout, that transcribe in opposite orientations. The Fin promoter drives the synthesis of transcripts that initiate around residue +6 and are directed toward the element.

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