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Resource: Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis
- Riu Yamashita,
- Nuankanya P. Sathira,
- Akinori Kanai,
- Kousuke Tanimoto,
- Takako Arauchi,
- Yoshiaki Tanaka,
- Shin-ichi Hashimoto,
- Sumio Sugano,
- Kenta Nakai,
- and Yutaka Suzuki
Genome Res. May 2011 21: 775-789; Published in Advance March 3, 2011, doi:10.1101/gr.110254.110
.... We also demonstrate that integrative interpretation of transcriptome data is essential for the selection of putative alternative promoter TSCs, two of which also have protein consequences. Furthermore, discriminative chromatin features that separate TSCs at different expression levels were found...
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Research: Redundant and incoherent regulations of multiple phenotypes suggest microRNAs’ role in stability control
- Zhongqi Liufu,
- Yixin Zhao,
- Li Guo,
- Guangxia Miao,
- Juan Xiao,
- Yang Lyu,
- Yuxin Chen,
- Suhua Shi,
- Tian Tang,
- and Chung-I Wu
Genome Res. October 2017 27: 1665-1673; Published in Advance September 13, 2017, doi:10.1101/gr.222505.117
...expression pattern of miR310s in D. melanogaster, we constructed themir310s-Gal4 strain by transforming the putative promoter region of mir310s into w1118 flies. A ∼2.0-kb fragment upstream of mir310s was amplified from the genomic DNA of w1118 with forward primer 5′-TTAGATCTGAGCAGCAATTGTCGCAGTA-3...
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Methods: Computational prediction of miRNAs in Arabidopsis thaliana
- Alex Adai,
- Cameron Johnson,
- Sizolwenkosi Mlotshwa,
- Sarah Archer-Evans,
- Varun Manocha,
- Vicki Vance,
- and Venkatesan Sundaresan
Genome Res. January 2005 15: 78-91; doi:10.1101/gr.2908205
...of the precursor in other species such as rice. For a singleton non-conserved precursor like miR161, an alternative approach is to look for the presence of conserved target sites within related transcripts within the Arabidopsis . If we use the above transcript, At1g06580, to perform a BLASTN search of all...
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Research: Impact of microRNA regulation on variation in human gene expression
- Jian Lu and
- Andrew G. Clark
Genome Res. July 2012 22: 1243-1254; Published in Advance March 28, 2012, doi:10.1101/gr.132514.111
...(Kertesz et al. 2007). We also used the Context Score in the TargetScan package (TSt) to identify non-conserved miRNA targets of conservedmiRNAs and targets of non-conservedmiRNAs (Grimson et al. 2007; Baek et al. 2008). With each of the five algorithms, we consistently found evidence that mRNAs targeted...
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Research: MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum
- Maria Ninova,
- Matthew Ronshaugen,
- and Sam Griffiths-Jones
Genome Res. January 2016 26: 85-96; Published in Advance October 30, 2015, doi:10.1101/gr.193367.115
...iriririririririririririririririririririririririririririririririririririririririririririririririririririrc-5 iririrl-4 irirl-3 ir1 Mb mir-3836 mir-3851Families: mir-3858 cluster of non-conserved miRs cluster of conserved miRs singleton Tribolium-specific miR (other than mir-3836/3851/3858) singleton conserved miR Figure 1. Genomic organization of known and novel microRNAs in T. castaneum. Horizontal...
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Methods: Transcriptional and post-transcriptional profile of human chromosome 21
- Sergey I. Nikolaev,
- Samuel Deutsch,
- Raphael Genolet,
- Christelle Borel,
- Leila Parand,
- Catherine Ucla,
- Frederic Schütz,
- Genevieve Duriaux Sail,
- Yann Dupré,
- Pascale Jaquier-Gubler,
- Tanguy Araud,
- Beatrice Conne,
- Patrick Descombes,
- Jean-Dominique Vassalli,
- Joseph Curran,
- and Stylianos E. Antonarakis
Genome Res. August 2009 19: 1471-1479; Published in Advance July 6, 2009, doi:10.1101/gr.089425.108
...across the human genome, a substantial fraction of which is not associated with any functional annotation. However, very little is known regarding the post-transcriptional processes that operate within the different classes of RNA molecules. To characterize the post-transcriptional properties...
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ARTICLE: Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression
- Wei Deng,
- Xiaopeng Zhu,
- Geir Skogerbø,
- Yi Zhao,
- Zhuo Fu,
- Yudong Wang,
- Housheng He,
- Lun Cai,
- Hong Sun,
- Changning Liu,
- Biao Li,
- Baoyan Bai,
- Jie Wang,
- Dong Jia,
- Shiwei Sun,
- Hang He,
- Yan Cui,
- Yu Wang,
- Dongbo Bu,
- and Runsheng Chen
Genome Res. January 2006 16: 20-29; Published in Advance December 12, 2005, doi:10.1101/gr.4139206
...of ncRNA-specific upstream promoter elements. Furthermore, the transcription levels of at least 60% of the ncRNAs vary with developmental stages. We identified two new classes of ncRNAs, stem-bulge RNAs (sbRNAs) and snRNA-like RNAs (snlRNAs), both featuring distinct internal motifs, secondary structures...
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LETTER: Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle
- Miri Cohen-Zinder,
- Eyal Seroussi,
- Denis M. Larkin,
- Juan J. Loor,
- Annelie Everts-van der Wind,
- Jun-Heon Lee,
- James K. Drackley,
- Mark R. Band,
- A.G. Hernandez,
- Moshe Shani,
- Harris A. Lewin,
- Joel I. Weller,
- and Micha Ron
Genome Res. July 2005 15: 936-944; doi:10.1101/gr.3806705
...) was shotgun sequenced. By aligning this sequence with bovine ESTs and human orthologous genes, we identified in this BAC the last 15 exons of the bovine ABCG2 gene, which included the whole putative polypeptide sequence of the ABCG2 transporter (protein CAI38796.1). In the opposite orientation on the BAC, we...

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