Background: Fully grown mammalian oocyte utilizes transcripts synthetized and stored during earlier development. In the mouse oocyte there are three forms of cap-dependent translational repressors: 4E-BP1, 4E-BP2, and 4E-BP3. The dominant form, 4E-BP1, inhibits cap-dependent translation by binding to the eIF4E translation initiation factor. Hyperphosphorylation of 4E-BP1 disrupts this inhibitor...

Chromosome territory (CT) organization and chromatin condensation have been linked to gene expression. Although individual genes can be transcribed from inside CTs, some regions that have constitutively high expression or are coordinately activated loop out from CTs and decondense. The relationship between epigenetic marks, such as DNA methylation, and higher-order chromatin structures is large...

Although it is established that some general transcription factors are inactivated at mitosis, many details of mitotic transcription inhibition (MTI) and its underlying mechanisms are largely unknown. We have identified mitotic transcriptional activation (MTA) as a key regulatory step to control transcription in mitosis for genes with transcriptionally engaged RNA polymerase II (Pol II) to acti...

Transcription in mammalian nuclei is highly compartmentalized in RNA polymerase II-enriched nuclear foci known as transcription factories. Genes in cis and trans can share the same factory, suggesting that genes migrate to preassembled transcription sites. We used fluorescent in situ hybridization to investigate the dynamics of gene association with transcription factories during immediate earl...

Expression of immediate early genes (IEG) is induced in brain neurons by synaptic activity and is frequently used to monitor neuronal activation. This unit describes a technique (cellular compartment analysis of temporal activity by fluorescence in situ hybridization or catFISH) that uses fluorescence in situ hybridization (FISH) of IEG RNAs to slide-mounted tissue sections, and confocal micros...

C. elegans Notch signaling maintains a pool of germline stem cells within their single-celled mesenchymal niche. Here we investigate the Notch transcriptional response in germline stem cells using single-molecule fluorescence in situ hybridization coupled with automated, high-throughput quantitation. This approach allows us to distinguish Notch-dependent nascent transcripts in the nucleus from ...