Searching journal content for articles similar to Veeramachaneni et al. 14 (2): 280.

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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...sequence can often be shared between two genes and in some occurrences, a gene is located completely within a different gene; these are known as host/nested gene pairs. In these instances, if both genes are transcribed, overlap can result in a transcriptional crosstalk where genes regulate each other...
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In memoriam: Sydney Brenner—a personal perspective
- Byrappa Venkatesh
Genome Res. June 2019 29: vii-ix; doi:10.1101/gr.251918.119
...AND TECHNOLOGY)Sydney Brenner (1927–2019), a pioneering molecular biologist and scientific giant, passed away recently at the age of 92. This is a personal perspective on Sydney based on my association with him during the last 28 years.Sydney was born on January 13, 1927 in Germiston, a small town in South...
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Research: Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
- Akanksha Bafna,
- Gareth Banks,
- Michael H. Hastings,
- and Patrick M. Nolan
Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
....bafna@har.mrc.ac.uk, pmnolan10@gmail.comAbstractThe mammalian suprachiasmatic nucleus (SCN), located in the ventral hypothalamus, synchronizes and maintains daily cellular and physiological rhythms across the body, in accordance with environmental and visceral cues. Consequently, the systematic regulation of spatiotemporal...
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Resource: dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development
- Xin Huang,
- Xiaohan Tang,
- Xuemei Bai,
- Honglei Li,
- Huan Tao,
- Junting Wang,
- Yaru Li,
- Yu Sun,
- Yang Zheng,
- Xiang Xu,
- Longteng Wang,
- Yang Ding,
- Meisong Lu,
- Pingkun Zhou,
- Xiaochen Bo,
- Hao Li,
- and Hebing Chen
Genome Res. August 2022 32: 1612-1625; Published in Advance August 17, 2022, doi:10.1101/gr.276744.122
...commitment. With breakthroughs in experimental and low-input chromatin analysis technologies adapted for the preimplantation of mammalian embryos, large amounts of sequencing data were generated, which provided us with a comprehensive perspective of the dynamics of epigenetic information mediating...
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Research: High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes
- Walter Muskovic,
- Eve Slavich,
- Ben Maslen,
- Dominik C. Kaczorowski,
- Joseph Cursons,
- Edmund Crampin,
- and Maria Kavallaris
Genome Res. August 2022 32: 1463-1473; Published in Advance June 27, 2022, doi:10.1101/gr.276818.122
.... Indeed, existing limited investigations of lncRNA dynamics in transitioning mammalian cells indicate that lncRNA production precedes activation of protein-coding genes (De Santa et al. 2010; Aitken et al. 2015; Arner et al. 2015), providing evidence for lncRNAs as ubiquitous cis-regulators of gene...
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Research: Global analyses of the dynamics of mammalian microRNA metabolism
- Elena R. Kingston and
- David P. Bartel
Genome Res. November 2019 29: 1777-1790; Published in Advance September 13, 2019, doi:10.1101/gr.251421.119
...of miR-7 by the Oip5os1 (also known as Cyrano) long noncoding RNA (lncRNA) in mammalian tissues (Kleaveland et al. 2018).Questions also remain regarding the rates of miRNA turnover and the extent to which degradation is regulated in a miRNA-specific manner. Most miRNAs that have been examined are highly...
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Research: A compendium of conserved cleavage and polyadenylation events in mammalian genes
- Ruijia Wang,
- Dinghai Zheng,
- Ghassan Yehia,
- and Bin Tian
Genome Res. October 2018 28: 1427-1441; Published in Advance August 24, 2018, doi:10.1101/gr.237826.118
...RNA isoforms with different 3′ UTRs and/or coding sequences. Here, we present a compendium of conserved cleavage and polyadenylation sites (PASs) in mammalian genes, based on approximately 1.2 billion 3′ end sequencing reads from more than 360 human, mouse, and rat samples. We show that ∼80% of mammalian m...
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Research: Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes
- Vedran Franke,
- Sravya Ganesh,
- Rosa Karlic,
- Radek Malik,
- Josef Pasulka,
- Filip Horvat,
- Maja Kuzman,
- Helena Fulka,
- Marketa Cernohorska,
- Jana Urbanova,
- Eliska Svobodova,
- Jun Ma,
- Yutaka Suzuki,
- Fugaku Aoki,
- Richard M. Schultz,
- Kristian Vlahovicek,
- and Petr Svoboda
Genome Res. August 2017 27: 1384-1394; Published in Advance May 18, 2017, doi:10.1101/gr.216150.116
...Retrotransposons are “copy-and-paste” insertional mutagens that substantially contribute to mammalian content. Retrotransposons often carry long terminal repeats (LTRs) for retrovirus-like reverse transcription and integration into the . We report an extraordinary impact of a group of LTRs from the mammalian...
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Research: Genomes of Ellobius species provide insight into the evolutionary dynamics of mammalian sex chromosomes
- Eskeatnaf Mulugeta,
- Evelyne Wassenaar,
- Esther Sleddens-Linkels,
- Wilfred F.J. van IJcken,
- Edith Heard,
- J. Anton Grootegoed,
- Walter Just,
- Joost Gribnau,
- and Willy M. Baarends
Genome Res. September 2016 26: 1202-1210; Published in Advance August 10, 2016, doi:10.1101/gr.201665.115
...Genomes of Ellobius species provide insight into the evolutionary dynamics of mammalian sex chromosomes Eskeatnaf Mulugeta 1 , 2 , Evelyne Wassenaar 1 , Esther Sleddens-Linkels 1 , Wilfred F.J. van IJcken 3 , Edith Heard 2 , J. Anton...
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Research: The life history of retrocopies illuminates the evolution of new mammalian genes
- Francesco Nicola Carelli,
- Takashi Hayakawa,
- Yasuhiro Go,
- Hiroo Imai,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. March 2016 26: 301-314; Published in Advance January 4, 2016, doi:10.1101/gr.198473.115
...Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan New genes contribute substantially to adaptive evolutionary innovation, but the functional evolution of new mammalian genes has been little explored at a broad scale. Previous work...

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