Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts

Abstract

Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form. We highlight how transcription of tandemly repetitive DNA sequences is organized in interphase nucleus and on lampbrush chromosomes. We offer LTR-activation hypotheses of widespread satellite DNA transcription initiation during oogenesis. Recent explanations are provided for the significance of high-yield production of non-coding RNA derived from tandemly organized highly repetitive DNA. In many cases the data on the transcription of satellite DNA can be extrapolated from lampbrush chromosomes to interphase chromosomes. Lampbrush chromosomes with applied novel technical approaches such as superresolution imaging, chromosome microdissection followed by high-throughput sequencing, dynamic observation in life-like conditions provide amazing opportunities for investigation mechanisms of the satellite DNA transcription.

Human pericentromeric tandemly repeated DNA is transcribed at the end of oocyte maturation and is associated with membraneless mitochondria-associated structures

“…This fact leads us to assume that the real quantity of HS transcripts in an oocyte is higher than could be expected according to the number of reads in SRR datasets. In other animals, transcription of TR DNA in oogenesis was observed 8,11,49 . Transcription of pericentromere TR DNA in ovaries of Drosophila 50 has been shown.…”

“…At the end of the last century, the first data appeared on the role of big satellites. Their transcription was shown in different organisms: mice 7 , amphibians 8 , fish 9 , birds 10 , 11 and humans 12 , 13 . The number of HS transcripts increases many fold at the beginning of proliferation, cell aging, cell differentiation, carcinogenesis, and cell stress 12 – 17 .…”

Subtelomeric Transcription and its Regulation

“…The role of these transcripts remains elusive, but their features suggest the existence of dsRNA generation and RNAi-dependent mechanisms involved in the assembly and maintenance of heterochromatin at subtelomeres [ 167 ]. Moreover, an interesting scenario concerning the role of these transcripts in embryo development has been proposed [ 167 ]: single-stranded G and C transcripts could form long dsRNAs, which could then be processed into short dsRNAs and accumulate in oocytes. After fertilization, the dsRNAs would be transferred into the embryo and play a role in the regulation of the early stages of embryogenesis before activation of the embryonic genome.…”

The Cytogenetic Map of the Nile Crocodile (Crocodylus niloticus, Crocodylidae, Reptilia) with Fluorescence In Situ Localization of Major Repetitive DNAs

“…Despite satellite DNA being earlier considered as “junk”, it has now become clear that these DNA arrays are integral to centromere function and stability and they are functionally significant at the level of the spatial organization of chromosomes, their pairing, and segregation during meiosis [ 24 , 30 , 31 , 32 ]. Satellite DNA transcripts are also involved in the formation and maintenance of the heterochromatin structure [ 33 , 34 ]. Very often satellite DNAs are co-localized with other tandemly arranged sequences, such as ribosomal RNA genes (rDNA) and telomeric sequences [ 35 , 36 ].…”