Aberrant nucleosome organization in mouse SCNT embryos revealed by ULI-MNase-seq

Yang, Lingyue; Xu, Xiaocui; Xu, Ruimin; Chen, Chuan; Zhang, Xiaolei; Chen, Mo; Kou, Xiaochen; Zhao, Yanhong; Wang, Hong; Liu, Xiaoyu; Gao, Shaorong; Li, Chong

doi:10.1016/j.stemcr.2022.05.020

Cited by 3 publications

(6 citation statements)

References 58 publications

(87 reference statements)

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“…To address these questions, we selected a mouse DNA sequence that is known to be bound by Nr5a2 during ZGA in two-cell embryos 19 . The nucleosome positions in early and late two-cell embryos were identified using published data from micrococcal nuclease digestion with deep sequencing (MNase-seq) 31 . We identified a genomic locus containing SINE B1 , at which nucleosome depletion occurs during the transition from the early to late two-cell stage.…”

Section: Resultsmentioning

confidence: 99%

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Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition

Kobayashi,

Sappler,

Bollschweiler

et al. 2024

Nat Struct Mol Biol

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Gene expression during natural and induced reprogramming is controlled by pioneer transcription factors that initiate transcription from closed chromatin. Nr5a2 is a key pioneer factor that regulates zygotic genome activation in totipotent embryos, pluripotency in embryonic stem cells and metabolism in adult tissues, but the mechanism of its pioneer activity remains poorly understood. Here, we present a cryo-electron microscopy structure of human NR5A2 bound to a nucleosome. The structure shows that the conserved carboxy-terminal extension (CTE) loop of the NR5A2 DNA-binding domain competes with a DNA minor groove anchor of the nucleosome and releases entry-exit site DNA. Mutational analysis showed that NR5A2 D159 of the CTE is dispensable for DNA binding but required for stable nucleosome association and persistent DNA ‘unwrapping’. These findings suggest that NR5A2 belongs to an emerging class of pioneer factors that can use DNA minor groove anchor competition to destabilize nucleosomes and facilitate gene expression during reprogramming.

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Section: Resultsmentioning

confidence: 99%

“… a , IGV snap snapshot showing Nr5a2 binding overlapped with MNase-seq profile in mouse two-cell (2C) embryos and embryonic stem (mES) cells 31 , 38 . The dashed rectangles highlight the region used to reconstitute mononucleosomes.…”

Section: Resultsmentioning

confidence: 99%

Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition

Kobayashi,

Sappler,

Bollschweiler

et al. 2024

Nat Struct Mol Biol

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“…These observations supported that failure to close accessible somatic promoters, or to open distal regulatory regions, maybe the major reprogramming barriers in SCNT embryos. 17,18 As gene expression control is largely determined by cis-elements in promoter regions of target genes, [64][65][66] AMRs, which were more prominent in ICM, would be expected to have a predominant influence on gene expression.…”

Section: Bffs In Bovine Nt Blastocystsmentioning

confidence: 99%

“…More than 60% of the bovine SCNT blastocysts that appear healthy, based on morphology examination, degenerate or disappear soon after transferring into the uterus, 8–10 suggesting that the normal blastocyst morphology is not a reliable predictive marker for the full‐term development of cloned embryos 4,11 . Extensive chromatin reorganization has been proven to occur during early embryonic development 12–16 and subsequent studies reveal that mouse SCNT embryos exhibit a different dynamic of chromatin reorganization from the fertilized ones 17,18 . Based on these findings, the obscured aberrant chromatin states in the transferred bovine embryos with visually satisfactory morphology are considered likely to be responsible for the low cloning efficiency.…”

Section: Introductionmentioning

confidence: 99%

“…4,11 Extensive chromatin reorganization has been proven to occur during early embryonic development [12][13][14][15][16] and subsequent studies reveal that mouse SCNT embryos exhibit a different dynamic of chromatin reorganization from the fertilized ones. 17,18 Based on these findings, the obscured aberrant chromatin states in the transferred bovine embryos with visually satisfactory morphology are considered likely to be responsible for the low cloning efficiency. Genome-wide analysis of chromatin accessibility provides valuable information on the regulatory elements, gene transcription activity, and regulatory mechanisms involved in cell function and fate commitment [19][20][21] ; however, comprehensive and in-depth investigations into chromatin accessibility in bovine SCNT embryos, especially in blastocysts, are still scarce.…”

Section: Introductionmentioning

confidence: 99%

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Chromatin accessibility memory of donor cells disrupts bovine somatic cell nuclear transfer blastocysts development

Huang¹,

Zhang²,

et al. 2023

The FASEB Journal

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The post‐transfer developmental capacity of bovine somatic cell nuclear transfer (SCNT) blastocysts is reduced, implying that abnormalities in gene expression regulation are present at blastocyst stage. Chromatin accessibility, as an indicator for transcriptional regulatory elements mediating gene transcription activity, has heretofore been largely unexplored in SCNT embryos, especially at blastocyst stage. In the present study, single‐cell sequencing assay for transposase‐accessible chromatin (scATAC‐seq) of in vivo and SCNT blastocysts were conducted to segregate lineages and demonstrate the aberrant chromatin accessibility of transcription factors (TFs) related to inner cell mass (ICM) development in SCNT blastocysts. Pseudotime analysis of lineage segregation further reflected dysregulated chromatin accessibility dynamics of TFs in the ICM of SCNT blastocysts compared to their in vivo counterparts. ATAC‐ and ChIP‐seq results of SCNT donor cells revealed that the aberrant chromatin accessibility in the ICM of SCNT blastocysts was due to the persistence of chromatin accessibility memory at corresponding loci in the donor cells, with strong enrichment of trimethylation of histone H3 at lysine 4 (H3K4me3) at these loci. Correction of the aberrant chromatin accessibility through demethylation of H3K4me3 by KDM5B diminished the expression of related genes (e.g., BCL11B) and significantly improved the ICM proliferation in SCNT blastocysts. This effect was confirmed by knocking down BCL11B in SCNT embryos to down‐regulate p21 and alleviate the inhibition of ICM proliferation. These findings expand our understanding of the chromatin accessibility abnormalities in SCNT blastocysts and BCL11B may be a potential target to improve SCNT efficiency.

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Cloning by SCNT: Integrating Technical and Biology-Driven Advances

Moura

2023

Methods in Molecular Biology

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Aberrant nucleosome organization in mouse SCNT embryos revealed by ULI-MNase-seq

Cited by 3 publications

References 58 publications

Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition

Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition

Chromatin accessibility memory of donor cells disrupts bovine somatic cell nuclear transfer blastocysts development

Cloning by SCNT: Integrating Technical and Biology-Driven Advances

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