Classification of loops of lampbrush chromosomes according to the arrangement of transcriptional complexes

Abstract

The arrangement of transcriptional units in the loops of lampbrush chromosomes from oocyte nuclei of urodele amphibia and from primary nuclei of the green alga Acetabularia have been studied in the electron microscope using spread preparations. Loops with different patterns of arrangement of matrix units (i.e. to a first approximation, transcriptional units) can be distinguished: (i) loops consisting of one active transcriptional unit; (ii) loops containing one active transcriptional unit plus additional fibril-free, i.e. apparently untranscribed, intercepts that may include ‘spacer’ regions; (iii) loops containing two or more transcriptional units arranged in identical or changing polarities, with or without interspersed apparent spacer regions. Morphological details of the transcriptional complexes are described. The observations are not compatible with the concept that one loop reflects one and only one transcriptional unit but, rather, lead to a classification of loop types according to the arrangement of their transcriptional units. We propose that the lampbrush chromosome loop can represent a unit for the coordinate transcription of either one gene or a set of several (different) genes.

The first chicken oocyte nucleus whole transcriptomic profile defines the spectrum of maternal mRNA and non-coding RNA genes transcribed by the lampbrush chromosomes

“…Another scenario - many genes of different polarity transcribed in a single lateral loop and separated by a chromatin knot (Figure 6) or even one by one without visible chromatin knots (Figure S9). Such arrangement of transcriptional units in lampbrush lateral loops completely corresponds to the classification of lateral loops in amphibian lampbrush chromosomes suggested according to electron-microscope observations of spread chromatin (Scheer et al . 1976).…”

“…2016; Morgan 2018). This is most likely achieved by the tight coverage of transcribed genes by elongating RNA polymerases as shown by chromosome spreading according to the Miller technique (Scheer et al . 1976).…”

“…Comparison of the chicken oocyte nucleus and cytoplasm RNA profiles clearly showed the nuclear retention of certain introns in the form of sisRNAs resistant to RNase R treatment. Interestingly, ring-like structures associated with the nascent RNP fibrils were observed during electron microscopy of spread lampbrush chromosome preparations (Figure 14 in Scheer et al 1976); these may correspond to sisRNAs being processed co-transcriptionally. sisRNA accumulation was previously demonstrated for Xenopus lampbrush stage oocyte nuclei (Gardner et al 2012).…”

“…The rate of nascent RNA synthesis is unusually high in lampbrush chromosomes (Gall and Callan 1962;Izawa et al 1963;Callebaut 1973;Hartley and Callan 1978;Deryusheva et al 2007;Kulikova et al 2016;Morgan 2018). This is most likely achieved by the tight coverage of transcribed genes by elongating RNA polymerases as shown by chromosome spreading according to the Miller technique (Scheer et al 1976). An increase in the rate of elongation by RNA polymerase II also cannot be ruled out.…”

Hybridization of nuclear matrix attached deoxyribonucleic acid fragments

“…The possibile relationship of DNA loops to transcriptional units has also been extensively discussed (Georgiev et al, 1978) . While the only definitive evidence for the organization of transcriptional units into distinct loops is derived from the specialized lampbrush chromosome systems (Scheer et al, 1979) , concluded that transcriptional sequences are arranged in a specific manner along the DNA loops in HeLa cells, and Pardoll & Vogelstein (1980) reported an enrichment in ribosomal RNA sequences in matrix-attached DNA. Our hybridization analysis indicates that transcribed sequences are randomly associated with attachment sites, though it is still an open question as to whether transcriptional units are arranged into specific orientations along the DNA loops during the actual process of transcription.…”