The 33 kb transcript of the chicken α‐globin gene domain is part of the nuclear matrix

Abstract

Giant nuclear transcripts, and in particular the RNAs of the globin gene domains which are much larger than their canonical pre-mRNAs, have been an enigma for many years. We show here that in avian erythroblastosis virus (AEV)-transformed chicken erythroleukaemic cells, where globin gene expression is abortive, the whole domain of alpha-globin genes is transcribed for about 33 kb in the globin direction and that this RNA is part of the nuclear matrix. Northern blot hybridisation with strand-specific riboprobes, recognising genes and intergenic sequences, and RT-PCR with downstream primers, show that the continuous full domain transcript (FDT) starts in the vicinity of a putative LCR and includes all the genes as well as known regulatory sites, the replication origin, and the DNA loop anchorage region in the upstream area. Absent in chicken fibroblasts, the globin FDT overlaps the major part of the ggPRX housekeeping gene that is transcribed in the opposite direction. RT-PCR and in situ hybridisation with genic and extra-genic globin probes demonstrated that the globin FDT is a component of the nuclear matrix. We suggest that the globin FDTs keep the domain in an active state, and the globin RNAs on the processing pathway are a component of the nuclear matrix. They may take part in the dynamic nuclear architecture when productively processed, or turn over slowly when globins are not synthesised.

Both the constitutive Cauliflower Mosaic Virus 35S and tissue-specific AGAMOUS enhancers activate transcription autonomously in Arabidopsis thaliana

“…For example, a series of overlapping, polyadenylated, intergenic RNAs of less than 3 kb were found to be generated by the HS2 enhancer towards its linked globin promoter at its endogenous loci (Ling et al 2005;Zhu et al 2007), whereas in an artificial vector the same enhancer synthesized intergenic transcripts that were initiated from multiple sites within the enhancer and elongated through the cis-linked promoter and into the reporter gene (Ling et al 2005). In contrast, the chicken a-globin gene locus has been found to generate enhancer-initiated intergenic RNAs of longer than 20 kb that span the sequence separating enhancer and promoter (Broders and Scherrer 1987;Razin et al 2004), while at the human prostrate specific antigen locus, the scanning of polymerase II from enhancer to promoter has not been found to generate intergenic RNAs at all (Wang et al 2005). Therefore, while scanning/ facilitated tracking seems to be a rather widespread means of establishing communication between regulatory elements, the mechanism by which this is accomplished appears to vary and a debate still exists whether long, enhancer-initiated transcripts are required for the proper expression of the target gene (for example Müller et al 1990).…”

Specific radial positions of centromeres of human chromosomes X, 1, and 19 remain unchanged in chromatin‐depleted nuclei of primary human fibroblasts: Evidence for the organizing role of the nuclear matrix

“…In some of recent publications the nuclear RNA is considered as an integral part of the nuclear matrix [Nickerson et al, 1989[Nickerson et al, , 2001Belgrader et al, 1991;Barboro et al, 2003;Razin et al, 2004b]. In particular, it was reported that residual chromosomal territories were disrupted in nuclear matrices treated with RNase A [Ma et al, 1999].…”

Chromatin Domains and Regulation of Transcription

“…Long intergenic or full domain transcripts were found in many genomic areas. 88,[94][95][96][97] It was demonstrated that in β globin gene domains of different vertebrates, RNA polymerase II was recruited to locus control regions and actually started transcription of the whole downstream domain. 98,99 Progressive modification of histones linked to polymerase II transcription was demonstrated in several studies.…”