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Research: NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors
- Joseph D. Fleming,
- Giulio Pavesi,
- Paolo Benatti,
- Carol Imbriano,
- Roberto Mantovani,
- and Kevin Struhl
Genome Res. August 2013 23: 1195-1209; Published in Advance April 17, 2013, doi:10.1101/gr.148080.112
...(Gatta and Mantovani 2011). 1196 Genome Research www..org Fleming et al. NF-Y binds to a diverse set of genomic features including nongenic regions We annotated the NF-Y bound regions in K562 to RefSeq genes, TSSs, maps of histone modifications and nucleosome-depleted regions, and RNA levels...
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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
...of our experimentally determined nTARs and compared it with the positive signals overlapping with RefSeq exons. In terms of conservation, as expected, expressed regions corresponding to RefSeq exons showed a substantial level of conservation with a median phastCons score of 0.425, whereas the majority...
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Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
- Nikolaos Vakirlis and
- Anne Kupczok
Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
...Corresponding authors: vakirlis@fleming.gr, anne.kupczok@wur.nlAbstractSpecies-specific genes, also known as orphans, are ubiquitous across life's domains. In prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in external elements such as viruses followed by horizontal gene...
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Research: Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant
- Haya H. Al-Balool,
- David Weber,
- Yilei Liu,
- Mark Wade,
- Kamlesh Guleria,
- Pitsien Lang Ping Nam,
- Jake Clayton,
- William Rowe,
- Jonathan Coxhead,
- Julie Irving,
- David J. Elliott,
- Andrew G. Hall,
- Mauro Santibanez-Koref,
- and Michael S. Jackson
Genome Res. November 2011 21: 1788-1799; Published in Advance September 23, 2011, doi:10.1101/gr.116442.110
...of novel human PTES transcripts As part of a pilot screen for novel splice variants and fusion genes within cancer s, a total of 9.7 Gb of Illumina and 454 Life Sciences (Roche) FLX sequence data was generated from seven human pediatric tumor samples and one cell line and was mapped to the RefSeq gene set...
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Research: The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients
- Zhaoshi Jiang,
- Suchit Jhunjhunwala,
- Jinfeng Liu,
- Peter M. Haverty,
- Michael I. Kennemer,
- Yinghui Guan,
- William Lee,
- Paolo Carnevali,
- Jeremy Stinson,
- Stephanie Johnson,
- Jingyu Diao,
- Stacy Yeung,
- Adrian Jubb,
- Weilan Ye,
- Thomas D. Wu,
- Sharookh B. Kapadia,
- Frederic J. de Sauvage,
- Robert C. Gentleman,
- Howard M. Stern,
- Somasekar Seshagiri,
- Krishna P. Pant,
- Zora Modrusan,
- Dennis G. Ballinger,
- and Zemin Zhang
Genome Res. April 2012 22: 593-601; Published in Advance January 20, 2012, doi:10.1101/gr.133926.111
...2010). The number of reads mapped to the exons of each RefSeq genewas calculated, and the corresponding RPKM (reads mapping to the per kilobase of transcript per million reads obtained fromsequencing) valuewas derived (SupplementalMaterial Section 3). Statistical analysis of differentially expressed...
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Perspective: Functional transcriptomics in the post-ENCODE era
- Jonathan M. Mudge,
- Adam Frankish,
- and Jennifer Harrow
Genome Res. December 2013 23: 1961-1973; Published in Advance October 30, 2013, doi:10.1101/gr.161315.113
.... There are several large-scale gene annotation projects in progress on the human , including RefSeq (Pruitt et al. 2005), GENCODE (Harrow et al. 2012), andUCSCGenes (Dreszer et al. 2012). In each ‘‘gene set’’ or ‘‘genebuild’’ produced, the vast majority of models are based upon transcriptomics data. Briefly, GENCODE...
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LETTER: Tandem chimerism as a means to increase protein complexity in the human genome
- Genís Parra,
- Alexandre Reymond,
- Noura Dabbouseh,
- Emmanouil T. Dermitzakis,
- Robert Castelo,
- Timothy M. Thomson,
- Stylianos E. Antonarakis,
- and Roderic Guigó
Genome Res. January 2006 16: 37-44; Published in Advance December 12, 2005, doi:10.1101/gr.4145906
...obtained from the UCSC Genome Browser database ( http://.cse.ucsc.edu/ ). The human NCBI33 (hg15, April 2003) assembly was used. The NCBI Reference Sequence (RefSeq; http://www.ncbi.nlm.nih.gov/RefSeq/ ) transcript coordinates were taken from the UCSC database refGenes.txt file. Coordinates of the EST...
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Research: Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency
- Chan-Shuo Wu,
- Chun-Ying Yu,
- Ching-Yu Chuang,
- Michael Hsiao,
- Cheng-Fu Kao,
- Hung-Chih Kuo,
- and Trees-Juen Chuang
Genome Res. January 2014 24: 25-36; Published in Advance October 16, 2013, doi:10.1101/gr.159483.113
...equally to this work. Abstract Trans -splicing is a post-transcriptional event that joins exons from separate pre-mRNAs. Detection of trans -splicing is usually severely hampered by experimental artifacts and genetic rearrangements. Here, we develop a new computational pipeline, TSscan, which...
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