ATF7IP2/MCAF2 directs H3K9 methylation and meiotic gene regulation in the male germline.

H3K9 trimethylation (H3K9me3) plays emerging roles in gene regulation, beyond its accumulation on pericentric constitutive heterochromatin. It remains a mystery why and how H3K9me3 undergoes dynamic regulation in male meiosis. Here, we identify a novel, critical regulator of H3K9 methylation and spermatogenic heterochromatin organization: the germline-specific protein ATF7IP2 (MCAF2). We show that in male meiosis, ATF7IP2 amasses on autosomal and X-pericentric heterochromatin, spreads through the entirety of the sex chromosomes, and accumulates on thousands of autosomal promoters and retrotransposon loci. On the sex chromosomes, which undergo meiotic sex chromosome inactivation (MSCI), the DNA damage response pathway recruits ATF7IP2 to X-pericentric heterochromatin, where it facilitates the recruitment of SETDB1, a histone methyltransferase that catalyzes H3K9me3. In the absence of ATF7IP2, male germ cells are arrested in meiotic prophase I. Analyses of ATF7IP2-deficient meiosis reveal the protein's essential roles in the maintenance of MSCI, suppression of retrotransposons, and global up-regulation of autosomal genes. We propose that ATF7IP2 is a downstream effector of the DDR pathway in meiosis that coordinates the organization of heterochromatin and gene regulation through the spatial regulation of SETDB1-mediated H3K9me3 deposition.

CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline.

Spermatogenesis is a unidirectional differentiation process that generates haploid sperm, but how the gene expression program that directs this process is established is largely unknown. Here we determine the high-resolution 3D chromatin architecture of male germ cells during spermatogenesis and show that CTCF-mediated 3D chromatin predetermines the gene expression program required for spermatogenesis. In undifferentiated spermatogonia, CTCF-mediated chromatin contacts on autosomes pre-establish meiosis-specific super-enhancers (SE). These meiotic SE recruit the master transcription factor A-MYB in meiotic spermatocytes, which strengthens their 3D contacts and instructs a burst of meiotic gene expression. We also find that at the mitosis-to-meiosis transition, the germline-specific Polycomb protein SCML2 resolves chromatin loops that are specific to mitotic spermatogonia. Moreover, SCML2 and A-MYB establish the unique 3D chromatin organization of sex chromosomes during meiotic sex chromosome inactivation. We propose that CTCF-mediated 3D chromatin organization enforces epigenetic priming that directs unidirectional differentiation, thereby determining the cellular identity of the male germline.

ATF7IP2/MCAF2 directs H3K9 methylation and meiotic gene regulation in the male germline.

H3K9 tri-methylation (H3K9me3) plays emerging roles in gene regulation, beyond its accumulation on pericentric constitutive heterochromatin. It remains a mystery why and how H3K9me3 undergoes dynamic regulation in male meiosis. Here, we identify a novel, critical regulator of H3K9 methylation and spermatogenic heterochromatin organization: the germline-specific protein ATF7IP2 (MCAF2). We show that, in male meiosis, ATF7IP2 amasses on autosomal and X pericentric heterochromatin, spreads through the entirety of the sex chromosomes, and accumulates on thousands of autosomal promoters and retrotransposon loci. On the sex chromosomes, which undergo meiotic sex chromosome inactivation (MSCI), the DNA damage response pathway recruits ATF7IP2 to X pericentric heterochromatin, where it facilitates the recruitment of SETDB1, a histone methyltransferase that catalyzes H3K9me3. In the absence of ATF7IP2, male germ cells are arrested in meiotic prophase I. Analyses of ATF7IP2-deficient meiosis reveal the protein's essential roles in the maintenance of MSCI, suppression of retrotransposons, and global upregulation of autosomal genes. We propose that ATF7IP2 is a downstream effector of the DDR pathway in meiosis that coordinates the organization of heterochromatin and gene regulation through the spatial regulation of SETDB1-mediated H3K9me3 deposition.

Active DNA damage response signaling initiates and maintains meiotic sex chromosome inactivation.

Meiotic sex chromosome inactivation (MSCI) is an essential process in the male germline. While genetic experiments have established that the DNA damage response (DDR) pathway directs MSCI, due to limitations to the experimental systems available, mechanisms underlying MSCI remain largely unknown. Here we establish a system to study MSCI ex vivo, based on a short-term culture method, and demonstrate that active DDR signaling is required both to initiate and maintain MSCI via a dynamic and reversible process. DDR-directed MSCI follows two layers of modifications: active DDR-dependent reversible processes and irreversible histone post-translational modifications. Further, the DDR initiates MSCI independent of the downstream repressive histone mark H3K9 trimethylation (H3K9me3), thereby demonstrating that active DDR signaling is the primary mechanism of silencing in MSCI. By unveiling the dynamic nature of MSCI, and its governance by active DDR signals, our study highlights the sex chromosomes as an active signaling hub in meiosis.

PRC1-mediated epigenetic programming is required to generate the ovarian reserve.

The ovarian reserve defines the female reproductive lifespan, which in humans spans decades due to robust maintenance of meiotic arrest in oocytes residing in primordial follicles. Epigenetic reprogramming, including DNA demethylation, accompanies meiotic entry, but the chromatin changes that underpin the generation and preservation of ovarian reserves are poorly defined. We report that the Polycomb Repressive Complex 1 (PRC1) establishes repressive chromatin states in perinatal mouse oocytes that directly suppress the gene expression program of meiotic prophase-I and thereby enable the transition to dictyate arrest. PRC1 dysfuction causes depletion of the ovarian reserve and leads to premature ovarian failure. Our study demonstrates a fundamental role for PRC1-mediated gene silencing in female reproductive lifespan, and reveals a critical window of epigenetic programming required to establish ovarian reserve.

Prediction of major microRNAs in follicular fluid regulating porcine oocyte development.

PURPOSE: The aim of the present study was to identify key microRNAs (miRNAs) in porcine follicular fluid (FF) that regulate oocyte growth. METHODS: miRNAs contained in FF were determined by small RNA-seq of exosome RNA. Upstream regulator miRNA was determined by ingenuity pathway analysis using differentially expressed genes in granulosa cells (GCs) between small follicles (1-2 mm in diameter) and large follicles (3-5 mm), and between follicles containing oocytes of high developmental ability and follicles containing oocytes of low developmental ability. The candidate miRNAs overlapping among the three miRNAs group were determined. Lastly, the effect of supplementation with FF, exosome-depleted FFs, or each miRNA on in vitro oocyte growth was examined. RESULTS: The miRNAs determined were miR-17, -27, -92a, and -145. These miRNAs were found in the spent culture medium of oocytes and granulosa cells complexes and serum by small RNA sequencing. Culturing of oocytes and granulosa cells complexes collected from porcine early antral follicles (0.5-0.7 mm in diameter) with FF for 14 days improved oocyte growth; depletion of exosomes from the FFs neutralized the beneficial effect observed. miR-92a mimic increased the antrum formation and diameter, together with acetylated levels of H4K12 in oocytes. In addition, supplementation of miRNA mimics miR-17b, -92a, and -145b improved the rate of chromatin configuration, and miR-17b and -92a mimics improved the developmental ability of oocytes to the blastocyst stage. CONCLUSION: miR-17, -92a, and -145 are major miRNA candidates in follicular fluids regulating oocyte growth.

Comparison of gene expression and mitochondria number between bovine blastocysts obtained in vitro and in vivo.

Embryo transfer uses embryos developed in vivo or in vitro for cattle production, however there is a difference in the quality of the embryos obtained by the two methods. This study addresses the differences in gene expression between blastocysts developed in vitro and in vivo. In vivo blastocysts were flushed from the uteri of super-ovulated cows and blastocysts developed in vitro were derived from in vitro matured and fertilized embryos. The same batch of frozen bull sperm was used for insemination and in vitro fertilization. Blastocysts were then subjected to RNA sequencing. Differentially expressed genes upregulated in in vitro blastocysts were annotated to focal adhesion, extracellular matrix (ECM)-receptor interaction, and PI3K-Akt signaling and the genes that were upregulated in in vivo blastocysts were annotated to oxidation-reduction processes, mitochondrion organization, and mitochondrial translation. Although the total cell number of the two types of blastocysts was similar, the mitochondrial quantity (determined by mitochondrial DNA copy numbers and expression levels of TOMM20), and ATP content in the blastocysts were lower in in vivo blastocysts compared with those developed in vitro. In conclusion, RNAseq revealed differential molecular backgrounds between in vitro and in vivo developed blastocysts and mitochondrial number and function are responsible for these differences.

Xanthan gum and Locust bean gum gel supports in vitro development of porcine oocytes derived from early antral follicles.

Early antral follicle (EAF)-derived porcine oocytes develop more readily on polyacrylamide-gel (PAG) than on plastic plates. Xanthan gum (XG) and locust bean gum (LBG) are edible polysaccharides. We investigated XG-LBG gel supports in the development of EAF-derived porcine oocytes. XG and LBG were mixed in a 1:1 ratio to form a substrate. We cultured oocyte granulosa cell complexes (OGCs) from the EAFs on XG-LBG gels of various concentrations. The oocyte diameters were comparable among the 0.3, 0.5, and 1.0% gels; granulosa cell proliferation was greater on the 1.0% gel. The proliferation and survival rates of the granulosa cells, and the histone H4 at lysine 12 acetylation levels were higher in OGCs cultured on 1.0% XG-LBG than those grown on 0.3% PAG. Development to the blastocyst stage was 13.8% for the XG-LBG gels and 9.4% for PAG. In conclusion, XG-LBG are safe and efficient substrates for in vitro culture of oocytes.

Mitochondrial cell-free DNA secreted from porcine granulosa cells.

Several studies have proposed that cell-free DNA (cfDNA) is a potential biomarker present in follicular fluid (FF) for oocyte quality. Recently we reported that mitochondria-derived cfDNA (mt-cfDNA) closely reflects the amount of cfDNA in FFs. The present study investigated the mechanism regulating mt-cfDNA secretion from porcine granulosa cells. Oocytes and cumulus cell complexes or granulosa cells (GCs) were cultured in maturation medium for 24 or 48 h respectively. Then, nuclear-derived cell-free DNA (n-cfDNA) or mt-cfDNA contents in the spent medium were examined using real-time polymerase chain reaction. When 10 µM of MG132, a proteasome inhibitor, was added to the culture medium, cellular viability of both COCs and GCs decreased and n-cfDNA significantly increased in the culture medium, whereas mt-cfDNA significantly decreased. Supplementation of the culture medium with GW4869, an inhibitor of intracellular vesicle formation, significantly decreased the mt-cfDNA, whereas no effect was observed on n-cfDNA in the medium of both COCs and GCs. Furthermore, the addition of bafilomycin, an inhibitor of autophagy to the culture medium significantly increased mt-cfDNA in the culture medium. After filtration (0.22 µm) and centrifugation (23,000 g), the mt-cfDNA content of the medium decreased significantly. In conclusion, the proteasomal mitochondrial quality control system is upstream of mt-cfDNA secretion and autophagy plays a role in cellular digestion of mitochondrial DNA in the cytoplasm. It is further suggested that dsDNA is enclosed in certain vesicles or associated with small molecules and secreted into the medium.

Modification of the medium volume and gel substrate under in vitro culture conditions improves growth of porcine oocytes derived from early antral follicles.

This study compared the effects of different volumes of culture medium for the in vitro growth of oocytes derived from porcine early antral follicles (EAFs). Oocyte granulosa cell complexes (OGCs) were collected from EAFs (0.5-0.7 mm in diameter) and individually cultured for 14 days. When OGCs were cultured in 1 ml of medium with or without polyacrylamide gel (PAG), the presence of PAG supported granulosa cell (GC) proliferation and oocyte growth. When OGCs were cultured in 0.2 or 1 ml of medium on PAG, the number of GC in the OGC culture and the developmental ability of the oocytes cultured in vitro were significantly higher for the 1 ml of culture medium group than for the 0.2 ml group. In conclusion, a combination of a large volume of culture medium with PAG improved the growth and developmental ability of the oocytes cultured in vitro, which were comparable to the oocytes collected from large antral follicles.

Cell-free DNA in medium is associated with the maturation ability of in vitro cultured oocytes.

Follicular fluid contains cell-free DNA (cfDNA), which may serve as a useful biomarker of oocyte ability. The present study evaluates whether nuclear and mitochondrial cfDNAs in conditioned oocyte growth medium determine the quality of oocytes cultured in vitro. Oocyte and granulosa cell complexes (OGCs) derived from early antral follicles of gilt ovaries were cultured for 14 days and the amount of cfDNA and lactate concentration in the conditioned culture medium were measured and compared to evaluate oocyte maturation ability. The amount of nuclear cfDNA, but not mitochondrial cfDNA, strongly correlated with the number of dead cells in OGCs. Furthermore, low mitochondrial cfDNA content and high lactate concentration in the medium was associated with high maturation ability of oocytes cultured in vitro. In conclusion, the amounts of nuclear and mitochondrial cfDNAs differentially reflect the conditions of OGCs, and low mitochondrial cfDNA, low glucose content, and high lactate concentration in the medium are associated with the proper maturation of oocytes.

Addition of granulosa cells collected from differential follicle stages supports development of oocytes derived from porcine early antral follicles.

PURPOSE: Improvement of in vitro oocyte growth by addition of granulosa cells derived from differential developmental stages of follicles. METHODS: Granulosa cells (GCs) collected from either early antral follicles (EAFs) or antral follicles (AFs) were added to oocyte-granulosa cell complexes (OGCs) derived from EAFs, and the in vitro growth of the oocytes was evaluated. RESULTS: Granulosa cells were incorporated into OGCs to form new OGCs within 2 days of culture. After 14 days of culture, the number of GCs surrounding oocytes was similar among the three OGCs conditions (unmanipulated "natural OGCs," "EAF-GCs add OGCs," and "AF-GCs add OGCs"), whereas the survival rate of the GCs and diameter of oocytes grown in vitro were the greatest for "AF-GCs added OGCs." After parthenogenetic activation, developmental rate till the blastocyst stage tended to be higher for "AF-GCs add OGCs" compared with other groups. Addition of AF-GCs significantly increased a hypoxic marker (pimonidazole staining) and increased the lipid content in oocytes grown in vitro compared with unmanipulated OGCs. CONCLUSION: Addition of GCs derived from more advanced stages of follicles to the OGCs changes the metabolism of oocytes and is beneficial for in vitro growth of oocytes derived from EAFs.

Aggregation of Human Trophoblast Cells into Three-Dimensional Culture System Enhances Anti-Inflammatory Characteristics through Cytoskeleton Regulation.

BACKGROUND: Three-dimensional (3D) culture changes cell characteristics and function, suggesting that 3D culture provides a more physiologically relevant environment for cells compared with 2D culture. We investigated the differences in cell functions depending on the culture model in human trophoblast cells (Sw.71). METHODS: Sw.71 cells were incubated in 2D monolayers or simple 3D spheroids. After incubation, cells were corrected to assess RNA-seq transcriptome or protein expression, and culture medium were corrected to detect cytokines. To clarify the role of actin cytoskeleton, spheroid Sw.71 cells were treated mycalolide B (inhibitor of actin polymerization) in a 3D culture. RESULTS: RNA-seq transcriptome analysis, results revealed that 3D-cultured cells had a different transcriptional profile compared with 2D-cultured cells, especially regarding inflammation-related molecules. Although interleukin-6 (IL-6) mRNA level was higher in 3D-culured cells, its secretion levels were higher in 2D-cultured cells. In addition, the levels of mRNA and protein expression of regnase-1, regulatory RNase of inflammatory cytokine, significantly increased in 3D culture, suggesting post-translational modification of IL-6 mRNA via regnase-1. Treatment with mycalolide B reduced cell-to-cell contact to build 3D formation and increased expression of actin cytoskeleton, resulting in increased IL-6 secretin. CONCLUSION: Cell dimensionality plays an essential role in governing the spatiotemporal cellular outcomes, including inflammatory cytokine production and its negative regulation associated with regnase-1.

Follicular factors determining granulosa cell number and developmental competence of porcine oocytes.

PURPOSE: Granulosa cell (GC) number in follicles is a simple characteristic of follicles. The present study examined the hypothesis that follicular fluid (FF) determines GC number and oocyte developmental ability and revealed the molecular background determining the number of follicular GCs. METHODS: FF was collected from antral follicles (3-5 mm in diameter), after which the number of GCs per follicle was determined for each donor gilt using real time PCR targeting single copy gene. GCs were analyzed by next-generation RNA sequencing and IPA pathway analysis. RESULTS: When oocyte cumulus cell-oocyte-complexes (COCs) were cultured in maturation medium containing 10% of each individual FF, the rate of development to the blastocyst stage was significantly correlated with the number of GCs in the donor gilt. In addition, when GCs were cultured in medium containing FF, the proliferative activity of the GCs was also significantly correlated to the number of GCs in the donor gilt. Moreover, when the FFs were categorized based on the number of GCs in the follicle, it was found that supplementation of culture media with GC-rich FF improved the developmental ability of oocytes compared to those supplemented with GC-poor FF. RNA sequencing and a pathway analysis of GCs from GC-rich and -poor follicles revealed the key regulatory pathway determining GC number in follicles. CONCLUSION: GC number may be a useful marker for "good" follicles and oocytes, and the characteristics of the FFs determine granulosa cell number and oocyte developmental ability.

Mitochondrial dysfunction in cumulus-oocyte complexes increases cell-free mitochondrial DNA.

This study examined the concentration of cell-free mitochondrial DNA (cf-mtDNA) in porcine follicular fluid (FF) and explored whether the cfDNA level in the culture medium could reflect mitochondrial dysfunction in cumulus cell-oocyte complexes (COCs). cfDNA concentration was higher in the fluid of small-sized follicles, compared to that in larger follicles. The length of cfDNA ranged from short (152 bp) to long (1,914 bp) mtDNA in FF, detected by polymerase chain reaction (PCR). cfDNA concentration in FF significantly correlated with the mtDNA copy number in FF but not with the number of one-copy gene (nuclear DNA) in FF. When the COCs were treated with the mitochondrial uncoupler, namely carbonyl cyanide m-chlorophenyl hydrazone (CCCP), for 2 h and incubated for 42 h, subsequent real-time PCR detected significantly higher amount of cf-mtDNA, compared to nuclear cfDNA, in the spent culture medium. The mtDNA number and viability of cumulus cells and oocytes remained unchanged. When the oocytes were denuded from the cumulus cells following CCCP treatment, PCR detected very low levels of cfDNA in the spent culture medium of the denuded oocytes. In contrast, CCCP treatment of granulosa cells significantly increased the amount of cf-mtDNA in the spent culture medium, without any effect on other markers, including survival rate, apoptosis of cumulus cells, and lactate dehydrogenase levels. Thus, cf-mtDNA was present in FF in a wide range of length, and mitochondrial dysfunction in COCs increased the active secretion of cf-mtDNA in the cultural milieu.

Promotion of glucose utilization by insulin enhances granulosa cell proliferation and developmental competence of porcine oocyte grown in vitro.

In vitro culture of the oocyte granulosa cell complexes (OGCs) from early antral follicles (EAFs) shows granulosa cell (GC) proliferation, but to a lesser extent than that observed in vivo during follicle development. As the number of GCs closely relates to energy sufficiency of the oocytes, enhancement of GC proliferation influences oocyte development. GC proliferation depends on glycolysis and insulin-mediated AKT/mTOR signaling pathway; therefore, addition of culture medium containing insulin and glucose may potentially promote GC proliferation and hence improve oocyte development. In the present study, we assessed the effect of exogenous insulin and glucose concentration on GC proliferation and oocyte energy status as well as developmental abilities of porcine oocytes grown in vitro. In the presence of 5.5 mM of glucose (Low), a comparison of 10 versus 20 µg/ml insulin showed that high insulin enhanced GC proliferation but exhausted glucose from the medium, which resulted in low energy status including lipid and adenosine triphosphate of the oocyte. Whereas, in the presence of 20 µg/ml insulin, medium with 11 mM glucose (High) enhanced GC proliferation and oocyte energy status as well as developmental ability up to the blastocyst stage. Considering that there was no difference in OGCs development observed with medium (10 µg/ml insulin) containing 5.5 versus 11 mM glucose, we concluded that the combination of high insulin and glucose enhanced GC proliferation and energy status of oocytes as well as the developmental ability of the oocytes grown in vitro.

Polyacrylamide gel as a culture substrate improves in vitro oocyte growth from porcine early antral follicles.

A major difference between in vivo and in vitro follicle culture is the stiffness of the substrate in which the follicles grow. In this study, we examined the effect of polyacrylamide gel (PAG), as a culture substrate, on the development of porcine oocytes derived from early antral follicles. Oocyte-granulosa cell complexes (OGCs) were collected from the early antral follicles of gilts, and incubated individually for 14 days in a 96-well culture plate without or with PAG. We then evaluated the number of granulosa cells present in OGCs as well as the abundance of ATP, lipid, and acetylated lysine in oocytes. OGCs cultured on PAG showed significantly greater antrum formation and granulosa cell proliferation than controls cultured on standard plastic. Oocytes grown on PAG also possessed significantly larger diameter, ATP and lipid content, and lysine acetylation, as well as competence to develop to the blastocyst stage. Transcriptome analysis of the granulosa cells revealed that genes involved in follicular development and mechanosensing are up-regulated under PAG culturing conditions. Thus, in vitro culturing OGCs on PAG profoundly induced granulosa cell proliferation, resulting in improved developmental competence of the oocytes. Mol. Reprod. Dev. 84: 44-54, 2017. © 2016 Wiley Periodicals, Inc.

Low oxygen level increases proliferation and metabolic changes in bovine granulosa cells.

The present study addresses molecular backgrounds underlying low oxygen induced metabolic changes and 1.2-fold change in bovine granulosa cell (GCs) proliferation. RNA-seq revealed that low oxygen (5%) upregulated genes associated with HIF-1 and glycolysis and downregulated genes associated with mitochondrial respiration than that in high oxygen level (21%). Low oxygen level induced high glycolytic activity and low mitochondrial function and biogenesis. Low oxygen level enhanced GC proliferation with high expression levels of HIF-1, VEGF, AKT, mTOR, and S6RP, whereas addition of anti-VEGF antibody decreased cellular proliferation with low phosphorylated AKT and mTOR expression levels. Low oxygen level reduced SIRT1, whereas activation of SIRT1 by resveratrol increased mitochondrial replication and decreased cellular proliferation with reduction of phosphorylated mTOR. These results suggest that low oxygen level stimulates the HIF1-VEGF-AKT-mTOR pathway and up-regulates glycolysis, which contributes to GC proliferation, and downregulation of SIRT1 contributes to hypoxia-associated reduction of mitochondria and cellular proliferation.

Relationship between the number of cells surrounding oocytes and energy states of oocytes.

Lipid content, ATP content, and histone acetylation are thought to reflect the energy state of cells. In addition, the energy state closely associates with growth and developmental ability of oocytes. Oocyte growth is accompanied by active proliferation of the surrounding granulosa cells (GCs), and GCs play a key role in the provision of energy substrates to the oocytes. In the present study, we first examined the relationship among the average number of GCs per follicle, the average number of cumulus cells (CCs) per oocyte, and the average lipid content in oocytes that developed in vivo within individual donor gilts. Second, we validated the relationship between the number of cells surrounding oocytes and the energy states of oocytes by using an IVC system of oocyte granulosa cell complexes (OGCs) derived from early antral follicles. We collected cumulus cells and oocyte complexes (COCs) from antral follicles (3-5 mm in diameter) and found that average lipid content in oocytes significantly correlated with the average number of both GCs/follicle and CCs/oocyte (P < 0.05). In the next series of experiments, we collected OGCs from early antral follicles (0.5-0.7 mm in diameter), and cultured them for 14 days, and then determined the cell number of OGCs, as well as the lipid content, ATP content, and acetylation level of H4K12 in oocytes grown in vitro. In addition, glucose consumption by OGCs was calculated from the sample media collected at Days 13 and 14. The lipid content of oocytes grown in vitro, significantly correlated with the number of cells surrounding the oocytes (P < 0.01) and with the level of glucose consumption by OGCs (P < 0.01). In addition, both ATP content and H4K12 acetylation levels of oocytes grown in vitro significantly correlated with the number of cells surrounding the oocytes (P < 0.05) and glucose consumption by OGCs (P < 0.05). In conclusion, the lipid content of oocytes depends on the number of cells surrounding the oocytes, and glucose uptake by OGCs is crucial for lipid content and ATP content, and H4K12 acetylation in oocytes.

Gene expression patterns in granulosa cells and oocytes at various stages of follicle development as well as in in vitro grown oocyte-and-granulosa cell complexes.

Follicle development is accompanied by proliferation of granulosa cells and increasing oocyte size. To obtain high-quality oocytes in vitro, it is important to understand the processes that occur in oocytes and granulosa cells during follicle development and the differences between in vivo and in vitro follicle development. In the present study, oocytes and granulosa cells were collected from early antral follicles (EAFs, 0.5-0.7 mm in diameter), small antral follicles (SAFs, 1-3 mm in diameter), large antral follicles (LAFs, 3-7 mm in diameter), and in vitro grown oocyte-and-granulosa cell complexes (OGCs), which were cultured for 14 days after collection from EAFs. Gene expression was analyzed comprehensively using the next-generation sequencing technology. We found top upstream regulators during the in vivo follicle development and compared them with those in in vitro developed OGCs. The comparison revealed that HIF1 is among the top regulators during both in vivo and in vitro development of OGCs. In addition, we found that HIF1-mediated upregulation of glycolysis in granulosa cells is important for the growth of OGCs, but the cellular metabolism differs between in vitro and in vivo grown OGCs. Furthermore, on the basis of comparison of upstream regulators between in vivo and in vitro development of OGCs, we believe that low expression levels of FLT1 (VEGFA receptor), SPP1, and PCSK6 can be considered causal factors of the suboptimal development under in vitro culture conditions.