Characterization of axolotl lampbrush chromosomes by fluorescence in situ hybridization and immunostaining

Keinath, Melissa C.; Davidian, Asya; Timoshevskiy, Vladimir A.; Timoshevskaya, Nataliya; Gall, Joseph G.

doi:10.1016/j.yexcr.2021.112523

Cited by 5 publications

(3 citation statements)

References 21 publications

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“…1989; Sallacz and Jantsch 2005). Recently, RNA-FISH with BAC clone based probes selected according to oocyte RNA-seq data identified transcripts overlapping with 13 protein-coding genes on axolotl ( Ambistoma mexicanum ) lampbrush chromosomes (Keinath et al . 2021).…”

Section: Discussionmentioning

confidence: 99%

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

Krasikova,

Kulikova,

Schelkunov

et al. 2024

Preprint

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Lampbrush chromosomes, with their unusually high rate of nascent RNA synthesis, provide a valuable model for studying the mechanisms of global transcriptome up-regulation. Here, we aimed to establish a full set of sequences transcribed on the lateral loops of chicken lampbrush chromosomes. For the first time, a whole-genomic profile of transcription along the entire length of all lampbrush chromosomes in the chicken karyotype including sex chromosomes and dot chromosomes was obtained. For that, we performed RNA-seq of oocyte nuclear and cytoplasmic total RNA, poly(A) RNA and small RNA libraries and aligned expressed RNA sequences against the chicken genome. This led to the identification of a full spectrum of maternal RNAs that accumulate in the nucleus and cytoplasm of chicken oocytes at the lampbrush chromosome stage, are then transferred to the zygote and can be used during the early stages of embryogenesis, including transcripts of protein-coding genes, long non-coding RNAs and small housekeeping non-coding RNAs. We also present the first high-throughput transcriptome characterisation of miRNAs and piRNAs in chicken oocytes at the lampbrush chromosome stage. Major targets of predicted piRNAs include CR1 and LTR containing retrotransposable elements. Transcription of tandem repeat arrays including 41bp higher-order repeats as well as unique centromere sequences was demonstrated by alignment against the whole telomere-to-telomere chromosome assemblies. We show that transcription of telomere-derived RNAs, including telomeric repeat-containing RNA (TERRA) and subtelomeric repeat-containing RNA, is initiated at adjacent LTR elements. With nuclear RNA-seq, we obtained information about a wider set of transcripts, including long non-coding RNAs retained in the nucleus and stable intronic sequence RNAs (sisRNAs). We identified 5’ UTR sisRNAs that may potentially support host gene transcription both during oogenesis and after activation of the embryonic genome. For a number of protein-coding genes, we visualised nascent transcripts and demonstrated their co-transcriptional splicing on the lateral loops of lampbrush chromosomes by RNA-FISH. The nuclear RNA-seq profile predicted the chromomere-loop organisation of the genomic regions. During oocyte maturation, transcriptional unit boundaries were maintained, while transcriptional output tended to decrease. We conclude that cytoplasmic and nuclear transcripts emerge from nascent transcripts on the lateral loops of lampbrush chromosomes. Most of gene transcripts are initiated at promoters, normally spliced, terminated and polyadenylated. The set of genes transcribed on the lampbrush chromosomes is required for basic cellular processes, is characterised by a broad expression pattern and is similar to sets of genes expressed in other hypertranscriptional systems. We conclude that hypertranscription on the lateral loops of giant lampbrush chromosomes is the main mechanism for synthesising large amounts of transferred to the embryo maternal RNA for thousands of genes.

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Section: Discussionmentioning

confidence: 99%

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

Krasikova,

Kulikova,

Schelkunov

et al. 2024

Preprint

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“…[2] The expression of a number of genes on the lateral loops of Ambystoma mexicanum and Gallus gallus lampbrush chromosomes was recently demonstrated by RNA fluorescence in situ hybridization (RNA-FISH) with nascent transcripts. [13][14][15] These new trends enable the establishment of a spectrum of maternal RNAs transcribed by the growing oocyte itself in a wide range of animals.…”

Section: Post-genomic Eramentioning

confidence: 99%

Lampbrush chromosome studies in the post‐genomic era

2023

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Extraordinary extended lampbrush chromosomes with thousands of transcription loops are favorable objects in chromosome biology. Chromosomes become lampbrushy due to unusually high rate of transcription during oogenesis. However, until recently, the information on the spectrum of transcribed sequences as well as genomic context of individual chromomeres was mainly limited to tandemly repetitive elements.Here we briefly outline novel findings and future directions in lampbrush chromosome studies in the post-genomic era. We emphasize the fruitfulness of combining genomewide approaches with microscopy imaging techniques using lampbrush chromosomes as a remarkable model object. We believe that new data on the spectrum of sequences transcribed on the lateral loops of lampbrush chromosomes and their structural organization push the boundaries in the discussion of their biological role. Also see the video

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“…20 This spectacular characteristic of the organism conclusively made it a prominent model for understanding regeneration. Additionally, they are easy to breed, they can be reproduced in laboratory conditions with a well-established husbandry protocol, 21 transgenesis is possible, 22 molecular techniques such as gene-silencing, immunocytochemistry, and in situ hybridization are extensively applicable [23][24][25][26] and they share many functional/structural proteins, and signaling pathways with mammals, which makes them a promising model organism for translational medicine studies.…”

Section: Axolotl: a Model Organism For Regenerationmentioning

confidence: 99%

Axolotl: A resourceful vertebrate model for regeneration and beyond

Bölük

Yavuz

Demircan

2022

Developmental Dynamics

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The regenerative capacity varies significantly among the animal kingdom. Successful regeneration program in some animals results in the functional restoration of tissues and lost structures. Among the highly regenerative animals, axolotl provides multiple experimental advantages with its many extraordinary characteristics. It has been positioned as a regeneration model organism due to its exceptional renewal capacity, including the internal organs, central nervous system, and appendages, in a scar-free manner. In addition to this unique regeneration ability, the observed low cancer incidence, its resistance to carcinogens, and the reversing effect of its cell extract on neoplasms strongly suggest its usability in cancer research. Axolotl's longevity and efficient utilization of several anti-aging mechanisms underline its potential to be employed in aging studies.

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Characterization of axolotl lampbrush chromosomes by fluorescence in situ hybridization and immunostaining

Cited by 5 publications

References 21 publications

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

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

Lampbrush chromosome studies in the post‐genomic era

Axolotl: A resourceful vertebrate model for regeneration and beyond

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