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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...of targeted BAC clone sequence) to the pig, human, and mouse assemblies. A comprehensive analysis of annotated X-linked orthologs in public databases demonstrated that the majority of ampliconic gene families were present on the ancestral placental X Chromosome. We generated a domestic cat Hi-C contact map...
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Research: Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania
- Matthew B. Rogers,
- James D. Hilley,
- Nicholas J. Dickens,
- Jon Wilkes,
- Paul A. Bates,
- Daniel P. Depledge,
- David Harris,
- Yerim Her,
- Pawel Herzyk,
- Hideo Imamura,
- Thomas D. Otto,
- Mandy Sanders,
- Kathy Seeger,
- Jean-Claude Dujardin,
- Matthew Berriman,
- Deborah F. Smith,
- Christiane Hertz-Fowler,
- and Jeremy C. Mottram
Genome Res. December 2011 21: 2129-2142; Published in Advance October 28, 2011, doi:10.1101/gr.122945.111
...(based on the homologous L. major chromosomes), while the latter are fused at the 39 endof chromosome36 and the 59 endof chromosome 20. The gene models and functional annotation, based on predicted orthology, were transferred from L. major to the L. mexicana U1103 using the Rapid Annotation Transfer Tool...
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ENSEMBL Special: The Otter Annotation System
- Stephen M.J. Searle,
- James Gilbert,
- Vivek Iyer,
- and Michele Clamp
Genome Res. May 2004 14: 963-970; doi:10.1101/gr.1864804
...Press References ↵ Collins, J.E., Goward, M.E., Cole, C.G., Smink, L.J., Huckle, E.J., Knowles, S., Bye, J.M., Beare, D.M., and Dunham, I. 2003 . Reevaluating human gene annotation: A second-generation analysis of chromosome 22. Genome Res. 13 : 27 -36. ↵ Deloukas, P., Matthews, L.H., Ashurst, J...
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LETTER: Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22
- Leonard Lipovich and
- Mary-Claire King
Genome Res. January 2006 16: 45-54; Published in Advance December 12, 2005, doi:10.1101/gr.3883606
.... In this report, we refer to TUs identical to known genes as “known genes,” or simply “genes,” and to TUs identified by our analysis but devoid of known-gene identities and public-database annotations as “novel TUs,” or simply “TUs.” The goal of the present study was to annotate TUs and UGPs on chromosome 22 (chr...
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Resource: The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
- Thomas Derrien,
- Rory Johnson,
- Giovanni Bussotti,
- Andrea Tanzer,
- Sarah Djebali,
- Hagen Tilgner,
- Gregory Guernec,
- David Martin,
- Angelika Merkel,
- David G. Knowles,
- Julien Lagarde,
- Lavanya Veeravalli,
- Xiaoan Ruan,
- Yijun Ruan,
- Timo Lassmann,
- Piero Carninci,
- James B. Brown,
- Leonard Lipovich,
- Jose M. Gonzalez,
- Mark Thomas,
- Carrie A. Davis,
- Ramin Shiekhattar,
- Thomas R. Gingeras,
- Tim J. Hubbard,
- Cedric Notredame,
- Jennifer Harrow,
- and Roderic Guigó
Genome Res. September 2012 22: 1775-1789; doi:10.1101/gr.132159.111
...studies have demonstrated compelling biological and disease roles for individual examples, analytical and experimental approaches to investigate these genes have been hampered by the lack of comprehensive lncRNA annotation. Here, we present and analyze the most complete human lncRNA annotation to date...
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Methods: Dragon Gene Start Finder: An Advanced System for Finding Approximate Locations of the Start of Gene Transcriptional Units
- Vladimir B. Bajic and
- Seng Hong Seah
Genome Res. August 2003 13: 1923-1929; Published in Advance July 17, 2003, doi:10.1101/gr.869803
...initiation site of human genes. In Silico Biol. 2 : 461 -465. ↵ Collins, J.E., Goward, M.E., Cole, C.G., Smink, L.J., Huckle, E.J., Knowles, S., Bye, J.M., Beare, D.M., and Dunham, I. 2003 . Reevaluating human gene annotation: A second-generation analysis of chromosome 22. Genome Res. 13 : 27 -36. ↵ Cross, S...
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Research: Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants
- Jing Xia,
- Aarthi Venkat,
- Rachel E. Bainbridge,
- Michael L. Reese,
- Karine G. Le Roch,
- Ferhat Ay,
- and Jon P. Boyle
Genome Res. May 2021 31: 834-851; Published in Advance April 27, 2021, doi:10.1101/gr.262816.120
...for these genes has been difficult to determine using first- and second-generation sequencing technologies and/or molecular biological experiments like Southern blotting. Therefore, we used a curated BLASTN approach to quantify copy number for each of these sequences across our respective Nanopore assemblies...
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Research: Ligand-induced native G-quadruplex stabilization impairs transcription initiation
- Conghui Li,
- Honghong Wang,
- Zhinang Yin,
- Pingping Fang,
- Ruijing Xiao,
- Ying Xiang,
- Wen Wang,
- Qiuzi Li,
- Beili Huang,
- Jian Huang,
- and Kaiwei Liang
Genome Res. September 2021 31: 1546-1560; Published in Advance August 16, 2021, doi:10.1101/gr.275431.121
...-wide annotation of HEK293T G4-CUT&Tag and G4 ChIP-seq peaks. G4-CUT&Tag detected more G4s at the promoter, gene body, and intergenic regions than the G4 ChIP-seq method. (F) Tracks example of G4 ChIP-seq, G4-CUT&Tag, Pol II (subunit: POLR2A), H3K27ac, H3K4me3, H3K4me2, H3K4me1 ChIP-seq, and chromatin...
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Method: Genome-reconstruction for eukaryotes from complex natural microbial communities
- Patrick T. West,
- Alexander J. Probst,
- Igor V. Grigoriev,
- Brian C. Thomas,
- and Jillian F. Banfield
Genome Res. April 2018 28: 569-580; Published in Advance March 1, 2018, doi:10.1101/gr.228429.117
...was determined as the average coverage depth of the scaffolds containing annotated ribosomal protein S3 (rpS3) genes. Abundances were normalized for comparison across samples by multiplying the average coverage depth by the sample read count and read length. (C) Normalized coverage of rpS3 containing scaffolds...
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ARTICLE: Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22
- Dione Kampa,
- Jill Cheng,
- Philipp Kapranov,
- Mark Yamanaka,
- Shane Brubaker,
- Simon Cawley,
- Jorg Drenkow,
- Antonio Piccolboni,
- Stefan Bekiranov,
- Gregg Helt,
- Hari Tammana,
- and Thomas R. Gingeras
Genome Res. March 2004 14: 331-342; doi:10.1101/gr.2094104
...their browser, is based on protein-coding genes from SWISS-PROT, TrEMBL, and TrEMBL-NEW and their corresponding mRNAs from GenBank. Transfrags overlapping with the set of Sanger annotated pseudogenes on Chromosome 22 ( Collins et al. 2003 ) were removed from our analyses because it is difficult to attribute...

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