1
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Li WX. Computational simulation of JAK/STAT signaling in somatic versus germline stem cells. Dev Dyn 2023. [PMID: 38126664 DOI: 10.1002/dvdy.684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 11/20/2023] [Accepted: 12/10/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND The Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling pathway regulates a variety of cellular processes. A major activation event in this pathway involves the phosphorylation of a tyrosine of STAT, converting unphosphorylated STAT (uSTAT) to phosphorylated STAT (pSTAT), an active transcription factor. In a noncanonical role, uSTAT contributes to the maintenance of heterochromatin stability. As such, an increase in pSTAT concurrently reduces uSTAT, resulting in heterochromatin loss, as observed in Drosophila somatic tissues. Paradoxically, an opposing phenomenon occurs in Drosophila male germline stem cells (GSCs), where the JAK/STAT pathway remains persistently active due to a continuous supply of ligands. Here, computational simulations were employed to dissect JAK/STAT pathway activation under different cellular contexts, mimicking somatic and germline cells. In these simulations, ordinary differential equations were leveraged to replicate the chemical reactions governing JAK/STAT signaling under different conditions. RESULTS The outcomes indicate that transient ligand stimulation, typical in somatic tissues, led to a momentary reduction in uSTAT levels. Conversely, sustained ligand stimulation, a characteristic feature of the GSC niche, resulted in elevated uSTAT levels at equilibrium. CONCLUSION The simulation suggests that the duration of ligand exposure could explain the observed opposite effects of JAK/STAT activation on heterochromatin in somatic versus GSCs.
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Affiliation(s)
- Willis X Li
- Department of Medicine, University of California San Diego, La Jolla, California, USA
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2
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Xing Y, Larson K, Li J, Li WX. Canonical and non-canonical functions of STAT in germline stem cell maintenance. Dev Dyn 2023; 252:728-741. [PMID: 36866634 PMCID: PMC10238624 DOI: 10.1002/dvdy.576] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/01/2023] [Accepted: 02/09/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Maintenance of the Drosophila male germline stem cells (GSCs) requires activation of the Janus kinase/signal transducer and activators of transcription (JAK/STAT) pathway by niche signals. The precise role of JAK/STAT signaling in GSC maintenance, however, remains incompletely understood. RESULTS Here, we show that, GSC maintenance requires both canonical and non-canonical JAK/STAT signaling, in which unphosphorylated STAT (uSTAT) maintains heterochromatin stability by binding to heterochromatin protein 1 (HP1). We found that GSC-specific overexpressing STAT, or even the transcriptionally inactive mutant STAT, increases GSC number and partially rescues the GSC-loss mutant phenotype due to reduced JAK activity. Furthermore, we found that both HP1 and STAT are transcriptional targets of the canonical JAK/STAT pathway in GSCs, and that GSCs exhibit higher heterochromatin content. CONCLUSIONS These results suggest that persistent JAK/STAT activation by niche signals leads to the accumulation of HP1 and uSTAT in GSCs, which promote heterochromatin formation important for maintaining GSC identity. Thus, the maintenance of Drosophila GSCs requires both canonical and non-canonical STAT functions within GSCs for heterochromatin regulation.
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Affiliation(s)
- Yalan Xing
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642
| | - Kimberly Larson
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642
| | - Jinghong Li
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093
| | - Willis X. Li
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642
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3
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Vidaurre V, Chen X. Epigenetic regulation of drosophila germline stem cell maintenance and differentiation. Dev Biol 2021; 473:105-118. [PMID: 33610541 DOI: 10.1016/j.ydbio.2021.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/26/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022]
Abstract
Gametogenesis is one of the most extreme cellular differentiation processes that takes place in Drosophila male and female germlines. This process begins at the germline stem cell, which undergoes asymmetric cell division (ACD) to produce a self-renewed daughter that preserves its stemness and a differentiating daughter cell that undergoes epigenetic and genomic changes to eventually produce haploid gametes. Research in molecular genetics and cellular biology are beginning to take advantage of the continually advancing genomic tools to understand: (1) how germ cells are able to maintain their identity throughout the adult reproductive lifetime, and (2) undergo differentiation in a balanced manner. In this review, we focus on the epigenetic mechanisms that address these two questions through their regulation of germline-soma communication to ensure germline stem cell identity and activity.
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Affiliation(s)
- Velinda Vidaurre
- Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Baltimore, MD, 21218, USA
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Baltimore, MD, 21218, USA.
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4
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Dutta P, Nath S, Li J, Li WX. Drosophila SERTAD domain protein Taranis is required in somatic cells for maintenance of male germline stem cells. Dev Dyn 2020; 250:237-248. [PMID: 32969117 DOI: 10.1002/dvdy.255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Polycomb proteins are essential for maintaining stem cell identity across different stem cell niches. However, how they function to maintain stem cell niches is not fully understood. RESULTS Here we show that the SERTAD protein Taranis (Tara), which is a Polycomb-trithorax group protein, is expressed in the adult testis niche and plays a role in its maintenance in Drosophila. We found that tara is expressed in early cyst cells, likely including somatic cyst stem cells (CySCs) of Drosophila male testis tip region, which houses both germline and somatic cyst stem cells along with the hub cells, forming the stem cell niche. Consistent with its expression, we found that, while loss of tara in germline cells only had minimal effects, tara knockdown in all cells or only in somatic cells of the niche reduced the number of not only somatic cells, but also germline stem cells (GSCs). We further found that Tara might antagonize Notch signaling in CySCs to maintain the stem cell niche. CONCLUSIONS Our studies suggest that Tara might function in somatic CySCs for GSC maintenance in the Drosophila testis.
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Affiliation(s)
- Pranabananda Dutta
- Department of Medicine, University of California San Diego, La Jolla, California, USA.,Division of Cancer Research and Training, Department of Medicine, Charles R. Drew University of Medicine and Science, Los Angeles, California, USA
| | - Soma Nath
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Jinghong Li
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Willis X Li
- Department of Medicine, University of California San Diego, La Jolla, California, USA
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5
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Tsurumi A, Li WX. Aging mechanisms-A perspective mostly from Drosophila. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 1:e10026. [PMID: 36619249 PMCID: PMC9744567 DOI: 10.1002/ggn2.10026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 04/04/2020] [Accepted: 04/08/2020] [Indexed: 01/11/2023]
Abstract
A mechanistic understanding of the natural aging process, which is distinct from aging-related disease mechanisms, is essential for developing interventions to extend lifespan or healthspan. Here, we discuss current trends in aging research and address conceptual and experimental challenges in the field. We examine various molecular markers implicated in aging with an emphasis on the role of heterochromatin and epigenetic changes. Studies in model organisms have been advantageous in elucidating conserved genetic and epigenetic mechanisms and assessing interventions that affect aging. We highlight the use of Drosophila, which allows controlled studies for evaluating genetic and environmental contributors to aging conveniently. Finally, we propose the use of novel methodologies and future strategies using Drosophila in aging research.
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Affiliation(s)
- Amy Tsurumi
- Department of SurgeryMassachusetts General Hospital, and Harvard Medical SchoolBostonMassachusettsUSA,Department of Microbiology and ImmunologyHarvard Medical SchoolBostonMassachusettsUSA,Shriners Hospitals for Children‐Boston®BostonMassachusettsUSA
| | - Willis X. Li
- Department of MedicineUniversity of California at San DiegoLa JollaCaliforniaUSA
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6
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Tsurumi A, Xue S, Zhang L, Li J, Li WX. Genome-wide Kdm4 histone demethylase transcriptional regulation in Drosophila. Mol Genet Genomics 2019; 294:1107-1121. [PMID: 31020413 PMCID: PMC6813854 DOI: 10.1007/s00438-019-01561-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 04/03/2019] [Indexed: 12/23/2022]
Abstract
The histone lysine demethylase 4 (Kdm4/Jmjd2/Jhdm3) family is highly conserved across species and reverses di- and tri-methylation of histone H3 lysine 9 (H3K9) and lysine 36 (H3K36) at the N-terminal tail of the core histone H3 in various metazoan species including Drosophila, C.elegans, zebrafish, mice and humans. Previous studies have shown that the Kdm4 family plays a wide variety of important biological roles in different species, including development, oncogenesis and longevity by regulating transcription, DNA damage response and apoptosis. Only two functional Kdm4 family members have been identified in Drosophila, compared to five in mammals, thus providing a simple model system. Drosophila Kdm4 loss-of-function mutants do not survive past the early 2nd instar larvae stage and display a molting defect phenotype associated with deregulated ecdysone hormone receptor signaling. To further characterize and identify additional targets of Kdm4, we employed a genome-wide approach to investigate transcriptome alterations in Kdm4 mutants versus wild-type during early development. We found evidence of increased deregulated transcripts, presumably associated with a progressive accumulation of H3K9 and H3K36 methylation through development. Gene ontology analyses found significant enrichment of terms related to the ecdysteroid hormone signaling pathway important in development, as expected, and additionally previously unidentified potential targets that warrant further investigation. Since Kdm4 is highly conserved across species, our results may be applicable more widely to other organisms and our genome-wide dataset may serve as a useful resource for further studies.
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Affiliation(s)
- Amy Tsurumi
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, 50 Blossom St., Their 340, Boston, MA, 02114, USA.
- Department of Microbiology and Immunology, Harvard Medical School, 77 Ave. Louis Pasteur, Boston, MA, 02115, USA.
- Shriners Hospitals for Children-Boston®, 51 Blossom St., Boston, MA, 02114, USA.
| | - Shuang Xue
- Department of Medicine, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Lin Zhang
- Department of Medicine, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Jinghong Li
- Department of Medicine, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Willis X Li
- Department of Medicine, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
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7
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Heterochromatin protein 1 (HP1) is intrinsically required for post-transcriptional regulation of Drosophila Germline Stem Cell (GSC) maintenance. Sci Rep 2019; 9:4372. [PMID: 30867469 PMCID: PMC6416348 DOI: 10.1038/s41598-019-40152-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/07/2019] [Indexed: 01/05/2023] Open
Abstract
A very important open question in stem cells regulation is how the fine balance between GSCs self-renewal and differentiation is orchestrated at the molecular level. In the past several years much progress has been made in understanding the molecular mechanisms underlying intrinsic and extrinsic controls of GSC regulation but the complex gene regulatory networks that regulate stem cell behavior are only partially understood. HP1 is a dynamic epigenetic determinant mainly involved in heterochromatin formation, epigenetic gene silencing and telomere maintenance. Furthermore, recent studies have revealed the importance of HP1 in DNA repair, sister chromatid cohesion and, surprisingly, in positive regulation of gene expression. Here, we show that HP1 plays a crucial role in the control of GSC homeostasis in Drosophila. Our findings demonstrate that HP1 is required intrinsically to promote GSC self-renewal and progeny differentiation by directly stabilizing the transcripts of key genes involved in GSCs maintenance.
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8
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Loza-Coll MA, Petrossian CC, Boyle ML, Jones DL. Heterochromatin Protein 1 (HP1) inhibits stem cell proliferation induced by ectopic activation of the Jak/STAT pathway in the Drosophila testis. Exp Cell Res 2019; 377:1-9. [PMID: 30817931 DOI: 10.1016/j.yexcr.2019.02.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/22/2019] [Accepted: 02/24/2019] [Indexed: 11/18/2022]
Abstract
Stem cells can divide asymmetrically with respect to cell fate, producing a copy of themselves (self-renewal), while giving rise to progeny that will differentiate along a specific lineage. Mechanisms that bias the balance towards self-renewal or extend the proliferative capacity of the differentiating progeny can result in tissue overgrowth and, eventually, the formation of tumors. Recent work has explored the role of heterochromatin and heterochromatin-associated proteins in the regulation of stem cell behavior under homeostatic conditions, but less is known about their possible roles in potentiating or suppressing stem cell overproliferation. Here we used ectopic activation of the Jak/STAT pathway in germline and somatic stem cells of the D. melanogaster testis as an in vivo model to probe the function of Heterochromatin Protein 1 (HP1) in stem cell overproliferation. Forced expression of HP1 in either early germ or somatic cells suppressed the overgrowth of testes in response to ectopic Jak/STAT activation. Interestingly, HP1 expression led to distinct phenotypes, depending on whether it was overexpressed in somatic or germ cells, possibly reflecting different cell-autonomous and non-autonomous effects in each cell type. Our results provide a new framework for further in vivo studies aimed at understanding the interactions between heterochromatin and uncontrolled stem cell proliferation, as well as the complex cross-regulatory interactions between the somatic and germline lineages in the Drosophila testis.
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Affiliation(s)
| | | | | | - D Leanne Jones
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
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9
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10
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Barton LJ, Duan T, Ke W, Luttinger A, Lovander KE, Soshnev AA, Geyer PK. Nuclear lamina dysfunction triggers a germline stem cell checkpoint. Nat Commun 2018; 9:3960. [PMID: 30262885 PMCID: PMC6160405 DOI: 10.1038/s41467-018-06277-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 08/13/2018] [Indexed: 12/13/2022] Open
Abstract
LEM domain (LEM-D) proteins are conserved components of the nuclear lamina (NL) that contribute to stem cell maintenance through poorly understood mechanisms. The Drosophila emerin homolog Otefin (Ote) is required for maintenance of germline stem cells (GSCs) and gametogenesis. Here, we show that ote mutants carry germ cell-specific changes in nuclear architecture that are linked to GSC loss. Strikingly, we found that both GSC death and gametogenesis are rescued by inactivation of the DNA damage response (DDR) kinases, ATR and Chk2. Whereas the germline checkpoint draws from components of the DDR pathway, genetic and cytological features of the GSC checkpoint differ from the canonical pathway. Instead, structural deformation of the NL correlates with checkpoint activation. Despite remarkably normal oogenesis, rescued oocytes do not support embryogenesis. Taken together, these data suggest that NL dysfunction caused by Otefin loss triggers a GSC-specific checkpoint that contributes to maintenance of gamete quality. Otefin is a nuclear lamina protein required for survival of Drosophila germ stem cells. Here the authors show that nuclear lamina dysfunction resulting from loss of Otefin activates a DNA damage-independent germ stem cell-specific checkpoint, mediated by the ATR and Chk2 kinases, which ensures that healthy gametes are passed on to the next generation.
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Affiliation(s)
- Lacy J Barton
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA.,Department of Cell Biology, Skirball Institute, NYU School of Medicine, 540 First Avenue, New York, NY, 10016, USA
| | - Tingting Duan
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Wenfan Ke
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA.,Department of Biology, University of Virginia, 485 McCormick Rd, Charlottesville, VA, 22904, USA
| | - Amy Luttinger
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Kaylee E Lovander
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Alexey A Soshnev
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA.,Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Pamela K Geyer
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA.
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11
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An J, Wu M, Xin X, Lin Z, Li X, Zheng Q, Gui X, Li T, Pu H, Li H, Lu D. Inflammatory related gene IKKα, IKKβ, IKKγ cooperates to determine liver cancer stem cells progression by altering telomere via heterochromatin protein 1-HOTAIR axis. Oncotarget 2018; 7:50131-50149. [PMID: 27367027 PMCID: PMC5226573 DOI: 10.18632/oncotarget.10321] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/13/2016] [Indexed: 12/12/2022] Open
Abstract
Cancer stem cells are associated with tumor recurrence. IKK is a protein kinase that is composed of IKKα, IKKβ, IKKγ. Herein, we demonstrate that IKKα plus IKKβ promoted and IKKγ inhibited liver cancer stem cell growth in vitro and in vivo. Mechanistically, IKKα plus IKKβ enhanced and IKKγ inhibited the interplay among HP1α, HP1β and HP1γ that competes for the interaction among HP1α, SUZ12, HEZ2. Therefore, IKKα plus IKKβ inhibited and IKKγ enhanced the activity of H3K27 methyltransferase SUZ12 and EZH2, which methylates H3K27 immediately sites on HOTAIR promoter region. Therefore, IKKα plus IKKβ increased and IKKγ decreased the HOTAIR expression. Strikingly, IKKα plus IKKβ decreases and IKKγ increases the HP1α interplays with DNA methyltransferase DNMT3b, which increases or decreases TERRA promoter DNA methylation. Thus IKKα plus IKKβ reduces and IKKγ increases to recruit TRF1 and RNA polymerase II deposition and elongation on the TERRA promoter locus, which increases or decreases TERRA expression. Furthermore, IKKα plus IKKβ decreases/increases and IKKγ increases/decreases the interplay between TERT and TRRRA/between TERT and TREC. Ultimately, IKKα plus IKKβ increases and IKKγ decreases the telomerase activity. On the other hand, at the telomere locus, IKKα plus IKKβ increases/drcreases and IKKγ decreases/increases TRF2, POT1, pPOT1, Exo1, pExo1, SNM1B, pSNM1B/CST-AAF binding, which keep active telomere regulatory genes and poised for telomere length. Strikingly, HOTAIR is required for IKKα plus IKKβ and IKKγ to control telomerase activity and telomere length. These observations suggest that HOTAIR operates the action of IKKα, IKKβ, IKKγ in liver cancer stem cells. This study provides a novel basis to elucidate the oncogenic action of IKKα, IKKβ, IKKγ and prompts that IKKα, IKKβ, IKKγ cooperate to HOTAR to be used as a novel therapeutic targets for liver cancer.
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Affiliation(s)
- Jiahui An
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Mengying Wu
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Xiaoru Xin
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Zhuojia Lin
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Xiaonan Li
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Qidi Zheng
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Xin Gui
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Tianming Li
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Hu Pu
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Haiyan Li
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Dongdong Lu
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
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12
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Clémot M, Molla-Herman A, Mathieu J, Huynh JR, Dostatni N. The replicative histone chaperone CAF-1 is essential for the maintenance of identity and genome integrity in adult stem cells. Development 2018; 145:dev.161190. [DOI: 10.1242/dev.161190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 07/20/2018] [Indexed: 12/14/2022]
Abstract
Chromatin packaging and modifications are important to define the identity of stem cells. How chromatin properties are retained over multiple cycles of stem cell replication, while generating differentiating progeny at the same time, remains a challenging question. The chromatin assembly factor CAF-1 is a conserved histone chaperone, which assembles histones H3 and H4 onto newly synthesized DNA during replication and repair. Here, we investigated the role of CAF-1 in the maintenance of germline stem cells (GSCs) in Drosophila ovaries. We depleted P180, the large subunit of CAF-1, in germ cells and found that it was required in GSCs to maintain their identity. In the absence of P180, GSCs still harbor stem cell properties but concomitantly express markers of differentiation. In addition, P180-depleted germ cells exhibit elevated levels of DNA damage and de-repression of the transposable I-element. These DNA damages activate p53- and Chk2-dependent checkpoints pathways, leading to cell death and female sterility. Altogether, our work demonstrates that chromatin dynamics mediated by CAF-1 play an important role in both the regulation of stem cell identity and genome integrity.
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Affiliation(s)
- Marie Clémot
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics, Paris, France
| | - Anahi Molla-Herman
- Institut Curie, PSL Research University, CNRS, Inserm, Sorbonne Université, Genetics and Developmental Biology, Paris, France
| | - Juliette Mathieu
- Institut Curie, PSL Research University, CNRS, Inserm, Sorbonne Université, Genetics and Developmental Biology, Paris, France
| | - Jean-René Huynh
- Institut Curie, PSL Research University, CNRS, Inserm, Sorbonne Université, Genetics and Developmental Biology, Paris, France
| | - Nathalie Dostatni
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics, Paris, France
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13
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Tsurumi A, Zhao C, Li WX. Canonical and non-canonical JAK/STAT transcriptional targets may be involved in distinct and overlapping cellular processes. BMC Genomics 2017; 18:718. [PMID: 28893190 PMCID: PMC5594485 DOI: 10.1186/s12864-017-4058-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 08/14/2017] [Indexed: 02/08/2023] Open
Abstract
Background The Janus kinase-signal transducer and activator of transcription (JAK/STAT) pathway has been well-characterized as a crucial signal transduction cascade that regulates vital biological responses including development, immunity and oncogenesis. Additionally to its canonical pathway that uses the phosphorylated form of the STAT transcription factor, recently the non-canonical pathway involving heterochromatin formation by unphosphorylated STAT was recently uncovered. Considering the significant role of the JAK/STAT pathway, we used the simple Drosophila system in which the non-canonical pathway was initially characterized, to compare putative canonical versus non-canonical transcriptional targets across the genome. We analyzed microarray expression patterns of wildtype, Jak gain- and loss-of-function mutants, as well as the Stat loss-of-function mutant during embryogenesis, since the contribution of the canonical signal transduction pathway has been well-characterized in these contexts. Previous studies have also demonstrated that Jak gain-of-function and Stat mutants counter heterochromatin silencing to de-repress target genes by the non-canonical pathway. Results Compared to canonical target genomic loci, non-canonical targets were significantly more associated with sites enriched with heterochromatin-related factors (p = 0.004). Furthermore, putative canonical and non-canonical transcriptional targets identified displayed some differences in biological pathways they regulate, as determined by Gene Ontology (GO) enrichment analyses. Canonical targets were enriched mainly with genes relevant to development and immunity, as expected, whereas the non-canonical target gene set mainly showed enrichment of genes for various metabolic responses and stress response, highlighting the possibility that some differences may exist between the two loci. Conclusions Canonical and non-canonical JAK/STAT genes may regulate distinct and overlapping sets of genes and may perform specific overall functions in physiology. Further studies at different developmental stages, or using distinct tissues may identify additional targets and provide insight into which gene targets are unique to the canonical or non-canonical pathway. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4058-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amy Tsurumi
- Department of Surgery, Massachusetts General Hospital, 50 Blossom St., Thier 340, Boston, MA, 02114, USA. .,Department of Microbiology and Immunology, Harvard Medical School, 77 Ave. Louis Pasteur, Boston, MA, 02115, USA. .,Shriners Hospitals for Children-Boston®, 51 Blossom St, Boston, MA, 02114, USA.
| | - Connie Zhao
- Genomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Willis X Li
- Department of Medicine, University of California at San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
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14
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Kogan GL, Akulenko NV, Abramov YA, Sokolova OA, Fefelova EA, Gvozdev VA. Nascent polypeptide-associated complex as tissue-specific cofactor during germinal cell differentiation in Drosophila testes. Mol Biol 2017. [DOI: 10.1134/s0026893317040112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Kim JJ, Bennett NK, Devita MS, Chahar S, Viswanath S, Lee EA, Jung G, Shao PP, Childers EP, Liu S, Kulesa A, Garcia BA, Becker ML, Hwang NS, Madabhushi A, Verzi MP, Moghe PV. Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells. Sci Rep 2017; 7:39406. [PMID: 28051095 PMCID: PMC5209743 DOI: 10.1038/srep39406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/23/2016] [Indexed: 12/22/2022] Open
Abstract
While distinct stem cell phenotypes follow global changes in chromatin marks, single-cell chromatin technologies are unable to resolve or predict stem cell fates. We propose the first such use of optical high content nanoscopy of histone epigenetic marks (epi-marks) in stem cells to classify emergent cell states. By combining nanoscopy with epi-mark textural image informatics, we developed a novel approach, termed EDICTS (Epi-mark Descriptor Imaging of Cell Transitional States), to discern chromatin organizational changes, demarcate lineage gradations across a range of stem cell types and robustly track lineage restriction kinetics. We demonstrate the utility of EDICTS by predicting the lineage progression of stem cells cultured on biomaterial substrates with graded nanotopographies and mechanical stiffness, thus parsing the role of specific biophysical cues as sensitive epigenetic drivers. We also demonstrate the unique power of EDICTS to resolve cellular states based on epi-marks that cannot be detected via mass spectrometry based methods for quantifying the abundance of histone post-translational modifications. Overall, EDICTS represents a powerful new methodology to predict single cell lineage decisions by integrating high content super-resolution nanoscopy and imaging informatics of the nuclear organization of epi-marks.
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Affiliation(s)
- Joseph J. Kim
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Neal K. Bennett
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - Mitchel S. Devita
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, USA
| | - Sanjay Chahar
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
| | - Satish Viswanath
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Eunjee A. Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Giyoung Jung
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
- Division of Heath Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paul P. Shao
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Erin P. Childers
- Department of Polymer Science, University of Akron, Akron, Ohio, USA
| | - Shichong Liu
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anthony Kulesa
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Benjamin A. Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Matthew L. Becker
- Department of Polymer Science, University of Akron, Akron, Ohio, USA
| | - Nathaniel S. Hwang
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Michael P. Verzi
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
| | - Prabhas V. Moghe
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey, USA
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