RNA‐dependent nuclear matrix contains a 33 kb globin full domain transcript as well as prosomes but no 26S proteasomes

Abstract

Previously, we have shown that in murine myoblasts prosomes are constituents of the nuclear matrix; a major part of the latter was found to be RNase sensitive. Here, we further define the RNA-dependent matrix in avian erythroblastosis virus (AEV) transformed erythroid cells in relation to its structure, presence of specific RNA, prosomes and/or proteasomes. These cells transcribe but do not express globin genes prior to induction. Electron micrographs show little difference in matrices treated with DNase alone or with both, DNase and RNase. In situ hybridization with alpha globin riboprobes shows that this matrix includes globin transcripts. Of particular interest is that, apparently, a nearly 35 kb long globin full domain transcript (FDT), including genes, intergenic regions and a large upstream domain is a part of the RNA-dependent nuclear matrix. The 23K-type of prosomes, previously shown to be co-localized with globin transcripts in the nuclear RNA processing centers, were found all over the nuclear matrix. Other types of prosomes show different distributions in the intact cell but similar distribution patterns on the matrix. Globin transcripts and at least 80% of prosomes disappear from matrices upon RNase treatment. Interestingly, the 19S proteasome modulator complex is insensitive to RNase treatment. Only 20S prosomes but not 26S proteasomes are thus part of the RNA-dependent nuclear matrix. We suggest that giant pre-mRNA and FDTs in processing, aligning prosomes and other RNA-binding proteins are involved in the organization of the dynamic nuclear matrix. It is proposed that the putative function of RNA within the nuclear matrix and, thus, the nuclear dynamic architecture, might explain the giant size and complex organization of primary transcripts and their introns.

DNA damage modulates interactions between microRNAs and the 26S proteasome

“…In this respect, it is important to note that several decades ago a number of reports described the proteasome (at least the 20S CP) as an RNA binding protein complex [19, 20]. Moreover, the same group of authors was able to show that the CP is also associated with nuclear matrix [21, 22] as well as with the cytoskeleton [23]. Interestingly, these 20S CP, or prosomes, displayed RNase activities [24, 25].…”

Mapping of the nuclear matrix-bound chromatin hubs by a new M3C experimental procedure

“…Cell nuclei were prepared according to protocols described elsewhere (27). To extract histones, 10 8 nuclei were suspended in 10 ml of ice-cold buffer A [10 mM PIPES (pH 7.8), 100 mM NaCl, 0.3 M Sucrose, 3 mM MgCl 2 , 0.5% Triton X-100, 0.1 mM PMSF].…”

Tightly bound to DNA proteins: Possible universal substrates for intranuclear processes

“…They degrade numerous nuclear proteins including transcription factors, repair enzymes (Nag et al, 2001), and the TBP C1D (Rothbarth et al, 2001b(Rothbarth et al, , 2002. Proteasomal proteins are well-characterized components of the nuclear matrix (De Conto et al, 1999Ioudinkova et al, 2005aIoudinkova et al, , 2005b. Several other proteins known as nuclear matrix components were found also among TBPs, this was the BAF factor (barrier-toautointegration factor), a DNA-binding protein interacting with lamin A and emerin, NMCP1 protein, and histone acetyl transferase HAC12 .…”

“…Intensity of hybridization with genomic probe microarrays for chicken α-globin domain. Compilation of data from (Bielskiene et al, 2008;Ioudinkova et al, 2005aIoudinkova et al, , 2005b. Probes correspond to domain sequences arranged at the interval of 2 kb.…”