Searching journal content for articles similar to Itzkovitz et al. 20 (11): 1582.

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  1. Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
    • Koichi Kitao,
    • Kenji Ichiyanagi,
    • and So Nakagawa
    Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
    ...Frequent loss of the Lyosin isoform raises the suspicion that these sequences have remained by chance and are not evolutionarily conserved as functional protein-coding exons. Therefore, we next investigated the conservation of the amino acid sequences of exon L. Alignment of the amino acid sequences revealed...
  2. Research: Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains
    • Vivek Hari Sundar G,
    • Chenna Swetha,
    • Debjani Basu,
    • Kannan Pachamuthu,
    • Steffi Raju,
    • Tania Chakraborty,
    • Rebecca A. Mosher,
    • and P.V. Shivaprasad
    Genome Res. May 2023 33: 715-728; Published in Advance June 5, 2023, doi:10.1101/gr.277353.122
    ...is mediated using several factors including chromatin modifiers. However, factors that avoid the intrusion of silencing signals into protein-coding genes are poorly understood. Here we show that a plant specific paralog of RNA polymerase (Pol) II, named Pol IV, is involved in avoidance of facultative...
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  3. 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
    ...Corresponding authors: w.muskovic@garvan.org.au, m.kavallaris@ccia.unsw.edu.auAbstractThe advent of massively parallel sequencing revealed extensive transcription beyond protein-coding genes, identifying tens of thousands of long noncoding RNAs (lncRNAs). Selected functional examples raised the possibility...
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  4. Method: Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease
    • Yi-Fei Huang and
    • Adam Siepel
    Genome Res. August 2019 29: 1310-1321; Published in Advance June 27, 2019, doi:10.1101/gr.245522.118
    ...protein-coding sequences in the human . This map is generally consistent with previous inferences of the bulk distribution of fitness effects but reveals pervasive weak negative selection against synonymous mutations. In addition, the estimated selection coefficients are highly predictive of inherited...
  5. Resource: Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
    • Jonathan M. Mudge,
    • Irwin Jungreis,
    • Toby Hunt,
    • Jose Manuel Gonzalez,
    • James C. Wright,
    • Mike Kay,
    • Claire Davidson,
    • Stephen Fitzgerald,
    • Ruth Seal,
    • Susan Tweedie,
    • Liang He,
    • Robert M. Waterhouse,
    • Yue Li,
    • Elspeth Bruford,
    • Jyoti S. Choudhary,
    • Adam Frankish,
    • and Manolis Kellis
    Genome Res. December 2019 29: 2073-2087; Published in Advance September 19, 2019, doi:10.1101/gr.246462.118
    ...CSF Regions overlapping protein-coding sequences in the same frame that were annotated in GENCODE v23. We also excluded 234,336 regions overlapping annotated coding sequences in the “antisense frame” (the frame on the opposite strand that shares the third codon position) and 23,443 overlapping pseudogenes...
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  6. Method: An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics
    • Ulrich Omasits,
    • Adithi R. Varadarajan,
    • Michael Schmid,
    • Sandra Goetze,
    • Damianos Melidis,
    • Marc Bourqui,
    • Olga Nikolayeva,
    • Maxime Québatte,
    • Andrea Patrignani,
    • Christoph Dehio,
    • Juerg E. Frey,
    • Mark D. Robinson,
    • Bernd Wollscheid,
    • and Christian H. Ahrens
    Genome Res. December 2017 27: 2083-2095; Published in Advance November 15, 2017, doi:10.1101/gr.218255.116
    ...Center Zurich, ETH & UZH Zurich, CH-8057 Zurich, Switzerland ↵6 These authors contributed equally to this work. Corresponding author: christian.ahrens@agroscope.admin.chAbstractAccurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing...
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  7. Research: Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity
    • Yamile Marquez,
    • Markus Höpfler,
    • Zahra Ayatollahi,
    • Andrea Barta,
    • and Maria Kalyna
    Genome Res. July 2015 25: 995-1007; Published in Advance May 1, 2015, doi:10.1101/gr.186585.114
    ...are protein-coding sequences directly flanked by protein-coding exonic sequences, they have a great potential to boost protein diversity via AS. Furthermore, these intrinsic features of exitrons raise questions about the origin and evolution of their splicing. Here, we present a comprehensive characterization...
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  8. Method: Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
    • Michael F. Lin,
    • Pouya Kheradpour,
    • Stefan Washietl,
    • Brian J. Parker,
    • Jakob S. Pedersen,
    • and Manolis Kellis
    Genome Res. November 2011 21: 1916-1928; Published in Advance October 12, 2011, doi:10.1101/gr.108753.110
    ...Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes Michael F. Lin 1 , 2 , Pouya Kheradpour 1 , 2 , Stefan Washietl 2 , Brian J. Parker 3 , Jakob S. Pedersen 3 , 5...
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  9. Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
    • Terence Gall-Duncan,
    • Nozomu Sato,
    • Ryan K.C. Yuen,
    • and Christopher E. Pearson
    Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
    ...and suggest that similar findings may follow in the future. LOF due to expansions within protein-coding genes: in CCHS, expansions of polyalanine-coding GCN repeats result in impaired function of the protein (Amiel et al. 2003). LOF due to expansions within introns: in Friedreich ataxia (Al-Mahdawi et al...
  10. Method: A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness
    • Panagiotis Katsonis and
    • Olivier Lichtarge
    Genome Res. December 2014 24: 2050-2058; Published in Advance September 12, 2014, doi:10.1101/gr.176214.114
    ...A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness Panagiotis Katsonis 1 and Olivier Lichtarge 1 , 2 , 3 , 4 1 Department of Molecular and Human Genetics...
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