Human ribosomal RNA variants from a single individual and their expression in different tissues

Abstract

We have investigated the extent of sequence variation in human ribosomal RNA (rRNA) genes and the expression of specific rRNA gene variants in different tissues of an individual. Focusing on the fifth variable region (V5; nt 2065-2244) of the 28S rRNA gene, we find that sequence differences between rRNA genes of a single individual are characterized by differences in number of repeats of simple sequences at four specific sites. These data support and extend previous findings which show similar V5 sequence variation in rRNA genes from a group of individuals. We performed experiments to determine if there is differential gene expression within the rRNA multigene family. From the analysis of data of six variant V5 probes protected from RNase digestion by rRNAs isolated from different tissues of the individual, we conclude that each variant rRNA is present in a similar proportion in these tissues, whereas the actual contributions of variants differ, their relative proportion is maintained from tissue to tissue in an individual. We favor the explanation of a gene dosage effect over that of a regulated gene effect to account for this pattern of rRNA gene expression. In addition, computer generated secondary structure models of each V5 clone structure predict the same three helix structure with the regions of sequence variation contained in one stem-loop structure.

Expression of distinct maternal and somatic 5.8S, 18S, and 28S rRNA types during zebrafish development

“…Also, 45S rDNA variants have been observed in several organisms (Kuo et al 1996;Rogers et al 1996;Ihara et al 2011). To study potential 5.8S, 18S, and 28S rRNA variations in zebrafish, we made an inventory of the zebrafish 45S rDNA units present in the current zebrafish genome assembly (GRCz10).…”

“…Usually not all 45S rDNA variants present in a genome are expressed (Kuo et al 1996), and therefore we analyzed the expression of the 18S, 5.8S, and 28S rRNAs in a range of zebrafish tissues to identify whether all three 45S rDNA variant types are transcribed. For 5.8S rRNA, we applied an adapted small-RNA-seq approach and for 18S as well as 28S rRNA a rRNA-seq approach (see Materials and Methods) on the following: an egg pool (51 M and 48 M reads, respectively), an embryonic time series (49 M reads and 79 M reads), whole-body adultmale samples (40 M and 40 M reads), and female-adult tail samples (7.7 M and 9.8 M reads) in order to include somatic female tissues without ovaries and developing oocytes.…”

“…But also within species, heterogeneity of the 45S rDNA was already discovered in the late seventies, which is reflected by the variability of the ribosomal transcription units in both length and sequence (Wellauer et al 1976;Arnheim and Southern 1977). Further investigations have since shown that the human 28S rRNA has several variants that differ in the sequence of a specific region (Kuo et al 1996).…”

The ribosome filter hypothesis

“…It was also noted that different human cell lines expressed different 28S rRNA genes. Similarly, an analysis of variants of expansion segment V5 within a single individual identified four sites of variability (73). In addition to the sequence variation that occurs in expansion segments, heterogeneity in the 28S rRNA genes has also been noted in regions that are conserved between species (70).…”

Identification and Genetic Diversity Analysis of Ascochyta Species Associated with Blight Complex of Pea in a Northwestern Hill State of India

“…Some of these differences were specific, e.g., changes in ITSI region of As43 (FJ156067) and 5.8S ribosomal RNA gene of As42 (FJ032642), As43 (FJ156067) and As44 (FJ-32643). The size variation within the isolates could be due to genetic changes as reported by DePriest [15] in lichenized-fungi or due to different number of simple sequence repeats [27].…”