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Research: Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors
- Martin Cusack,
- Hamish W. King,
- Paolo Spingardi,
- Benedikt M. Kessler,
- Robert J. Klose,
- and Skirmantas Kriaucionis
Genome Res. October 2020 30: 1393-1406; Published in Advance September 22, 2020, doi:10.1101/gr.257576.119
...perturbations (Supplemental Fig. S4E).Although all five transcription factors predominantly occupy gene promoter regions, the majority of ChIP-seq peaks that showed significant increases in occupancy upon DNA methylation loss or HDAC inhibition were situated at promoter distal genomic sites (Supplemental Fig. S...
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Research: Suppressor mutations in Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology
- Adebola Enikanolaiye,
- Julie Ruston,
- Rong Zeng,
- Christine Taylor,
- Marijke Schrock,
- Christie M. Buchovecky,
- Jay Shendure,
- Elif Acar,
- and Monica J. Justice
Genome Res. April 2020 30: 540-552; Published in Advance April 21, 2020, doi:10.1101/gr.258400.119
.... A network analysis shows that 63% of the genes cluster into the functional categories of transcriptional repression, chromatin modification, or DNA repair, delineating a pathway relationship with MECP2. Many mutations lie in genes that modulate synaptic signaling or lipid homeostasis. Mutations in genes...
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Research: Numerical and spatial patterning of yeast meiotic DNA breaks by Tel1
- Neeman Mohibullah and
- Scott Keeney
Genome Res. February 2017 27: 278-288; Published in Advance December 6, 2016, doi:10.1101/gr.213587.116
.../threonine kinase ATM/Tel1 (ataxia telangiectasia mutated in mammals; telomere maintenance in S. cerevisiae). ATM controls cell-cycle checkpoints and promotes DNA repair in somatic cells and is essential for meiosis in mammals (Shiloh and Ziv 2013). Testes from Atm−/− mice display a large increase in DSB numbers...
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RESEARCH: Strategies for Mutational Analysis of the Large Multiexon ATM Gene Using High-Density Oligonucleotide Arrays
- Joseph G. Hacia,
- Bryan Sun,
- Nathaniel Hunt,
- Keith Edgemon,
- Deborah Mosbrook,
- Christiane Robbins,
- Stephen P.A. Fodor,
- Danilo A. Tagle,
- and Francis S. Collins
Genome Res. December 1, 1998 8: 1245-1258; doi:10.1101/gr.8.12.1245
...truncation of the ATM protein. DNA chip-based assays should play a valuable role in high throughput sequence analysis of complex genes. The Human Genome Project will soon provide the scientific community with the complete sequence of all human genes. A major challenge for medical genetics will be in using...
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ARTICLE: Identification and characterization of a new gene physically linked to the ATM gene.
- T Imai,
- M Yamauchi,
- N Seki,
- T Sugawara,
- T Saito,
- Y Matsuda,
- H Ito,
- T Nagase,
- N Nomura,
- and T Hori
Genome Res. May 1996 6: 439-447; doi:10.1101/gr.6.5.439
...to ionizing radiation. Although AT has been divided into four complementation groups by its radioresistant-DNA synthesis phenotype, the ATM gene has been isolated as the candidate gene responsible for all AT groups. We identified a new gene, designated NPAT, from the major AT locus on human chromosome 11q22-q...
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LETTER: Identification and analysis of expression of human VACM-1, a cullin gene family member located on chromosome 11q22-23.
- P J Byrd,
- T Stankovic,
- C M McConville,
- A D Smith,
- P R Cooper,
- and A M Taylor
Genome Res. January 1997 7: 71-75; doi:10.1101/gr.7.1.71
...have localized the human homolog of the rabbit vasopressin-activated calcium-mobilizing receptor VACM-1 to a region close to the gene for ataxia telangiectasia ATM on chromosome 11q22-23. We have determined the complete amino acid sequence of the human Hs-VACM-1 protein, which is 780 amino acids long...
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Research: L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis
- Stephanie N. Schauer,
- Patricia E. Carreira,
- Ruchi Shukla,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Francisco J. Sanchez-Luque,
- Paola Nicoli,
- Michaela Kindlova,
- Serena Ghisletti,
- Alexandre Dos Santos,
- Delphine Rapoud,
- Didier Samuel,
- Jamila Faivre,
- Adam D. Ewing,
- Sandra R. Richardson,
- and Geoffrey J. Faulkner
Genome Res. May 2018 28: 639-653; Published in Advance April 11, 2018, doi:10.1101/gr.226993.117
...Element-1 (LINE-1 or L1), which accounts for 19.9% and 17.5% of mouse and human genomic DNA, respectively (Smit et al. 2013). Although the vast majority of L1 copies are no longer mobile, 80–100 human L1s and 2000–3000 mouse L1s, per individual, are full-length and retain retrotransposition potential...
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Research: Heritable L1 retrotransposition in the mouse primordial germline and early embryo
- Sandra R. Richardson,
- Patricia Gerdes,
- Daniel J. Gerhardt,
- Francisco J. Sanchez-Luque,
- Gabriela-Oana Bodea,
- Martin Muñoz-Lopez,
- J. Samuel Jesuadian,
- Marie-Jeanne H.C. Kempen,
- Patricia E. Carreira,
- Jeffrey A. Jeddeloh,
- Jose L. Garcia-Perez,
- Haig H. Kazazian, Jr.,
- Adam D. Ewing,
- and Geoffrey J. Faulkner
Genome Res. August 2017 27: 1395-1405; Published in Advance May 8, 2017, doi:10.1101/gr.219022.116
...the first intron of the gene Suclg2 on Chr 6 is shown. (D) 5′ junction PCR validation for insertion #7. (E) A quantitative PCR (qPCR) assay for the prevalence of insertion #7. A forward primer (P1, gray) is situated within flanking genomic DNA, and a reverse primer (P2, gray/red) spans the junction between...
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LETTER: Complex SNP-Based Haplotypes in Three Human Helicases: Implications for Cancer Association Studies
- Dimitra Trikka,
- Zhe Fang,
- Alex Renwick,
- Sally H. Jones,
- Ranajit Chakraborty,
- Marek Kimmel,
- and David L. Nelson
Genome Res. April 1, 2002 12: 627-639; doi:10.1101/gr.176702
...groups. Linkage disequilibrium and recombination effects showed that each locus has taken a diverse evolutionary path. Primate DNA analysis of the same loci revealed one human haplotype per gene shared with the great apes, indicating that the observed diversity occurred since the divergence of humans...
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Letter: Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts
- Jeremy R. Sanford,
- Xin Wang,
- Matthew Mort,
- Natalia VanDuyn,
- David N. Cooper,
- Sean D. Mooney,
- Howard J. Edenberg,
- and Yunlong Liu
Genome Res. March 2009 19: 381-394; Published in Advance December 30, 2008, doi:10.1101/gr.082503.108
..., see Wang and Cooper 2007 ). Studies of the BRCA1 , SMN , CFTR , GH1 , and ATM genes (among others) have demonstrated that all classes of point mutations, including nonsense mutations, can disrupt exonic splicing regulatory elements and induce aberrant alternative splicing ( Teraoka et al. 1999 ; Liu...

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