Organization of chromatin and histone modifications at a transcription site

Abstract

According to the transcription factory model, localized transcription sites composed of immobilized polymerase molecules transcribe chromatin by reeling it through the transcription site and extruding it to form a surrounding domain of recently transcribed decondensed chromatin. Although transcription sites have been identified in various cells, surrounding domains of recently transcribed decondensed chromatin have not. We report evidence that transcription sites associated with a tandem gene array in mouse cells are indeed surrounded by or adjacent to a domain of decondensed chromatin composed of sequences from the gene array. Formation of this decondensed domain requires transcription and topoisomerase IIα activity. The decondensed domain is enriched for the trimethyl H3K36 mark that is associated with recently transcribed chromatin in yeast and several mammalian systems. Consistent with this, chromatin immunoprecipitation demonstrates a comparable enrichment of this mark in transcribed sequences at the tandem gene array. These results provide new support for the pol II factory model, in which an immobilized polymerase molecule extrudes decondensed, transcribed sequences into its surroundings.

Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays

“…It has been shown that actively transcribed DNA sequences at the ~2 Mbase mammary tumor virus (MMTV) array are extruded from transcription sites as highly decondensed domains not detected by conventional DNA FISH protocols (Muller et al, 2007). Although we failed to obtain any experimental evidence for extended loops, whether snoRNA gene arrays reflect the same chromatin configuration as MMTV array remains an open question.…”

Dynamics and interplay of nuclear architecture, genome organization, and gene expression

“…When released after termination, a gene would still be near a factory and still carry the active histone modifications that could keep it in an open state, leading to efficient reinitiation (Bartlett et al 2006). In agreement with this concept, domains of decondensed and recently transcribed chromatin carry histone marks that are associated with active transcription (Muller et al 2007).…”

Co-expressed genes prepositioned in spatial neighborhoods stochastically associate with SC35 speckles and RNA polymerase II factories

“…BrUtP incorporation the protocol followed that in [67], with the following modifications. the permeabilization buffer contained 10 μg/ml instead of 25 μg/ml digitonin, dexamethasone was omitted.…”