Distinct epigenetic features of differentiation-regulated replication origins

Owen K. Smith, Ryanguk Kim, Haiqing Fu, Melvenia M. Martin, Chii Mei Lin, Koichi Utani, Ya Zhang, Anna B. Marks, Marc Lalande, Stormy Chamberlain, Maxwell W. Libbrecht, Eric E. Bouhassira, Michael C. Ryan, William S. Noble, Mirit I. Aladjem

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

Background: Eukaryotic genome duplication starts at discrete sequences (replication origins) that coordinate cell cycle progression, ensure genomic stability and modulate gene expression. Origins share some sequence features, but their activity also responds to changes in transcription and cellular differentiation status. Results: To identify chromatin states and histone modifications that locally mark replication origins, we profiled origin distributions in eight human cell lines representing embryonic and differentiated cell types. Consistent with a role of chromatin structure in determining origin activity, we found that cancer and non-cancer cells of similar lineages exhibited highly similar replication origin distributions. Surprisingly, our study revealed that DNase hypersensitivity, which often correlates with early replication at large-scale chromatin domains, did not emerge as a strong local determinant of origin activity. Instead, we found that two distinct sets of chromatin modifications exhibited strong local associations with two discrete groups of replication origins. The first origin group consisted of about 40,000 regions that actively initiated replication in all cell types and preferentially colocalized with unmethylated CpGs and with the euchromatin markers, H3K4me3 and H3K9Ac. The second group included origins that were consistently active in cells of a single type or lineage and preferentially colocalized with the heterochromatin marker, H3K9me3. Shared origins replicated throughout the S-phase of the cell cycle, whereas cell-type-specific origins preferentially replicated during late S-phase. Conclusions: These observations are in line with the hypothesis that differentiation-associated changes in chromatin and gene expression affect the activation of specific replication origins.

Original languageEnglish (US)
Article number18
JournalEpigenetics and Chromatin
Volume9
Issue number1
DOIs
StatePublished - May 10 2016

Fingerprint

Replication Origin
Epigenomics
Chromatin
S Phase
Cell Cycle
Histone Code
Euchromatin
Gene Expression
Deoxyribonucleases
Heterochromatin
Genomic Instability
Cell Lineage
Hypersensitivity
Genome
Cell Line
Neoplasms

Keywords

  • Cell cycle
  • Cellular differentiation
  • Chromatin
  • CpG islands
  • H3K4me3
  • H3K9Ac
  • H3K9me3
  • Histone modification
  • Origin of replication
  • Proliferation

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology

Cite this

Smith, O. K., Kim, R., Fu, H., Martin, M. M., Lin, C. M., Utani, K., ... Aladjem, M. I. (2016). Distinct epigenetic features of differentiation-regulated replication origins. Epigenetics and Chromatin, 9(1), [18]. https://doi.org/10.1186/s13072-016-0067-3

Distinct epigenetic features of differentiation-regulated replication origins. / Smith, Owen K.; Kim, Ryanguk; Fu, Haiqing; Martin, Melvenia M.; Lin, Chii Mei; Utani, Koichi; Zhang, Ya; Marks, Anna B.; Lalande, Marc; Chamberlain, Stormy; Libbrecht, Maxwell W.; Bouhassira, Eric E.; Ryan, Michael C.; Noble, William S.; Aladjem, Mirit I.

In: Epigenetics and Chromatin, Vol. 9, No. 1, 18, 10.05.2016.

Research output: Contribution to journalArticle

Smith, OK, Kim, R, Fu, H, Martin, MM, Lin, CM, Utani, K, Zhang, Y, Marks, AB, Lalande, M, Chamberlain, S, Libbrecht, MW, Bouhassira, EE, Ryan, MC, Noble, WS & Aladjem, MI 2016, 'Distinct epigenetic features of differentiation-regulated replication origins', Epigenetics and Chromatin, vol. 9, no. 1, 18. https://doi.org/10.1186/s13072-016-0067-3
Smith, Owen K. ; Kim, Ryanguk ; Fu, Haiqing ; Martin, Melvenia M. ; Lin, Chii Mei ; Utani, Koichi ; Zhang, Ya ; Marks, Anna B. ; Lalande, Marc ; Chamberlain, Stormy ; Libbrecht, Maxwell W. ; Bouhassira, Eric E. ; Ryan, Michael C. ; Noble, William S. ; Aladjem, Mirit I. / Distinct epigenetic features of differentiation-regulated replication origins. In: Epigenetics and Chromatin. 2016 ; Vol. 9, No. 1.
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AB - Background: Eukaryotic genome duplication starts at discrete sequences (replication origins) that coordinate cell cycle progression, ensure genomic stability and modulate gene expression. Origins share some sequence features, but their activity also responds to changes in transcription and cellular differentiation status. Results: To identify chromatin states and histone modifications that locally mark replication origins, we profiled origin distributions in eight human cell lines representing embryonic and differentiated cell types. Consistent with a role of chromatin structure in determining origin activity, we found that cancer and non-cancer cells of similar lineages exhibited highly similar replication origin distributions. Surprisingly, our study revealed that DNase hypersensitivity, which often correlates with early replication at large-scale chromatin domains, did not emerge as a strong local determinant of origin activity. Instead, we found that two distinct sets of chromatin modifications exhibited strong local associations with two discrete groups of replication origins. The first origin group consisted of about 40,000 regions that actively initiated replication in all cell types and preferentially colocalized with unmethylated CpGs and with the euchromatin markers, H3K4me3 and H3K9Ac. The second group included origins that were consistently active in cells of a single type or lineage and preferentially colocalized with the heterochromatin marker, H3K9me3. Shared origins replicated throughout the S-phase of the cell cycle, whereas cell-type-specific origins preferentially replicated during late S-phase. Conclusions: These observations are in line with the hypothesis that differentiation-associated changes in chromatin and gene expression affect the activation of specific replication origins.

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