MtDNA Chromatin-like Organization Is Gradually Established during Mammalian Embryogenesis

Shani Marom,Amit Blumberg,Anshul Kundaje,Dan Mishmar

doi:10.1016/j.isci.2018.12.032

Abstract

SummaryUnlike the nuclear genome, the mammalian mitochondrial genome (mtDNA) is thought to be coated solely by mitochondrial transcription factor A (TFAM), whose binding sequence preferences are debated. Therefore, higher-order mtDNA organization is considered much less regulated than both the bacterial nucleoid and the nuclear chromatin. However, our recently identified conserved DNase footprinting pattern in human mtDNA, which co-localizes with regulatory elements and responds to physiological conditions, likely reflects a structured higher-order mtDNA organization. We hypothesized that this pattern emerges during embryogenesis. To test this hypothesis, we analyzed assay for transposase-accessible chromatin sequencing (ATAC-seq) results collected during the course of mouse and human early embryogenesis. Our results reveal, for the first time, a gradual and dynamic emergence of the adult mtDNA footprinting pattern during embryogenesis of both mammals. Taken together, our findings suggest that the structured adult chromatin-like mtDNA organization is gradually formed during mammalian embryogenesis.

Highlights

During metazoan embryogenesis, the transition to zygotic gene expression occurs during the blastocyst stage
Taken together our study reveals for the first time a dynamic chromatin-like mtDNA organization during the course of early mammalian embryogenesis, which associates with regulatory sites of mtDNA transcription and replication
To increase the stringency of our comparison of mtASFP dynamics during mouse development, sites that overlapped at least in one nucleotide position were merged. Such a stringent approach was applied to avoid false identification of mt-ATAC-seq footprinting sites (ASFPs) site changes and dynamics, reducing potential noise. This approach was applied to ATAC-seq experimental data collected from mouse pre-implanted embryos at the following developmental stages: early 2-cell, 2-cell, 4-cell, 8-cell, and inner cell mass (ICM) stages (Wu et al, 2016), as well as from mouse embryonic day 6 (E6) and E7.2 embryos from another dataset (Neijts et al, 2016)

Summary

Introduction

The transition to zygotic gene expression occurs during the blastocyst stage. During the early 1970s, strand-specific mtDNA polycistron transcripts have been identified in human cells (Aloni and Attardi, 1971), which subsequently were determined in the mouse mtDNA (Barshad et al, 2018; Battey and Clayton, 1978; Blumberg et al, 2017) This bacterial-like pattern of transcription urged many to isolate the core elements of mtDNA transcriptional regulation, namely, mitochondrial transcription factor A (TFAM) (Fisher et al, 1987; Parisi and Clayton, 1991), the mitochondrial RNA polymerase (POLRMT) (Reid and Parsons, 1971; Ringel et al, 2011), mitochondrial transcription factor B2 (Falkenberg et al, 2002; Gustafsson et al, 2016; Morozov et al, 2014), and the transcription termination factor, mTERF (Daga et al, 1993).

Results

Discussion

Conclusion