PAP-LMPCR for improved, allele-specific footprinting and automated chromatin fine structure analysis

R Ingram, C Gao, J Lebon, Q Liu, RJ Mayoral, SS Sommer, Maarten Hoogenkamp, AD Riggs, Constanze Bonifer

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)


The analysis of chromatin fine structure and transcription factor occupancy of differentially expressed genes by in vivo footprinting and ligation-mediated-PCR (LMPCR) is a powerful tool to understand the impact of chromatin on gene expression. However, as with all PCR-based techniques, the accuracy of the experiments has often been reduced by sequence similarities and the presence of GC-rich or repeat sequences, and some sequences are completely refractory to analysis. Here we describe a novel method, pyrophosphorolysis activated polymerization LMPCR or PAP-LMPCR, which is capable of generating accurate and reproducible footprints specific for individual alleles and can read through sequences previously not accessible for analysis. In addition, we have adapted this technique for automation, thus enabling the simultaneous and rapid analysis of chromatin structure at many different genes.
Original languageEnglish
Article numbere19
JournalNucleic Acids Research
Issue number3
Early online date21 Jan 2008
Publication statusPublished - 1 Feb 2008



ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)


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