Searching journal content for articles similar to Dinger et al. 18 (9): 1433.

Displaying results 1-10 of 258
For checked items
  1. Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
    • Marcel Tarbier,
    • Sebastian D. Mackowiak,
    • Vaishnovi Sekar,
    • Franziska Bonath,
    • Etka Yapar,
    • Bastian Fromm,
    • Omid R. Faridani,
    • Inna Biryukova,
    • and Marc R. Friedländer
    Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
    ...target expression variation and covariation, but these observations have been limited to a few microRNAs. Here we systematically study microRNA alternative functions in mouse embryonic stem cells (mESCs) by genetically deleting Drosha, leading to global loss of microRNAs. We apply complementary single...
    OPEN ACCESS ARTICLE
  2. Research: Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
    • Uditi Bhatt,
    • Anne Cucchiarini,
    • Yu Luo,
    • Cameron W. Evans,
    • Jean-Louis Mergny,
    • K. Swaminathan Iyer,
    • and Nicole M. Smith
    Genome Res. February 2024 34: 217-230; Published in Advance February 14, 2024, doi:10.1101/gr.278236.123
    ...the expression of a key transcription factor and oncogene, SOX2, a critical factor in maintaining pluripotency and embryonic and neural stem cells (Schaefer and Lengerke 2020; Mirzaei et al. 2022). Consequently, SOX2-OT participates in tumorigenic pathways for multiple cancer types, including lung cancer...
  3. Research: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
    • Richard D.W. Kelly,
    • Kristy R. Stengel,
    • Aditya Chandru,
    • Lyndsey C. Johnson,
    • Scott W. Hiebert,
    • and Shaun M. Cowley
    Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
    ...(HDACs). Deacetylation of histone tails results in chromatin tightening, and therefore, HDACs are generally regarded as transcriptional repressors. Counterintuitively, simultaneous deletion of Hdac1 and Hdac2 in embryonic stem cells (ESCs) reduces expression of the pluripotency-associated transcription...
    OPEN ACCESS ARTICLE
  4. Research: H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells
    • Haifen Chen,
    • Bo Hu,
    • Cynthia Horth,
    • Eric Bareke,
    • Phillip Rosenbaum,
    • Sin Young Kwon,
    • Jacinthe Sirois,
    • Daniel N. Weinberg,
    • Faith M. Robison,
    • Benjamin A. Garcia,
    • Chao Lu,
    • William A. Pastor,
    • and Jacek Majewski
    Genome Res. May 2022 32: 825-837; Published in Advance April 8, 2022, doi:10.1101/gr.276383.121
    ...interactions. Here, we use the mouse embryonic stem cell (mESC) model to describe in detail the relationships within the H3K27-H3K36-DNA methylation subnetwork. In particular, we focus on the major epigenetic reorganization caused by deletion of the histone 3 lysine 36 methyltransferase NSD1, which in m...
    OPEN ACCESS ARTICLE
  5. Research: Critical roles of long noncoding RNAs in Drosophila spermatogenesis
    • Kejia Wen,
    • Lijuan Yang,
    • Tuanlin Xiong,
    • Chao Di,
    • Danhui Ma,
    • Menghua Wu,
    • Zhaoyu Xue,
    • Xuedi Zhang,
    • Li Long,
    • Weimin Zhang,
    • Jiaying Zhang,
    • Xiaolin Bi,
    • Junbiao Dai,
    • Qiangfeng Zhang,
    • Zhi John Lu,
    • and Guanjun Gao
    Genome Res. September 2016 26: 1233-1244; Published in Advance August 11, 2016, doi:10.1101/gr.199547.115
    ...Critical roles of long noncoding RNAs in Drosophila spermatogenesis Kejia Wen 1 , 6 , Lijuan Yang 1 , 2 , 6 , Tuanlin Xiong 1 , 6 , Chao Di 1 , Danhui Ma 1 , Menghua Wu 1 , Zhaoyu Xue 1 , Xuedi Zhang 1...
  6. Research: A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells
    • Gurdeep Singh,
    • Shanelle Mullany,
    • Sakthi D. Moorthy,
    • Richard Zhang,
    • Tahmid Mehdi,
    • Ruxiao Tian,
    • Andrew G. Duncan,
    • Alan M. Moses,
    • and Jennifer A. Mitchell
    Genome Res. April 2021 31: 564-575; Published in Advance March 12, 2021, doi:10.1101/gr.272468.120
    ...reveals that pluripotent stem cell enhancers contain a conserved regulatory codeTo decipher the regulatory code in pluripotent cells, we investigated regions bound by multiple transcription factors in mouse and human embryonic stem cells (ESCs) (* in Fig. 1A), as these regions are more likely to show...
  7. Research: Embryonic LTR retrotransposons supply promoter modules to somatic tissues
    • Kosuke Hashimoto,
    • Eeva-Mari Jouhilahti,
    • Virpi Töhönen,
    • Piero Carninci,
    • Juha Kere,
    • and Shintaro Katayama
    Genome Res. November 2021 31: 1983-1993; Published in Advance October 21, 2021, doi:10.1101/gr.275354.121
    ...-implantation embryos. Nat Commun 10: 364. doi:10.1038/s41467-018-08244-0 ↵Lu X, Sachs F, Ramsay LA, Jacques PÉ, Göke J, Bourque G, Ng HH. 2014. The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. Nat Struct Mol Biol 21: 423–425. doi:10.1038/nsmb.2799 ↵Mager DL, Goodchild NL...
  8. Research: Noncoding regions underpin avian bill shape diversification at macroevolutionary scales
    • Leeban Yusuf,
    • Matthew C. Heatley,
    • Joseph P.G. Palmer,
    • Henry J. Barton,
    • Christopher R. Cooney,
    • and Toni I. Gossmann
    Genome Res. April 2020 30: 553-565; Published in Advance April 8, 2020, doi:10.1101/gr.255752.119
    ...with embryonic stem cell pathways, including BMP and Wnt signaling, both of which have repeatedly been implicated in the morphological development of avian beaks. This suggests that identifying genotype-phenotype association on a -wide scale over macroevolutionary time is feasible. Although the coding...
  9. Research: Regulation of the ESC transcriptome by nuclear long noncoding RNAs
    • Jan H. Bergmann,
    • Jingjing Li,
    • Mélanie A. Eckersley-Maslin,
    • Frank Rigo,
    • Susan M. Freier,
    • and David L. Spector
    Genome Res. September 2015 25: 1336-1346; Published in Advance June 5, 2015, doi:10.1101/gr.189027.114
    ..., The Babraham Institute, Babraham Research Campus, Cambridge CB22 AT, UK Abstract Long noncoding (lnc)RNAs have recently emerged as key regulators of gene expression. Here, we performed high-depth poly(A)+ RNA sequencing across multiple clonal populations of mouse embryonic stem cells (ESCs...
  10. Resource: The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
    • Christine E. Schnitzler,
    • E. Sally Chang,
    • Justin Waletich,
    • Gonzalo Quiroga-Artigas,
    • Wai Yee Wong,
    • Anh-Dao Nguyen,
    • Sofia N. Barreira,
    • Liam B. Doonan,
    • Paul Gonzalez,
    • Sergey Koren,
    • James M. Gahan,
    • Steven M. Sanders,
    • Brian Bradshaw,
    • Timothy Q. DuBuc,
    • Febrimarsa,
    • Danielle de Jong,
    • Eric P. Nawrocki,
    • Alexandra Larson,
    • Samantha Klasfeld,
    • Sebastian G. Gornik,
    • R. Travis Moreland,
    • Tyra G. Wolfsberg,
    • Adam M. Phillippy,
    • James C. Mullikin,
    • Oleg Simakov,
    • Paulyn Cartwright,
    • Matthew Nicotra,
    • Uri Frank,
    • and Andreas D. Baxevanis
    Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
    ...and tentaculozooids). The colonies lend themselves to experimental study as they are easily cultured on glass microscope slides (Fig. 1A). Marine hydroids, including Hydractinia, have fascinated biologists since the late 1800s (Weismann 1883) owing to their population of pluripotent stem cells, called “i-cells” given...
    OPEN ACCESS ARTICLE
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research