Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.

By S. Cawley, S. Bekiranov, Huck-Hui Ng, Philipp Kapranov, E. Sekinger, D. Kampa, A. Piccolboni, V. Sementchenko, Jill Cheng, A. J. Williams and 10 more. Cell, 2004

1,160 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3316bdc5cea1af09f6d1b3969e3811358f252510

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In Molecular Biology

1. John S. Mattick
2. S. Yamanaka
3. David Haussler
4. R. Jaenisch
5. D. Reinberg
6. Eric S. Lander
7. A. Bird
8. Steven L. Salzberg

Citations in the corpus

• Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. (2008, background): “Genome-wide mapping studies reveal abundant binding sites for different TFs in mammalian cells (Bieda et al., 2006; Birney et al., 2007; Cawley et al., 2004).”
• Protocol for the fast chromatin immunoprecipitation (ChIP) method (2006, background): “Alternatively, an interaction of the factor with multiple genomic locations can be detected simultaneously by applying the isolated DNA to a DNA microarray (ChIP on chip”
• DNA methylation profiling of human chromosomes 6, 20 and 22 (2006, methodology): “For the analysis of individual transcription factor binding sites, we selected 94 amplicons containing experimentally verified Sp1 binding sites on chromosome 22 that were previously identified in ref”
• p53 in health and disease (2007, background): “Numerous studies, including the recently reported genome-wide ChIP analyses”
• PeakSeq: Systematic Scoring of ChIP-Seq Experiments Relative to Controls (2009, neutral): “This is similar to the maxgap/minrun approach that is commonly used for analyzing ChIP-chip tiling array dat”
• Genome-wide transcription and the implications for genomic organization (2007, background): “Unbiased efforts to map transcription factor binding sites found that only 22% of MYC and SP1 binding sites lie proximal to the 5′ ends of well annotated genes, whereas 36% lie within gene boundarie”
• Chromosome 21 and Down syndrome: from genomics to pathophysiology (2004, background): “Another study combined chromatin immunoprecipitation and high-density oligonucleotide arrays to map more than 300 binding sites of the three transcription factors, Sp1, cMyc, and p53 on HSA21 (Ref”
• Chromatin Structure and the Inheritance of Epigenetic Information (2010, background): “, and common transcription factors (such as MYC and SP1) are involved in their regulatio”
• Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene (2004, positive): “The nine probes used were antisense oligonucleotides corresponding to the following positions relative to the SER3 ATG:2650 to2724 (1),2467 to2541 (2),2341 to2415 (3),2217 to2291 (4), 2118 to2192 (5),þ39 to236 (6),þ223 toþ149 (7),þ530 toþ456 (8),þ891 toþ817 (9).”