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Poly(A)-Selected Intergenic Transcripts in In Vivo Developed Bovine Oocytes and Pre-Implantation Embryos.

Saurav Ranjitkar1, Mohammad Shiri2, Jiangwen Sun2

  • 1Department of Animal Science, University of Connecticut, Storrs, Connecticut, USA.

Molecular Reproduction and Development
|February 23, 2025
PubMed
Summary
This summary is machine-generated.

In vivo developed bovine embryos and oocytes exhibit abundant intergenic transcripts, termed read-outs and read-ins, with limited read-through transcription. These transcripts are associated with developmental stages and gene expression, independent of DNA methylation patterns.

Keywords:
intergenic transcriptionpolyadenylationread‐inread‐outread‐through (downstream of gene)

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Area of Science:

  • Developmental Biology
  • Genomics
  • Epigenetics

Background:

  • Intergenic transcription, including read-through transcription and transcription initiation in intergenic regions, is observed in cultured cells and can be enhanced by stressors.
  • This phenomenon has not been well-characterized in natural biological samples, particularly during pre-implantation development, a period marked by extensive gene expression and DNA methylation changes.

Purpose of the Study:

  • To characterize intergenic transcription in vivo during bovine oocyte and pre-implantation embryo development.
  • To investigate the relationship between intergenic transcription, gene expression, and DNA methylation in these early developmental stages.

Main Methods:

  • Utilized Automatic Readthrough Transcription Detection (ARTDeco) and poly(A)-selected RNA-sequencing (RNA-seq) on in vivo developed bovine oocytes and embryos.
  • Analyzed intergenic transcript types (read-outs, read-ins, read-throughs), their association with reference genes, differential expression, and correlation with DNA methylation.

Main Results:

  • Abundant intergenic transcripts, termed read-outs and read-ins, were identified, with read-throughs being less common.
  • Many intergenic transcripts were associated with common reference genes across developmental stages and showed stage-specific differential expression.
  • No significant correlation was found between intergenic transcription and DNA methylation levels in flanking regions, despite observed decreases in methylation.

Conclusions:

  • Bovine oocytes and pre-implantation embryos express substantial levels of intergenic transcripts, including novel read-outs and read-ins.
  • Intergenic transcription is not random, is linked to developmental stage and gene expression, and appears to be regulated independently of broad DNA methylation changes.
  • The presence of transcription factor binding motifs and polyadenylation signals suggests active regulation of novel transcription initiation and RNA processing within intergenic regions.