Literature DB >> 31043413

Illuminating Genomic Dark Matter with RNA Imaging.

Arjun Raj1, John L Rinn2.   

Abstract

In the postgenomic era, it is clear that the human genome encodes thousands of long noncoding RNAs (lncRNAs). Along the way, RNA imaging (e.g., RNA fluorescence in situ hybridization [RNA-FISH]) has been instrumental in identifying powerful roles for lncRNAs based on their subcellular localization patterns. Here, we explore how RNA imaging technologies have shed new light on how, when, and where lncRNAs may play functional roles. Specifically, we will synthesize the underlying principles of RNA imaging techniques by exploring several landmark lncRNA imaging studies that have illuminated key insights into lncRNA biology.
Copyright © 2019 Cold Spring Harbor Laboratory Press; all rights reserved.

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Year:  2019        PMID: 31043413      PMCID: PMC6496349          DOI: 10.1101/cshperspect.a032094

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Biol        ISSN: 1943-0264            Impact factor:   10.005


  91 in total

1.  A quick and simple FISH protocol with hybridization-sensitive fluorescent linear oligodeoxynucleotide probes.

Authors:  Dan Ohtan Wang; Hitomi Matsuno; Shuji Ikeda; Akiko Nakamura; Hiroyuki Yanagisawa; Yasunori Hayashi; Akimitsu Okamoto
Journal:  RNA       Date:  2011-11-18       Impact factor: 4.942

Review 2.  Noncoding RNAs and enhancers: complications of a long-distance relationship.

Authors:  Ulf Andersson Orom; Ramin Shiekhattar
Journal:  Trends Genet       Date:  2011-08-09       Impact factor: 11.639

3.  Telomeric noncoding RNA TERRA is induced by telomere shortening to nucleate telomerase molecules at short telomeres.

Authors:  Emilio Cusanelli; Carmina Angelica Perez Romero; Pascal Chartrand
Journal:  Mol Cell       Date:  2013-09-26       Impact factor: 17.970

4.  Single molecule imaging of RNA in situ.

Authors:  Mona Batish; Arjun Raj; Sanjay Tyagi
Journal:  Methods Mol Biol       Date:  2011

Review 5.  Biogenesis and function of nuclear bodies.

Authors:  Yuntao S Mao; Bin Zhang; David L Spector
Journal:  Trends Genet       Date:  2011-06-15       Impact factor: 11.639

6.  The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus.

Authors:  C J Brown; B D Hendrich; J L Rupert; R G Lafrenière; Y Xing; J Lawrence; H F Willard
Journal:  Cell       Date:  1992-10-30       Impact factor: 41.582

Review 7.  A single molecule view of gene expression.

Authors:  Daniel R Larson; Robert H Singer; Daniel Zenklusen
Journal:  Trends Cell Biol       Date:  2009-10-08       Impact factor: 20.808

8.  Single-Molecule Imaging Reveals a Switch between Spurious and Functional ncRNA Transcription.

Authors:  Tineke L Lenstra; Antoine Coulon; Carson C Chow; Daniel R Larson
Journal:  Mol Cell       Date:  2015-11-05       Impact factor: 17.970

9.  Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation.

Authors:  Marshall J Levesque; Arjun Raj
Journal:  Nat Methods       Date:  2013-02-17       Impact factor: 28.547

10.  Live-cell CRISPR imaging in plants reveals dynamic telomere movements.

Authors:  Steven Dreissig; Simon Schiml; Patrick Schindele; Oda Weiss; Twan Rutten; Veit Schubert; Evgeny Gladilin; Michael F Mette; Holger Puchta; Andreas Houben
Journal:  Plant J       Date:  2017-07-14       Impact factor: 6.417

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  9 in total

1.  Single-cell imaging reveals unexpected heterogeneity of telomerase reverse transcriptase expression across human cancer cell lines.

Authors:  Teisha J Rowland; Gabrijela Dumbović; Evan P Hass; John L Rinn; Thomas R Cech
Journal:  Proc Natl Acad Sci U S A       Date:  2019-08-26       Impact factor: 11.205

2.  Using RNA Sequencing and Spike-in RNAs to Measure Intracellular Abundance of lncRNAs and mRNAs.

Authors:  Megan D Schertzer; McKenzie M Murvin; J Mauro Calabrese
Journal:  Bio Protoc       Date:  2020-10-05

Review 3.  Long Noncoding RNAs and Human Liver Disease.

Authors:  Johanna K DiStefano; Glenn S Gerhard
Journal:  Annu Rev Pathol       Date:  2021-08-20       Impact factor: 32.350

Review 4.  lncRNAs in T lymphocytes: RNA regulation at the heart of the immune response.

Authors:  Leah M Plasek; Saba Valadkhan
Journal:  Am J Physiol Cell Physiol       Date:  2020-12-09       Impact factor: 4.249

5.  Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA is driven by intron retention.

Authors:  Gabrijela Dumbović; Ulrich Braunschweig; Heera K Langner; Michael Smallegan; Josep Biayna; Evan P Hass; Katarzyna Jastrzebska; Benjamin Blencowe; Thomas R Cech; Marvin H Caruthers; John L Rinn
Journal:  Nat Commun       Date:  2021-06-03       Impact factor: 14.919

Review 6.  New insights into the functional role of retrotransposon dynamics in mammalian somatic cells.

Authors:  Arianna Mangiavacchi; Peng Liu; Francesco Della Valle; Valerio Orlando
Journal:  Cell Mol Life Sci       Date:  2021-05-14       Impact factor: 9.261

Review 7.  A mechanistic view of long noncoding RNAs in cancer.

Authors:  Lauren Winkler; Nadya Dimitrova
Journal:  Wiley Interdiscip Rev RNA       Date:  2021-10-19       Impact factor: 9.349

8.  ALKBH5-mediated N6-methyladenosine modification of TRERNA1 promotes DLBCL proliferation via p21 downregulation.

Authors:  Wei Song; Fei Fei; Fengchang Qiao; Zuyi Weng; Yuanxun Yang; Bei Cao; Jing Yue; Jiaxuan Xu; Meihong Zheng; Juan Li
Journal:  Cell Death Discov       Date:  2022-01-14

9.  LNCAROD is stabilized by m6A methylation and promotes cancer progression via forming a ternary complex with HSPA1A and YBX1 in head and neck squamous cell carcinoma.

Authors:  Yuanyuan Ban; Pingqing Tan; Jing Cai; Junjun Li; Meng Hu; Ying Zhou; Yan Mei; Yixin Tan; Xiaoling Li; Zhaoyang Zeng; Wei Xiong; Guiyuan Li; Xiayu Li; Mei Yi; Bo Xiang
Journal:  Mol Oncol       Date:  2020-04-13       Impact factor: 6.603

  9 in total

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