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Zhang YW, Wu SX, Wang GW, Wan RD, Yang QE. Single-cell analysis identifies critical regulators of spermatogonial development and differentiation in cattle-yak bulls. J Dairy Sci 2024; 107:7317-7336. [PMID: 38642661 DOI: 10.3168/jds.2023-24442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/11/2024] [Indexed: 04/22/2024]
Abstract
Spermatogenesis is a continuous process in which functional sperm are produced through a series of mitotic and meiotic divisions and morphological changes in germ cells. The aberrant development and fate transitions of spermatogenic cells cause hybrid sterility in mammals. Cattle-yak, a hybrid animal between taurine cattle (Bos taurus) and yak (Bos grunniens), exhibits male-specific sterility due to spermatogenic failure. In the present study, we performed single-cell RNA sequencing analysis to identify differences in testicular cell composition and the developmental trajectory of spermatogenic cells between yak and cattle-yak. The composition and molecular signatures of spermatogonial subtypes were dramatically different between these 2 animals, and the expression of genes associated with stem cell maintenance, cell differentiation and meiotic entry was altered in cattle-yak, indicating the impairment of undifferentiated spermatogonial fate decisions. Cell communication analysis revealed that signaling within different spermatogenic cell subpopulations was weakened, and progenitor spermatogonia were unable to or delayed receiving and sending signals for transformation to the next stage in cattle-yak. Simultaneously, the communication between niche cells and germ cells was also abnormal. Collectively, we obtained the expression profiles of transcriptome signatures of different germ cells and testicular somatic cell populations at the single-cell level and identified critical regulators of spermatogonial differentiation and meiosis in yak and sterile cattle-yak. The findings of this study shed light on the genetic mechanisms that lead to hybrid sterility and speciation in bovid species.
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Affiliation(s)
- Yi-Wen Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shi-Xin Wu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guo-Wen Wang
- Qinghai Academy of Animal Husbandry and Veterinary Sciences, Xining, Qinghai 810016, China
| | - Rui-Dong Wan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi-En Yang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810000, China; University of Chinese Academy of Sciences, Beijing 100049, China; Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, China.
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2
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Robinson M, Zhou K, Kung SHY, Karaoğlanoğlu F, Golin A, Safa A, Cai C, Witherspoon L, Hach F, Flannigan R. A novel sorting method for the enrichment of early human spermatocytes from clinical biopsies. F&S SCIENCE 2024; 5:130-140. [PMID: 38369016 DOI: 10.1016/j.xfss.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
OBJECTIVE To determine if early spermatocytes can be enriched from a human testis biopsy using fluorescence-activated cell sorting (FACS). DESIGN Potential surface markers for early spermatocytes were identified using bioinformatics analysis of single-cell RNA-sequenced human testis tissue. Testicular sperm extraction samples from three participants with normal spermatogenesis were digested into single-cell suspensions and cryopreserved. Two to four million cells were obtained from each and sorted by FACS as separate biologic replicates using antibodies for the identified surface markers. A portion from each biopsy remained unsorted to serve as controls. The sorted cells were then characterized for enrichment of early spermatocytes. SETTING A laboratory study. PATIENTS Three men with a diagnosis of obstructive azoospermia (age range, 30-40 years). INTERVENTION None. MAIN OUTCOME MEASURES Sorted cells were characterized for RNA expression of markers encompassing the stages of spermatogenesis. Sorting markers were validated by their reactivity on human testis formalin-fixed paraffin-embedded tissue. RESULTS Serine protease 50 (TSP50) and SWI5-dependent homologous recombination repair protein 1 were identified as potential surface proteins specific for early spermatocytes. After FACS sorting, the TSP50-sorted populations accounted for 1.6%-8.9% of total populations and exhibited the greatest average-fold increases in RNA expression for the premeiotic marker stimulated by retinoic acid (STRA8), by 23-fold. Immunohistochemistry showed the staining pattern for TSP50 to be strong in premeiotic undifferentiated embryonic cell transcription factor 1-/doublesex and Mab-3 related transcription factor 1-/STRA8+ spermatogonia as well as SYCP3+/protamine 2- spermatocytes. CONCLUSION This work shows that TSP50 can be used to enrich early STRA8-expressing spermatocytes from human testicular biopsies, providing a means for targeted single-cell RNA sequencing analysis and in vitro functional interrogation of germ cells during the onset of meiosis. This could enable investigation into details of the regulatory pathways underlying this critical stage of spermatogenesis, previously difficult to enrich from whole tissue samples.
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Affiliation(s)
- Meghan Robinson
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Kevin Zhou
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sonia H Y Kung
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Fatih Karaoğlanoğlu
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; School of Computing Science, Department of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Andrew Golin
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Armita Safa
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charley Cai
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Luke Witherspoon
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada; Department of Urology, the Ottawa Hospital, Ottawa, Ontario, Canada
| | - Faraz Hach
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan Flannigan
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada; Department of Urology, Weill Cornell Medicine, New York, New York.
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3
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Pugacheva EM, Bhatt DN, Rivero-Hinojosa S, Tajmul M, Fedida L, Price E, Ji Y, Loukinov D, Strunnikov AV, Ren B, Lobanenkov VV. BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites. Genome Biol 2024; 25:40. [PMID: 38297316 PMCID: PMC10832218 DOI: 10.1186/s13059-024-03175-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Pervasive usage of alternative promoters leads to the deregulation of gene expression in carcinogenesis and may drive the emergence of new genes in spermatogenesis. However, little is known regarding the mechanisms underpinning the activation of alternative promoters. RESULTS Here we describe how alternative cancer-testis-specific transcription is activated. We show that intergenic and intronic CTCF binding sites, which are transcriptionally inert in normal somatic cells, could be epigenetically reprogrammed into active de novo promoters in germ and cancer cells. BORIS/CTCFL, the testis-specific paralog of the ubiquitously expressed CTCF, triggers the epigenetic reprogramming of CTCF sites into units of active transcription. BORIS binding initiates the recruitment of the chromatin remodeling factor, SRCAP, followed by the replacement of H2A histone with H2A.Z, resulting in a more relaxed chromatin state in the nucleosomes flanking the CTCF binding sites. The relaxation of chromatin around CTCF binding sites facilitates the recruitment of multiple additional transcription factors, thereby activating transcription from a given binding site. We demonstrate that the epigenetically reprogrammed CTCF binding sites can drive the expression of cancer-testis genes, long noncoding RNAs, retro-pseudogenes, and dormant transposable elements. CONCLUSIONS Thus, BORIS functions as a transcription factor that epigenetically reprograms clustered CTCF binding sites into transcriptional start sites, promoting transcription from alternative promoters in both germ cells and cancer cells.
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Affiliation(s)
- Elena M Pugacheva
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Dharmendra Nath Bhatt
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Samuel Rivero-Hinojosa
- Center for Cancer and Immunology Research, Children's National Research Institute, Washington, DC, 20010, USA
| | - Md Tajmul
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Liron Fedida
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Emma Price
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yon Ji
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Dmitri Loukinov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alexander V Strunnikov
- Guangzhou Institutes of Biomedicine and Health, Molecular Epigenetics Laboratory, 190 Kai Yuan Avenue, Science Park, Guangzhou, 510530, China
| | - Bing Ren
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Cellular and Molecular Medicine, Center for Epigenomics, Moores Cancer Center and Institute of Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, CA, 92093-0653, USA
| | - Victor V Lobanenkov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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von Stromberg K, Seddar L, Ip WH, Günther T, Gornott B, Weinert SC, Hüppner M, Bertzbach LD, Dobner T. The human adenovirus E1B-55K oncoprotein coordinates cell transformation through regulation of DNA-bound host transcription factors. Proc Natl Acad Sci U S A 2023; 120:e2310770120. [PMID: 37883435 PMCID: PMC10622919 DOI: 10.1073/pnas.2310770120] [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: 06/27/2023] [Accepted: 09/13/2023] [Indexed: 10/28/2023] Open
Abstract
The multifunctional adenovirus E1B-55K oncoprotein can induce cell transformation in conjunction with adenovirus E1A gene products. Previous data from transient expression studies and in vitro experiments suggest that these growth-promoting activities correlate with E1B-55K-mediated transcriptional repression of p53-targeted genes. Here, we analyzed genome-wide occupancies and transcriptional consequences of species C5 and A12 E1B-55Ks in transformed mammalian cells by combinatory ChIP and RNA-seq analyses. E1B-55K-mediated repression correlates with tethering of the viral oncoprotein to p53-dependent promoters via DNA-bound p53. Moreover, we found that E1B-55K also interacts with and represses transcription of numerous p53-independent genes through interactions with transcription factors that play central roles in cancer and stress signaling. Our results demonstrate that E1B-55K oncoproteins function as promiscuous transcriptional repressors of both p53-dependent and -independent genes and further support the model that manipulation of cellular transcription is central to adenovirus-induced cell transformation and oncogenesis.
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Affiliation(s)
| | - Laura Seddar
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Wing-Hang Ip
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Thomas Günther
- Virus Genomics, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Britta Gornott
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Sophie-Celine Weinert
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Max Hüppner
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Luca D. Bertzbach
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Thomas Dobner
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
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Akhtar MS, Akhter N, Talat A, Alharbi RA, Sindi AAA, Klufah F, Alyahyawi HE, Alruwetei A, Ahmad A, Zamzami MA, Deo S, Husain SA, Badi OA, Khan MJ. Association of mutation and expression of the brother of the regulator of imprinted sites (BORIS) gene with breast cancer progression. Oncotarget 2023; 14:528-541. [PMID: 37235839 DOI: 10.18632/oncotarget.28442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
INTRODUCTION The BORIS, 11 zinc-finger transcription factors, is a member of the cancer-testis antigen (CTA) family. It is mapped to chromosome number 20q13.2 and this region is genetically linked to the early onset of breast cancer. The current study analyzed the correlation between BORIS mutations and the expression of the protein in breast cancer cases. MATERIALS AND METHODS A population-based study including a total of 155 breast cancer tissue samples and an equal number of normal adjacent tissues from Indian female breast cancer patients was carried out. Mutations of the BORIS gene were detected by polymerase chain reaction-single standard confirmation polymorphisms (PCR-SSCP) and automated DNA sequencing and by immunohistochemistry for BORIS protein expression were performed. The observed findings were correlated with several clinicopathological parameters to find out the clinical relevance of associations. RESULTS Of all the cases 16.12% (25/155) showed mutations in the BORIS gene. The observed mutations present on codon 329 are missense, leading to Val> Ile (G>A) change on exon 5 of the BORIS gene. A significant association was observed between mutations of the BORIS gene and some clinicopathological features like nodal status (p = 0.013), estrogen receptor (ER) expression (p = 0.008), progesterone receptor (PR) expression (p = 0.039), clinical stage (p = 0.010) and menopausal status (p = 0.023). The protein expression analysis showed 20.64% (32/155) samples showing low or no expression (+), 34.19% (53/155) with moderate expression (++), and 45.17% (70/155) showing high expression (+++) of BORIS protein. A significant association was observed between the expression of BORIS protein and clinicopathological features like clinical stage (p = 0.013), nodal status (p = 0.049), ER expression (p = 0.039), and PR expression (p = 0.027). When mutation and protein expression were correlated in combination with clinicopathological parameters a significant association was observed in the category of high (+++) level of BORIS protein expression (p = 0.017). CONCLUSION The BORIS mutations and high protein expression occur frequently in carcinoma of the breast suggesting their association with the onset and progression of breast carcinoma. Further, the BORIS has the potential to be used as a biomarker.
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Affiliation(s)
- Mohammad Salman Akhtar
- Department of Basic Medical Sciences, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Naseem Akhter
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
- Department of Neurology, Henry Ford Health System, Detroit, MI 48202, USA
| | - Arshi Talat
- Department of Orthodontics and Dentofacial Orthopedics, ITS Dental College, Hospital and Research Centre, Greater Noida, Delhi-NCR, India
| | - Raed A Alharbi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Abdulmajeed A A Sindi
- Department of Basic Medical Sciences, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Faisal Klufah
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Hanan E Alyahyawi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Abdulmohsen Alruwetei
- Department of Medical Laboratory, College of Applied Medical Sciences, Qassim University, Qassim, Saudi Arabia
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Svs Deo
- Department of Surgical Oncology, BRA- IRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Syed Akhtar Husain
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Osama A Badi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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6
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Del Moral-Morales A, Salgado-Albarrán M, Sánchez-Pérez Y, Wenke NK, Baumbach J, Soto-Reyes E. CTCF and Its Multi-Partner Network for Chromatin Regulation. Cells 2023; 12:1357. [PMID: 37408191 DOI: 10.3390/cells12101357] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 07/07/2023] Open
Abstract
Architectural proteins are essential epigenetic regulators that play a critical role in organizing chromatin and controlling gene expression. CTCF (CCCTC-binding factor) is a key architectural protein responsible for maintaining the intricate 3D structure of chromatin. Because of its multivalent properties and plasticity to bind various sequences, CTCF is similar to a Swiss knife for genome organization. Despite the importance of this protein, its mechanisms of action are not fully elucidated. It has been hypothesized that its versatility is achieved through interaction with multiple partners, forming a complex network that regulates chromatin folding within the nucleus. In this review, we delve into CTCF's interactions with other molecules involved in epigenetic processes, particularly histone and DNA demethylases, as well as several long non-coding RNAs (lncRNAs) that are able to recruit CTCF. Our review highlights the importance of CTCF partners to shed light on chromatin regulation and pave the way for future exploration of the mechanisms that enable the finely-tuned role of CTCF as a master regulator of chromatin.
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Affiliation(s)
- Aylin Del Moral-Morales
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Marisol Salgado-Albarrán
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Yesennia Sánchez-Pérez
- Subdirección de Investigación, Instituto Nacional de Cancerología, Mexico City 14080, Mexico
| | - Nina Kerstin Wenke
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
- Computational BioMedicine Lab., University of Southern Denmark, DK-5230 Odense, Denmark
| | - Ernesto Soto-Reyes
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
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7
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Zhou S, Li L, Zhang M, Qin Y, Li B. The function of brother of the regulator of imprinted sites in cancer development. Cancer Gene Ther 2023; 30:236-244. [PMID: 36376421 DOI: 10.1038/s41417-022-00556-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 11/15/2022]
Abstract
As Douglas Hanahan and Robert Weinberg compiled, there are nine hallmarks of cancer that are conducive to cancer cell development and survival. Previous studies showed that brother of the regulator of imprinted sites (BORIS) might promote cancer progression through these aspects. The competition between BORIS and CCCTC-binding factor (CTCF), which is crucial in the formation of chromatin loops, affects the normal function of CTCF and leads to neoplasia and deformity. In addition, BORIS belongs to the cancer-testis antigen families, which are potential targets in cancer diagnosis and treatment. Herein, we discuss the function and mechanisms of BORIS, especially in cancer development.
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Affiliation(s)
- Siqi Zhou
- Department of Liver Surgery, West China Hospital, Sichuan University Medical School, 37 Guo Xue Road, Chengdu, 610041, Sichuan Province, China
| | - Lian Li
- Department of Liver Surgery, West China Hospital, Sichuan University Medical School, 37 Guo Xue Road, Chengdu, 610041, Sichuan Province, China
| | - Ming Zhang
- Department of Liver Surgery, West China Hospital, Sichuan University Medical School, 37 Guo Xue Road, Chengdu, 610041, Sichuan Province, China
| | - Yang Qin
- Department of Biochemistry and Molecular Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, No. 17, Section 3, South Renmin Road, Chengdu, 610041, Sichuan Province, China.
| | - Bo Li
- Department of Liver Surgery, West China Hospital, Sichuan University Medical School, 37 Guo Xue Road, Chengdu, 610041, Sichuan Province, China.
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8
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Barsoum M, Stenzel AT, Bochyńska A, Kuo CC, Tsompanidis A, Sayadi-Boroujeni R, Bussmann P, Lüscher-Firzlaff J, Costa IG, Lüscher B. Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes reduces chromatin accessibility at promoters. Sci Rep 2022; 12:21506. [PMID: 36513698 PMCID: PMC9747801 DOI: 10.1038/s41598-022-25881-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Changes in gene expression programs are intimately linked to cell fate decisions. Post-translational modifications of core histones contribute to control gene expression. Methylation of lysine 4 of histone H3 (H3K4) correlates with active promoters and gene transcription. This modification is catalyzed by KMT2 methyltransferases, which require interaction with 4 core subunits, WDR5, RBBP5, ASH2L and DPY30, for catalytic activity. Ash2l is necessary for organismal development and for tissue homeostasis. In mouse embryo fibroblasts (MEFs), Ash2l loss results in gene repression, provoking a senescence phenotype. We now find that upon knockout of Ash2l both H3K4 mono- and tri-methylation (H3K4me1 and me3, respectively) were deregulated. In particular, loss of H3K4me3 at promoters correlated with gene repression, especially at CpG island promoters. Ash2l loss resulted in increased loading of histone H3 and reduced chromatin accessibility at promoters, accompanied by an increase of repressing and a decrease of activating histone marks. Moreover, we observed altered binding of CTCF upon Ash2l loss. Lost and gained binding was noticed at promoter-associated and intergenic sites, respectively. Thus, Ash2l loss and reduction of H3K4me3 correlate with altered chromatin accessibility and transcription factor binding. These findings contribute to a more detailed understanding of mechanistic consequences of H3K4me3 loss and associated repression of gene transcription and thus of the observed cellular consequences.
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Affiliation(s)
- Mirna Barsoum
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Alexander T. Stenzel
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Agnieszka Bochyńska
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Chao-Chung Kuo
- grid.1957.a0000 0001 0728 696XInstitute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany ,grid.1957.a0000 0001 0728 696XInterdisciplinary Center for Clinical Research (IZKF), Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Alexander Tsompanidis
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Roksaneh Sayadi-Boroujeni
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Philip Bussmann
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Juliane Lüscher-Firzlaff
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Ivan G. Costa
- grid.1957.a0000 0001 0728 696XInstitute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany.
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9
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Rabbani M, Zheng X, Manske GL, Vargo A, Shami AN, Li JZ, Hammoud SS. Decoding the Spermatogenesis Program: New Insights from Transcriptomic Analyses. Annu Rev Genet 2022; 56:339-368. [PMID: 36070560 PMCID: PMC10722372 DOI: 10.1146/annurev-genet-080320-040045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Spermatogenesis is a complex differentiation process coordinated spatiotemporally across and along seminiferous tubules. Cellular heterogeneity has made it challenging to obtain stage-specific molecular profiles of germ and somatic cells using bulk transcriptomic analyses. This has limited our ability to understand regulation of spermatogenesis and to integrate knowledge from model organisms to humans. The recent advancement of single-cell RNA-sequencing (scRNA-seq) technologies provides insights into the cell type diversity and molecular signatures in the testis. Fine-grained cell atlases of the testis contain both known and novel cell types and define the functional states along the germ cell developmental trajectory in many species. These atlases provide a reference system for integrated interspecies comparisons to discover mechanistic parallels and to enable future studies. Despite recent advances, we currently lack high-resolution data to probe germ cell-somatic cell interactions in the tissue environment, but the use of highly multiplexed spatial analysis technologies has begun to resolve this problem. Taken together, recent single-cell studies provide an improvedunderstanding of gametogenesis to examine underlying causes of infertility and enable the development of new therapeutic interventions.
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Affiliation(s)
- Mashiat Rabbani
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
| | - Xianing Zheng
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
| | - Gabe L Manske
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexander Vargo
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
| | - Adrienne N Shami
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Saher Sue Hammoud
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Urology, University of Michigan, Ann Arbor, Michigan, USA
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
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10
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Farini D, De Felici M. The Beginning of Meiosis in Mammalian Female Germ Cells: A Never-Ending Story of Intrinsic and Extrinsic Factors. Int J Mol Sci 2022; 23:ijms232012571. [PMID: 36293427 PMCID: PMC9604137 DOI: 10.3390/ijms232012571] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/06/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Meiosis is the unique division of germ cells resulting in the recombination of the maternal and paternal genomes and the production of haploid gametes. In mammals, it begins during the fetal life in females and during puberty in males. In both cases, entering meiosis requires a timely switch from the mitotic to the meiotic cell cycle and the transition from a potential pluripotent status to meiotic differentiation. Revealing the molecular mechanisms underlying these interrelated processes represents the essence in understanding the beginning of meiosis. Meiosis facilitates diversity across individuals and acts as a fundamental driver of evolution. Major differences between sexes and among species complicate the understanding of how meiosis begins. Basic meiotic research is further hindered by a current lack of meiotic cell lines. This has been recently partly overcome with the use of primordial-germ-cell-like cells (PGCLCs) generated from pluripotent stem cells. Much of what we know about this process depends on data from model organisms, namely, the mouse; in mice, the process, however, appears to differ in many aspects from that in humans. Identifying the mechanisms and molecules controlling germ cells to enter meiosis has represented and still represents a major challenge for reproductive medicine. In fact, the proper execution of meiosis is essential for fertility, for maintaining the integrity of the genome, and for ensuring the normal development of the offspring. The main clinical consequences of meiotic defects are infertility and, probably, increased susceptibility to some types of germ-cell tumors. In the present work, we report and discuss data mainly concerning the beginning of meiosis in mammalian female germ cells, referring to such process in males only when pertinent. After a brief account of this process in mice and humans and an historical chronicle of the major hypotheses and progress in this topic, the most recent results are reviewed and discussed.
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11
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Ectopic expression of meiotic cohesin generates chromosome instability in cancer cell line. Proc Natl Acad Sci U S A 2022; 119:e2204071119. [PMID: 36179046 PMCID: PMC9549395 DOI: 10.1073/pnas.2204071119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
This work originated from mining of cancer genome data and proceeded to analyze the effects of ectopic expression of meiotic cohesins in mitotic cells in culture. In the process, apart from conclusively answering the question on mechanisms for RAD21L toxicity and its underrepresentation in tumor transcriptomes, we found an association of meiotic cohesin binding with BORIS/CTCFL sites in the normal testis. We also elucidated the patterns and outcomes of meiotic cohesin binding to chromosomes in model cell lines. Furthermore, we uncovered that RAD21L-based meiotic cohesin possesses a self-contained chromosome restructuring activity able to trigger sustainable but imperfect mitotic arrest leading to chromosomal instability. The discovered epigenomic and genetic mechanisms can be relevant to chromosome instability in cancer. Many tumors express meiotic genes that could potentially drive somatic chromosome instability. While germline cohesin subunits SMC1B, STAG3, and REC8 are widely expressed in many cancers, messenger RNA and protein for RAD21L subunit are expressed at very low levels. To elucidate the potential of meiotic cohesins to contribute to genome instability, their expression was investigated in human cell lines, predominately in DLD-1. While the induction of the REC8 complex resulted in a mild mitotic phenotype, the expression of the RAD21L complex produced an arrested but viable cell pool, thus providing a source of DNA damage, mitotic chromosome missegregation, sporadic polyteny, and altered gene expression. We also found that genomic binding profiles of ectopically expressed meiotic cohesin complexes were reminiscent of their corresponding specific binding patterns in testis. Furthermore, meiotic cohesins were found to localize to the same sites as BORIS/CTCFL, rather than CTCF sites normally associated with the somatic cohesin complex. These findings highlight the existence of a germline epigenomic memory that is conserved in cells that normally do not express meiotic genes. Our results reveal a mechanism of action by unduly expressed meiotic cohesins that potentially links them to aneuploidy and chromosomal mutations in affected cells.
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12
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Zhang Y, Fang M, Li S, Xu H, Ren J, Tu L, Zuo B, Yao W, Liang G. BTApep-TAT peptide inhibits ADP-ribosylation of BORIS to induce DNA damage in cancer. Mol Cancer 2022; 21:158. [PMID: 35918747 PMCID: PMC9344678 DOI: 10.1186/s12943-022-01621-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Brother of regulator of imprinted sites (BORIS) is expressed in most cancers and often associated with short survival and poor prognosis in patients. BORIS inhibits apoptosis and promotes proliferation of cancer cells. However, its mechanism of action has not been elucidated, and there is no known inhibitor of BORIS. METHODS A phage display library was used to find the BORIS inhibitory peptides and BTApep-TAT was identified. The RNA sequencing profile of BTApep-TAT-treated H1299 cells was compared with that of BORIS-knockdown cells. Antitumor activity of BTApep-TAT was evaluated in a non-small cell lung cancer (NSCLC) xenograft mouse model. BTApep-TAT was also used to investigate the post-translational modification (PTM) of BORIS and the role of BORIS in DNA damage repair. Site-directed mutants of BORIS were constructed and used for investigating PTM and the function of BORIS. RESULTS BTApep-TAT induced DNA damage in cancer cells and suppressed NSCLC xenograft tumor progression. Investigation of the mechanism of action of BTApep-TAT demonstrated that BORIS underwent ADP ribosylation upon double- or single-strand DNA damage. Substitution of five conserved glutamic acid (E) residues with alanine residues (A) between amino acids (AAs) 198 and 228 of BORIS reduced its ADP ribosylation. Inhibition of ADP ribosylation of BORIS by a site-specific mutation or by BTApep-TAT treatment blocked its interaction with Ku70 and impaired the function of BORIS in DNA damage repair. CONCLUSIONS The present study identified an inhibitor of BORIS, highlighted the importance of ADP ribosylation of BORIS, and revealed a novel function of BORIS in DNA damage repair. The present work provides a practical method for the future screening or optimization of drugs targeting BORIS.
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Affiliation(s)
- Yanmei Zhang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China.
| | - Mengdie Fang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China.,College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Shouye Li
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China.,Zhejiang Eyoung Pharmaceutical Research and Development Center, Hangzhou, 311258, Zhejiang, China
| | - Hao Xu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Juan Ren
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Linglan Tu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Bowen Zuo
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Wanxin Yao
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Guang Liang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China. .,College of Pharmacy, Hangzhou Medical College, Hangzhou, 311300, Zhejiang, China.
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13
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Ghieh F, Barbotin AL, Swierkowski-Blanchard N, Leroy C, Fortemps J, Gerault C, Hue C, Mambu Mambueni H, Jaillard S, Albert M, Bailly M, Izard V, Molina-Gomes D, Marcelli F, Prasivoravong J, Serazin V, Dieudonne MN, Delcroix M, Garchon HJ, Louboutin A, Mandon-Pepin B, Ferlicot S, Vialard F. OUP accepted manuscript. Hum Reprod 2022; 37:1334-1350. [PMID: 35413094 PMCID: PMC9156845 DOI: 10.1093/humrep/deac057] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 03/07/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- F Ghieh
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- École Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - A L Barbotin
- Institut de Biologie de la Reproduction-Spermiologie-CECOS, Hôpital Jeanne de Flandre, Centre Hospitalier et Universitaire, Lille, France
| | - N Swierkowski-Blanchard
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- École Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
- Département de Gynécologie Obstétrique, CHI de Poissy/Saint-Germain-en-Laye, Poissy, France
| | - C Leroy
- Institut de Biologie de la Reproduction-Spermiologie-CECOS, Hôpital Jeanne de Flandre, Centre Hospitalier et Universitaire, Lille, France
| | - J Fortemps
- Service d’Anatomie Pathologique, CHI de Poissy/Saint-Germain-en-Laye, Saint-Germain-en-Laye, France
| | - C Gerault
- Département de Génétique, Laboratoire de Biologie Médicale, CHI de Poissy/Saint-Germain-en-Laye, Poissy, France
| | - C Hue
- Department of Biotechnology and Health, UVSQ, Université Paris-Saclay, Inserm UMR 1173, Montigny-le-Bretonneux, France
| | - H Mambu Mambueni
- Department of Biotechnology and Health, UVSQ, Université Paris-Saclay, Inserm UMR 1173, Montigny-le-Bretonneux, France
| | - S Jaillard
- Service de Cytogénétique, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET—UMR_S 1085, Université Rennes 1, Rennes, France
| | - M Albert
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- École Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - M Bailly
- Département de Gynécologie Obstétrique, CHI de Poissy/Saint-Germain-en-Laye, Poissy, France
| | - V Izard
- Service d’Urologie, AP-HP, Université Paris-Saclay, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - D Molina-Gomes
- Département de Génétique, Laboratoire de Biologie Médicale, CHI de Poissy/Saint-Germain-en-Laye, Poissy, France
| | - F Marcelli
- Institut de Biologie de la Reproduction-Spermiologie-CECOS, Hôpital Jeanne de Flandre, Centre Hospitalier et Universitaire, Lille, France
| | - J Prasivoravong
- Institut de Biologie de la Reproduction-Spermiologie-CECOS, Hôpital Jeanne de Flandre, Centre Hospitalier et Universitaire, Lille, France
| | - V Serazin
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- École Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
- Département de Génétique, Laboratoire de Biologie Médicale, CHI de Poissy/Saint-Germain-en-Laye, Poissy, France
| | - M N Dieudonne
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- École Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - M Delcroix
- Département de Génétique, Laboratoire de Biologie Médicale, CHI de Poissy/Saint-Germain-en-Laye, Poissy, France
| | - H J Garchon
- Department of Biotechnology and Health, UVSQ, Université Paris-Saclay, Inserm UMR 1173, Montigny-le-Bretonneux, France
| | - A Louboutin
- Service d’Anatomie Pathologique, CHI de Poissy/Saint-Germain-en-Laye, Saint-Germain-en-Laye, France
| | - B Mandon-Pepin
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- École Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - S Ferlicot
- Service d’Anatomie Pathologique, AP-HP, Université Paris-Saclay, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - F Vialard
- Correspondence address. Tel: +33-139-274-700; E-mail:
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14
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Umer N, Arévalo L, Phadke S, Lohanadan K, Kirfel G, Sons D, Sofia D, Witke W, Schorle H. Loss of Profilin3 Impairs Spermiogenesis by Affecting Acrosome Biogenesis, Autophagy, Manchette Development and Mitochondrial Organization. Front Cell Dev Biol 2021; 9:749559. [PMID: 34869336 PMCID: PMC8632698 DOI: 10.3389/fcell.2021.749559] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/28/2021] [Indexed: 11/28/2022] Open
Abstract
Profilins (PFNs) are key regulatory proteins for the actin polymerization in cells and are encoded in mouse and humans by four Pfn genes. PFNs are involved in cell mobility, cell growth, neurogenesis, and metastasis of tumor cells. The testes-specific PFN3 is localized in the acroplaxome-manchette complex of developing spermatozoa. We demonstrate that PFN3 further localizes in the Golgi complex and proacrosomal vesicles during spermiogenesis, suggesting a role in vesicle transport for acrosome formation. Using CRISPR/Cas9 genome editing, we generated mice deficient for Pfn3. Pfn3-/- males are subfertile, displaying a type II globozoospermia. We revealed that Pfn3-/- sperm display abnormal manchette development leading to an amorphous sperm head shape. Additionally, Pfn3-/- sperm showed reduced sperm motility resulting from flagellum deformities. We show that acrosome biogenesis is impaired starting from the Golgi phase, and mature sperm seems to suffer from a cytoplasm removal defect. An RNA-seq analysis revealed an upregulation of Trim27 and downregulation of Atg2a. As a consequence, mTOR was activated and AMPK was suppressed, resulting in the inhibition of autophagy. This dysregulation of AMPK/mTOR affected the autophagic flux, which is hallmarked by LC3B accumulation and increased SQSTM1 protein levels. Autophagy is involved in proacrosomal vesicle fusion and transport to form the acrosome. We conclude that this disruption leads to the observed malformation of the acrosome. TRIM27 is associated with PFN3 as determined by co-immunoprecipitation from testis extracts. Further, actin-related protein ARPM1 was absent in the nuclear fraction of Pfn3-/- testes and sperm. This suggests that lack of PFN3 leads to destabilization of the PFN3-ARPM1 complex, resulting in the degradation of ARPM1. Interestingly, in the Pfn3-/- testes, we detected increased protein levels of essential actin regulatory proteins, cofilin-1 (CFL1), cofilin-2 (CFL2), and actin depolymerizing factor (ADF). Taken together, our results reveal the importance for PFN3 in male fertility and implicate this protein as a candidate for male factor infertility in humans.
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Affiliation(s)
- Naila Umer
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Lena Arévalo
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Sharang Phadke
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | | | - Gregor Kirfel
- Institute for Cell Biology, University of Bonn, Bonn, Germany
| | - Dominik Sons
- Department of Membrane Biochemistry, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Denise Sofia
- Institute of Genetics, University of Bonn, Bonn, Germany
| | - Walter Witke
- Institute of Genetics, University of Bonn, Bonn, Germany
| | - Hubert Schorle
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, Bonn, Germany
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15
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CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells. Nat Cell Biol 2021; 23:881-893. [PMID: 34326481 DOI: 10.1038/s41556-021-00722-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 06/24/2021] [Indexed: 12/12/2022]
Abstract
The 11 zinc finger (ZF) protein CTCF regulates topologically associating domain formation and transcription through selective binding to thousands of genomic sites. Here, we replaced endogenous CTCF in mouse embryonic stem cells with green-fluorescent-protein-tagged wild-type or mutant proteins lacking individual ZFs to identify additional determinants of CTCF positioning and function. While ZF1 and ZF8-ZF11 are not essential for cell survival, ZF8 deletion strikingly increases the DNA binding off-rate of mutant CTCF, resulting in reduced CTCF chromatin residence time. Loss of ZF8 results in widespread weakening of topologically associating domains, aberrant gene expression and increased genome-wide DNA methylation. Thus, important chromatin-templated processes rely on accurate CTCF chromatin residence time, which we propose depends on local sequence and chromatin context as well as global CTCF protein concentration.
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16
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Rivero-Hinojosa S, Pugacheva EM, Kang S, Méndez-Catalá CF, Kovalchuk AL, Strunnikov AV, Loukinov D, Lee JT, Lobanenkov VV. The combined action of CTCF and its testis-specific paralog BORIS is essential for spermatogenesis. Nat Commun 2021; 12:3846. [PMID: 34158481 PMCID: PMC8219828 DOI: 10.1038/s41467-021-24140-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 05/28/2021] [Indexed: 01/03/2023] Open
Abstract
CTCF is a key organizer of the 3D genome. Its specialized paralog, BORIS, heterodimerizes with CTCF but is expressed only in male germ cells and in cancer states. Unexpectedly, BORIS-null mice have only minimal germ cell defects. To understand the CTCF-BORIS relationship, mouse models with varied CTCF and BORIS levels were generated. Whereas Ctcf+/+Boris+/+, Ctcf+/-Boris+/+, and Ctcf+/+Boris-/- males are fertile, Ctcf+/-Boris-/- (Compound Mutant; CM) males are sterile. Testes with combined depletion of both CTCF and BORIS show reduced size, defective meiotic recombination, increased apoptosis, and malformed spermatozoa. Although CM germ cells exhibit only 25% of CTCF WT expression, chromatin binding of CTCF is preferentially lost from CTCF-BORIS heterodimeric sites. Furthermore, CM testes lose the expression of a large number of spermatogenesis genes and gain the expression of developmentally inappropriate genes that are "toxic" to fertility. Thus, a combined action of CTCF and BORIS is required to both repress pre-meiotic genes and activate post-meiotic genes for a complete spermatogenesis program.
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Affiliation(s)
- Samuel Rivero-Hinojosa
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
- Center for Cancer and Immunology Research, Children's National Research Institute, Washington, DC, USA.
| | - Elena M Pugacheva
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Sungyun Kang
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Claudia Fabiola Méndez-Catalá
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Genetics and Molecular Oncology, Building A4, Faculty of Higher Studies (FES) Iztacala, National Autonomous University of Mexico (UNAM), Tlalnepantla, State of Mexico, Mexico
| | - Alexander L Kovalchuk
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alexander V Strunnikov
- Guangzhou Institutes of Biomedicine and Health, Molecular Epigenetics Laboratory, Guangzhou, China
| | - Dmitri Loukinov
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Victor V Lobanenkov
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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17
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Schield DR, Pasquesi GIM, Perry BW, Adams RH, Nikolakis ZL, Westfall AK, Orton RW, Meik JM, Mackessy SP, Castoe TA. Snake Recombination Landscapes Are Concentrated in Functional Regions despite PRDM9. Mol Biol Evol 2021; 37:1272-1294. [PMID: 31926008 DOI: 10.1093/molbev/msaa003] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Meiotic recombination in vertebrates is concentrated in hotspots throughout the genome. The location and stability of hotspots have been linked to the presence or absence of PRDM9, leading to two primary models for hotspot evolution derived from mammals and birds. Species with PRDM9-directed recombination have rapid turnover of hotspots concentrated in intergenic regions (i.e., mammals), whereas hotspots in species lacking PRDM9 are concentrated in functional regions and have greater stability over time (i.e., birds). Snakes possess PRDM9, yet virtually nothing is known about snake recombination. Here, we examine the recombination landscape and test hypotheses about the roles of PRDM9 in rattlesnakes. We find substantial variation in recombination rate within and among snake chromosomes, and positive correlations between recombination rate and gene density, GC content, and genetic diversity. Like mammals, snakes appear to have a functional and active PRDM9, but rather than being directed away from genes, snake hotspots are concentrated in promoters and functional regions-a pattern previously associated only with species that lack a functional PRDM9. Snakes therefore provide a unique example of recombination landscapes in which PRDM9 is functional, yet recombination hotspots are associated with functional genic regions-a combination of features that defy existing paradigms for recombination landscapes in vertebrates. Our findings also provide evidence that high recombination rates are a shared feature of vertebrate microchromosomes. Our results challenge previous assumptions about the adaptive role of PRDM9 and highlight the diversity of recombination landscape features among vertebrate lineages.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | | | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | - Richard H Adams
- Department of Biology, University of Texas at Arlington, Arlington, TX.,Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL
| | | | | | - Richard W Orton
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX
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18
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Sati L, Soygur B, Goksu E, Bassorgun CI, McGrath J. CTCFL expression is associated with cerebral vascular abnormalities. Tissue Cell 2021; 72:101528. [PMID: 33756271 DOI: 10.1016/j.tice.2021.101528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 02/06/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
CTCFL is expressed in testis, oocytes and embryonic stem cells, and is aberrantly expressed in malignant cells, and is classified as a cancer-testis gene. We have previously shown by using a tetracycline-inducible Ctcfl transgene that inappropriate expression of Ctcfl negatively impacts fetal development and causes early postnatal lethality in the mouse. The affected pups displayed severe vascular abnormalities and localized hemorrhages in the brain evocative of cerebral cavernous malformations (CCM) and arteriovenous malformations (AVM) in humans. Thus, we aim to analyze; a) the presence of CCM-related proteins CCM1/KRIT1, CCM2/malcavernin and CCM3/PDCD10 in Ctcfl transgenic animals and, b) whether there is CTCFL expression in human CCM and AVM tissues. Ctcfl transgenic animals exhibited increased CD31 expression in vascular areas of the dermis and periadnexal regions but no difference was observed for vWF and α-SMA expressions. CCM-related proteins CCM1/KRIT1, CCM2/malcavernin and CCM3/PDCD10 were aberrantly expressed in coronal sections of the head in transgenic animals. We also observed CTCFL expression in human CCMs and AVMs. The induced expression of CTCFL resulting in vascular brain malformations in mice combined with the presence of CTCFL in human vascular malformations provide new insights into the role of this gene in vascular development in humans.
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Affiliation(s)
- Leyla Sati
- Department of Histology and Embryology, Akdeniz University School of Medicine, Antalya, Turkey.
| | - Bikem Soygur
- Department of Histology and Embryology, Akdeniz University School of Medicine, Antalya, Turkey; Department of Obstetrics, Gynecology and Reproductive Sciences, Center for Reproductive Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Ethem Goksu
- Department of Neurosurgery, Akdeniz University School of Medicine, Antalya, Turkey
| | | | - James McGrath
- Departments of Genetics and Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
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19
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Browne JA, NandyMazumdar M, Paranjapye A, Leir SH, Harris A. The Bromodomain Containing 8 (BRD8) transcriptional network in human lung epithelial cells. Mol Cell Endocrinol 2021; 524:111169. [PMID: 33476703 PMCID: PMC8035426 DOI: 10.1016/j.mce.2021.111169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/18/2020] [Accepted: 01/07/2021] [Indexed: 12/17/2022]
Abstract
Mechanisms regulating gene expression in the airway epithelium underlie its response to the environment. A network of transcription factors (TFs) and architectural proteins, modulate chromatin accessibility and recruit activating or repressive signals. Bromodomain-containing proteins function as TFs or by engaging methyltransferase or acetyltransferase activity to induce chromatin modifications. Here we investigate the role of Bromodomain Containing 8 (BRD8) in coordinating lung epithelial function. Sites of BRD8 occupancy genome-wide were mapped in human lung epithelial cell lines (Calu-3 and 16HBE14o-). CCCTC-Binding Factor (CTCF) was identified as a predicted co-factor of BRD8, based upon motif over-representation under BRD8 ChIP-seq peaks. Following siRNA-mediated depletion of BRD8, differentially expressed genes with nearby peaks of BRD8 occupancy were subject to gene ontology process enrichment analysis. BRD8 targets are enriched for genes involved in the innate immune response and the cell cycle. Depletion of BRD8 increased the secretion of the antimicrobial peptide beta-defensin 1 and multiple chemokines, and reduced cell proliferation.
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Affiliation(s)
- James A Browne
- Department of Genetics and Genome Sciences, Cleveland, OH, USA
| | | | | | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Cleveland, OH, USA; Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Cleveland, OH, USA; Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
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20
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Nora EP, Caccianini L, Fudenberg G, So K, Kameswaran V, Nagle A, Uebersohn A, Hajj B, Saux AL, Coulon A, Mirny LA, Pollard KS, Dahan M, Bruneau BG. Molecular basis of CTCF binding polarity in genome folding. Nat Commun 2020; 11:5612. [PMID: 33154377 PMCID: PMC7645679 DOI: 10.1038/s41467-020-19283-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/07/2020] [Indexed: 11/09/2022] Open
Abstract
Current models propose that boundaries of mammalian topologically associating domains (TADs) arise from the ability of the CTCF protein to stop extrusion of chromatin loops by cohesin. While the orientation of CTCF motifs determines which pairs of CTCF sites preferentially stabilize loops, the molecular basis of this polarity remains unclear. By combining ChIP-seq and single molecule live imaging we report that CTCF positions cohesin, but does not control its overall binding dynamics on chromatin. Using an inducible complementation system, we find that CTCF mutants lacking the N-terminus cannot insulate TADs properly. Cohesin remains at CTCF sites in this mutant, albeit with reduced enrichment. Given the orientation of CTCF motifs presents the N-terminus towards cohesin as it translocates from the interior of TADs, these observations explain how the orientation of CTCF binding sites translates into genome folding patterns.
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Affiliation(s)
- Elphège P Nora
- Gladstone Institutes, San Francisco, CA, 94158, USA.
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, 94158, USA.
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94143, USA.
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94143, USA.
| | - Laura Caccianini
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 26 Rue D'Ulm, Paris, 75005, France
| | | | - Kevin So
- Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Vasumathi Kameswaran
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, 94158, USA
| | - Abigail Nagle
- Gladstone Institutes, San Francisco, CA, 94158, USA
- University of Washington, Seattle, WA, USA
| | - Alec Uebersohn
- Gladstone Institutes, San Francisco, CA, 94158, USA
- University of California Berkeley, Berkeley, CA, USA
| | - Bassam Hajj
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 26 Rue D'Ulm, Paris, 75005, France
| | - Agnès Le Saux
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Mammalian Developmental Epigenetics group, F-75005, Paris, France
- Sorbonne Université, F-75005, Paris, France
| | - Antoine Coulon
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 26 Rue D'Ulm, Paris, 75005, France
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Nuclear Dynamics unit, F-75005, Paris, France
| | - Leonid A Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Epidemiology & Biostatistics, Institute for Human Genetics, Quantitative Biology Institute, and Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Maxime Dahan
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 26 Rue D'Ulm, Paris, 75005, France
| | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA, 94158, USA.
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, 94158, USA.
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94143, USA.
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, 94143, USA.
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21
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Zhang Y, Song Y, Li C, Ren J, Fang M, Fang J, Wang X. Brother of regulator of imprinted sites inhibits cisplatin-induced DNA damage in non-small cell lung cancer. Oncol Lett 2020; 20:251. [PMID: 32994814 PMCID: PMC7509674 DOI: 10.3892/ol.2020.12114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
Cisplatin (DDP) chemotherapy is the primary modality of treatment for non-small cell lung cancer (NSCLC). However, due to the occurrence of DDP resistance, only a limited number of patients benefit from this treatment regimen. Brother of Regulator of Imprinted Sites (BORIS) is expressed elevated in NSCLC. Whether BORIS is involved in the DDP resistance of NSCLC is currently undetermined. The association between BORIS expression and overall survival rate of 156 patients with NSCLC who received DDP chemotherapy was analyzed in the present study. In order to investigate the function of BORIS in DDP chemotherapy, BORIS was silenced or overexpressed in four NSCLC cell lines. The cell viabilities, apoptosis and DNA damage induced by DDP were evaluated in these cell lines. In addition, the regulations of DNA repair genes were assessed, including POLH, ERCC1, BRCA1, MSH6 and XPA. The present study demonstrated that high BORIS expression was associated with decreased overall survival rate in patients with NSCLC who received DDP chemotherapy. The patients who benefited and went into remission following DDP therapy expressed a relatively low level of BORIS, suggesting the potential function of BORIS in DDP resistance. Cell experiments revealed that NSCLC cells that had a higher proliferation rate and resisted DDP treatment expressed a relatively higher level of BORIS. Knockdown of BORIS in NSCLC cells induced DNA damage; inhibiting cell proliferation and sensitizing cells to DDP treatment. In contrast, BORIS overexpression suppressed DDP-induced DNA damage. Notably, the mismatch repair factor mutS homolog 6 (MSH6) was regulated by BORIS, indicating its association with BORIS-associated DDP resistance in NSCLC. The findings of the present study suggest that BORIS suppresses DNA damage and promotes the progression of NSCLC and DDP resistance. The present study indicates the potential application of BORIS in NSCLC therapy and prognosis.
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Affiliation(s)
- Yanmei Zhang
- Center for Molecular Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310012, P.R. China
| | - Yongfei Song
- Center for Molecular Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310012, P.R. China
| | - Chao Li
- Center for Molecular Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310012, P.R. China
| | - Juan Ren
- Center for Molecular Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310012, P.R. China
| | - Mengdie Fang
- Center for Molecular Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310012, P.R. China
| | - Jianfei Fang
- Center for Molecular Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310012, P.R. China.,Department of Pathology, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Xiaoju Wang
- Center for Molecular Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310012, P.R. China
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22
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Nishana M, Ha C, Rodriguez-Hernaez J, Ranjbaran A, Chio E, Nora EP, Badri SB, Kloetgen A, Bruneau BG, Tsirigos A, Skok JA. Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation. Genome Biol 2020; 21:108. [PMID: 32393311 PMCID: PMC7212617 DOI: 10.1186/s13059-020-02024-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/16/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Ubiquitously expressed CTCF is involved in numerous cellular functions, such as organizing chromatin into TAD structures. In contrast, its paralog, CTCFL, is normally only present in the testis. However, it is also aberrantly expressed in many cancers. While it is known that shared and unique zinc finger sequences in CTCF and CTCFL enable CTCFL to bind competitively to a subset of CTCF binding sites as well as its own unique locations, the impact of CTCFL on chromosome organization and gene expression has not been comprehensively analyzed in the context of CTCF function. Using an inducible complementation system, we analyze the impact of expressing CTCFL and CTCF-CTCFL chimeric proteins in the presence or absence of endogenous CTCF to clarify the relative and combined contribution of CTCF and CTCFL to chromosome organization and transcription. RESULTS We demonstrate that the N terminus of CTCF interacts with cohesin which explains the requirement for convergent CTCF binding sites in loop formation. By analyzing CTCF and CTCFL binding in tandem, we identify phenotypically distinct sites with respect to motifs, targeting to promoter/intronic intergenic regions and chromatin folding. Finally, we reveal that the N, C, and zinc finger terminal domains play unique roles in targeting each paralog to distinct binding sites to regulate transcription, chromatin looping, and insulation. CONCLUSION This study clarifies the unique and combined contribution of CTCF and CTCFL to chromosome organization and transcription, with direct implications for understanding how their co-expression deregulates transcription in cancer.
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Affiliation(s)
| | - Caryn Ha
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA
| | | | - Ali Ranjbaran
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA
| | - Erica Chio
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA
| | - Elphege P Nora
- Gladstone Institutes, San Francisco, CA, 94158, USA.,Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, 94158, USA.,Cardiovascular Research Institute, University of California, San Francisco, CA, 94158, USA
| | - Sana B Badri
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA
| | - Andreas Kloetgen
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY, 10016, USA
| | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA, 94158, USA.,Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, 94158, USA.,Cardiovascular Research Institute, University of California, San Francisco, CA, 94158, USA.,Department of Pediatrics, University of California, San Francisco, CA, 94158, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA.,Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY, 10016, USA
| | - Jane A Skok
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA. .,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, 10016, USA.
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23
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Debaugny RE, Skok JA. CTCF and CTCFL in cancer. Curr Opin Genet Dev 2020; 61:44-52. [PMID: 32334335 PMCID: PMC7893514 DOI: 10.1016/j.gde.2020.02.021] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/11/2020] [Accepted: 02/22/2020] [Indexed: 12/28/2022]
Abstract
CTCF plays a key role in organizing chromatin into TAD structures but it can also function as a transcription factor. CTCFL (CTCF-like), the paralog of CTCF, is normally transiently expressed in pre-meiotic male germ cells together with ubiquitously expressed CTCF. It plays a unique role in spermatogenesis by regulating expression of testis-specific genes. Genetic alterations in CTCF and its paralog CTCFL have both been found in numerous cancers, but it remains unknown to what extent CTCFL deregulates transcription on its own or by opposing CTCF. Here, we discuss some of the potential mechanisms by which these two proteins could alter gene regulation and contribute to oncogenic transcriptional programs.
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Affiliation(s)
- Roxanne E Debaugny
- Dept. of Pathology, New York University Langone Health, New York, NY 10016, USA
| | - Jane A Skok
- Dept. of Pathology, New York University Langone Health, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
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24
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Janssen SM, Moscona R, Elchebly M, Papadakis AI, Redpath M, Wang H, Rubin E, van Kempen LC, Spatz A. BORIS/CTCFL promotes a switch from a proliferative towards an invasive phenotype in melanoma cells. Cell Death Discov 2020; 6:1. [PMID: 32123577 PMCID: PMC7026120 DOI: 10.1038/s41420-019-0235-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/27/2019] [Accepted: 12/03/2019] [Indexed: 12/19/2022] Open
Abstract
Melanoma is among the most aggressive cancers due to its tendency to metastasize early. Phenotype switching between a proliferative and an invasive state has been suggested as a critical process for metastasis, though the mechanisms that regulate state transitions are complex and remain poorly understood. Brother of Regulator of Imprinted Sites (BORIS), also known as CCCTC binding factor-Like (CTCFL), is a transcriptional modulator that becomes aberrantly expressed in melanoma. Yet, the role of BORIS in melanoma remains elusive. Here, we show that BORIS is involved in melanoma phenotype switching. Genetic modification of BORIS expression in melanoma cells combined with whole-transcriptome analysis indicated that BORIS expression contributes to an invasion-associated transcriptome. In line with these findings, inducible BORIS overexpression in melanoma cells reduced proliferation and increased migration and invasion, demonstrating that the transcriptional switch is accompanied by a phenotypic switch. Mechanistically, we reveal that BORIS binds near the promoter of transforming growth factor-beta 1 (TFGB1), a well-recognized factor involved in the transition towards an invasive state, which coincided with increased expression of TGFB1. Overall, our study indicates a pro-invasive role for BORIS in melanoma via transcriptional reprogramming.
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Affiliation(s)
- Sanne Marlijn Janssen
- Lady Davis Institute for Medical Research, Montréal, QC Canada
- Department of Pathology, McGill University, Montréal, QC Canada
| | - Roy Moscona
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Mounib Elchebly
- Lady Davis Institute for Medical Research, Montréal, QC Canada
| | | | - Margaret Redpath
- Lady Davis Institute for Medical Research, Montréal, QC Canada
- Department of Pathology, McGill University, Montréal, QC Canada
- Division of Pathology, Department of Laboratory medicine, McGill University Health Center, Montreal, QC Canada
| | - Hangjun Wang
- Lady Davis Institute for Medical Research, Montréal, QC Canada
- Department of Pathology, McGill University, Montréal, QC Canada
- Division of Pathology, Department of Laboratory medicine, McGill University Health Center, Montreal, QC Canada
| | - Eitan Rubin
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Léon Cornelis van Kempen
- Lady Davis Institute for Medical Research, Montréal, QC Canada
- Department of Pathology, McGill University, Montréal, QC Canada
- Department of Pathology, Laboratory for Molecular Pathology, University Medical Center Groningen, Groningen, The Netherlands
| | - Alan Spatz
- Lady Davis Institute for Medical Research, Montréal, QC Canada
- Department of Pathology, McGill University, Montréal, QC Canada
- Division of Pathology, Department of Laboratory medicine, McGill University Health Center, Montreal, QC Canada
- Department of Oncology, McGill University, Montréal, QC Canada
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25
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The Role of Insulation in Patterning Gene Expression. Genes (Basel) 2019; 10:genes10100767. [PMID: 31569427 PMCID: PMC6827083 DOI: 10.3390/genes10100767] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/16/2022] Open
Abstract
Development is orchestrated by regulatory elements that turn genes ON or OFF in precise spatial and temporal patterns. Many safety mechanisms prevent inappropriate action of a regulatory element on the wrong gene promoter. In flies and mammals, dedicated DNA elements (insulators) recruit protein factors (insulator binding proteins, or IBPs) to shield promoters from regulatory elements. In mammals, a single IBP called CCCTC-binding factor (CTCF) is known, whereas genetic and biochemical analyses in Drosophila have identified a larger repertoire of IBPs. How insulators function at the molecular level is not fully understood, but it is currently thought that they fold chromosomes into conformations that affect regulatory element-promoter communication. Here, we review the discovery of insulators and describe their properties. We discuss recent genetic studies in flies and mice to address the question: Is gene insulation important for animal development? Comparing and contrasting observations in these two species reveal that they have different requirements for insulation, but that insulation is a conserved and critical gene regulation strategy.
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26
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High-Throughput Single-Cell Sequencing with Linear Amplification. Mol Cell 2019; 76:676-690.e10. [PMID: 31495564 DOI: 10.1016/j.molcel.2019.08.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 05/22/2019] [Accepted: 08/01/2019] [Indexed: 11/22/2022]
Abstract
Conventional methods for single-cell genome sequencing are limited with respect to uniformity and throughput. Here, we describe sci-L3, a single-cell sequencing method that combines combinatorial indexing (sci-) and linear (L) amplification. The sci-L3 method adopts a 3-level (3) indexing scheme that minimizes amplification biases while enabling exponential gains in throughput. We demonstrate the generalizability of sci-L3 with proof-of-concept demonstrations of single-cell whole-genome sequencing (sci-L3-WGS), targeted sequencing (sci-L3-target-seq), and a co-assay of the genome and transcriptome (sci-L3-RNA/DNA). We apply sci-L3-WGS to profile the genomes of >10,000 sperm and sperm precursors from F1 hybrid mice, mapping 86,786 crossovers and characterizing rare chromosome mis-segregation events in meiosis, including instances of whole-genome equational chromosome segregation. We anticipate that sci-L3 assays can be applied to fully characterize recombination landscapes, to couple CRISPR perturbations and measurements of genome stability, and to other goals requiring high-throughput, high-coverage single-cell sequencing.
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27
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Large-scale chromatin organisation in interphase, mitosis and meiosis. Biochem J 2019; 476:2141-2156. [DOI: 10.1042/bcj20180512] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 01/17/2023]
Abstract
AbstractThe spatial configuration of chromatin is fundamental to ensure any given cell can fulfil its functional duties, from gene expression to specialised cellular division. Significant technological innovations have facilitated further insights into the structure, function and regulation of three-dimensional chromatin organisation. To date, the vast majority of investigations into chromatin organisation have been conducted in interphase and mitotic cells leaving meiotic chromatin relatively unexplored. In combination, cytological and genome-wide contact frequency analyses in mammalian germ cells have recently demonstrated that large-scale chromatin structures in meiotic prophase I are reminiscent of the sequential loop arrays found in mitotic cells, although interphase-like segmentation of transcriptionally active and inactive regions are also evident along the length of chromosomes. Here, we discuss the similarities and differences of such large-scale chromatin architecture, between interphase, mitotic and meiotic cells, as well as their functional relevance and the proposed modulatory mechanisms which underlie them.
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28
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Bergmaier P, Weth O, Dienstbach S, Boettger T, Galjart N, Mernberger M, Bartkuhn M, Renkawitz R. Choice of binding sites for CTCFL compared to CTCF is driven by chromatin and by sequence preference. Nucleic Acids Res 2019; 46:7097-7107. [PMID: 29860503 PMCID: PMC6101590 DOI: 10.1093/nar/gky483] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/23/2018] [Indexed: 01/22/2023] Open
Abstract
The two paralogous zinc finger factors CTCF and CTCFL differ in expression such that CTCF is ubiquitously expressed, whereas CTCFL is found during spermatogenesis and in some cancer types in addition to other cell types. Both factors share the highly conserved DNA binding domain and are bound to DNA sequences with an identical consensus. In contrast, both factors differ substantially in the number of bound sites in the genome. Here, we addressed the molecular features for this binding specificity. In contrast to CTCF we found CTCFL highly enriched at ‘open’ chromatin marked by H3K27 acetylation, H3K4 di- and trimethylation, H3K79 dimethylation and H3K9 acetylation plus the histone variant H2A.Z. CTCFL is enriched at transcriptional start sites and regions bound by transcription factors. Consequently, genes deregulated by CTCFL are highly cell specific. In addition to a chromatin-driven choice of binding sites, we determined nucleotide positions critical for DNA binding by CTCFL, but not by CTCF.
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Affiliation(s)
- Philipp Bergmaier
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Oliver Weth
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Sven Dienstbach
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Thomas Boettger
- Department Cardiac Development and Remodelling, Max-Planck-Institute, D61231 Bad Nauheim, Germany
| | - Niels Galjart
- Department of Cell Biology and Genetics, Erasmus MC, 3000CA Rotterdam, The Netherlands
| | - Marco Mernberger
- Institute of Molecular Oncology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Rainer Renkawitz
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
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29
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Hillman JC, Pugacheva EM, Barger CJ, Sribenja S, Rosario S, Albahrani M, Truskinovsky AM, Stablewski A, Liu S, Loukinov DI, Zentner GE, Lobanenkov VV, Karpf AR, Higgins MJ. BORIS Expression in Ovarian Cancer Precursor Cells Alters the CTCF Cistrome and Enhances Invasiveness through GALNT14. Mol Cancer Res 2019; 17:2051-2062. [PMID: 31292201 DOI: 10.1158/1541-7786.mcr-19-0310] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/07/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022]
Abstract
High-grade serous carcinoma (HGSC) is the most aggressive and predominant form of epithelial ovarian cancer and the leading cause of gynecologic cancer-related death. We have previously shown that CTCFL (also known as BORIS, Brother of the Regulator of Imprinted Sites) is expressed in most ovarian cancers, and is associated with global and promoter-specific DNA hypomethylation, advanced tumor stage, and poor prognosis. To explore its role in HGSC, we expressed BORIS in human fallopian tube secretory epithelial cells (FTSEC), the presumptive cells of origin for HGSC. BORIS-expressing cells exhibited increased motility and invasion, and BORIS expression was associated with alterations in several cancer-associated gene expression networks, including fatty acid metabolism, TNF signaling, cell migration, and ECM-receptor interactions. Importantly, GALNT14, a glycosyltransferase gene implicated in cancer cell migration and invasion, was highly induced by BORIS, and GALNT14 knockdown significantly abrogated BORIS-induced cell motility and invasion. In addition, in silico analyses provided evidence for BORIS and GALNT14 coexpression in several cancers. Finally, ChIP-seq demonstrated that expression of BORIS was associated with de novo and enhanced binding of CTCF at hundreds of loci, many of which correlated with activation of transcription at target genes, including GALNT14. Taken together, our data indicate that BORIS may promote cell motility and invasion in HGSC via upregulation of GALNT14, and suggests BORIS as a potential therapeutic target in this malignancy. IMPLICATIONS: These studies provide evidence that aberrant expression of BORIS may play a role in the progression to HGSC by enhancing the migratory and invasive properties of FTSEC.
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Affiliation(s)
- Joanna C Hillman
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Elena M Pugacheva
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland
| | - Carter J Barger
- Eppley Institute and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sirinapa Sribenja
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Spencer Rosario
- Department of Cancer Genetics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Mustafa Albahrani
- Eppley Institute and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | | | - Aimee Stablewski
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Dmitri I Loukinov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland
| | - Gabriel E Zentner
- Department of Biology, Indiana University, Bloomington, Indiana.,Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana
| | - Victor V Lobanenkov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland
| | - Adam R Karpf
- Eppley Institute and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska.
| | - Michael J Higgins
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York.
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30
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Wang DC, Wang W, Zhang L, Wang X. A tour of 3D genome with a focus on CTCF. Semin Cell Dev Biol 2019; 90:4-11. [PMID: 30031214 DOI: 10.1016/j.semcdb.2018.07.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022]
Abstract
The complex three-dimensional (3D) structure of the genome plays critical roles in the maintenance of genome stability, organization, and dynamics and in regulation of gene expression for understanding molecular mechanisms and diseases. Chromatin maintains biological functions and transcriptional activities through long distance interaction and interactions between loops and enhancers-promoters. We firstly overview the architecture and biology of chromatin and loops, topologically associated domains (TADs) and interactions, and compartments and functions. We specifically focus on CCCTC-binding factor (CTCF) in 3D genome organization and function to furthermore understand the significance of CTCF biology, transcriptional regulations, interactions with cohesin, roles in DNA binding, influences of CTCF degradation, and communication with wings-apart like (Wapl) protein. We also summarize the advanced single cell approaches to further monitor dynamics of CTCF functions and structures in the maintenance of 3D genome organization and function at single cell level.
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Affiliation(s)
- Diane C Wang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - William Wang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Linlin Zhang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China.
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31
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Ernst C, Eling N, Martinez-Jimenez CP, Marioni JC, Odom DT. Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis. Nat Commun 2019; 10:1251. [PMID: 30890697 PMCID: PMC6424977 DOI: 10.1038/s41467-019-09182-1] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/15/2019] [Indexed: 12/21/2022] Open
Abstract
Male gametes are generated through a specialised differentiation pathway involving a series of developmental transitions that are poorly characterised at the molecular level. Here, we use droplet-based single-cell RNA-Sequencing to profile spermatogenesis in adult animals and at multiple stages during juvenile development. By exploiting the first wave of spermatogenesis, we both precisely stage germ cell development and enrich for rare somatic cell-types and spermatogonia. To capture the full complexity of spermatogenesis including cells that have low transcriptional activity, we apply a statistical tool that identifies previously uncharacterised populations of leptotene and zygotene spermatocytes. Focusing on post-meiotic events, we characterise the temporal dynamics of X chromosome re-activation and profile the associated chromatin state using CUT&RUN. This identifies a set of genes strongly repressed by H3K9me3 in spermatocytes, which then undergo extensive chromatin remodelling post-meiosis, thus acquiring an active chromatin state and spermatid-specific expression.
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Affiliation(s)
- Christina Ernst
- European Molecular Biology Laboratory, European Bioinformatics Institute, (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Nils Eling
- European Molecular Biology Laboratory, European Bioinformatics Institute, (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Celia P Martinez-Jimenez
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics, 69120, Heidelberg, Germany.
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32
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Halldorsson BV, Palsson G, Stefansson OA, Jonsson H, Hardarson MT, Eggertsson HP, Gunnarsson B, Oddsson A, Halldorsson GH, Zink F, Gudjonsson SA, Frigge ML, Thorleifsson G, Sigurdsson A, Stacey SN, Sulem P, Masson G, Helgason A, Gudbjartsson DF, Thorsteinsdottir U, Stefansson K. Characterizing mutagenic effects of recombination through a sequence-level genetic map. Science 2019; 363:363/6425/eaau1043. [DOI: 10.1126/science.aau1043] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 05/16/2018] [Accepted: 12/07/2018] [Indexed: 12/14/2022]
Abstract
Genetic diversity arises from recombination and de novo mutation (DNM). Using a combination of microarray genotype and whole-genome sequence data on parent-child pairs, we identified 4,531,535 crossover recombinations and 200,435 DNMs. The resulting genetic map has a resolution of 682 base pairs. Crossovers exhibit a mutagenic effect, with overrepresentation of DNMs within 1 kilobase of crossovers in males and females. In females, a higher mutation rate is observed up to 40 kilobases from crossovers, particularly for complex crossovers, which increase with maternal age. We identified 35 loci associated with the recombination rate or the location of crossovers, demonstrating extensive genetic control of meiotic recombination, and our results highlight genes linked to the formation of the synaptonemal complex as determinants of crossovers.
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33
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Loukinov D. Targeting CTCFL/BORIS for the immunotherapy of cancer. Cancer Immunol Immunother 2018; 67:1955-1965. [PMID: 30390146 PMCID: PMC11028242 DOI: 10.1007/s00262-018-2251-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 07/13/2018] [Indexed: 10/27/2022]
Abstract
Cancer vaccines have great potential in the fight against metastatic malignancies. Current anti-tumor immunotherapy is hindered by existing tolerance to tumor-associated antigens (TAA) and tumor escape using various mechanisms, highlighting the need for improved targets for immunotherapy. The cancer-testis antigen CTCFL/BORIS was discovered 16 years ago and possesses all features necessary for an ideal TAA. Recently CTCFL/BORIS has received additional attention as a target expressed in cancer stem cells (CSC). These cells drive tumor growth recurrence, metastasis, and treatment resistance. CTCFL/BORIS silencing leads to senescence and death of CSC. Therefore, an immunotherapeutic strategy that targets CTCFL/BORIS may lead to the selective destruction of CSC and potential eradication of metastatic disease. The high immunotherapeutic potential of CTCFL/BORIS antigen was shown in a stringent 4T1 mouse model of breast cancer. Using these highly metastatic, poorly immunogenic carcinoma cells inoculated into T-helper2 prone mice, we showed that DC fed with recombinant CTCFL/BORIS as an immunogen inhibited tumor growth and reduced the number of metastases in distant organs. About 20% of CTCFL/BORIS immunized animals were tumor free. 50% of animals remained metastasis free. Those having metastasis showed at least tenfold fewer metastases compared to controls. In a rat model of breast cancer, we showed that alphavirus-based CTCFL/BORIS immunotherapy was capable of cancer elimination as we were able to cure 50% of animals. Based on the above data, we believe that translation of CTCFL/BORIS-targeting immunotherapeutic strategies to the clinic will provide new avenues for improving survival of breast cancer patients with advanced metastatic disease.
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Affiliation(s)
- Dmitri Loukinov
- Molecular Pathology Section, Laboratory of Immunogenetics, NIAID/NIH, Twinbrook 1, Room 1329, 5640 Fishers Lane, Rockville, MD, 20852, USA.
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34
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Soltanian S, Dehghani H. BORIS: a key regulator of cancer stemness. Cancer Cell Int 2018; 18:154. [PMID: 30323717 PMCID: PMC6173857 DOI: 10.1186/s12935-018-0650-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023] Open
Abstract
BORIS (CTCFL) is a DNA binding protein which is involved in tumorigenesis. Although, there are different opinions on the level of gene expression and function of BORIS in normal and cancer tissues, the results of many studies have classified BORIS as a protein belonging to cancer/testis (CT) genes, which are identified as a group of genes that are expressed normally in testis, and abnormally in various types of cancers. In testis, BORIS induces the expression of some male germ cell/testis specific genes, and plays crucial roles during spermatogenesis and production of sperm. In tumorigenesis, the role of BORIS in the expression induction of some CT genes and oncogenes, as well as increasing proliferation/viability of cancer cells has been demonstrated in many researches. In addition to cancer cells, some believe that BORIS is also expressed in normal conditions and plays a universal function in cell division and regulation of genes. The following is a comprehensive review on contradictory views on the expression pattern and biological function of BORIS in normal, as well as cancer cells/tissues, and presents some evidence that support the expression of BORIS in cancer stem cells (CSCs) and advanced stage/poorer differentiation grade of cancers. Boris is involved in the regulation of CSC cellular and molecular features such as self-renewal, chemo-resistance, tumorigenicity, sphere-forming ability, and migration capacity. Finally, the role of BORIS in regulating two important signaling pathways including Wnt/β-catenin and Notch in CSCs, and its ability in recruiting transcription factors or chromatin-remodeling proteins to induce tumorigenesis is discussed.
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Affiliation(s)
- Sara Soltanian
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hesam Dehghani
- Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, 91775-1793 Iran
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Stem Cells and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
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Gambetta MC, Furlong EEM. The Insulator Protein CTCF Is Required for Correct Hox Gene Expression, but Not for Embryonic Development in Drosophila. Genetics 2018; 210:129-136. [PMID: 30021792 PMCID: PMC6116963 DOI: 10.1534/genetics.118.301350] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/12/2018] [Indexed: 02/07/2023] Open
Abstract
Insulator binding proteins (IBPs) play an important role in regulating gene expression by binding to specific DNA sites to facilitate appropriate gene regulation. There are several IBPs in Drosophila, each defined by their ability to insulate target gene promoters in transgenic assays from the activating or silencing effects of neighboring regulatory elements. Of these, only CCCTC-binding factor (CTCF) has an obvious ortholog in mammals. CTCF is essential for mammalian cell viability and is an important regulator of genome architecture. In flies, CTCF is both maternally deposited and zygotically expressed. Flies lacking zygotic CTCF die as young adults with homeotic defects, suggesting that specific Hox genes are misexpressed in inappropriate body segments. The lack of any major embryonic defects was assumed to be due to the maternal supply of CTCF protein, as maternally contributed factors are often sufficient to progress through much of embryogenesis. Here, we definitively determined the requirement of CTCF for developmental progression in Drosophila We generated animals that completely lack both maternal and zygotic CTCF and found that, contrary to expectation, these mutants progress through embryogenesis and larval life. They develop to pharate adults, which fail to eclose from their pupal case. These mutants show exacerbated homeotic defects compared to zygotic mutants, misexpressing the Hox gene Abdominal-B outside of its normal expression domain early in development. Our results indicate that loss of Drosophila CTCF is not accompanied by widespread effects on gene expression, which may be due to redundant functions with other IBPs. Rather, CTCF is required for correct Hox gene expression patterns and for the viability of adult Drosophila.
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Affiliation(s)
| | - Eileen E M Furlong
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
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36
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Green CD, Ma Q, Manske GL, Shami AN, Zheng X, Marini S, Moritz L, Sultan C, Gurczynski SJ, Moore BB, Tallquist MD, Li JZ, Hammoud SS. A Comprehensive Roadmap of Murine Spermatogenesis Defined by Single-Cell RNA-Seq. Dev Cell 2018; 46:651-667.e10. [PMID: 30146481 DOI: 10.1016/j.devcel.2018.07.025] [Citation(s) in RCA: 296] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 07/03/2018] [Accepted: 07/30/2018] [Indexed: 02/07/2023]
Abstract
Spermatogenesis requires intricate interactions between the germline and somatic cells. Within a given cross section of a seminiferous tubule, multiple germ and somatic cell types co-occur. This cellular heterogeneity has made it difficult to profile distinct cell types at different stages of development. To address this challenge, we collected single-cell RNA sequencing data from ∼35,000 cells from the adult mouse testis and identified all known germ and somatic cells, as well as two unexpected somatic cell types. Our analysis revealed a continuous developmental trajectory of germ cells from spermatogonia to spermatids and identified candidate transcriptional regulators at several transition points during differentiation. Focused analyses delineated four subtypes of spermatogonia and nine subtypes of Sertoli cells; the latter linked to histologically defined developmental stages over the seminiferous epithelial cycle. Overall, this high-resolution cellular atlas represents a community resource and foundation of knowledge to study germ cell development and in vivo gametogenesis.
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Affiliation(s)
| | - Qianyi Ma
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel L Manske
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | | | - Xianing Zheng
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Simone Marini
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Lindsay Moritz
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Caleb Sultan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Bethany B Moore
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | | | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
| | - Saher Sue Hammoud
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA; Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan, Ann Arbor, MI, USA.
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37
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PRDM Histone Methyltransferase mRNA Levels Increase in Response to Curative Hormone Treatment for Cryptorchidism-Dependent Male Infertility. Genes (Basel) 2018; 9:genes9080391. [PMID: 30071651 PMCID: PMC6116052 DOI: 10.3390/genes9080391] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/16/2018] [Accepted: 07/24/2018] [Indexed: 12/17/2022] Open
Abstract
There is a correlation between cryptorchidism and an increased risk of testicular cancer and infertility. During orchidopexy, testicular biopsies are performed to confirm the presence of type A dark (Ad) spermatogonia, which are a marker for low infertility risk (LIR). The Ad spermatogonia are absent in high infertility risk (HIR) patients, who are treated with a gonadotropin-releasing hormone agonist (GnRHa) to significantly lower the risk of infertility. Despite its prevalence, little is known about the molecular events involved in cryptorchidism. Previously, we compared the transcriptomes of LIR versus HIR patients treated with and without hormones. Here, we interpreted data regarding members of the positive regulatory domain-containing (PRDM) family; some of which encoded histone methyltransferases that are important for reproduction. We found there were lower levels of PRDM1, PRDM6, PRDM9, PRDM13, and PRDM14 mRNA in the testes of HIR patients compared with LIR patients, and that PRDM7, PRDM9, PRDM12, and PRDM16 were significantly induced after GnRHa treatment. Furthermore, we observed PRDM9 protein staining in the cytoplasm of germ cells in the testes from LIR and HIR patients, indicating that the mRNA and protein levels corresponded. This result indicated that the curative hormonal therapy for cryptorchidism involved conserved chromatin modification enzymes.
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38
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Jabbari K, Heger P, Sharma R, Wiehe T. The Diverging Routes of BORIS and CTCF: An Interactomic and Phylogenomic Analysis. Life (Basel) 2018; 8:life8010004. [PMID: 29385718 PMCID: PMC5871936 DOI: 10.3390/life8010004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 01/25/2018] [Accepted: 01/25/2018] [Indexed: 12/11/2022] Open
Abstract
The CCCTC-binding factor (CTCF) is multi-functional, ubiquitously expressed, and highly conserved from Drosophila to human. It has important roles in transcriptional insulation and the formation of a high-dimensional chromatin structure. CTCF has a paralog called “Brother of Regulator of Imprinted Sites” (BORIS) or “CTCF-like” (CTCFL). It binds DNA at sites similar to those of CTCF. However, the expression profiles of the two proteins are quite different. We investigated the evolutionary trajectories of the two proteins after the duplication event using a phylogenomic and interactomic approach. We find that CTCF has 52 direct interaction partners while CTCFL only has 19. Almost all interactors already existed before the emergence of CTCF and CTCFL. The unique secondary loss of CTCF from several nematodes is paralleled by a loss of two of its interactors, the polycomb repressive complex subunit SuZ12 and the multifunctional transcription factor TYY1. In contrast to earlier studies reporting the absence of BORIS from birds, we present evidence for a multigene synteny block containing CTCFL that is conserved in mammals, reptiles, and several species of birds, indicating that not the entire lineage of birds experienced a loss of CTCFL. Within this synteny block, BORIS and its genomic neighbors seem to be partitioned into two nested chromatin loops. The high expression of SPO11, RAE1, RBM38, and PMEPA1 in male tissues suggests a possible link between CTCFL, meiotic recombination, and fertility-associated phenotypes. Using the 65,700 exomes and the 1000 genomes data, we observed a higher number of intergenic, non-synonymous, and loss-of-function mutations in CTCFL than in CTCF, suggesting a reduced strength of purifying selection, perhaps due to less functional constraint.
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Affiliation(s)
- Kamel Jabbari
- Cologne Biocenter, Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Köln, Germany.
| | - Peter Heger
- Cologne Biocenter, Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Köln, Germany.
| | - Ranu Sharma
- Cologne Biocenter, Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Köln, Germany.
| | - Thomas Wiehe
- Cologne Biocenter, Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Köln, Germany.
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Sharifi-Zarchi A, Gerovska D, Adachi K, Totonchi M, Pezeshk H, Taft RJ, Schöler HR, Chitsaz H, Sadeghi M, Baharvand H, Araúzo-Bravo MJ. DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism. BMC Genomics 2017; 18:964. [PMID: 29233090 PMCID: PMC5727985 DOI: 10.1186/s12864-017-4353-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 11/28/2017] [Indexed: 12/21/2022] Open
Abstract
Background DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is expected. Actually, there exist contradictory reports about positive and negative correlations between DNA methylation and H3K4me1, a chromatin hallmark of enhancers. Results We investigated the relationship between DNA methylation and active chromatin marks through genome-wide correlations, and found anti-correlation between H3K4me1 and H3K4me3 enrichment at low and intermediate DNA methylation loci. We hypothesized “seesaw” dynamics between H3K4me1 and H3K4me3 in the low and intermediate DNA methylation range, in which DNA methylation discriminates between enhancers and promoters, marked by H3K4me1 and H3K4me3, respectively. Low methylated regions are H3K4me3 enriched, while those with intermediate DNA methylation levels are progressively H3K4me1 enriched. Additionally, the enrichment of H3K27ac, distinguishing active from primed enhancers, follows a plateau in the lower range of the intermediate DNA methylation level, corresponding to active enhancers, and decreases linearly in the higher range of the intermediate DNA methylation. Thus, the decrease of the DNA methylation switches smoothly the state of the enhancers from a primed to an active state. We summarize these observations into a rule of thumb of one-out-of-three methylation marks: “In each genomic region only one out of these three methylation marks {DNA methylation, H3K4me1, H3K4me3} is high. If it is the DNA methylation, the region is inactive. If it is H3K4me1, the region is an enhancer, and if it is H3K4me3, the region is a promoter”. To test our model, we used available genome-wide datasets of H3K4 methyltransferases knockouts. Our analysis suggests that CXXC proteins, as readers of non-methylated CpGs would regulate the “seesaw” mechanism that focuses H3K4me3 to unmethylated sites, while being repulsed from H3K4me1 decorated enhancers and CpG island shores. Conclusions Our results show that DNA methylation discriminates promoters from enhancers through H3K4me1-H3K4me3 seesaw mechanism, and suggest its possible function in the inheritance of chromatin marks after cell division. Our analyses suggest aberrant formation of promoter-like regions and ectopic transcription of hypomethylated regions of DNA. Such mechanism process can have important implications in biological process in where it has been reported abnormal DNA methylation status such as cancer and aging. Electronic supplementary material The online version of this article (10.1186/s12864-017-4353-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ali Sharifi-Zarchi
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.,Computer Science Department, Colorado State University, Fort Collins, CO, USA.,Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014, San Sebastián, Spain
| | - Kenjiro Adachi
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Mehdi Totonchi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Hamid Pezeshk
- School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, Tehran, Iran.,School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | | | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Medical Faculty, University of Münster, Münster, Germany
| | - Hamidreza Chitsaz
- Computer Science Department, Colorado State University, Fort Collins, CO, USA
| | - Mehdi Sadeghi
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.,National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran. .,Department of Developmental Biology, University of Science and Culture, Tehran, Iran.
| | - Marcos J Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014, San Sebastián, Spain. .,Computational Biology and Bioinformatics Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany. .,IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain.
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40
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Abstract
CCCTC-binding factor (CTCF) is a conserved, essential regulator of chromatin architecture containing a unique array of 11 zinc fingers (ZFs). Gene duplication and sequence divergence during early amniote evolution generated the CTCF paralog Brother Of the Regulator of Imprinted Sites (BORIS), which has a DNA binding specificity identical to that of CTCF but divergent N- and C-termini. While healthy somatic tissues express only CTCF, CTCF and BORIS are normally co-expressed in meiotic and post-meiotic germ cells, and aberrant activation of BORIS occurs in tumors and some cancer cell lines. This has led to a model in which CTCF and BORIS compete for binding to some but not all genomic target sites; however, regulation of CTCF and BORIS genomic co-occupancy is not well understood. We recently addressed this issue, finding evidence for two major classes of CTCF target sequences, some of which contain single CTCF target sites (1xCTSes) and others containing two adjacent CTCF motifs (2xCTSes). The functional and chromatin structural features of 2xCTSes are distinct from those of 1xCTS-containing regions bound by a CTCF monomer. We suggest that these previously overlooked classes of CTCF binding regions may have different roles in regulating diverse chromatin-based phenomena, and may impact our understanding of heritable epigenetic regulation in cancer cells and normal germ cells.
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Affiliation(s)
- Victor V Lobanenkov
- a Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health , 5601 Fishers Ln, Rockville , MD , USA
| | - Gabriel E Zentner
- b Department of Biology , Indiana University , 915 E 3rd St, Bloomington , IN 47405 , USA
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41
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Altemose N, Noor N, Bitoun E, Tumian A, Imbeault M, Chapman JR, Aricescu AR, Myers SR. A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis. eLife 2017; 6:e28383. [PMID: 29072575 PMCID: PMC5705219 DOI: 10.7554/elife.28383] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 10/24/2017] [Indexed: 12/31/2022] Open
Abstract
PRDM9 binding localizes almost all meiotic recombination sites in humans and mice. However, most PRDM9-bound loci do not become recombination hotspots. To explore factors that affect binding and subsequent recombination outcomes, we mapped human PRDM9 binding sites in a transfected human cell line and measured PRDM9-induced histone modifications. These data reveal varied DNA-binding modalities of PRDM9. We also find that human PRDM9 frequently binds promoters, despite their low recombination rates, and it can activate expression of a small number of genes including CTCFL and VCX. Furthermore, we identify specific sequence motifs that predict consistent, localized meiotic recombination suppression around a subset of PRDM9 binding sites. These motifs strongly associate with KRAB-ZNF protein binding, TRIM28 recruitment, and specific histone modifications. Finally, we demonstrate that, in addition to binding DNA, PRDM9's zinc fingers also mediate its multimerization, and we show that a pair of highly diverged alleles preferentially form homo-multimers.
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Affiliation(s)
- Nicolas Altemose
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Nudrat Noor
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Emmanuelle Bitoun
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Afidalina Tumian
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Michael Imbeault
- Global Health InstituteÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - J Ross Chapman
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - A Radu Aricescu
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Simon R Myers
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
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Intragenic DNA methylation and BORIS-mediated cancer-specific splicing contribute to the Warburg effect. Proc Natl Acad Sci U S A 2017; 114:11440-11445. [PMID: 29073069 PMCID: PMC5664520 DOI: 10.1073/pnas.1708447114] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recent advances in cancer epigenetics have shown the involvement of epigenetic abnormalities in the initiation and progression of cancer, but their role in cancer-specific aberrant splicing is not clear. The identification of upstream epigenetic regulators of cancer-specific splicing will enable us to therapeutically target aberrant splicing and provide an approach to cancer therapy. Here we have demonstrated a mechanism of intragenic DNA methylation-mediated regulation of alternative splicing by Brother of Regulator of Imprinted Sites (BORIS), which can contribute to breast cancer tumorigenesis by favoring the Warburg effect. The reversal of the Warburg effect was achieved by the inhibition of DNA methylation or down-regulation of BORIS, which may serve as a useful approach to inhibit the growth of breast cancer cells. Aberrant alternative splicing and epigenetic changes are both associated with various cancers, but epigenetic regulation of alternative splicing in cancer is largely unknown. Here we report that the intragenic DNA methylation-mediated binding of Brother of Regulator of Imprinted Sites (BORIS) at the alternative exon of Pyruvate Kinase (PKM) is associated with cancer-specific splicing that promotes the Warburg effect and breast cancer progression. Interestingly, the inhibition of DNA methylation, BORIS depletion, or CRISPR/Cas9-mediated deletion of the BORIS binding site leads to a splicing switch from cancer-specific PKM2 to normal PKM1 isoform. This results in the reversal of the Warburg effect and the inhibition of breast cancer cell growth, which may serve as a useful approach to inhibit the growth of breast cancer cells. Importantly, our results show that in addition to PKM splicing, BORIS also regulates the alternative splicing of several genes in a DNA methylation-dependent manner. Our findings highlight the role of intragenic DNA methylation and DNA binding protein BORIS in cancer-specific splicing and its role in tumorigenesis.
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43
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Genetic and epigenetic features direct differential efficiency of Xist-mediated silencing at X-chromosomal and autosomal locations. Nat Commun 2017; 8:690. [PMID: 28947736 PMCID: PMC5612955 DOI: 10.1038/s41467-017-00528-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 07/06/2017] [Indexed: 02/02/2023] Open
Abstract
Xist is indispensable for X chromosome inactivation. However, how Xist RNA directs chromosome-wide silencing and why some regions are more efficiently silenced than others remains unknown. Here, we explore the function of Xist by inducing ectopic Xist expression from multiple different X-linked and autosomal loci in mouse aneuploid and female diploid embryonic stem cells in which Xist-mediated silencing does not lead to lethal functional monosomy. We show that ectopic Xist expression faithfully recapitulates endogenous X chromosome inactivation from any location on the X chromosome, whereas long-range silencing of autosomal genes is less efficient. Long interspersed elements facilitate inactivation of genes located far away from the Xist transcription locus, and genes escaping X chromosome inactivation show enrichment of CTCF on X chromosomal but not autosomal loci. Our findings highlight important genomic and epigenetic features acquired during sex chromosome evolution to facilitate an efficient X chromosome inactivation process.Xist RNA is required for X chromosome inactivation but it is not well understood how Xist silences some regions more efficiently than others. Here, the authors induce ectopic Xist expression from multiple different X-linked and autosomal loci in cells to explore Xist function.
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44
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Teplyakov E, Wu Q, Liu J, Pugacheva EM, Loukinov D, Boukaba A, Lobanenkov V, Strunnikov A. The downregulation of putative anticancer target BORIS/CTCFL in an addicted myeloid cancer cell line modulates the expression of multiple protein coding and ncRNA genes. Oncotarget 2017; 8:73448-73468. [PMID: 29088719 PMCID: PMC5650274 DOI: 10.18632/oncotarget.20627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/23/2017] [Indexed: 12/27/2022] Open
Abstract
The BORIS/CTCFL gene, is a testis-specific CTCF paralog frequently erroneously activated in cancer, although its exact role in cancer remains unclear. BORIS is both a transcription factor and an architectural chromatin protein. BORIS' normal role is to establish a germline-like gene expression and remodel the epigenetic landscape in testis; it similarly remodels chromatin when activated in human cancer. Critically, at least one cancer cell line, K562, is dependent on BORIS for its self-renewal and survival. Here, we downregulate BORIS expression in the K562 cancer cell line to investigate downstream pathways regulated by BORIS. RNA-seq analyses of both mRNA and small ncRNAs, including miRNA and piRNA, in the knock-down cells revealed a set of differentially expressed genes and pathways, including both testis-specific and general proliferation factors, as well as proteins involved in transcription regulation and cell physiology. The differentially expressed genes included important transcriptional regulators such as SOX6 and LIN28A. Data indicate that both direct binding of BORIS to promoter regions and locus-control activity via long-distance chromatin domain regulation are involved. The sum of findings suggests that BORIS activation in leukemia does not just recapitulate the germline, but creates a unique regulatory network.
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Affiliation(s)
- Evgeny Teplyakov
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China.,The University of the Chinese Academy of Sciences, Beijing, China
| | - Qiongfang Wu
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Jian Liu
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | | | - Dmitry Loukinov
- NIH, NIAID, Laboratory of Immunogenetics, Rockville, MD, USA
| | - Abdelhalim Boukaba
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | | | - Alexander Strunnikov
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China.,The University of the Chinese Academy of Sciences, Beijing, China
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45
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Liu Q, Chen K, Liu Z, Huang Y, Zhao R, Wei L, Yu X, He J, Liu J, Qi J, Qin Y, Li B. BORIS up-regulates OCT4 via histone methylation to promote cancer stem cell-like properties in human liver cancer cells. Cancer Lett 2017. [DOI: 10.1016/j.canlet.2017.06.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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46
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Nora EP, Goloborodko A, Valton AL, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG. Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. Cell 2017; 169:930-944.e22. [PMID: 28525758 PMCID: PMC5538188 DOI: 10.1016/j.cell.2017.05.004] [Citation(s) in RCA: 1050] [Impact Index Per Article: 150.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/14/2017] [Accepted: 05/02/2017] [Indexed: 01/17/2023]
Abstract
The molecular mechanisms underlying folding of mammalian chromosomes remain poorly understood. The transcription factor CTCF is a candidate regulator of chromosomal structure. Using the auxin-inducible degron system in mouse embryonic stem cells, we show that CTCF is absolutely and dose-dependently required for looping between CTCF target sites and insulation of topologically associating domains (TADs). Restoring CTCF reinstates proper architecture on altered chromosomes, indicating a powerful instructive function for CTCF in chromatin folding. CTCF remains essential for TAD organization in non-dividing cells. Surprisingly, active and inactive genome compartments remain properly segregated upon CTCF depletion, revealing that compartmentalization of mammalian chromosomes emerges independently of proper insulation of TADs. Furthermore, our data support that CTCF mediates transcriptional insulator function through enhancer blocking but not as a direct barrier to heterochromatin spreading. Beyond defining the functions of CTCF in chromosome folding, these results provide new fundamental insights into the rules governing mammalian genome organization.
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Affiliation(s)
- Elphège P Nora
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA.
| | - Anton Goloborodko
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anne-Laure Valton
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Johan H Gibcus
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Alec Uebersohn
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Nezar Abdennur
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Job Dekker
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, CA 94143, USA; Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA.
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47
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Testis-specific transcriptional regulators selectively occupy BORIS-bound CTCF target regions in mouse male germ cells. Sci Rep 2017; 7:41279. [PMID: 28145452 PMCID: PMC5286509 DOI: 10.1038/srep41279] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/19/2016] [Indexed: 12/14/2022] Open
Abstract
Despite sharing the same sequence specificity in vitro and in vivo, CCCTC-binding factor (CTCF) and its paralog brother of the regulator of imprinted sites (BORIS) are simultaneously expressed in germ cells. Recently, ChIP-seq analysis revealed two classes of CTCF/BORIS-bound regions: single CTCF target sites (1xCTSes) that are bound by CTCF alone (CTCF-only) or double CTCF target sites (2xCTSes) simultaneously bound by CTCF and BORIS (CTCF&BORIS) or BORIS alone (BORIS-only) in germ cells and in BORIS-positive somatic cancer cells. BORIS-bound regions (CTCF&BORIS and BORIS-only sites) are, on average, enriched for RNA polymerase II (RNAPII) binding and histone retention in mature spermatozoa relative to CTCF-only sites, but little else is known about them. We show that subsets of CTCF&BORIS and BORIS-only sites are occupied by several testis-specific transcriptional regulators (TSTRs) and associated with highly expressed germ cell-specific genes and histone retention in mature spermatozoa. We also demonstrate a physical interaction between BORIS and one of the analyzed TSTRs, TATA-binding protein (TBP)-associated factor 7-like (TAF7L). Our data suggest that CTCF and BORIS cooperate with additional TSTRs to regulate gene expression in developing male gametes and histone retention in mature spermatozoa, potentially priming certain regions of the genome for rapid activation following fertilization.
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48
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Herzig Y, Nevo S, Bornstein C, Brezis MR, Ben-Hur S, Shkedy A, Eisenberg-Bord M, Levi B, Delacher M, Goldfarb Y, David E, Weinberger L, Viukov S, Ben-Dor S, Giraud M, Hanna JH, Breiling A, Lyko F, Amit I, Feuerer M, Abramson J. Transcriptional programs that control expression of the autoimmune regulator gene Aire. Nat Immunol 2017; 18:161-172. [PMID: 27941786 DOI: 10.1038/ni.3638] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/17/2016] [Indexed: 12/15/2022]
Abstract
Aire is a transcriptional regulator that induces promiscuous expression of thousands of genes encoding tissue-restricted antigens (TRAs) in medullary thymic epithelial cells (mTECs). While the target genes of Aire are well characterized, the transcriptional programs that regulate its own expression have remained elusive. Here we comprehensively analyzed both cis-acting and trans-acting regulatory mechanisms and found that the Aire locus was insulated by the global chromatin organizer CTCF and was hypermethylated in cells and tissues that did not express Aire. In mTECs, however, Aire expression was facilitated by concurrent eviction of CTCF, specific demethylation of exon 2 and the proximal promoter, and the coordinated action of several transcription activators, including Irf4, Irf8, Tbx21, Tcf7 and Ctcfl, which acted on mTEC-specific accessible regions in the Aire locus.
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Affiliation(s)
- Yonatan Herzig
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Shir Nevo
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Chamutal Bornstein
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Miriam R Brezis
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Sharon Ben-Hur
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Aya Shkedy
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Ben Levi
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Delacher
- Research Group Immune Tolerance, Tumor Immunology Program, German Cancer Research Center, Heidelberg, Germany
| | - Yael Goldfarb
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Leehee Weinberger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Viukov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Bioinformatics Unit, Biological Services Department, Weizmann Institute of Science, Rehovot, Israel
| | - Matthieu Giraud
- Department of Infection Immunity and Inflammation, Cochin Institute, Paris, France
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Achim Breiling
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Markus Feuerer
- Research Group Immune Tolerance, Tumor Immunology Program, German Cancer Research Center, Heidelberg, Germany
| | - Jakub Abramson
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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49
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Abstract
Genome function, replication, integrity, and propagation rely on the dynamic structural organization of chromosomes during the cell cycle. Genome folding in interphase provides regulatory segmentation for appropriate transcriptional control, facilitates ordered genome replication, and contributes to genome integrity by limiting illegitimate recombination. Here, we review recent high-resolution chromosome conformation capture and functional studies that have informed models of the spatial and regulatory compartmentalization of mammalian genomes, and discuss mechanistic models for how CTCF and cohesin control the functional architecture of mammalian chromosomes.
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Affiliation(s)
- Matthias Merkenschlager
- MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom;
| | - Elphège P Nora
- Gladstone Institute of Cardiovascular Disease, San Francisco, California 94158;
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50
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Pugacheva EM, Teplyakov E, Wu Q, Li J, Chen C, Meng C, Liu J, Robinson S, Loukinov D, Boukaba A, Hutchins AP, Lobanenkov V, Strunnikov A. The cancer-associated CTCFL/BORIS protein targets multiple classes of genomic repeats, with a distinct binding and functional preference for humanoid-specific SVA transposable elements. Epigenetics Chromatin 2016; 9:35. [PMID: 27588042 PMCID: PMC5007689 DOI: 10.1186/s13072-016-0084-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/18/2016] [Indexed: 12/20/2022] Open
Abstract
Background A common aberration in cancer is the activation of germline-specific proteins. The DNA-binding proteins among them could generate novel chromatin states, not found in normal cells. The germline-specific transcription factor BORIS/CTCFL, a paralog of chromatin architecture protein CTCF, is often erroneously activated in cancers and rewires the epigenome for the germline-like transcription program. Another common feature of malignancies is the changed expression and epigenetic states of genomic repeats, which could alter the transcription of neighboring genes and cause somatic mutations upon transposition. The role of BORIS in transposable elements and other repeats has never been assessed. Results The investigation of BORIS and CTCF binding to DNA repeats in the K562 cancer cells dependent on BORIS for self-renewal by ChIP-chip and ChIP-seq revealed three classes of occupancy by these proteins: elements cohabited by BORIS and CTCF, CTCF-only bound, or BORIS-only bound. The CTCF-only enrichment is characteristic for evolutionary old and inactive repeat classes, while BORIS and CTCF co-binding predominately occurs at uncharacterized tandem repeats. These repeats form staggered cluster binding sites, which are a prerequisite for CTCF and BORIS co-binding. At the same time, BORIS preferentially occupies a specific subset of the evolutionary young, transcribed, and mobile genomic repeat family, SVA. Unlike CTCF, BORIS prominently binds to the VNTR region of the SVA repeats in vivo. This suggests a role of BORIS in SVA expression regulation. RNA-seq analysis indicates that BORIS largely serves as a repressor of SVA expression, alongside DNA and histone methylation, with the exception of promoter capture by SVA. Conclusions Thus, BORIS directly binds to, and regulates SVA repeats, which are essentially movable CpG islands, via clusters of BORIS binding sites. This finding uncovers a new function of the global germline-specific transcriptional regulator BORIS in regulating and repressing the newest class of transposable elements that are actively transposed in human genome when activated. This function of BORIS in cancer cells is likely a reflection of its roles in the germline. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0084-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Evgeny Teplyakov
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530 Guangdong China
| | - Qiongfang Wu
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530 Guangdong China
| | - Jingjing Li
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530 Guangdong China
| | - Cheng Chen
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530 Guangdong China
| | - Chengcheng Meng
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530 Guangdong China
| | - Jian Liu
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530 Guangdong China
| | - Susan Robinson
- Laboratory of Immunogenetics, NIH, NIAID, Rockville, MD 20852 USA
| | - Dmitry Loukinov
- Laboratory of Immunogenetics, NIH, NIAID, Rockville, MD 20852 USA
| | - Abdelhalim Boukaba
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530 Guangdong China
| | - Andrew Paul Hutchins
- Department of Biology, Southern University of Science and Technology of China, Shenzhen, 518055 Guangdong China
| | | | - Alexander Strunnikov
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530 Guangdong China
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