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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
...and its dynamic use during the development of a vertebrate embryo. By using cap analysis of gene expression (CAGE), we mapped transcription initiation events at single nucleotide resolution across 12 stages of zebrafish development. These CAGE-based transcriptome maps reveal -wide rules of core promoter...
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Research: Genome-wide promoter assembly in E. coli measured at single-base resolution
- Jordan John,
- Javaid Jabbar,
- Nitika Badjatia,
- Matthew J. Rossi,
- William K.M. Lai,
- and B. Franklin Pugh
Genome Res. May 2022 32: 878-892; Published in Advance April 28, 2022, doi:10.1101/gr.276544.121
...al. 2015). This has allowed promoter regions that are enriched with these factors to be defined. Yet, the structural organization of proteins at promoters has yet to be defined on a genomic scale at single-base-pair resolution.E. coli has over 4000 genes, with many transcribed into a single...
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Research: Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing
- Sergey Aganezov,
- Sara Goodwin,
- Rachel M. Sherman,
- Fritz J. Sedlazeck,
- Gayatri Arun,
- Sonam Bhatia,
- Isac Lee,
- Melanie Kirsche,
- Robert Wappel,
- Melissa Kramer,
- Karen Kostroff,
- David L. Spector,
- Winston Timp,
- W. Richard McCombie,
- and Michael C. Schatz
Genome Res. September 2020 30: 1258-1273; Published in Advance September 4, 2020, doi:10.1101/gr.260497.119
...instability.Somatic mutations that drive cancer development range across all genomic scales, from single-nucleotide variants through large-scale rearrangements, and have been observed in nearly all types of cancer at every stage of the disease progression (Martincorena and Campbell 2015). Better detection...
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LETTER: Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms
- Wei Zhang,
- Weihong Qi,
- Thomas J. Albert,
- Alifiya S. Motiwala,
- David Alland,
- Eija K. Hyytia-Trees,
- Efrain M. Ribot,
- Patricia I. Fields,
- Thomas S. Whittam,
- and Bala Swaminathan
Genome Res. June 2006 16: 757-767; Published in Advance April 10, 2006, doi:10.1101/gr.4759706
...protein-coding genes, limiting the use of nucleotide sequences to study the evolution and epidemiology of this bacterial pathogen. To systematically examine single nucleotide polymorphisms (SNPs) at a genome scale, we designed comparative genome sequencing microarrays and analyzed 1199 chromosomal genes...
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Method: Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
- Jakob Skou Pedersen,
- Eivind Valen,
- Amhed M. Vargas Velazquez,
- Brian J. Parker,
- Morten Rasmussen,
- Stinus Lindgreen,
- Berit Lilje,
- Desmond J. Tobin,
- Theresa K. Kelly,
- Søren Vang,
- Robin Andersson,
- Peter A. Jones,
- Cindi A. Hoover,
- Alexei Tikhonov,
- Egor Prokhortchouk,
- Edward M. Rubin,
- Albin Sandelin,
- M. Thomas P. Gilbert,
- Anders Krogh,
- Eske Willerslev,
- and Ludovic Orlando
Genome Res. March 2014 24: 454-466; Published in Advance December 3, 2013, doi:10.1101/gr.163592.113
...Material SI2.9). We first looked at the single nucleotide distribution across the top quartile of nucleosome calls in unique regions (n = 1.37M, FDR = 8.5%). Base frequencies show the expected 10.2-bp periodicity corresponding to the turn of the slightly stretched DNA helix around nucleosomes (Brogaard et...
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Resource: High-resolution mapping of open chromatin in the rice genome
- Wenli Zhang,
- Yufeng Wu,
- James C. Schnable,
- Zixian Zeng,
- Michael Freeling,
- Gregory E. Crawford,
- and Jiming Jiang
Genome Res. January 2012 22: 151-162; Published in Advance November 22, 2011, doi:10.1101/gr.131342.111
...High-resolution mapping of open chromatin in the rice genome Wenli Zhang 1 , 4 , Yufeng Wu 1 , 4 , James C. Schnable 2 , Zixian Zeng 1 , Michael Freeling 2 , Gregory E. Crawford 3 and Jiming Jiang 1 , 5...
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Methods: High-resolution nucleosome mapping reveals transcription-dependent promoter packaging
- Assaf Weiner,
- Amanda Hughes,
- Moran Yassour,
- Oliver J. Rando,
- and Nir Friedman
Genome Res. January 2010 20: 90-100; Published in Advance October 21, 2009, doi:10.1101/gr.098509.109
.... cerevisiaehas been a tremendously productive method for illuminating the principles underlying chromatin structure and function. Deep sequencing methods have multiple advantages over tiling microarrays for genomic localization studies such as nucleosome mapping studies, including single-nucleotide resolution...
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Method: Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods
- Michael Stevens,
- Jeffrey B. Cheng,
- Daofeng Li,
- Mingchao Xie,
- Chibo Hong,
- Cécile L. Maire,
- Keith L. Ligon,
- Martin Hirst,
- Marco A. Marra,
- Joseph F. Costello,
- and Ting Wang
Genome Res. September 2013 23: 1541-1553; Published in Advance June 26, 2013, doi:10.1101/gr.152231.112
...differences with reasonable statistical significance. Additionally, bisulfite-converted s have lower sequence complexity. This not only causes problems in library construction and cluster formation on a sequencing plate, but also more profoundly affects alignment of bisulfite reads to the , i.e., mapping...
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Method: A fine-scale recombination map of the human–chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion
- Kasper Munch,
- Thomas Mailund,
- Julien Y. Dutheil,
- and Mikkel Heide Schierup
Genome Res. March 2014 24: 467-474; Published in Advance November 4, 2013, doi:10.1101/gr.158469.113
...of adaptive and nonadaptive evolution. Understanding how the recombination landscape has evolved in humans is thus key to the interpretation of human genomic evolution. Comparison of fine-scale recombination maps of human and chimpanzee has revealed large changes at fine genomic scales and conservation over...
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Methods: Generic eukaryotic core promoter prediction using structural features of DNA
- Thomas Abeel,
- Yvan Saeys,
- Eric Bonnet,
- Pierre Rouzé,
- and Yves Van de Peer
Genome Res. February 2008 18: 310-323; Published in Advance December 20, 2007, doi:10.1101/gr.6991408
...recognize structural features instead of specific nucleotide sequences. Structural properties are known to have long-range interactions (up to 10 kb), so they can exhibit properties that are not visible in the sequence ( Merling et al. 2003 ; Faiger et al. 2006 ). The Human Genomic Melting Map ( Liu et al...

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