YAC clone contigs covering 5 Mb of a repeat sequence island on the mouse X chromosome

Profiling of DNA replication timing in unsynchronized cell populations

Profiling chromatin in a particular cell type provides a valuable 'signature' for cell identity and developmental stage. One approach has been to assay and use the timing of DNA replication across a panel of loci as an indicator of chromatin structure. This epigenetic profiling used on pluripotent embryonic stem (ES) cells has reliably distinguished them from cells that have a more restricted lineage potential. Thus, such an approach may become increasingly useful for understanding the molecular basis of pluripotency and lineage induction, especially in the context of stem-cell therapy. Here I describe in detail the DNA replication timing method, whereby unsynchronized cell populations are pulse-labeled with 5-bromo-2'-deoxyuridine (BrdU), fractionated according to cell-cycle stage and the abundance of candidate sequences within newly replicated DNA is determined by PCR. This robust protocol has been used consistently by several laboratories and might offer some advantages over conventional transcription-based profiling for characterizing cell populations. The procedure requires 3-4 d to complete.

Heritable gene silencing in lymphocytes delays chromatid resolution without affecting the timing of DNA replication

Temporal control of DNA replication has been implicated in epigenetic regulation of gene expression on the basis of observations that certain tissue-specific genes replicate earlier in expressing than non-expressing cells. Here, we show evidence that several leukocyte-specific genes replicate early in lymphocytes regardless of their transcription and also in fibroblasts, where these genes are never normally expressed. Instead, the heritable silencing of some genes (Rag-1, TdT, CD8alpha and lambda5) and their spatial recruitment to heterochromatin domains within the nucleus of lymphocytes resulted in a markedly delayed resolution of sister chromatids into doublet signals discernable by 3D fluorescence in situ hybridization (FISH). Integration of transgenes within heterochromatin (in cis) did, however, confer late replication and this was reversed after variegated transgene expression. These findings emphasise that chromosomal location is important for defining the replication timing of genes and show that retarded sister-chromatid resolution is a novel feature of inactive chromatin.

Chromatin structure analysis of the mouse Xist locus

The Xist gene is expressed exclusively from the inactive X chromosome and plays a central role in regulating X chromosome inactivation. Here we describe experiments aimed at defining the extent of the active chromatin domain of the expressed Xist allele. By using an allele-specific general DNaseI sensitivity assay we show that there is preferential digestion of the expressed allele at sites within the transcribed locus but not in flanking sites located up to 70 kb 5'. A putative proximal boundary for the Xist domain is located within 10 kb upstream of promoter P1. Chromatin in the expressed domain was found to be acetylated at H4 in XX somatic cells but also in XY cells, where Xist is never expressed. A single clear exception to this was the Xist promoter, which is acetylated only in XX cells. These observations concur with the view that H4 acetylation may not be a general marker of active chromatin domains and further support data implicating local promoter acetylation as being of primary functional significance in vivo.

Physical mapping of the mouse genome

This review is intended to provide an overview of techniques and a source of reagents for physical mapping of the mouse genome. It focuses on those applications, methods, or resources unique to the mouse and on the generation of comparative physical maps. The reference list is not comprehensive; rather, recent reviews on each topic and selected representative examples are given.