Searching journal content for articles similar to Pauli et al. 22 (3): 577.

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  1. Research: Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis
    • Paola Cornejo-Páramo,
    • Kathrein Roper,
    • Sandie M. Degnan,
    • Bernard M. Degnan,
    • and Emily S. Wong
    Genome Res. March 2022 32: 474-487; Published in Advance January 19, 2022, doi:10.1101/gr.275864.121
    ...repertoire is complex and animal-like. Amphimedon displays an extensive repertoire of noncoding elements, including microRNAs, long noncoding RNAs, and piwiRNAs (Grimson et al. 2008; Gaiti et al. 2017; Calcino et al. 2018). The larval and adult stages possess metazoan regulatory innovations, including distal...
  2. Resource: Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis
    • Yingshu Li,
    • Yongjie Liu,
    • Hang Yang,
    • Ting Zhang,
    • Kiyoshi Naruse,
    • and Qiang Tu
    Genome Res. June 2020 30: 924-937; Published in Advance June 26, 2020, doi:10.1101/gr.258871.119
    ...scores of novel genes showed a bimodal distribution, indicating that a large portion of them are noncoding genes (Supplemental Fig. S5). In the end, 1135 lncRNAs were identified (Supplemental Table S3). This work is a great expansion of lncRNA annotation in the medaka as no systematic survey had been...
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  3. Method: High-confidence coding and noncoding transcriptome maps
    • Bo-Hyun You,
    • Sang-Ho Yoon,
    • and Jin-Wu Nam
    Genome Res. June 2017 27: 1050-1062; Published in Advance April 10, 2017, doi:10.1101/gr.214288.116
    ....0 (Cabili et al. 2011), and MiTranscriptome (Iyer et al. 2015), have massively reconstructed whole transcriptomes by assembling large-scale RNA-seq data and have characterized transcriptome-wide noncoding RNAs (ncRNAs). The majority of RNAs in the noncoding transcriptome were longncRNAs (lncRNAs...
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  4. Research: Antisense RNAs during early vertebrate development are divided in groups with distinct features
    • Sanjana Pillay,
    • Hazuki Takahashi,
    • Piero Carninci,
    • and Aditi Kanhere
    Genome Res. June 2021 31: 995-1010; Published in Advance April 1, 2021, doi:10.1101/gr.262964.120
    ...and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK Corresponding author: a.kanhere@liverpool.ac.ukAbstractLong noncoding RNAs or lncRNAs are a class of non-protein-coding RNAs that are >200 nt in length. Almost 50% of lncRNAs during zebrafish development are transcribed in an antisense...
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  5. Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
    • Hyung Joo Lee,
    • Yiran Hou,
    • Ju Heon Maeng,
    • Nakul M. Shah,
    • Yujie Chen,
    • Heather A. Lawson,
    • Hongbo Yang,
    • Feng Yue,
    • and Ting Wang
    Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
    ...). This is similar to the work revealing the contribution of a human-specific endogenous retrovirus to TP53 binding sites in the human (Wang et al. 2007). Additionally, it has been shown that zebrafish TEs can contribute to long noncoding RNAs (Kapusta et al. 2013). However, a systemic analysis of the contribution...
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  6. Resource: Long noncoding RNAs in C. elegans
    • Jin-Wu Nam and
    • David P. Bartel
    Genome Res. December 2012 22: 2529-2540; Published in Advance June 15, 2012, doi:10.1101/gr.140475.112
    ...Long noncoding RNAs in C. elegans Jin-Wu Nam 1 , 2 , 3 , 4 and David P. Bartel 1 , 2 , 3 , 5 1 Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA; 2 Howard Hughes Medical Institute, Massachusetts...
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  7. Research: Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals
    • Stefan Washietl,
    • Manolis Kellis,
    • and Manuel Garber
    Genome Res. April 2014 24: 616-628; Published in Advance January 15, 2014, doi:10.1101/gr.165035.113
    ...Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals Stefan Washietl 1 , Manolis Kellis 1 , 2 , 5 , 6 and Manuel Garber 2 , 3 , 4 , 5 , 6 1 Computer Science and Artificial Intelligence Laboratory...
  8. Resource: High resolution annotation of zebrafish transcriptome using long-read sequencing
    • German Nudelman,
    • Antonio Frasca,
    • Brandon Kent,
    • Kirsten C. Sadler,
    • Stuart C. Sealfon,
    • Martin J. Walsh,
    • and Elena Zaslavsky
    Genome Res. September 2018 28: 1415-1425; Published in Advance July 30, 2018, doi:10.1101/gr.223586.117
    ..., progress has been hampered by gaps in the annotation of the zebrafish and transcriptome. Recent studies profiling the zebrafish transcriptome using short-read RNA-sequencing technology during early embryogenesis suggest that thousands of transcripts are missing from the reference annotation (Aanes et al...
  9. Research: Dehydration stress extends mRNA 3′ untranslated regions with noncoding RNA functions in Arabidopsis
    • Hai-Xi Sun,
    • Yan Li,
    • Qi-Wen Niu,
    • and Nam-Hai Chua
    Genome Res. August 2017 27: 1427-1436; Published in Advance May 18, 2017, doi:10.1101/gr.218669.116
    ...′ UTRs have characteristics of long noncoding RNAs and likely do not interact with miRNAs. Functional studies using T-DNA insertion mutants reveal that they can act as antisense transcripts to repress expression levels of sense genes from the opposite strand or can activate the transcription or lead...
  10. Resource: Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis
    • Chirag Nepal,
    • Yavor Hadzhiev,
    • Christopher Previti,
    • Vanja Haberle,
    • Nan Li,
    • Hazuki Takahashi,
    • Ana Maria M. Suzuki,
    • Ying Sheng,
    • Rehab F. Abdelhamid,
    • Santosh Anand,
    • Jochen Gehrig,
    • Altuna Akalin,
    • Christel E.M. Kockx,
    • Antoine A.J. van der Sloot,
    • Wilfred F.J. van IJcken,
    • Olivier Armant,
    • Sepand Rastegar,
    • Craig Watson,
    • Uwe Strähle,
    • Elia Stupka,
    • Piero Carninci,
    • Boris Lenhard,
    • and Ferenc Müller
    Genome Res. November 2013 23: 1938-1950; Published in Advance September 3, 2013, doi:10.1101/gr.153692.112
    ...splice donor site-associated intronic RNA (sRNA) to be specific to genes of the splicingmachinery. For the identification of conserved features, we compared the zebrafish data sets to the first CAGE promoter map of Tetraodon and the existing human CAGE data. We show that a number of features...
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