Literature DB >> 27700226

LncRNAs: Bridging environmental sensing and gene expression.

Zachary T Beck1, Zheng Xing1, Elizabeth J Tran1,2.   

Abstract

The survival of all organisms is dependent on complex, coordinated responses to environmental cues. Non-coding RNAs have been identified as major players in regulation of gene expression, with recent evidence supporting roles for long non-coding (lnc)RNAs in both transcriptional and post-transcriptional control. Evidence from our laboratory shows that lncRNAs have the ability to form hybridized structures called R-loops with specific DNA target sequences in S. cerevisiae, thereby modulating gene expression. In this Point of View, we provide an overview of the nature of lncRNA-mediated control of gene expression in the context of our studies using the GAL gene cluster as a model for controlling the timing of transcription.

Entities:  

Keywords:  Environment; R-loops; gene expression; helicase; long non-coding; metabolism; ncRNA

Mesh:

Substances:

Year:  2016        PMID: 27700226      PMCID: PMC5207385          DOI: 10.1080/15476286.2016.1240139

Source DB:  PubMed          Journal:  RNA Biol        ISSN: 1547-6286            Impact factor:   4.652


  109 in total

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2.  Gene activation by dissociation of an inhibitor from a transcriptional activation domain.

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Authors:  M Muramatsu; J L Hodnett; H Busch
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Review 4.  Yeast Gal4: a transcriptional paradigm revisited.

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5.  A role for noncoding transcription in activation of the yeast PHO5 gene.

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6.  Regulation of glucose-dependent gene expression by the RNA helicase Dbp2 in Saccharomyces cerevisiae.

Authors:  Zachary T Beck; Sara C Cloutier; Matthew J Schipma; Christopher J Petell; Wai Kit Ma; Elizabeth J Tran
Journal:  Genetics       Date:  2014-08-27       Impact factor: 4.562

7.  The transcriptional landscape of the mammalian genome.

Authors:  P Carninci; T Kasukawa; S Katayama; J Gough; M C Frith; N Maeda; R Oyama; T Ravasi; B Lenhard; C Wells; R Kodzius; K Shimokawa; V B Bajic; S E Brenner; S Batalov; A R R Forrest; M Zavolan; M J Davis; L G Wilming; V Aidinis; J E Allen; A Ambesi-Impiombato; R Apweiler; R N Aturaliya; T L Bailey; M Bansal; L Baxter; K W Beisel; T Bersano; H Bono; A M Chalk; K P Chiu; V Choudhary; A Christoffels; D R Clutterbuck; M L Crowe; E Dalla; B P Dalrymple; B de Bono; G Della Gatta; D di Bernardo; T Down; P Engstrom; M Fagiolini; G Faulkner; C F Fletcher; T Fukushima; M Furuno; S Futaki; M Gariboldi; P Georgii-Hemming; T R Gingeras; T Gojobori; R E Green; S Gustincich; M Harbers; Y Hayashi; T K Hensch; N Hirokawa; D Hill; L Huminiecki; M Iacono; K Ikeo; A Iwama; T Ishikawa; M Jakt; A Kanapin; M Katoh; Y Kawasawa; J Kelso; H Kitamura; H Kitano; G Kollias; S P T Krishnan; A Kruger; S K Kummerfeld; I V Kurochkin; L F Lareau; D Lazarevic; L Lipovich; J Liu; S Liuni; S McWilliam; M Madan Babu; M Madera; L Marchionni; H Matsuda; S Matsuzawa; H Miki; F Mignone; S Miyake; K Morris; S Mottagui-Tabar; N Mulder; N Nakano; H Nakauchi; P Ng; R Nilsson; S Nishiguchi; S Nishikawa; F Nori; O Ohara; Y Okazaki; V Orlando; K C Pang; W J Pavan; G Pavesi; G Pesole; N Petrovsky; S Piazza; J Reed; J F Reid; B Z Ring; M Ringwald; B Rost; Y Ruan; S L Salzberg; A Sandelin; C Schneider; C Schönbach; K Sekiguchi; C A M Semple; S Seno; L Sessa; Y Sheng; Y Shibata; H Shimada; K Shimada; D Silva; B Sinclair; S Sperling; E Stupka; K Sugiura; R Sultana; Y Takenaka; K Taki; K Tammoja; S L Tan; S Tang; M S Taylor; J Tegner; S A Teichmann; H R Ueda; E van Nimwegen; R Verardo; C L Wei; K Yagi; H Yamanishi; E Zabarovsky; S Zhu; A Zimmer; W Hide; C Bult; S M Grimmond; R D Teasdale; E T Liu; V Brusic; J Quackenbush; C Wahlestedt; J S Mattick; D A Hume; C Kai; D Sasaki; Y Tomaru; S Fukuda; M Kanamori-Katayama; M Suzuki; J Aoki; T Arakawa; J Iida; K Imamura; M Itoh; T Kato; H Kawaji; N Kawagashira; T Kawashima; M Kojima; S Kondo; H Konno; K Nakano; N Ninomiya; T Nishio; M Okada; C Plessy; K Shibata; T Shiraki; S Suzuki; M Tagami; K Waki; A Watahiki; Y Okamura-Oho; H Suzuki; J Kawai; Y Hayashizaki
Journal:  Science       Date:  2005-09-02       Impact factor: 47.728

8.  The homologous recombination machinery modulates the formation of RNA-DNA hybrids and associated chromosome instability.

Authors:  Lamia Wahba; Steven K Gore; Douglas Koshland
Journal:  Elife       Date:  2013-06-11       Impact factor: 8.140

9.  RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships.

Authors:  Julie Nadel; Rodoniki Athanasiadou; Christophe Lemetre; N Ari Wijetunga; Pilib Ó Broin; Hanae Sato; Zhengdong Zhang; Jeffrey Jeddeloh; Cristina Montagna; Aaron Golden; Cathal Seoighe; John M Greally
Journal:  Epigenetics Chromatin       Date:  2015-11-16       Impact factor: 4.954

10.  Recruitment, Duplex Unwinding and Protein-Mediated Inhibition of the Dead-Box RNA Helicase Dbp2 at Actively Transcribed Chromatin.

Authors:  Wai Kit Ma; Bishnu P Paudel; Zheng Xing; Ivan G Sabath; David Rueda; Elizabeth J Tran
Journal:  J Mol Biol       Date:  2016-02-11       Impact factor: 5.469

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  10 in total

1.  Antisense transcription represses Arabidopsis seed dormancy QTL DOG1 to regulate drought tolerance.

Authors:  Ruslan Yatusevich; Halina Fedak; Arkadiusz Ciesielski; Katarzyna Krzyczmonik; Anna Kulik; Grazyna Dobrowolska; Szymon Swiezewski
Journal:  EMBO Rep       Date:  2017-10-13       Impact factor: 8.807

2.  Developmental transitions in Arabidopsis are regulated by antisense RNAs resulting from bidirectionally transcribed genes.

Authors:  Katarzyna Krzyczmonik; Agata Wroblewska-Swiniarska; Szymon Swiezewski
Journal:  RNA Biol       Date:  2017-05-17       Impact factor: 4.652

3.  Natural temperature fluctuations promote COOLAIR regulation of FLC.

Authors:  Yusheng Zhao; Pan Zhu; Jo Hepworth; Rebecca Bloomer; Rea Laila Antoniou-Kourounioti; Jade Doughty; Amelie Heckmann; Congyao Xu; Hongchun Yang; Caroline Dean
Journal:  Genes Dev       Date:  2021-05-13       Impact factor: 11.361

4.  The lncRNA PCAT1 is correlated with poor prognosis and promotes cell proliferation, invasion, migration and EMT in osteosarcoma.

Authors:  Xuedong Zhang; Yakui Zhang; Yong Mao; Xinlong Ma
Journal:  Onco Targets Ther       Date:  2018-01-31       Impact factor: 4.147

5.  LINC01016 promotes the malignant phenotype of endometrial cancer cells by regulating the miR-302a-3p/miR-3130-3p/NFYA/SATB1 axis.

Authors:  Xin Pan; Da Li; Jianing Huo; Fanfei Kong; Hui Yang; Xiaoxin Ma
Journal:  Cell Death Dis       Date:  2018-02-21       Impact factor: 8.469

6.  Long noncoding RNA myocardial infarction‑associated transcript is associated with the microRNA‑150‑5p/P300 pathway in cardiac hypertrophy.

Authors:  Zhao Li; Yamin Liu; Xiaofan Guo; Guozhe Sun; Qun Ma; Ying Dai; Guangshuo Zhu; Yingxian Sun
Journal:  Int J Mol Med       Date:  2018-05-21       Impact factor: 4.101

7.  Linc00423 as a tumor suppressor in retroperitoneal liposarcoma via activing MAPK signaling pathway through destabilizing of NFATC3.

Authors:  Yong Zhang; Hanxing Tong; Junyi He; Yebo Shao; Xi Guo; Rongyuan Zhuang; Jue Yang; Ju Liu; Yuqin Ding; Wenshuai Liu; Weiqi Lu; Yuhong Zhou
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8.  The Expression of the Cancer-Associated lncRNA Snhg15 Is Modulated by EphrinA5-Induced Signaling.

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Review 9.  Long Noncoding RNAs and Mitochondrial Homeostasis in the Development of Diabetic Retinopathy.

Authors:  Renu A Kowluru
Journal:  Front Endocrinol (Lausanne)       Date:  2022-06-06       Impact factor: 6.055

10.  Inference of Crosstalk Effects between DNA Methylation and lncRNA Regulation in NSCLC.

Authors:  Binhua Tang
Journal:  Biomed Res Int       Date:  2018-06-24       Impact factor: 3.411

  10 in total

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