Chromatin accessibility analysis from fresh and cryopreserved human ovarian follicles

Jennifer Shannon, Aishwarya Sundaresan, Orhan Bukulmez, Zexu Jiao, Kaitlin Doody, Sarah Capelouto, Bruce Carr, Laura A. Banaszynski

Research output: Contribution to journalArticlepeer-review

Abstract

Understanding how gene regulatory elements influence ovarian follicle development has important implications in clinically relevant settings. This includes understanding decreased fertility with age and understanding the short-lived graft function commonly observed after ovarian tissue cryopreservation and subsequent autologous transplantation as a fertility preservation treatment. The Assay for Transposase-Accessible Chromatin by sequencing (ATAC-seq) is a powerful tool to identify distal and proximal regulatory elements important for activity-dependent gene regulation and hormonal and environmental responses such as those involved in germ cell maturation and human fertility. Original ATAC protocols were optimized for fresh cells, a major barrier to implementing this technique for clinical tissue samples which are more often than not frozen and stored. While recent advances have improved data obtained from stored samples, this technique has yet to be applied to human ovarian follicles, perhaps due to the difficulty in isolating follicles in sufficient quantities from stored clinical samples. Further, it remains unknown whether the process of cryopreservation affects the quality of the data obtained from ovarian follicles. Here, we generate ATAC-seq data sets from matched fresh and cryopreserved human ovarian follicles. We find that data obtained from cryopreserved samples are of reduced quality but consistent with data obtained from fresh samples, suggesting that the act of cryopreservation does not significantly affect biological interpretation of chromatin accessibility data. Our study encourages the use of this method to uncover the role of chromatin regulation in a number of clinical settings with the ultimate goal of improving fertility.

Original languageEnglish (US)
Article numbergaac020
JournalMolecular Human Reproduction
Volume28
Issue number6
DOIs
StatePublished - Jun 1 2022

Keywords

  • ATAC-seq
  • chromatin accessibility
  • cryopreservation
  • ovarian follicles
  • regulatory elements

ASJC Scopus subject areas

  • Reproductive Medicine
  • Embryology
  • Molecular Biology
  • Genetics
  • Obstetrics and Gynecology
  • Developmental Biology
  • Cell Biology

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