The Transcriptional Landscape of the Mammalian Genome

Carninci, Piero; Kasukawa, Takeya; Katayama, Shintaro; Gough, Julian; Frith, Martin C.; Maeda, Norihiro; Oyama, Rieko; Ravasi, Timothy; Lenhard, Boris; Wells, Christine A.; Kodzius, Rimantas; Shimokawa, Kuniyasu; Bajic, Vladimir B.; Brenner, Steven E.; Batalov, Serge; Forrest, Alistair R.R.; Zavolan, Mihaela; Davis, Melissa J.; Wilming, Laurens G.; Aidinis, Vassilis; Allen, Jonathan; Ambesi-Impiombato, Alberto; Apweiler, Rolf; Aturaliya, Rajith; Bailey, Timothy L.; Bansal, Mukul S.; Baxter, Laura L.; Beisel, Kirk W.; Bersano, Tom; Bono, Hidemasa; Chalk, Alistair M.; Chiu, Kuo Ping; Choudhary, Vijayata; Christoffels, Alan; Clutterbuck, D. R.; Crowe, Mark L.; Dalla, Emiliano; Dalrymple, Brian P.; Bono, Bernard de; Gatta, Giusy Della; Bernardo, Diego di; Down, Thomas A.; Engström, Pär G.; Fagiolini, Michela; Faulkner, Geoffrey J.; Fletcher, Colin; Fukushima, Tatsuya; Furuno, Masaaki; Futaki, Sugiko; Gariboldi, Manuela; Georgii-Hemming, Patrik; Gingeras, T; Gojobori, Takashi; Green, Edward; Gustincich, Stefano; Harbers, Matthias; Hayashi, Yoshitaka; Hensch, Takao K.; Hirokawa, Nobutaka; Hill, David E.; Huminiecki, Łukasz; Iacono, Michele; Ikeo, Kazuho; Iwama, Atsushi; Ishikawa, Takanori; Jakt, M.; Kanapin, Alexander; Katoh, Masaru; Kawasawa, Yuka Imamura; Kelso, Janet; Kitamura, Hiroshi; Kitano, Hiroaki; Kollias, George; Krishnan, S. P. T.; Kruger, Adéle; Kummerfeld, Sarah; Kurochkin, Igor V.; Lareau, Liana F.; Lazarevic, Dejan; Lipovich, Leonard; Liu, J.; Liuni, Sabino; McWilliam, Sean; Babu, M. Madan; Madera, Martin; Marchionni, Luigi; Matsuda, Hideo; Matsuzawa, Shu‐ichi; Miki, Hiroaki; Mignone, Flavio; Miyake, S.; Morris, Ken A.; Mottagui‐Tabar, Salim; Mulder, Nicola; Nakano, Norio; Nakauchi, Hiromitsu; Ng, Patrick; Nilsson, Roland; Nishiguchi, Seiji; Nishikawa, Shigemichi; Nori, Franco; Ohara, Osamu; Okazaki, Yasushi; Orlando, Valerio; Pang, Ken C; Pavan, William J.; Pavesi, Giulio; Pesole, Graziano; Petrovsky, Nikolai; Piazza, Silvano; Reed, James; Reid, James; Ring, Brian Z.; Ringwald, Martin; Rost, Burkhard; Ruan, Yijun; Salzberg, Steven L.; Sandelin, Albin; Schneider, Claudio; Schönbach, Christian; Sekiguchi, Kiyotoshi; Semple, Colin A.; Seno, Shigeto; Sessa, Luca; Sheng, Ying; Shibata, Yûkô; Shimada, Hiroshi; Shimada, Kiyo; Silva, D.; Sinclair, Bella; Sperling, Silke; Stupka, Elia; Sugiura, Koji; Sultana, Răzvan; Takenaka, Yasuhiro; Taki, Kohei; Tammoja, Kairi; Tan, Sin Lam; Suisheng, Tang; Taylor, Martin S.; Tegnér, Jesper; Teichmann, Sarah A.; Ueda, Hiroki R.; Nimwegen, Erik van; Verardo, Roberto; Wei, Chia Lin; Yagi, Ken; Yamanishi, Hiromichi; Zabarovsky, Eugene R.; Zhu, Shanshan; Zimmer, Andreas; Hide, Winston; Bult, Carol J.; Grimmond, Sean M.; Teasdale, Rohan D.; Liu, E. T.; Brusic, Vladimir; Quackenbush, John; Wahlestedt, Claes; Mattick, John S.; Hume, David; Cui, Kai; Sasaki, Daisuke; Tomaru, Yuji; Fukuda, Shiro; Kanamori-Katayama, Mutsumi; Suzuki, Masanori; Aoki, Juliana Ide; Arakawa, Takahiro; Iida, Juri; Imamura, Kengo; Itoh, Masayoshi; Kato, Tomomi; Kawaji, Hideya; Kawagashira, Nobuyuki; Kawashima, Tsugumi; Kojima, Miki; Kondo, Shinji; Konno, Hiroyuki; Nakano, Kenji; Ninomiya, Noriko; Nishio, Tomoaki; Okada, Mitsuhiro; Plessy, Charles; Shibata, Kazuhiro; Shiraki, Toshiyuki; Suzuki, Satoru; Tagami, Michihira; Waki, Kazunori; Watahiki, Akira; Okamura-Oho, Yuko; Suzuki, Harukazu; Kawai, Jun; Hayashizaki, Yoshihide

doi:10.1126/science.1112014

Cited by 3,066 publications

(1,314 citation statements)

References 18 publications

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“…As these RNA transcripts do not encode for any proteins, they are grouped as ncRNAs. The noncoding genomic regions serve as a template for the transcription of a large number of ncRNAs in addition to their role as a substrate for DNA binding protein (Carninci et al 2005). Based on the size of the ncRNAs, they are categorized into two groups including short ncRNAs and long ncRNAs.…”

Section: Noncoding Ribonucleic Acids (Ncrnas)mentioning

confidence: 99%

Long noncoding RNAs: emerging players in thyroid cancer pathogenesis

Murugan

Munirajan

Alzahrani

2018

Endocrine-Related Cancer

110

100

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Thyroid cancer continues to be the most common malignancy of endocrine glands. The incidence of thyroid cancer has risen significantly over the past 4 decades and has emerged as a major health issue. In recent years, significant progress has been achieved in our understanding of the molecular mechanisms of thyroid carcinogenesis, resulting in significant diagnostic, prognostic and therapeutic implications; yet, it has not reached a satisfactory level. Identifying novel molecular therapeutic targets and molecules for diagnosis and prognosis is expected to advance the overall management of this common malignancy. Long noncoding RNAs (lncRNAs) are implicated in the regulation of various key cellular genes involved in cell differentiation, proliferation, cell cycle, apoptosis, migration and invasion mainly through modulation of gene expression. Recent studies have established that lncRNAs are deregulated in thyroid cancer. In this review, we discuss extensively the tumor-suppressive (for example, LINC00271, MEG3, NAMA, PTCSC1/2/3, etc.) and oncogenic (for example, ANRIL, FAL1, H19, PVT1, etc.) roles of various lncRNAs and their possible disease associations implicated in thyroid carcinogenesis. We briefly summarize the strategies and mechanisms of lncRNA-targeting agents. We also describe the potential role of lncRNAs as prospective novel therapeutic targets, and diagnostic and prognostic markers in thyroid cancer.

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Section: Noncoding Ribonucleic Acids (Ncrnas)mentioning

confidence: 99%

Long noncoding RNAs: emerging players in thyroid cancer pathogenesis

Murugan

Munirajan

Alzahrani

2018

Endocrine-Related Cancer

110

100

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“…Since the introduction of CAGE, a great effort has been made by the FANTOM consortium to map genome-wide TSSs in numerous mouse and human samples [27,32,33]. This has led to the discovery of distinct classes of promoters with respect to TSS distribution that correlates with both underlying sequence features and gene function [12], and implies distinct modes of their regulation (reviewed in [34]).…”

Section: Cap Analysis Of Gene Expression (Cage)mentioning

confidence: 99%

Promoter architectures and developmental gene regulation

Haberle

Lenhard

2016

Seminars in Cell & Developmental Biology

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Core promoters are minimal regions sufficient to direct accurate initiation of transcription and are crucial for regulation of gene expression. They are highly diverse in terms of associated core promoter motifs, underlying sequence composition and patterns of transcription initiation.Distinctive features of promoters are also seen at the chromatin level, including nucleosome positioning patterns and presence of specific histone modifications. Recent advances in identifying and characterizing promoters using next-generation sequencing-based technologies have provided the basis for their classification into functional groups and have shed light on their modes of regulation, with important implications for transcriptional regulation in development.This review discusses the methodology and the results of genome-wide studies that provided insight into the diversity of RNA polymerase II promoter architectures in vertebrates and other Metazoa, and the association of these architectures with distinct modes of regulation in embryonic development and differentiation.

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“…18 Thus far, many lncRNAs have been shown to control the expression of protein-coding genes by recruiting chromatin remodeling factors to specific gene loci. 19 Histone modifying enzymes and nucleosome remodeling proteins that interact with lncRNAs include G9a, 20 LSD1, 21 PRC2, 21,22 SWI/SNF, 23 and MLL, 24 indicating a diversity of interactions.…”

mentioning

confidence: 99%

LncRNAs: Bridging environmental sensing and gene expression

2016

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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.

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The Transcriptional Landscape of the Mammalian Genome

Cited by 3,066 publications

References 18 publications

Long noncoding RNAs: emerging players in thyroid cancer pathogenesis

Long noncoding RNAs: emerging players in thyroid cancer pathogenesis

Promoter architectures and developmental gene regulation

LncRNAs: Bridging environmental sensing and gene expression

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