Project description:The manuscript by D. Licastro and colleagues “Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved sequence elements” presents an overview of experimental and computational approaches employed by the authors to perform a multi-facet characterization of ultraconserved elements (UCEs). The authors present an interesting analysis where they investigate the transcription of UCEs in mouse development at different stages by conductin an microarray experiment. Some of these results are further verified by RT-PCR. 12 Samples, 4 groups 3 samples per group.
Project description:The manuscript by D. Licastro and colleagues “Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved sequence elements” presents an overview of experimental and computational approaches employed by the authors to perform a multi-facet characterization of ultraconserved elements (UCEs). The authors present an interesting analysis where they investigate the transcription of UCEs in mouse development at different stages by conductin an microarray experiment. Some of these results are further verified by RT-PCR.
Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Here, we optimised the FAIRE and MNase assays for application upon heavily-fixed tissues as is typically found in historical formalin-preserved museum specimens. We demonstrate these assays in formalin-fixed mouse specimens and compare the chromatin signatures to specimen-matched fresh tissues. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are reproducible, tissue-specific and sex-specific in vertebrate specimens.
Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Here, we optimised the FAIRE and MNase assays for application upon heavily-fixed tissues as is typically found in historical formalin-preserved museum specimens. We demonstrate these assays in formalin-fixed mouse specimens and compare the chromatin signatures to specimen-matched fresh tissues. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are reproducible, tissue-specific and sex-specific in vertebrate specimens.
Project description:Sequence capture and phylogenetic utility of genomic ultraconserved elements obtained from pinned insect specimens more than 100 years-old
