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Adams M, Vollmers C. Generation and analysis of a mouse multi-tissue genome annotation atlas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578267. [PMID: 38352519 PMCID: PMC10862843 DOI: 10.1101/2024.01.31.578267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Generating an accurate and complete genome annotation for an organism is complex because the cells within each tissue can express a unique set of transcript isoforms from a unique set of genes. A comprehensive genome annotation should contain information on what tissues express what transcript isoforms at what level. This tissue-level isoform information can then inform a wide range of research questions as well as experiment designs. Long-read sequencing technology combined with advanced full-length cDNA library preparation methods has now achieved throughput and accuracy where generating these types of annotations is achievable. Here, we show this by generating a genome annotation of the mouse (Mus musculus). We used the nanopore-based R2C2 long-read sequencing method to generate 64 million highly accurate full length cDNA consensus reads - averaging 5.4 million reads per tissue for a dozen tissues. Using the Mandalorion tool we processed these reads to generate the Tissue-level Atlas of Mouse Isoforms (TAMI - available at https://genome.ucsc.edu/s/vollmers/TAMI) which we believe will be a valuable complement to conventional, manually curated reference genome annotations.
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Affiliation(s)
- Matthew Adams
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Cruz
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2
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Luna-Arias JP, Castro-Muñozledo F. Participation of the TBP-associated factors (TAFs) in cell differentiation. J Cell Physiol 2024; 239:e31167. [PMID: 38126142 DOI: 10.1002/jcp.31167] [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: 09/18/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The understanding of the mechanisms that regulate gene expression to establish differentiation programs and determine cell lineages, is one of the major challenges in Developmental Biology. Besides the participation of tissue-specific transcription factors and epigenetic processes, the role of general transcription factors has been ignored. Only in recent years, there have been scarce studies that address this issue. Here, we review the studies on the biological activity of some TATA-box binding protein (TBP)-associated factors (TAFs) during the proliferation of stem/progenitor cells and their involvement in cell differentiation. Particularly, the accumulated evidence suggests that TAF4, TAF4b, TAF7L, TAF8, TAF9, and TAF10, among others, participate in nervous system development, adipogenesis, myogenesis, and epidermal differentiation; while TAF1, TAF7, TAF15 may be involved in the regulation of stem cell proliferative abilities and cell cycle progression. On the other hand, evidence suggests that TBP variants such as TBPL1 and TBPL2 might be regulating some developmental processes such as germ cell maturation and differentiation, myogenesis, or ventral specification during development. Our analysis shows that it is necessary to study in greater depth the biological function of these factors and its participation in the assembly of specific transcription complexes that contribute to the differential gene expression that gives rise to the great diversity of cell types existing in an organism. The understanding of TAFs' regulation might lead to the development of new therapies for patients which suffer from mutations, alterations, and dysregulation of these essential elements of the transcriptional machinery.
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Affiliation(s)
- Juan Pedro Luna-Arias
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
| | - Federico Castro-Muñozledo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
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Moreno-Irusta A, Dominguez EM, Iqbal K, Zhang X, Wang N, Soares MJ. TAF7L regulates early stages of male germ cell development in the rat. FASEB J 2024; 38:e23376. [PMID: 38112167 PMCID: PMC11246239 DOI: 10.1096/fj.202301716rr] [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: 08/24/2023] [Revised: 11/14/2023] [Accepted: 12/04/2023] [Indexed: 12/20/2023]
Abstract
Male germ cell development is dependent on the orchestrated regulation of gene networks. TATA-box binding protein associated factors (TAFs) facilitate interactions of TATA-binding protein with the TATA element, which is known to coordinate gene transcription during organogenesis. TAF7 like (Taf7l) is situated on the X chromosome and has been implicated in testis development. We examined the biology of TAF7L in testis development using the rat. Taf7l was prominently expressed in preleptotene to leptotene spermatocytes. To study the impact of TAF7L on the testis we generated a global loss-of-function rat model using CRISPR/Cas9 genome editing. Exon 3 of the Taf7l gene was targeted. A founder was generated possessing a 110 bp deletion within the Taf7l locus, which resulted in a frameshift and the premature appearance of a stop codon. The mutation was effectively transmitted through the germline. Deficits in TAF7L did not adversely affect pregnancy or postnatal survival. However, the Taf7l disruption resulted in male infertility due to compromised testis development and failed sperm production. Mutant germ cells suffer meiotic arrest at late zygotene/early pachynema stages, with defects in sex body formation. This testis phenotype was more pronounced than previously described for the subfertile Taf7l null mouse. We conclude that TAF7L is essential for male germ cell development in the rat.
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Affiliation(s)
- Ayelen Moreno-Irusta
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Esteban M. Dominguez
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Khursheed Iqbal
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Xiaoyu Zhang
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Ning Wang
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Michael J. Soares
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, Kansas, USA
- Center for Perinatal Research, Children’s Mercy Research Institute, Children’s Mercy, Kansas City, Missouri, USA
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Moreno-Irusta A, Dominguez EM, Iqbal K, Zhang X, Wang N, Soares MJ. TAF7L REGULATES EARLY STAGES OF MALE GERM CELL DEVELOPMENT. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.08.561408. [PMID: 37873461 PMCID: PMC10592675 DOI: 10.1101/2023.10.08.561408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Male germ cell development is dependent on the orchestrated regulation of gene networks. TATA-box binding protein associated factors (TAFs) facilitate interactions of TATA-binding protein with the TATA element, which is known to coordinate gene transcription during organogenesis. TAF7 like (Taf7l) is situated on the X chromosome and has been implicated in testis development. We examined the biology of TAF7L in testis development using the rat. Taf7l was prominently expressed in preleptotene to leptotene spermatocytes. To study the impact of TAF7L on the testis we generated a global loss-of-function rat model using CRISPR/Cas9 genome editing. Exon 3 of the Taf7l gene was targeted. A founder was generated possessing a 110 bp deletion within the Taf7l locus, which resulted in a frameshift and the premature appearance of a stop codon. The mutation was effectively transmitted through the germline. Deficits in TAF7L did not adversely affect pregnancy or postnatal survival. However, the Taf7l disruption resulted in male infertility due to compromised testis development and failed sperm production. Mutant germ cells suffer meiotic arrest at the zygotene stage, with defects in sex body formation and meiotic sex chromosome inactivation. This testis phenotype was more pronounced than previously described for the subfertile Taf7l null mouse. We conclude that TAF7L is essential for male germ cell development in the rat.
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Affiliation(s)
- Ayelen Moreno-Irusta
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS
| | - Esteban M. Dominguez
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS
| | - Khursheed Iqbal
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS
| | - Xiaoyu Zhang
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS
| | - Ning Wang
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS
| | - Michael J. Soares
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS
- Center for Perinatal Research, Children’s Mercy Research Institute, Children’s Mercy, Kansas City, MO
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Gao J, Wang Y, Liu J, Chen F, Guo Y, Ke H, Wang X, Luo M, Fu S. Genome-wide association study reveals genomic loci of sex differentiation and gonadal development in Plectropomus leopardus. Front Genet 2023; 14:1229242. [PMID: 37645057 PMCID: PMC10461086 DOI: 10.3389/fgene.2023.1229242] [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: 06/12/2023] [Accepted: 07/17/2023] [Indexed: 08/31/2023] Open
Abstract
Introduction: Plectropomus leopardus, a commercially significant marine fish, is primarily found in the Western Pacific regions and along the coast of Southeast Asia. A thorough analysis of the molecular mechanisms involved in sex differentiation is crucial for gaining a comprehensive understanding of gonadal development and improving sex control breeding. However, the relevant fundamental studies of P. leopardus are relatively lacking. Methods: In this study, a genome-wide association study (GWAS) was conducted to investigate the genetic basis mechanism of sex differentiation and gonadal developmental traits in P. leopardus utilizing about 6,850,000 high-quality single-nucleotide polymorphisms (SNPs) derived from 168 individuals (including 126 females and 42 males) by the genome-wide efficient mixed-model association (GEMMA) algorithm. Results: The results of these single-trait GWASs showed that 46 SNP loci (-log10 p > 7) significantly associated with sex differentiation, and gonadal development traits were distributed in multiple different chromosomes, which suggested the analyzed traits were all complex traits under multi-locus control. A total of 1,838 potential candidate genes were obtained by considering a less-stringent threshold (-log10 p > 6) and ±100 kb regions surrounding the significant genomic loci. Moreover, 31 candidate genes were identified through a comprehensive analysis of significant GWAS peaks, gene ontology (GO) annotations, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, including taf7, ddx6, apoeb, sgk1, a2m, usf1, hsd3b7, dll4, xbp1, tet3, esr1, and gli3. These trait-associated genes have been shown to be involved in germline development, male sex differentiation, gonad morphogenesis, hormone receptor binding, oocyte development, male gonad development, steroidogenesis, estrogen-synthetic pathway, etc. Discussion: In the present study, multiple genomic loci of P. leopardus associated with sex differentiation and gonadal development traits were identified for the first time by using GWAS, providing a valuable resource for further research on the molecular genetic mechanism and sex control in P. leopardus. Our results also can contribute to understanding the genetic basis of the sex differentiation mechanism and gonadal development process in grouper fish.
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Affiliation(s)
- Jin Gao
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Hainan Tropical Ocean University Yazhou Bay Innovation Institute, Sanya, China
| | - Yongbo Wang
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Hainan Tropical Ocean University Yazhou Bay Innovation Institute, Sanya, China
| | - Jinye Liu
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Hainan Provincial Engineering Research Center for Tropical Sea-Farming, Haikou, China
| | - Fuxiao Chen
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Hainan Tropical Ocean University Yazhou Bay Innovation Institute, Sanya, China
| | - Yilan Guo
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Hongji Ke
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Xulei Wang
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Ming Luo
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Shuyuan Fu
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Hainan Tropical Ocean University Yazhou Bay Innovation Institute, Sanya, China
- Hainan Provincial Engineering Research Center for Tropical Sea-Farming, Haikou, China
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Gene Expression and DNA Methylation in Human Papillomavirus Positive and Negative Head and Neck Squamous Cell Carcinomas. Int J Mol Sci 2022; 23:ijms231810967. [PMID: 36142875 PMCID: PMC9504918 DOI: 10.3390/ijms231810967] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
High-risk human papillomaviruses (HPV) are important agents, responsible for a large percentage of the 745,000 cases of head and neck squamous cell carcinomas (HNSCC), which were identified worldwide in 2020. In addition to being virally induced, tobacco and heavy alcohol consumption are believed to cause DNA damage contributing to the high number of HNSCC cases. Gene expression and DNA methylation differ between HNSCC based on HPV status. We used publicly available gene expression and DNA methylation profiles from the Cancer Genome Atlas and compared HPV positive and HPV negative HNSCC groups. We used differential gene expression analysis, differential methylation analysis, and a combination of these two analyses to identify the differences. Differential expression analysis identified 1854 differentially expressed genes, including PCNA, TNFRSF14, TRAF1, TRAF2, BCL2, and BIRC3. SYCP2 was identified as one of the top deregulated genes in the differential methylation analysis and in the combined differential expression and methylation analyses. Additionally, pathway and ontology analyses identified the extracellular matrix and receptor interaction pathway as the most altered between HPV negative and HPV positive HNSCC groups. Combining gene expression and DNA methylation can help in elucidating the genes involved in HPV positive HNSCC tumorigenesis, such as SYCP2 and TAF7L.
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Ambulkar PS, Waghmare JE, Verma Shivkumar P, Chaudhari AR, Gangane NM, Narang P, Pal AK. The association of testis-specific hTAF7L gene variants with idiopathic azoospermic and severe oligozoospermic male infertility. Andrologia 2022; 54:e14581. [PMID: 36068176 DOI: 10.1111/and.14581] [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: 01/13/2022] [Revised: 05/27/2022] [Accepted: 08/25/2022] [Indexed: 12/01/2022] Open
Abstract
Spermatogenesis is regulated by complex tissue specific gene expression in the testis to achieve normal male fertility. X-chromosome specific TATA binding protein (TBP)-associated factor 7L (hTAF7L) is one of the transcriptional regulator genes considered essential for spermatogenesis. The aim of this study was to evaluate the role of variants/mutations in the testis-specific hTAF7L gene in non-obstructive azoospermia and severe oligozoospermia male infertility. We studied 156 idiopathic non-obstructive azoospermic, severe oligozoospermic infertile males and 50 fertile proven controls. Infertile males and control subjects were genotyped for variants of the hTAF7L gene using polymerase chain reaction and a direct Sanger sequencing approach. The odds ratio evaluated the association of hTAF7L gene variants with idiopathic male infertility. The variants found in the hTAF7L gene were subjected to an in-silico analysis study. In infertile study subjects, we observed 11 single base pair nucleotide changes at various exons and three frameshift variants at exon 10 in the hTAF7L gene. We also found more than one variant in some non-obstructive azoospermia and severe oligozoospermia infertile males along with control subjects. All these variants changed the amino acid sequences in the hTAF7L gene. However, similar changes were also seen in fertile subjects, and the differences were not statistically significant. In-silico tools also predicted that the variants were likely to be benign. The variants in cDNA of the hTAF7L gene were typical SNPs. It is found that the hTAF7L gene is highly polymorphic and these missense variants are not directly associated with male infertility. However, we feel that more studies are needed to elucidate the role of multiple variants of the hTAF7L gene in the process of normal spermatogenesis.
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Affiliation(s)
- Prafulla S Ambulkar
- Centre for Genetics & Genomics, Department of Anatomy, Mahatma Gandhi Institute of Medical Sciences, Wardha, Maharashtra, India
| | - Jwalant E Waghmare
- Centre for Genetics & Genomics, Department of Anatomy, Mahatma Gandhi Institute of Medical Sciences, Wardha, Maharashtra, India
| | - Poonam Verma Shivkumar
- Department of Obstetrics & Gynaecology, Mahatma Gandhi Institute of Medical Sciences, Wardha, Maharashtra, India
| | - Ajay R Chaudhari
- Department of Physiology, Mahatma Gandhi Institute of Medical Sciences, Wardha, Maharashtra, India
| | - Nitin M Gangane
- Centre for Genetics & Genomics, Department of Anatomy, Mahatma Gandhi Institute of Medical Sciences, Wardha, Maharashtra, India.,Department of Pathology, Mahatma Gandhi Institute of Medical Sciences, Wardha, Maharashtra, India
| | - Pratibha Narang
- Centre for Genetics & Genomics, Department of Anatomy, Mahatma Gandhi Institute of Medical Sciences, Wardha, Maharashtra, India.,Department of Microbiology, Mahatma Gandhi Institute of Medical Sciences, Wardha, Maharashtra, India
| | - Asoke K Pal
- Centre for Genetics & Genomics, Department of Anatomy, Mahatma Gandhi Institute of Medical Sciences, Wardha, Maharashtra, India
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Ling L, Li F, Yang P, Oates RD, Silber S, Kurischko C, Luca FC, Leu NA, Zhang J, Yue Q, Skaletsky H, Brown LG, Rozen S, Page DC, Wang PJ, Zheng K. Genetic characterization of a missense mutation in the X-linked TAF7L gene identified in an oligozoospermic man. Biol Reprod 2022; 107:157-167. [PMID: 35554494 PMCID: PMC9310510 DOI: 10.1093/biolre/ioac093] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 04/18/2022] [Accepted: 05/02/2022] [Indexed: 11/14/2022] Open
Abstract
While hundreds of knockout mice show infertility as a major phenotype, causative genic mutations of male infertility in humans remain rather limited. Here we report the identification of a missense mutation (D136G) in the X-linked TAF7L gene as a potential cause of oligozoospermia in men. The human aspartate (D136) is evolutionally conserved across species, and its change to glycine (G) is predicted to be detrimental. Genetic complementation experiments in budding yeast demonstrate that the conserved aspartate or its analogous asparagine (N) residue in yeast TAF7 is essential for cell viability and thus its mutation to glycine is lethal. Although the corresponding D144G substitution in the mouse Taf7l gene does not affect male fertility, RNA-seq analyses reveal alterations in transcriptome profiles in the Taf7l (D144G) mutant testes. These results support this TAF7L mutation as a risk factor for oligozoospermia in humans.
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Affiliation(s)
- Li Ling
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Fangfang Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Pinglan Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Robert D Oates
- Department of Urology, Boston University Medical Center, Boston, MA 02118, USA
| | - Sherman Silber
- Infertility Center of St. Louis, St. Luke's Hospital, St. Louis, MO 63017, USA
| | - Cornelia Kurischko
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Francis C Luca
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - N Adrian Leu
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Jinwen Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Qiuling Yue
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Helen Skaletsky
- Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 455 Main Street, Cambridge, MA 02142, USA
| | - Laura G Brown
- Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 455 Main Street, Cambridge, MA 02142, USA
| | - Steve Rozen
- Duke-NUS Graduate Medical School Singapore, 8 College Road, 169857, Singapore
| | - David C Page
- Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 455 Main Street, Cambridge, MA 02142, USA
| | - P Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
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Gura MA, Relovská S, Abt KM, Seymour KA, Wu T, Kaya H, Turner JMA, Fazzio TG, Freiman RN. TAF4b transcription networks regulating early oocyte differentiation. Development 2022; 149:dev200074. [PMID: 35043944 PMCID: PMC8918801 DOI: 10.1242/dev.200074] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/04/2022] [Indexed: 01/11/2023]
Abstract
Establishment of a healthy ovarian reserve is contingent upon numerous regulatory pathways during embryogenesis. Previously, mice lacking TBP-associated factor 4b (Taf4b) were shown to exhibit a diminished ovarian reserve. However, potential oocyte-intrinsic functions of TAF4b have not been examined. Here, we use a combination of gene expression profiling and chromatin mapping to characterize TAF4b-dependent gene regulatory networks in mouse oocytes. We find that Taf4b-deficient oocytes display inappropriate expression of meiotic, chromatin modification/organization, and X-linked genes. Furthermore, dysregulated genes in Taf4b-deficient oocytes exhibit an unexpected amount of overlap with dysregulated genes in oocytes from XO female mice, a mouse model of Turner Syndrome. Using Cleavage Under Targets and Release Using Nuclease (CUT&RUN), we observed TAF4b enrichment at genes involved in chromatin remodeling and DNA repair, some of which are differentially expressed in Taf4b-deficient oocytes. Interestingly, TAF4b target genes were enriched for Sp/Klf family and NFY target motifs rather than TATA-box motifs, suggesting an alternative mode of promoter interaction. Together, our data connect several gene regulatory nodes that contribute to the precise development of the mammalian ovarian reserve.
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Affiliation(s)
- Megan A. Gura
- MCB Graduate Program, Brown University, 70 Ship Street, Box G-E4, Providence, RI 02903, USA
| | - Soňa Relovská
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 70 Ship Street, Box G-E4, Providence, RI 02903, USA
| | - Kimberly M. Abt
- MCB Graduate Program, Brown University, 70 Ship Street, Box G-E4, Providence, RI 02903, USA
| | - Kimberly A. Seymour
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 70 Ship Street, Box G-E4, Providence, RI 02903, USA
| | - Tong Wu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Haskan Kaya
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - James M. A. Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Thomas G. Fazzio
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Richard N. Freiman
- MCB Graduate Program, Brown University, 70 Ship Street, Box G-E4, Providence, RI 02903, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 70 Ship Street, Box G-E4, Providence, RI 02903, USA
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10
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Bai H, Sha Y, Tan Y, Li P, Zhang Y, Xu J, Xu S, Ji Z, Wang X, Chen W, Zhang J, Yao C, Li Z, Zhi E. Deleterious variants in TAF7L cause human oligoasthenoteratozoospermia and its impairing histone to protamine exchange inducing reduced in vitro fertilization. Front Endocrinol (Lausanne) 2022; 13:1099270. [PMID: 36714566 PMCID: PMC9874084 DOI: 10.3389/fendo.2022.1099270] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/05/2022] [Indexed: 01/12/2023] Open
Abstract
INTRODUCTION Oligoasthenoteratozoospermia (OAT) is a major cause of infertility in males. Only a few pathogenic genes of OAT have been clearly identified till now. A large number of OAT-affected cases remain largely unknown. METHODS Here, Whole-exome sequencing (WES) in 725 idiopathic OAT patients was performed. Ejaculated spermatozoa by OAT patients were microinjected into mouse oocytes to estimate fertilization potential. Diff-quick staining and transmission electron microscopy were performed to evaluate sperm morphology and ultrastructure. The protein expression level and localization In vitro were detected by Western Blotting and Immunocytochemistry. RESULTS We identified four X-linked hemizygous deleterious variants of TAF7L-namely, c.1301_1302del;(p.V434Afs*5), c.699G>T;(p.R233S), c.508delA; (p. T170fs), c.719dupA;(p.K240fs) -in five probands. Intracytoplasmic sperm injection (ICSI) were carried out in M1, M2-1and M3 patient's wife. However only M1 patient's wife became pregnant after embryo transfer. In vitro study demonstrated significantly reduced fertilization ability in patient with TAF7L mutation. The TAF7L mutation let to abnormal sperm head and impaired histone-to protamine exchange. Variant 719dupA (p. K240fs) resulted in producing a truncated TAF7L protein and localized massively within the nucleus. In addition, TAF7L expression were not able to be detected due to variants c.1301_1302del (p. V434Afs*5) and c.508delA (p. T170fs) In vitro. CONCLUSION Our findings support that TAF7L is one of pathogenic genes of OAT and deleterious mutations in TAF7L may cause impaired histone-to-protamine affected the chromatin compaction of sperm head.
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Affiliation(s)
- Haowei Bai
- Department of Andrology, Center for Men’s Health, Department of ART, Institute of Urologic Medical Center, Shanghai General Hospital, Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanwei Sha
- Department of Andrology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yueqiu Tan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Peng Li
- Department of Andrology, Center for Men’s Health, Department of ART, Institute of Urologic Medical Center, Shanghai General Hospital, Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuxiang Zhang
- Department of Andrology, Center for Men’s Health, Department of ART, Institute of Urologic Medical Center, Shanghai General Hospital, Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junwei Xu
- Department of Andrology, Center for Men’s Health, Department of ART, Institute of Urologic Medical Center, Shanghai General Hospital, Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuai Xu
- Department of Andrology, Center for Men’s Health, Department of ART, Institute of Urologic Medical Center, Shanghai General Hospital, Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyong Ji
- Department of Andrology, Center for Men’s Health, Department of ART, Institute of Urologic Medical Center, Shanghai General Hospital, Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaobo Wang
- Department of Andrology, Center for Men’s Health, Department of ART, Institute of Urologic Medical Center, Shanghai General Hospital, Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Chen
- Department of Andrology, Center for Men’s Health, Department of ART, Institute of Urologic Medical Center, Shanghai General Hospital, Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianxiong Zhang
- Department of Andrology, Center for Men’s Health, Department of ART, Institute of Urologic Medical Center, Shanghai General Hospital, Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chencheng Yao
- Department of Andrology, Center for Men’s Health, Department of ART, Institute of Urologic Medical Center, Shanghai General Hospital, Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Chencheng Yao, ; Zheng Li, ; Erlei Zhi,
| | - Zheng Li
- Department of Andrology, Center for Men’s Health, Department of ART, Institute of Urologic Medical Center, Shanghai General Hospital, Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Chencheng Yao, ; Zheng Li, ; Erlei Zhi,
| | - Erlei Zhi
- Department of Andrology, Center for Men’s Health, Department of ART, Institute of Urologic Medical Center, Shanghai General Hospital, Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Chencheng Yao, ; Zheng Li, ; Erlei Zhi,
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11
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Wu SC, Münger K. Role and Clinical Utility of Cancer/Testis Antigens in Head and Neck Squamous Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13225690. [PMID: 34830845 PMCID: PMC8616139 DOI: 10.3390/cancers13225690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/03/2021] [Accepted: 11/11/2021] [Indexed: 12/15/2022] Open
Abstract
Cancer/testis (CT) antigens exhibit selective expression predominantly in immunoprivileged tissues in non-pathological contexts but are aberrantly expressed in diverse cancers. Due to their expression pattern, they have historically been attractive targets for immunotherapies. A growing number of studies implicate CT antigens in almost all hallmarks of cancer, suggesting that they may act as cancer drivers. CT antigens are expressed in head and neck squamous cell carcinomas. However, their role in the pathogenesis of these cancers remains poorly studied. Given that CT antigens hold intriguing potential as therapeutic targets and as biomarkers for prognosis and that they can provide novel insights into oncogenic mechanisms, their further study in the context of head and squamous cell carcinoma is warranted.
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Affiliation(s)
- Sharon Changshan Wu
- Molecular Microbiology Program, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA;
| | - Karl Münger
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
- Correspondence:
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12
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Novel variations in spermatogenic transcription regulators RFX2 and TAF7 increase risk of azoospermia. J Assist Reprod Genet 2021; 38:3195-3212. [PMID: 34762273 DOI: 10.1007/s10815-021-02352-5] [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: 08/23/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022] Open
Abstract
PURPOSE Genetic etiology of idiopathic male infertility is enigmatic owing to involvement of multiple gene regulatory networks in spermatogenesis process. Any change in optimal function of the transcription factors involved in this process owing to polymorphisms/mutations may increase the risk of infertility. We investigated polymorphisms/mutations of spermatogenic transcription regulators TAF7 and RFX2 and analysed their association with incidence of azoospermia among the men from West Bengal, India. METHODS Genotyping was carried by Sanger's dideoxy sequencing of 130 azoospermic men who were detected negative in Y chromosome microdeletion screening and 140 healthy controls. Association study was done by suitable statistical methods. In silico analysis was performed to infer the intuitive damaging effects of detected variants at transcripts and protein level. RESULTS We found significant association of TAF7 C16T (MW827584 G > A), RFX2 562delT (MZ560629delA), rs11547633 A > C, rs17606721 A > G, MW827583 C > T, and MZ379836 C > T variants with the incidence of azoospermia. In silico analysis predicted that the variants either alter the natural splice junctions of the transcript or cause probable damage in the structure of proteins of respective genes. CONCLUSION Polymorphisms/mutations of TAF7 and RFX2 genes increase risk of male infertility in Bengali population. The novel variants may be used as markers for male infertility screening in ART practise.
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13
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Liao J, Suen HC, Luk ACS, Yang L, Lee AWT, Qi H, Lee TL. Transcriptomic and epigenomic profiling of young and aged spermatogonial stem cells reveals molecular targets regulating differentiation. PLoS Genet 2021; 17:e1009369. [PMID: 34237055 PMCID: PMC8291634 DOI: 10.1371/journal.pgen.1009369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/20/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
Spermatogonial stem cells (SSC), the foundation of spermatogenesis and male fertility, possess lifelong self-renewal activity. Aging leads to the decline in stem cell function and increased risk of paternal age-related genetic diseases. In the present study, we performed a comparative genomic analysis of mouse SSC-enriched undifferentiated spermatogonia (Oct4-GFP+/KIT-) and differentiating progenitors (Oct4-GFP+/KIT+) isolated from young and aged testes. Our transcriptome data revealed enormous complexity of expressed coding and non-coding RNAs and alternative splicing regulation during SSC differentiation. Further comparison between young and aged undifferentiated spermatogonia suggested these differentiation programs were affected by aging. We identified aberrant expression of genes associated with meiosis and TGF-β signaling, alteration in alternative splicing regulation and differential expression of specific lncRNAs such as Fendrr. Epigenetic profiling revealed reduced H3K27me3 deposition at numerous pro-differentiation genes during SSC differentiation as well as aberrant H3K27me3 distribution at genes in Wnt and TGF-β signaling upon aging. Finally, aged undifferentiated spermatogonia exhibited gene body hypomethylation, which is accompanied by an elevated 5hmC level. We believe this in-depth molecular analysis will serve as a reference for future analysis of SSC aging.
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Affiliation(s)
- Jinyue Liao
- Developmental and Regenerative Biology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hoi Ching Suen
- Developmental and Regenerative Biology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Alfred Chun Shui Luk
- Developmental and Regenerative Biology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Lele Yang
- Guangzhou Regenerative Medicine and Health Bioland Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Annie Wing Tung Lee
- Developmental and Regenerative Biology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Huayu Qi
- Guangzhou Regenerative Medicine and Health Bioland Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Tin-Lap Lee
- Developmental and Regenerative Biology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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14
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Li JY, Liu YF, Xu HY, Zhang JY, Lv PP, Liu ME, Ying YY, Qian YQ, Li K, Li C, Huang Y, Xu GF, Ding GL, Mao YC, Xu CM, Liu XM, Sheng JZ, Zhang D, Huang HF. Basonuclin 1 deficiency causes testicular premature aging: BNC1 cooperates with TAF7L to regulate spermatogenesis. J Mol Cell Biol 2021; 12:71-83. [PMID: 31065688 PMCID: PMC7052986 DOI: 10.1093/jmcb/mjz035] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/19/2019] [Accepted: 03/21/2019] [Indexed: 12/19/2022] Open
Abstract
Basonuclin (BNC1) is expressed primarily in proliferative keratinocytes and gametogenic cells. However, its roles in spermatogenesis and testicular aging were not clear. Previously we discovered a heterozygous BNC1 truncation mutation in a premature ovarian insufficiency pedigree. In this study, we found that male mice carrying the truncation mutation exhibited progressively fertility loss and testicular premature aging. Genome-wide expression profiling and direct binding studies (by chromatin immunoprecipitation sequencing) with BNC1 in mouse testis identified several spermatogenesis-specific gene promoters targeted by BNC1 including kelch-like family member 10 (Klhl10), testis expressed 14 (Tex14), and spermatogenesis and centriole associated 1 (Spatc1). Moreover, biochemical analysis showed that BNC1 was associated with TATA-box binding protein-associated factor 7 like (TAF7L), a germ cell-specific paralogue of the transcription factor IID subunit TAF7, both in vitro and in testis, suggesting that BNC1 might directly cooperate with TAF7L to regulate spermatogenesis. The truncation mutation disabled nuclear translocation of the BNC1/TAF7L complex, thus, disturbing expression of related genes and leading to testicular premature aging. Similarly, expressions of BNC1, TAF7L, Y-box-binding protein 2 (YBX2), outer dense fiber of sperm tails 1 (ODF1), and glyceraldehyde-3-phosphate dehydrogenase, spermatogenic (GAPDHS) were significantly decreased in the testis of men with non-obstructive azoospermia. The present study adds to the understanding of the physiology of male reproductive aging and the mechanism of spermatogenic failure in infertile men.
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Affiliation(s)
- Jing-Yi Li
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Yi-Feng Liu
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Hai-Yan Xu
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Jun-Yu Zhang
- International Peace Maternal and Child Health Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Ping-Ping Lv
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Miao-E Liu
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Yan-Yun Ying
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Ye-Qing Qian
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Kun Li
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Cheng Li
- International Peace Maternal and Child Health Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yun Huang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Gu-Feng Xu
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Guo-Lian Ding
- International Peace Maternal and Child Health Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yu-Chan Mao
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Chen-Ming Xu
- International Peace Maternal and Child Health Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xin-Mei Liu
- International Peace Maternal and Child Health Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jian-Zhong Sheng
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China.,Department of Pathology & Pathophysiology, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - He-Feng Huang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China.,International Peace Maternal and Child Health Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
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15
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Ge W, Wang JJ, Zhang RQ, Tan SJ, Zhang FL, Liu WX, Li L, Sun XF, Cheng SF, Dyce PW, De Felici M, Shen W. Dissecting the initiation of female meiosis in the mouse at single-cell resolution. Cell Mol Life Sci 2021; 78:695-713. [PMID: 32367190 PMCID: PMC11072979 DOI: 10.1007/s00018-020-03533-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/22/2020] [Accepted: 04/17/2020] [Indexed: 01/22/2023]
Abstract
Meiosis is one of the most finely orchestrated events during gametogenesis with distinct developmental patterns in males and females. However, the molecular mechanisms involved in this process remain not well known. Here, we report detailed transcriptome analyses of cell populations present in the mouse female gonadal ridges (E11.5) and the embryonic ovaries from E12.5 to E14.5 using single-cell RNA sequencing (scRNA seq). These periods correspond with the initiation and progression of meiosis throughout the first stage of prophase I. We identified 13 transcriptionally distinct cell populations and 7 transcriptionally distinct germ cell subclusters that correspond to mitotic (3 clusters) and meiotic (4 clusters) germ cells. By analysing cluster-specific gene expression profiles, we found four cell clusters correspond to different cell stages en route to meiosis and characterized their detailed transcriptome dynamics. Our scRNA seq analysis here represents a new important resource for deciphering the molecular pathways driving female meiosis initiation.
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Affiliation(s)
- Wei Ge
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jun-Jie Wang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Rui-Qian Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shao-Jing Tan
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Fa-Li Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wen-Xiang Liu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lan Li
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiao-Feng Sun
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shun-Feng Cheng
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Paul W Dyce
- Department of Animal Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Massimo De Felici
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Wei Shen
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China.
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16
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Nakamura S, Hira S, Kojima M, Kondo A, Mukai M. Expression of the core promoter factors TATA box binding protein and TATA box binding protein-related factor 2 in Drosophila germ cells and their distinct functions in germline development. Dev Growth Differ 2020; 62:540-553. [PMID: 33219538 DOI: 10.1111/dgd.12701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 10/15/2020] [Accepted: 10/22/2020] [Indexed: 11/30/2022]
Abstract
In Drosophila, the expression of germline genes is initiated in primordial germ cells (PGCs) and is known to be associated with germline establishment. However, the transcriptional regulation of germline genes remains elusive. Previously, we found that the BTB/POZ-Zn-finger protein, Mamo, is necessary for the expression of the germline gene, vasa, in PGCs. Moreover, truncated Mamo lacking the BTB/POZ domain (MamoAF) is a potent vasa activator. In this study, we investigated the genetic interaction between MamoAF and specific transcriptional regulators to gain insight into the transcriptional regulation of germline development. We identified a general transcription factor, TATA box binding protein (TBP)-associated factor 3 (TAF3/BIP2), and a member of the TBP-like proteins, TBP-related factor 2 (TRF2), as new genetic modifiers of MamoAF. In contrast to TRF2, TBP was found to show no genetic interaction with MamoAF, suggesting that Trf2 has a selective function. Therefore, we focused on Trf2 expression and investigated its function in germ cells. We found that Trf2 mRNA, rather than Tbp mRNA, was preferentially expressed in PGCs during embryogenesis. Depletion of TRF2 in PGCs resulted in decreased mRNA expression of vasa. RNA interference-mediated knockdown showed that, while Trf2 is required for maintenance of germ cells, Tbp is needed for their differentiation during oogenesis. Therefore, these results suggest that Trf2 and Tbp expression is differentially regulated in germ cells and that these factors have distinct functions in Drosophila germline development.
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Affiliation(s)
- Shoichi Nakamura
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan.,Graduate School of Natural Science, Konan University, Kobe, Japan.,Institute for Integrative Neurosciences, Hyogo, Japan.,Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Hyogo, Japan
| | - Seiji Hira
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan.,Graduate School of Natural Science, Konan University, Kobe, Japan.,Institute for Integrative Neurosciences, Hyogo, Japan
| | - Makoto Kojima
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan
| | - Akane Kondo
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan.,Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Masanori Mukai
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan.,Graduate School of Natural Science, Konan University, Kobe, Japan.,Institute for Integrative Neurosciences, Hyogo, Japan
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17
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Gustafson EA, Seymour KA, Sigrist K, Rooij DGDE, Freiman RN. ZFP628 Is a TAF4b-Interacting Transcription Factor Required for Mouse Spermiogenesis. Mol Cell Biol 2020; 40:e00228-19. [PMID: 31932482 PMCID: PMC7076252 DOI: 10.1128/mcb.00228-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/11/2019] [Accepted: 12/20/2019] [Indexed: 12/28/2022] Open
Abstract
TAF4b is a subunit of the TFIID complex that is highly expressed in the ovary and testis and required for mouse fertility. TAF4b-deficient male mice undergo a complex series of developmental defects that result in the inability to maintain long-term spermatogenesis. To decipher the transcriptional mechanisms upon which TAF4b functions in spermatogenesis, we used two-hybrid screening to identify a novel TAF4b-interacting transcriptional cofactor, ZFP628. Deletion analysis of both proteins reveals discrete and novel domains of ZFP628 and TAF4b protein that function to bridge their direct interaction in vitro Moreover, coimmunoprecipitation of ZFP628 and TAF4b proteins in testis-derived protein extracts supports their endogenous association. Using CRISPR-Cas9, we disrupted the expression of ZFP628 in the mouse and uncovered a postmeiotic germ cell arrest at the round spermatid stage in the seminiferous tubules of the testis in ZFP628-deficient mice that results in male infertility. Coincident with round spermatid arrest, we find reduced mRNA expression of transition protein (Tnp1 and Tnp2) and protamine (Prm1 and Prm2) genes, which are critical for the specialized maturation of haploid male germ cells called spermiogenesis. These data delineate a novel association of two transcription factors, TAF4b and ZFP628, and identify ZFP628 as a novel transcriptional regulator of stage-specific spermiogenesis.
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Affiliation(s)
- Eric A Gustafson
- Brown University, Department of Molecular and Cell Biology and Biochemistry, Providence, Rhode Island, USA
| | - Kimberly A Seymour
- Brown University, Department of Molecular and Cell Biology and Biochemistry, Providence, Rhode Island, USA
| | - Kirsten Sigrist
- Brown University, Department of Molecular and Cell Biology and Biochemistry, Providence, Rhode Island, USA
| | - Dirk G D E Rooij
- Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Richard N Freiman
- Brown University, Department of Molecular and Cell Biology and Biochemistry, Providence, Rhode Island, USA
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18
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Gura MA, Mikedis MM, Seymour KA, de Rooij DG, Page DC, Freiman RN. Dynamic and regulated TAF gene expression during mouse embryonic germ cell development. PLoS Genet 2020; 16:e1008515. [PMID: 31914128 PMCID: PMC7010400 DOI: 10.1371/journal.pgen.1008515] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 02/10/2020] [Accepted: 11/11/2019] [Indexed: 12/02/2022] Open
Abstract
Germ cells undergo many developmental transitions before ultimately becoming either eggs or sperm, and during embryonic development these transitions include epigenetic reprogramming, quiescence, and meiosis. To begin understanding the transcriptional regulation underlying these complex processes, we examined the spatial and temporal expression of TAF4b, a variant TFIID subunit required for fertility, during embryonic germ cell development. By analyzing published datasets and using our own experimental system to validate these expression studies, we determined that both Taf4b mRNA and protein are highly germ cell-enriched and that Taf4b mRNA levels dramatically increase from embryonic day 12.5–18.5. Surprisingly, additional mRNAs encoding other TFIID subunits are coordinately upregulated through this time course, including Taf7l and Taf9b. The expression of several of these germ cell-enriched TFIID genes is dependent upon Dazl and/or Stra8, known regulators of germ cell development and meiosis. Together, these data suggest that germ cells employ a highly specialized and dynamic form of TFIID to drive the transcriptional programs that underlie mammalian germ cell development. Assisted reproductive therapy and fertility preservation are increasingly used to improve human reproduction across the world, yet there are still many unanswered questions regarding what factors govern the development of eggs and sperm and how these factors work together. We previously identified a subunit of the general transcription factor TFIID, TAF4b, that is essential for fertility. However, many basic characteristics of how Taf4b and its associated TFIID family members contribute to the formation of healthy sperm and eggs in mice and humans remain unknown. In this study, we find that mouse Taf4b and several closely related TFIID subunits become highly abundant during mouse embryonic gonad development, specifically in the cells that ultimately become eggs and sperm. Here, we analyzed data from public repositories and isolated these developing cells to examine their gene expression patterns throughout embryonic development. Together these data suggest that the dynamic expression of Taf4b and other TFIID family members are dependent on the well-established reproductive cell regulators Dazl and Stra8. This understanding of Taf4b gene expression and regulation in mouse reproductive cell development is likely conserved during development of human cells and offers novel insights into the interconnectedness of the factors that govern the formation of healthy eggs and sperm.
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Affiliation(s)
- Megan A. Gura
- Brown University, MCB Graduate Program and Department of Molecular Biology, Cell Biology and Biochemistry, Providence, RI, United States of America
| | | | - Kimberly A. Seymour
- Brown University, MCB Graduate Program and Department of Molecular Biology, Cell Biology and Biochemistry, Providence, RI, United States of America
| | | | - David C. Page
- Whitehead Institute, Cambridge, MA, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, United States of America
| | - Richard N. Freiman
- Brown University, MCB Graduate Program and Department of Molecular Biology, Cell Biology and Biochemistry, Providence, RI, United States of America
- * E-mail:
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19
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Pandey A, Yadav SK, Vishvkarma R, Singh B, Maikhuri JP, Rajender S, Gupta G. The dynamics of gene expression during and post meiosis sets the sperm agenda. Mol Reprod Dev 2019; 86:1921-1939. [DOI: 10.1002/mrd.23278] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 09/16/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Aastha Pandey
- Division of EndocrinologyCSIR‐Central Drug Research Institute Lucknow India
| | | | - Rahul Vishvkarma
- Division of EndocrinologyCSIR‐Central Drug Research Institute Lucknow India
| | - Bineta Singh
- Division of EndocrinologyCSIR‐Central Drug Research Institute Lucknow India
| | | | - Singh Rajender
- Division of EndocrinologyCSIR‐Central Drug Research Institute Lucknow India
| | - Gopal Gupta
- Division of EndocrinologyCSIR‐Central Drug Research Institute Lucknow India
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20
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The RNA Polymerase II Core Promoter in Drosophila. Genetics 2019; 212:13-24. [PMID: 31053615 DOI: 10.1534/genetics.119.302021] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 03/05/2019] [Indexed: 11/18/2022] Open
Abstract
Transcription by RNA polymerase II initiates at the core promoter, which is sometimes referred to as the "gateway to transcription." Here, we describe the properties of the RNA polymerase II core promoter in Drosophila The core promoter is at a strategic position in the expression of genes, as it is the site of convergence of the signals that lead to transcriptional activation. Importantly, core promoters are diverse in terms of their structure and function. They are composed of various combinations of sequence motifs such as the TATA box, initiator (Inr), and downstream core promoter element (DPE). Different types of core promoters are transcribed via distinct mechanisms. Moreover, some transcriptional enhancers exhibit specificity for particular types of core promoters. These findings indicate that the core promoter is a central component of the transcriptional apparatus that regulates gene expression.
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21
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Antonova SV, Boeren J, Timmers HTM, Snel B. Epigenetics and transcription regulation during eukaryotic diversification: the saga of TFIID. Genes Dev 2019; 33:888-902. [PMID: 31123066 PMCID: PMC6672047 DOI: 10.1101/gad.300475.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this perspective, Antonova et al. determine the evolutionary history of all TFIID subunits and place them in a functional context to understand their diversification. This analysis of TFIID evolution exemplifies how phylogenetic protein interrogation aids in uncovering existing structures, drawing parallels between related complexes and challenges offered by genome expansions that can be countered by exploiting chromatin modifications. The basal transcription factor TFIID is central for RNA polymerase II-dependent transcription. Human TFIID is endowed with chromatin reader and DNA-binding domains and protein interaction surfaces. Fourteen TFIID TATA-binding protein (TBP)-associated factor (TAF) subunits assemble into the holocomplex, which shares subunits with the Spt–Ada–Gcn5–acetyltransferase (SAGA) coactivator. Here, we discuss the structural and functional evolution of TFIID and its divergence from SAGA. Our orthologous tree and domain analyses reveal dynamic gains and losses of epigenetic readers, plant-specific functions of TAF1 and TAF4, the HEAT2-like repeat in TAF2, and, importantly, the pre-LECA origin of TFIID and SAGA. TFIID evolution exemplifies the dynamic plasticity in transcription complexes in the eukaryotic lineage.
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Affiliation(s)
- Simona V Antonova
- Molecular Cancer Research and Regenerative Medicine, University Medical Centre Utrecht, 3584 CT Utrecht, The Netherlands
| | - Jeffrey Boeren
- Department of Developmental Biology, Erasmus MC, 3015 CN Rotterdam, The Netherlands
| | - H T Marc Timmers
- Molecular Cancer Research and Regenerative Medicine, University Medical Centre Utrecht, 3584 CT Utrecht, The Netherlands.,Department of Urology, Medical Centre-University of Freiburg, 79106 Freiburg, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK) Standort Freiburg, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
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22
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Neves A, Eisenman RN. Distinct gene-selective roles for a network of core promoter factors in Drosophila neural stem cell identity. Biol Open 2019; 8:8/4/bio042168. [PMID: 30948355 PMCID: PMC6504003 DOI: 10.1242/bio.042168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The transcriptional mechanisms that allow neural stem cells (NSC) to balance self-renewal with differentiation are not well understood. Employing an in vivo RNAi screen we identify here NSC-TAFs, a subset of nine TATA-binding protein associated factors (TAFs), as NSC identity genes in Drosophila We found that depletion of NSC-TAFs results in decreased NSC clone size, reduced proliferation, defective cell polarity and increased hypersensitivity to cell cycle perturbation, without affecting NSC survival. Integrated gene expression and genomic binding analyses revealed that NSC-TAFs function with both TBP and TRF2, and that NSC-TAF-TBP and NSC-TAF-TRF2 shared target genes encode different subsets of transcription factors and RNA-binding proteins with established or emerging roles in NSC identity and brain development. Taken together, our results demonstrate that core promoter factors are selectively required for NSC identity in vivo by promoting cell cycle progression and NSC cell polarity. Because pathogenic variants in a subset of TAFs have all been linked to human neurological disorders, this work may stimulate and inform future animal models of TAF-linked neurological disorders.
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Affiliation(s)
- Alexandre Neves
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Robert N Eisenman
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
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23
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Kojima ML, de Rooij DG, Page DC. Amplification of a broad transcriptional program by a common factor triggers the meiotic cell cycle in mice. eLife 2019; 8:43738. [PMID: 30810530 PMCID: PMC6392498 DOI: 10.7554/elife.43738] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 02/10/2019] [Indexed: 12/22/2022] Open
Abstract
The germ line provides the cellular link between generations of multicellular organisms, its cells entering the meiotic cell cycle only once each generation. However, the mechanisms governing this initiation of meiosis remain poorly understood. Here, we examined cells undergoing meiotic initiation in mice, and we found that initiation involves the dramatic upregulation of a transcriptional network of thousands of genes whose expression is not limited to meiosis. This broad gene expression program is directly upregulated by STRA8, encoded by a germ cell-specific gene required for meiotic initiation. STRA8 binds its own promoter and those of thousands of other genes, including meiotic prophase genes, factors mediating DNA replication and the G1-S cell-cycle transition, and genes that promote the lengthy prophase unique to meiosis I. We conclude that, in mice, the robust amplification of this extraordinarily broad transcription program by a common factor triggers initiation of meiosis.
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Affiliation(s)
- Mina L Kojima
- Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | | | - David C Page
- Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, United States
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24
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Genetic Factors Affecting Sperm Chromatin Structure. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1166:1-28. [PMID: 31301043 DOI: 10.1007/978-3-030-21664-1_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Spermatozoa genome has unique features that make it a fascinating field of investigation: first, because, with oocyte genome, it can be transmitted generation after generation; second, because of genetic shuffling during meiosis, each spermatozoon is virtually unique in terms of genetic content, with consequences for species evolution; and finally, because its chromatin organization is very different from that of somatic cells or oocytes, as it is not based on nucleosomes but on nucleoprotamines which confer a higher order of packaging. Histone-to-protamine transition involves many actors, such as regulators of spermatid gene expression, components of the nuclear envelop, histone-modifying enzymes and readers, chaperones, histone variants, transition proteins, protamines, and certainly many more to be discovered.In this book chapter, we will present what is currently known about sperm chromatin structure and how it is established during spermiogenesis, with the aim to list the genetic factors that regulate its organization.
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25
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Chen Y, Zheng Y, Gao Y, Lin Z, Yang S, Wang T, Wang Q, Xie N, Hua R, Liu M, Sha J, Griswold MD, Li J, Tang F, Tong MH. Single-cell RNA-seq uncovers dynamic processes and critical regulators in mouse spermatogenesis. Cell Res 2018; 28:879-896. [PMID: 30061742 PMCID: PMC6123400 DOI: 10.1038/s41422-018-0074-y] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 06/25/2018] [Accepted: 07/05/2018] [Indexed: 12/12/2022] Open
Abstract
A systematic interrogation of male germ cells is key to complete understanding of molecular mechanisms governing spermatogenesis and the development of new strategies for infertility therapies and male contraception. Here we develop an approach to purify all types of homogeneous spermatogenic cells by combining transgenic labeling and synchronization of the cycle of the seminiferous epithelium, and subsequent single-cell RNA-sequencing. We reveal extensive and previously uncharacterized dynamic processes and molecular signatures in gene expression, as well as specific patterns of alternative splicing, and novel regulators for specific stages of male germ cell development. Our transcriptomics analyses led us to discover discriminative markers for isolating round spermatids at specific stages, and different embryo developmental potentials between early and late stage spermatids, providing evidence that maturation of round spermatids impacts on embryo development. This work provides valuable insights into mammalian spermatogenesis, and a comprehensive resource for future studies towards the complete elucidation of gametogenesis.
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Affiliation(s)
- Yao Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yuxuan Zheng
- Beijing Advanced Innovation Center for Genomics, Biomedical Institute for Pioneering Investigation via Convergence, College of Life Sciences, Peking University, Beijing, 100871, China.,Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yun Gao
- Beijing Advanced Innovation Center for Genomics, Biomedical Institute for Pioneering Investigation via Convergence, College of Life Sciences, Peking University, Beijing, 100871, China.,Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Zhen Lin
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Suming Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Tongtong Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qiu Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Nannan Xie
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Rong Hua
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Mingxi Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Jiahao Sha
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Michael D Griswold
- School of Molecular Biosciences and the Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Jinsong Li
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, Biomedical Institute for Pioneering Investigation via Convergence, College of Life Sciences, Peking University, Beijing, 100871, China. .,Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China. .,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Ming-Han Tong
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
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26
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Bai S, Fu K, Yin H, Cui Y, Yue Q, Li W, Cheng L, Tan H, Liu X, Guo Y, Zhang Y, Xie J, He W, Wang Y, Feng H, Xin C, Zhang J, Lin M, Shen B, Sun Z, Guo X, Zheng K, Ye L. Sox30 initiates transcription of haploid genes during late meiosis and spermiogenesis in mouse testes. Development 2018; 145:dev.164855. [PMID: 29866902 DOI: 10.1242/dev.164855] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/23/2018] [Indexed: 12/17/2022]
Abstract
Transcription factors of the Sox protein family contain a DNA-binding HMG box and are key regulators of progenitor cell fate. Here, we report that expression of Sox30 is restricted to meiotic spermatocytes and postmeiotic haploids. Sox30 mutant males are sterile owing to spermiogenic arrest at the early round spermatid stage. Specifically, in the absence of Sox30, proacrosomic vesicles fail to form a single acrosomal organelle, and spermatids arrest at step 2-3. Although most Sox30 mutant spermatocytes progress through meiosis, accumulation of diplotene spermatocytes indicates a delayed or impaired transition from meiotic to postmeiotic stages. Transcriptome analysis of isolated stage-specific spermatogenic cells reveals that Sox30 controls a core postmeiotic gene expression program that initiates as early as the late meiotic cell stage. ChIP-seq analysis shows that Sox30 binds to specific DNA sequences in mouse testes, and its genomic occupancy correlates positively with expression of many postmeiotic genes including Tnp1, Hils1, Ccdc54 and Tsks These results define Sox30 as a crucial transcription factor that controls the transition from a late meiotic to a postmeiotic gene expression program and subsequent round spermatid development.
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Affiliation(s)
- Shun Bai
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Kaiqiang Fu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Huiqi Yin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Yiqiang Cui
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Qiuling Yue
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Wenbo Li
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Le Cheng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Huanhuan Tan
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Xiaofei Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Yingwen Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Jie Xie
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Wenxiu He
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Yuanyuan Wang
- Department of Neurobiology, School of Basic Medical Science, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Hua Feng
- Omics Core of Bio-Med Big Data Center, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Changpeng Xin
- Omics Core of Bio-Med Big Data Center, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Jinwen Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Mingyan Lin
- Department of Neurobiology, School of Basic Medical Science, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Zheng Sun
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Lan Ye
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
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27
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Zhang D, Xie D, Lin X, Ma L, Chen J, Zhang D, Wang Y, Duo S, Feng Y, Zheng C, Jiang B, Ning Y, Han C. The transcription factor SOX30 is a key regulator of mouse spermiogenesis. Development 2018; 145:145/11/dev164723. [PMID: 29848638 DOI: 10.1242/dev.164723] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/30/2018] [Indexed: 01/01/2023]
Abstract
The postmeiotic development of male germ cells, also known as spermiogenesis, features the coordinated expression of a large number of spermatid-specific genes. However, only a limited number of key transcription factors have been identified and the underlying regulatory mechanisms remain largely unknown. Here, we report that SOX30, the most-divergent member of the Sry-related high-motility group box (SOX) family of transcription factors, is essential for mouse spermiogenesis. The SOX30 protein was predominantly expressed in spermatids, while its transcription was regulated by retinoic acid and by MYBL1 before and during meiosis. Sox30 knockout mice arrested spermiogenesis at step 3 round spermatids, which underwent apoptosis and abnormal chromocenter formation. We also determined that SOX30 regulated the expression of hundreds of spermatid-specific protein-coding and long non-coding RNA genes. SOX30 bound to the proximal promoter of its own gene and activated its transcription. These results reveal SOX30 as a novel key regulator of spermiogenesis that regulates its own transcription to enforce and activate this meiotic regulatory pathway.
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Affiliation(s)
- Daoqin Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan Xie
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiwen Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Longfei Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Daoqi Zhang
- Department of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yang Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuguang Duo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanmin Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunwei Zheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Binjie Jiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Ning
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunsheng Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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28
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Biswas B, Batista F, Sundaram S, Stanley P. MGAT1 and Complex N-Glycans Regulate ERK Signaling During Spermatogenesis. Sci Rep 2018; 8:2022. [PMID: 29386567 PMCID: PMC5792458 DOI: 10.1038/s41598-018-20465-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 01/19/2018] [Indexed: 12/21/2022] Open
Abstract
Mechanisms that regulate spermatogenesis in mice are important to define as they often apply to fertility in man. We previously showed that conditional deletion of the mouse Mgat1 gene (Mgat1 cKO) in spermatogonia causes a germ-cell autonomous defect leading to infertility. MGAT1 is the N-acetylglucosaminyltransferase (GlcNAcT-I) that initiates the synthesis of complex N-glycans. Mechanistic bases of MGAT1 loss were investigated in germ cells from 22- and 23-day males, before any changes in germ cell morphology were apparent. Gene expression changes induced by deletion of Mgat1 were determined using the Affymetrix gene chip Mouse Mogene 2.0 ST array, and relationships were investigated by bioinformatics including Gene Ontology (GO), Ingenuity Pathway Analysis (IPA), and Gene Set Enrichment Analysis (GSEA). The loss of complex N-glycans promoted the premature up-regulation of genes normally expressed later in spermatogenesis and spermiogenesis, and IPA and GSEA implicated ERK signaling. EGFR and PDGFRA transcripts and ERK1/2 signaling were reduced in 22-day Mgat1 cKO germ cells. Basigin, a germ cell target of MGAT1, activated ERK1/2 in CHO cells, but not in a Lec1 CHO mutant that lacks MGAT1 and complex N-glycans. Thus, MGAT1 is required to regulate ERK1/2 signaling during spermatogenesis, potentially via different mechanisms.
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Affiliation(s)
- Barnali Biswas
- 0000000121791997grid.251993.5Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461 USA
| | - Frank Batista
- 0000000121791997grid.251993.5Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461 USA ,0000 0001 1088 8582grid.7122.6Present Address: Biochemistry and Molecular Biology Department, University of Debrecen, Debrecen, Hungary
| | - Subha Sundaram
- 0000000121791997grid.251993.5Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461 USA
| | - Pamela Stanley
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, 10461, USA.
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29
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Sisakhtnezhad S, Heshmati P. Comparative analysis of single-cell RNA sequencing data from mouse spermatogonial and mesenchymal stem cells to identify differentially expressed genes and transcriptional regulators of germline cells. J Cell Physiol 2018; 233:5231-5242. [PMID: 29194616 DOI: 10.1002/jcp.26303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022]
Abstract
Identifying effective internal factors for regulating germline commitment during development and for maintaining spermatogonial stem cells (SSCs) self-renewal is important to understand the molecular basis of spermatogenesis process, and to develop new protocols for the production of the germline cells from other cell sources. Therefore, this study was designed to investigate single-cell RNA-sequencing data for identification of differentially expressed genes (DEGs) in 12 mouse-derived single SSCs (mSSCs) in compare with 16 mouse-derived single mesenchymal stem cells. We also aimed to find transcriptional regulators of DEGs. Collectively, 1,584 up-regulated DEGs were identified that are associated with 32 biological processes. Moreover, investigation of the expression profiles of genes including in spermatogenesis process revealed that Dazl, Ddx4, Sall4, Fkbp6, Tex15, Tex19.1, Rnf17, Piwil2, Taf7l, Zbtb16, and Cadm1 are presented in the first 30 up-regulated DEGs. We also found 12 basal transcription factors (TFs) and three sequence-specific TFs that control the expression of DEGs. Our findings also indicated that MEIS1, SMC3, TAF1, KAT2A, STAT3, GTF3C2, SIN3A, BDP1, PHC1, and EGR1 are the main central regulators of DEGs in mSSCs. In addition, we collectively detected two significant protein complexes in the protein-protein interactions network for DEGs regulators. Finally, this study introduces the major upstream kinases for the main central regulators of DEGs and the components of core protein complexes. In conclusion, this study provides a molecular blueprint to uncover the molecular mechanisms behind the biology of SSCs and offers a list of candidate factors for cell type conversion approaches and production of germ cells.
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Affiliation(s)
| | - Parvin Heshmati
- Faculty of Dentistry, Department of Endodontics, Kermanshah University of Medical Sciences, Kermanshah, Iran
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30
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31
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Röpke A, Tüttelmann F. MECHANISMS IN ENDOCRINOLOGY: Aberrations of the X chromosome as cause of male infertility. Eur J Endocrinol 2017; 177:R249-R259. [PMID: 28611019 DOI: 10.1530/eje-17-0246] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/22/2017] [Accepted: 06/13/2017] [Indexed: 11/08/2022]
Abstract
Male infertility is most commonly caused by spermatogenetic failure, clinically noted as oligo- or a-zoospermia. Today, in approximately 20% of azoospermic patients, a causal genetic defect can be identified. The most frequent genetic causes of azoospermia (or severe oligozoospermia) are Klinefelter syndrome (47,XXY), structural chromosomal abnormalities and Y-chromosomal microdeletions. Consistent with Ohno's law, the human X chromosome is the most stable of all the chromosomes, but contrary to Ohno's law, the X chromosome is loaded with regions of acquired, rapidly evolving genes, which are of special interest because they are predominantly expressed in the testis. Therefore, it is not surprising that the X chromosome, considered as the female counterpart of the male-associated Y chromosome, may actually play an essential role in male infertility and sperm production. This is supported by the recent description of a significantly increased copy number variation (CNV) burden on both sex chromosomes in infertile men and point mutations in X-chromosomal genes responsible for male infertility. Thus, the X chromosome seems to be frequently affected in infertile male patients. Four principal X-chromosomal aberrations have been identified so far: (1) aneuploidy of the X chromosome as found in Klinefelter syndrome (47,XXY or mosaicism for additional X chromosomes). (2) Translocations involving the X chromosome, e.g. nonsyndromic 46,XX testicular disorders of sex development (XX-male syndrome) or X-autosome translocations. (3) CNVs affecting the X chromosome. (4) Point mutations disrupting X-chromosomal genes. All these are reviewed herein and assessed concerning their importance for the clinical routine diagnostic workup of the infertile male as well as their potential to shape research on spermatogenic failure in the next years.
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32
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Nettersheim D, Jostes S, Schneider S, Schorle H. Elucidating human male germ cell development by studying germ cell cancer. Reproduction 2017; 152:R101-13. [PMID: 27512122 DOI: 10.1530/rep-16-0114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/07/2016] [Indexed: 12/19/2022]
Abstract
Human germ cell development is regulated in a spatio-temporal manner by complex regulatory networks. Here, we summarize results obtained in germ cell tumors and respective cell lines and try to pinpoint similarities to normal germ cell development. This comparison allows speculating about the critical and error-prone mechanisms, which when disturbed, lead to the development of germ cell tumors. Short after specification, primordial germ cells express markers of pluripotency, which, in humans, persists up to the stage of fetal/infantile spermatogonia. Aside from the rare spermatocytic tumors, virtually all seminomas and embryonal carcinomas express markers of pluripotency and show signs of pluripotency or totipotency. Therefore, it appears that proper handling of the pluripotency program appears to be the most critical step in germ cell development in terms of tumor biology. Furthermore, data from mice reveal that germline cells display an epigenetic signature, which is highly similar to pluripotent cells. This signature (poised histone code, DNA hypomethylation) is required for the rapid induction of toti- and pluripotency upon fertilization. We propose that adult spermatogonial cells, when exposed to endocrine disruptors or epigenetic active substances, are prone to reinitiate the pluripotency program, giving rise to a germ cell tumor. The fact that pluripotent cells can be derived from adult murine and human testicular cells further corroborates this idea.
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Affiliation(s)
- Daniel Nettersheim
- Department of Developmental PathologyInstitute of Pathology, University of Bonn Medical School, Bonn, Germany
| | - Sina Jostes
- Department of Developmental PathologyInstitute of Pathology, University of Bonn Medical School, Bonn, Germany
| | - Simon Schneider
- Department of Developmental PathologyInstitute of Pathology, University of Bonn Medical School, Bonn, Germany
| | - Hubert Schorle
- Department of Developmental PathologyInstitute of Pathology, University of Bonn Medical School, Bonn, Germany
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33
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Bardot P, Vincent SD, Fournier M, Hubaud A, Joint M, Tora L, Pourquié O. The TAF10-containing TFIID and SAGA transcriptional complexes are dispensable for early somitogenesis in the mouse embryo. Development 2017; 144:3808-3818. [PMID: 28893950 DOI: 10.1242/dev.146902] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 09/02/2017] [Indexed: 01/09/2023]
Abstract
During development, tightly regulated gene expression programs control cell fate and patterning. A key regulatory step in eukaryotic transcription is the assembly of the pre-initiation complex (PIC) at promoters. PIC assembly has mainly been studied in vitro, and little is known about its composition during development. In vitro data suggest that TFIID is the general transcription factor that nucleates PIC formation at promoters. Here we show that TAF10, a subunit of TFIID and of the transcriptional co-activator SAGA, is required for the assembly of these complexes in the mouse embryo. We performed Taf10 conditional deletions during mesoderm development and show that Taf10 loss in the presomitic mesoderm (PSM) does not prevent cyclic gene transcription or PSM segmental patterning, whereas lateral plate differentiation is profoundly altered. During this period, global mRNA levels are unchanged in the PSM, with only a minor subset of genes dysregulated. Together, our data strongly suggest that the TAF10-containing canonical TFIID and SAGA complexes are dispensable for early paraxial mesoderm development, arguing against the generic role in transcription proposed for these fully assembled holo-complexes.
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Affiliation(s)
- Paul Bardot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France.,Université de Strasbourg, Illkirch 67400, France
| | - Stéphane D Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France.,Université de Strasbourg, Illkirch 67400, France
| | - Marjorie Fournier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France.,Université de Strasbourg, Illkirch 67400, France
| | - Alexis Hubaud
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France.,Université de Strasbourg, Illkirch 67400, France
| | - Mathilde Joint
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France.,Université de Strasbourg, Illkirch 67400, France
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France.,Université de Strasbourg, Illkirch 67400, France
| | - Olivier Pourquié
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France.,Université de Strasbourg, Illkirch 67400, France
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Abstract
This review by Vo ngoc et al. expands the view of the RNA polymerase II core promoter, which is comprised of classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure. The signals that direct the initiation of transcription ultimately converge at the core promoter, which is the gateway to transcription. Here we provide an overview of the RNA polymerase II core promoter in bilateria (bilaterally symmetric animals). The core promoter is diverse in terms of its composition and function yet is also punctilious, as it acts with strict rules and precision. We additionally describe an expanded view of the core promoter that comprises the classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure. This model may eventually lead to a more unified conceptual understanding of the core promoter.
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Affiliation(s)
- Long Vo Ngoc
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Yuan-Liang Wang
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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35
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Zhou L, Canagarajah B, Zhao Y, Baibakov B, Tokuhiro K, Maric D, Dean J. BTBD18 Regulates a Subset of piRNA-Generating Loci through Transcription Elongation in Mice. Dev Cell 2017; 40:453-466.e5. [PMID: 28292424 DOI: 10.1016/j.devcel.2017.02.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/18/2016] [Accepted: 02/09/2017] [Indexed: 11/27/2022]
Abstract
PIWI-interacting RNAs (piRNAs) are small non-coding RNAs essential for animal germ cell development. Despite intense investigation of post-transcriptional processing, chromatin regulators for piRNA biogenesis in mammals remain largely unexplored. Here we document that BTBD18 is a pachytene nuclear protein in mouse testes that occupies a subset of pachytene piRNA-producing loci. Ablation of Btbd18 in mice disrupts piRNA biogenesis, prevents spermiogenesis, and results in male sterility. Transcriptome profiling, chromatin accessibility, and RNA polymerase II occupancy demonstrate that BTBD18 facilitates expression of pachytene piRNA precursors by promoting transcription elongation. Thus, our study identifies BTBD18 as a specific controller for transcription activation through RNA polymerase II elongation at a subset of genomic piRNA loci.
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Affiliation(s)
- Liquan Zhou
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Bertram Canagarajah
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yangu Zhao
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Boris Baibakov
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keizo Tokuhiro
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dragan Maric
- NINDS Flow Cytometry Core Facility, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jurrien Dean
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
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36
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Testis Transcriptome Modulation in Klinefelter Patients with Hypospermatogenesis. Sci Rep 2017; 7:45729. [PMID: 28361989 PMCID: PMC5374630 DOI: 10.1038/srep45729] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 03/02/2017] [Indexed: 12/15/2022] Open
Abstract
The main genetic cause of male infertility is represented by the Klinefelter Syndrome (KS), a condition accounting for 3% of all cases of infertility and up to15% of cases of azoospermia. KS is generally characterized by azoospermia; approximately 10% of cases have severe oligozoospermia. Among these, the 30-40% of patients show hypospermatogenesis. The mechanisms leading to adult testis dysfunctions are not completely understood. A microarray transcriptome analysis was performed on testis biopsies obtained from three KS patients with hypospermatogenesis and three control subjects. KS testis showed a differential up- and down-regulation of 303 and 747 transcripts, respectively, as compared to controls. The majority of down-regulated transcripts were involved in spermiogenesis failure and testis morphological defects, whereas up-regulated genes were responsible for testis apoptotic processes. Functional analysis of the transcriptionally altered genes indicated a deregulation in cell death, germ cell function and morphology as well as blood-testis-barrier maintenance and Leydig cells activity. These data support a complex scenario in which spermatogenic impairment is the result of functional and morphological alterations in both germinal and somatic components of KS testis. These findings could represent the basis for evaluating new markers of KS spermatogenesis and potential targets of therapeutic intervention to preserve residual spermatogenesis.
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37
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An Orchestrated Intron Retention Program in Meiosis Controls Timely Usage of Transcripts during Germ Cell Differentiation. Dev Cell 2017; 41:82-93.e4. [PMID: 28366282 PMCID: PMC5392497 DOI: 10.1016/j.devcel.2017.03.003] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 01/24/2017] [Accepted: 03/03/2017] [Indexed: 12/11/2022]
Abstract
Global transcriptome reprogramming during spermatogenesis ensures timely expression of factors in each phase of male germ cell differentiation. Spermatocytes and spermatids require particularly extensive reprogramming of gene expression to switch from mitosis to meiosis and to support gamete morphogenesis. Here, we uncovered an extensive alternative splicing program during this transmeiotic differentiation. Notably, intron retention was largely the most enriched pattern, with spermatocytes showing generally higher levels of retention compared with spermatids. Retained introns are characterized by weak splice sites and are enriched in genes with strong relevance for gamete function. Meiotic intron-retaining transcripts (IRTs) were exclusively localized in the nucleus. However, differently from other developmentally regulated IRTs, they are stable RNAs, showing longer half-life than properly spliced transcripts. Strikingly, fate-mapping experiments revealed that IRTs are recruited onto polyribosomes days after synthesis. These studies reveal an unexpected function for regulated intron retention in modulation of the timely expression of select transcripts during spermatogenesis.
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38
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Li Y, Li J, Wang Y, Zhang Y, Chu J, Sun C, Fu Z, Huang Y, Zhang H, Yuan H, Yin Y. Roles of cancer/testis antigens (CTAs) in breast cancer. Cancer Lett 2017; 399:64-73. [PMID: 28274891 DOI: 10.1016/j.canlet.2017.02.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 12/19/2022]
Abstract
Breast cancer is the most common cancer diagnosed and is the second leading cause of cancer death among women in the US. For breast cancer, early diagnosis and efficient therapy remains a significant clinical challenge. Therefore, it is necessary to identify novel tumor associated molecules to target for biomarker development and immunotherapy. In this regard, cancer testis antigens (CTAs) have emerged as a potential clinical biomarker targeting immunotherapy for various malignancies due to the nature of its characteristics. CTAs are a group of tumor associated antigens (TAAs) that display normal expression in immune-privileged organs, but display aberrant expression in several types of cancers, particularly in advanced cancers. Investigation of CTAs for the clinical management of breast malignancies indicates that these TAAs have potential roles as novel biomarkers, with increased specificity and sensitivity compared to those currently used in the clinic. Moreover, TAAs could be therapeutic targets for cancer immunotherapy. This review is an attempt to address the promising CTAs in breast cancer and their possible clinical implications as biomarkers and immunotherapeutic targets with particular focus on challenges and future interventions.
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Affiliation(s)
- Yongfei Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University. Nanjing 210004, China
| | - Jun Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University. Nanjing 210004, China
| | - Yifan Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University. Nanjing 210004, China
| | - Yanhong Zhang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University. Nanjing 210004, China
| | - Jiahui Chu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University. Nanjing 210004, China
| | - Chunxiao Sun
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University. Nanjing 210004, China
| | - Ziyi Fu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University. Nanjing 210004, China; Nanjing Maternity and Child Health Medical Institute, Affiliated Obstetrics and Gynecology Hospital, Nanjing Medical University, Nanjing 210004, China
| | - Yi Huang
- Department of Pharmacology and Chemical Biology, Magee Women's Research Institute, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Hansheng Zhang
- School of Public Health, University of Maryland, College Park, MD 20742, USA
| | - Hongyan Yuan
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Yongmei Yin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University. Nanjing 210004, China.
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39
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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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40
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TRF2 is recruited to the pre-initiation complex as a testis-specific subunit of TFIIA/ALF to promote haploid cell gene expression. Sci Rep 2016; 6:32069. [PMID: 27576952 PMCID: PMC5006001 DOI: 10.1038/srep32069] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/28/2016] [Indexed: 11/08/2022] Open
Abstract
Mammalian genomes encode two genes related to the TATA-box binding protein (TBP), TBP-related factors 2 and 3 (TRF2 and TRF3). Male Trf2−/− mice are sterile and characterized by arrested spermatogenesis at the transition from late haploid spermatids to early elongating spermatids. Despite this characterization, the molecular function of murine Trf2 remains poorly characterized and no direct evidence exists to show that it acts as a bona fide chromatin-bound transcription factor. We show here that Trf2 forms a stable complex with TFIIA or the testis expressed paralogue ALF chaperoned in the cytoplasm by heat shock proteins. We demonstrate for the first time that Trf2 is recruited to active haploid cell promoters together with Tbp, Taf7l and RNA polymerase II. RNA-seq analysis identifies a set of genes activated in haploid spermatids during the first wave of spermatogenesis whose expression is down-regulated by Trf2 inactivation. We therefore propose that Trf2 is recruited to the preinitiation complex as a testis-specific subunit of TFIIA/ALF that cooperates with Tbp and Taf7l to promote haploid cell gene expression.
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41
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Kistler WS, Baas D, Lemeille S, Paschaki M, Seguin-Estevez Q, Barras E, Ma W, Duteyrat JL, Morlé L, Durand B, Reith W. RFX2 Is a Major Transcriptional Regulator of Spermiogenesis. PLoS Genet 2015; 11:e1005368. [PMID: 26162102 PMCID: PMC4498915 DOI: 10.1371/journal.pgen.1005368] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 06/17/2015] [Indexed: 11/21/2022] Open
Abstract
Spermatogenesis consists broadly of three phases: proliferation of diploid germ cells, meiosis, and finally extensive differentiation of the haploid cells into effective delivery vehicles for the paternal genome. Despite detailed characterization of many haploid developmental steps leading to sperm, only fragmentary information exists on the control of gene expression underlying these processes. Here we report that the RFX2 transcription factor is a master regulator of genes required for the haploid phase. A targeted mutation of Rfx2 was created in mice. Rfx2-/- mice are perfectly viable but show complete male sterility. Spermatogenesis appears to progress unperturbed through meiosis. However, haploid cells undergo a complete arrest in spermatid development just prior to spermatid elongation. Arrested cells show altered Golgi apparatus organization, leading to a deficit in the generation of a spreading acrosomal cap from proacrosomal vesicles. Arrested cells ultimately merge to form giant multinucleated cells released to the epididymis. Spermatids also completely fail to form the flagellar axoneme. RNA-Seq analysis and ChIP-Seq analysis identified 139 genes directly controlled by RFX2 during spermiogenesis. Gene ontology analysis revealed that genes required for cilium function are specifically enriched in down- and upregulated genes showing that RFX2 allows precise temporal expression of ciliary genes. Several genes required for cell adhesion and cytoskeleton remodeling are also downregulated. Comparison of RFX2-regulated genes with those controlled by other major transcriptional regulators of spermiogenesis showed that each controls independent gene sets. Altogether, these observations show that RFX2 plays a major and specific function in spermiogenesis. Failure of spermatogenesis, which is presumed to often result from genetic defects, is a common cause of male sterility. Although numerous genes associated with defects in male spermatogenesis have been identified, numerous cases of genetic male infertility remain unelucidated. We report here that the transcription factor RFX2 is a master regulator of gene expression programs required for progression through the haploid phase of spermatogenesis. Male RFX2-deficient mice are completely sterile. Spermatogenesis progresses through meiosis, but haploid cells undergo a complete block in development just prior to spermatid elongation. Gene expression profiling and ChIP-Seq analysis revealed that RFX2 controls key pathways implicated in cilium/flagellum formation, as well as genes implicated in microtubule and vesicle associated transport. The set of genes activated by RFX2 in spermatids exhibits virtually no overlap with those controlled by other known transcriptional regulators of spermiogenesis, establishing RFX2 as an essential new player in this developmental process. RFX2-deficient mice should therefore represent a valuable new model for deciphering the regulatory networks that direct sperm formation, and thereby contribute to the identification of causes of human male infertility.
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Affiliation(s)
- W. Stephen Kistler
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, United States of America
- * E-mail: (WSK); (BD)
| | - Dominique Baas
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, Villeurbanne, Lyon, France
| | - Sylvain Lemeille
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Marie Paschaki
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, Villeurbanne, Lyon, France
| | - Queralt Seguin-Estevez
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Emmanuèle Barras
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Wenli Ma
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, United States of America
| | - Jean-Luc Duteyrat
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, Villeurbanne, Lyon, France
| | - Laurette Morlé
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, Villeurbanne, Lyon, France
| | - Bénédicte Durand
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, Villeurbanne, Lyon, France
- * E-mail: (WSK); (BD)
| | - Walter Reith
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
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42
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de Camargo GMF, Porto-Neto LR, Kelly MJ, Bunch RJ, McWilliam SM, Tonhati H, Lehnert SA, Fortes MRS, Moore SS. Non-synonymous mutations mapped to chromosome X associated with andrological and growth traits in beef cattle. BMC Genomics 2015; 16:384. [PMID: 25975716 PMCID: PMC4432507 DOI: 10.1186/s12864-015-1595-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 04/28/2015] [Indexed: 12/31/2022] Open
Abstract
Background Previous genome-wide association analyses identified QTL regions in the X chromosome for percentage of normal sperm and scrotal circumference in Brahman and Tropical Composite cattle. These traits are important to be studied because they are indicators of male fertility and are correlated with female sexual precocity and reproductive longevity. The aim was to investigate candidate genes in these regions and to identify putative causative mutations that influence these traits. In addition, we tested the identified mutations for female fertility and growth traits. Results Using a combination of bioinformatics and molecular assay technology, twelve non-synonymous SNPs in eleven genes were genotyped in a cattle population. Three and nine SNPs explained more than 1% of the additive genetic variance for percentage of normal sperm and scrotal circumference, respectively. The SNPs that had a major influence in percentage of normal sperm were mapped to LOC100138021 and TAF7L genes; and in TEX11 and AR genes for scrotal circumference. One SNP in TEX11 was explained ~13% of the additive genetic variance for scrotal circumference at 12 months. The tested SNP were also associated with weight measurements, but not with female fertility traits. Conclusions The strong association of SNPs located in X chromosome genes with male fertility traits validates the QTL. The implicated genes became good candidates to be used for genetic evaluation, without detrimentally influencing female fertility traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1595-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gregório Miguel Ferreira de Camargo
- Departamento de Zootecnia, Universidade Estadual Paulista (Unesp), Jaboticabal, SP, 14884-900, Brazil. .,Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St Lucia, QLD, 4067, Australia. .,School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia Brisbane, QLD, 4072, Australia.
| | - Laercio R Porto-Neto
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St Lucia, QLD, 4067, Australia.
| | - Matthew J Kelly
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia Brisbane, QLD, 4072, Australia.
| | - Rowan J Bunch
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St Lucia, QLD, 4067, Australia.
| | - Sean M McWilliam
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St Lucia, QLD, 4067, Australia.
| | - Humberto Tonhati
- Departamento de Zootecnia, Universidade Estadual Paulista (Unesp), Jaboticabal, SP, 14884-900, Brazil.
| | - Sigrid A Lehnert
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St Lucia, QLD, 4067, Australia.
| | - Marina R S Fortes
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia Brisbane, QLD, 4072, Australia.
| | - Stephen S Moore
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4067, Australia.
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43
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Danino YM, Even D, Ideses D, Juven-Gershon T. The core promoter: At the heart of gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1116-31. [PMID: 25934543 DOI: 10.1016/j.bbagrm.2015.04.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/19/2015] [Accepted: 04/23/2015] [Indexed: 12/17/2022]
Abstract
The identities of different cells and tissues in multicellular organisms are determined by tightly controlled transcriptional programs that enable accurate gene expression. The mechanisms that regulate gene expression comprise diverse multiplayer molecular circuits of multiple dedicated components. The RNA polymerase II (Pol II) core promoter establishes the center of this spatiotemporally orchestrated molecular machine. Here, we discuss transcription initiation, diversity in core promoter composition, interactions of the basal transcription machinery with the core promoter, enhancer-promoter specificity, core promoter-preferential activation, enhancer RNAs, Pol II pausing, transcription termination, Pol II recycling and translation. We further discuss recent findings indicating that promoters and enhancers share similar features and may not substantially differ from each other, as previously assumed. Taken together, we review a broad spectrum of studies that highlight the importance of the core promoter and its pivotal role in the regulation of metazoan gene expression and suggest future research directions and challenges.
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Affiliation(s)
- Yehuda M Danino
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dan Even
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel.
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44
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Abstract
Transcriptional regulation is pivotal for development and differentiation of organisms. Transcription of eukaryotic protein-coding genes by RNA polymerase II (Pol II) initiates at the core promoter. Core promoters, which encompass the transcription start site, may contain functional core promoter elements, such as the TATA box, initiator, TCT and downstream core promoter element. TRF2 (TATA-box-binding protein-related factor 2) does not bind TATA box-containing promoters. Rather, it is recruited to core promoters via sequences other than the TATA box. We review the recent findings implicating TRF2 as a basal transcription factor in the regulation of diverse biological processes and specialized transcriptional programs.
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Key Words
- BREd, downstream TFIIB recognition element
- BREu, upstream TFIIB recognition element
- ChIP, Chromatin immunoprecipitation
- DPE
- DPE, downstream core promoter element
- Inr, initiator
- MTE, motif ten element
- PIC, preinitiation complex
- Pol II, RNA polymerase II
- RNA Pol II transcription
- TAF, TBP-associated factor
- TBP, TATA-box binding protein
- TBP-related factors
- TCT
- TFIIA (transcription factor, RNA polymerase II A)
- TFIIB (transcription factor, RNA polymerase II B)
- TFIID (transcription factor, RNA polymerase II D)
- TRF, TATA-box-binding protein-related factor
- TRF2
- TSS, transcription start site
- core promoter elements/motifs
- embryonic development
- histone gene cluster
- ribosomal protein genes
- spermiogenesis
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Affiliation(s)
- Yonathan Zehavi
- a The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University , Ramat Gan , 5290002 , Israel
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de Boer P, de Vries M, Ramos L. A mutation study of sperm head shape and motility in the mouse: lessons for the clinic. Andrology 2014; 3:174-202. [PMID: 25511638 DOI: 10.1111/andr.300] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 09/19/2014] [Accepted: 09/24/2014] [Indexed: 12/11/2022]
Abstract
Mouse mutants that show effects on sperm head shape, the sperm tail (flagellum), and motility were analysed in a systematic way. This was achieved by grouping mutations in the following classes: manchette, acrosome, Sertoli cell contact, chromatin remodelling, and mutations involved in complex regulations such as protein (de)phosphorylation and RNA stability, and flagellum/motility mutations. For all mutant phenotypes, flagellum function (motility) was affected. Head shape, including the nucleus, was also affected in spermatozoa of most mouse models, though with considerable variation. For the mutants that were categorized in the flagellum/motility group, generally normal head shapes were found, even when the flagellum did not develop or only poorly so. Most mutants are sterile, an occasional one semi-sterile. For completeness, the influence of the sex chromosomes on sperm phenotype is included. Functionally, the genes involved can be categorized as regulators of spermiogenesis. When extrapolating these data to human sperm samples, in vivo selection for motility would be the tool for weeding out the products of suboptimal spermiogenesis and epididymal sperm maturation. The striking dependency of motility on proper sperm head development is not easy to understand, but likely is of evolutionary benefit. Also, sperm competition after mating can never act against the long-term multi-generation interest of genetic integrity. Hence, it is plausible to suggest that short-term haplophase fitness i.e., motility, is developmentally integrated with proper nucleus maturation, including genetic integrity to protect multi-generation fitness. We hypothesize that, when the prime defect is in flagellum formation, apparently a feedback loop was not necessary as head morphogenesis in these mutants is mostly normal. Extrapolating to human-assisted reproductive techniques practice, this analysis would supply the arguments for the development of tools to select for motility as a continuous (non-discrete) parameter.
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Affiliation(s)
- P de Boer
- Department of Obstetrics and Gynaecology, Radboud University Medical Centre, Nijmegen, The Netherlands
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tBRD-1 selectively controls gene activity in the Drosophila testis and interacts with two new members of the bromodomain and extra-terminal (BET) family. PLoS One 2014; 9:e108267. [PMID: 25251222 PMCID: PMC4177214 DOI: 10.1371/journal.pone.0108267] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/04/2014] [Indexed: 01/29/2023] Open
Abstract
Multicellular organisms have evolved specialized mechanisms to control transcription in a spatial and temporal manner. Gene activation is tightly linked to histone acetylation on lysine residues that can be recognized by bromodomains. Previously, the testis-specifically expressed bromodomain protein tBRD-1 was identified in Drosophila. Expression of tBRD-1 is restricted to highly transcriptionally active primary spermatocytes. tBRD-1 is essential for male fertility and proposed to act as a co-factor of testis-specific TATA box binding protein-associated factors (tTAFs) for testis-specific transcription. Here, we performed microarray analyses to compare the transcriptomes of tbrd-1 mutant testes and wild-type testes. Our data confirmed that tBRD-1 controls gene activity in male germ cells. Additionally, comparing the transcriptomes of tbrd-1 and tTAF mutant testes revealed a subset of common target genes. We also characterized two new members of the bromodomain and extra-terminal (BET) family, tBRD-2 and tBRD-3. In contrast to other members of the BET family in animals, both possess only a single bromodomain, a characteristic feature of plant BET family members. Immunohistology techniques not only revealed that tBRD-2 and tBRD-3 partially co-localize with tBRD-1 and tTAFs in primary spermatocytes, but also that their proper subcellular distribution was impaired in tbrd-1 and tTAF mutant testes. Treating cultured male germ cells with inhibitors showed that localization of tBRD-2 and tBRD-3 depends on the acetylation status within primary spermatocytes. Yeast two-hybrid assays and co-immunoprecipitations using fly testes protein extracts demonstrated that tBRD-1 is able to form homodimers as well as heterodimers with tBRD-2, tBRD-3, and tTAFs. These data reveal for the first time the existence of single bromodomain BET proteins in animals, as well as evidence for a complex containing tBRDs and tTAFs that regulates transcription of a subset of genes with relevance for spermiogenesis.
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Abstract
Transcription of protein-coding genes is highly dependent on the RNA polymerase II core promoter. Core promoters, generally defined as the regions that direct transcription initiation, consist of functional core promoter motifs (such as the TATA-box, initiator [Inr], and downstream core promoter element [DPE]) that confer specific properties to the core promoter. The known basal transcription factors that support TATA-dependent transcription are insufficient for in vitro transcription of DPE-dependent promoters. In search of a transcription factor that supports DPE-dependent transcription, we used a biochemical complementation approach and identified the Drosophila TBP (TATA-box-binding protein)-related factor 2 (TRF2) as an enriched factor in the fractions that support DPE-dependent transcription. We demonstrate that the short TRF2 isoform preferentially activates DPE-dependent promoters. DNA microarray analysis reveals the enrichment of DPE promoters among short TRF2 up-regulated genes. Using primer extension analysis and reporter assays, we show the importance of the DPE in transcriptional regulation of TRF2 target genes. It was previously shown that, unlike TBP, TRF2 fails to bind DNA containing TATA-boxes. Using microfluidic affinity analysis, we discovered that short TRF2-bound DNA oligos are enriched for Inr and DPE motifs. Taken together, our findings highlight the role of short TRF2 as a preferential core promoter regulator.
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Herrera FJ, Yamaguchi T, Roelink H, Tjian R. Core promoter factor TAF9B regulates neuronal gene expression. eLife 2014; 3:e02559. [PMID: 25006164 PMCID: PMC4083437 DOI: 10.7554/elife.02559] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Emerging evidence points to an unexpected diversification of core promoter recognition complexes that serve as important regulators of cell-type specific gene transcription. Here, we report that the orphan TBP-associated factor TAF9B is selectively up-regulated upon in vitro motor neuron differentiation, and is required for the transcriptional induction of specific neuronal genes, while dispensable for global gene expression in murine ES cells. TAF9B binds to both promoters and distal enhancers of neuronal genes, partially co-localizing at binding sites of OLIG2, a key activator of motor neuron differentiation. Surprisingly, in this neuronal context TAF9B becomes preferentially associated with PCAF rather than the canonical TFIID complex. Analysis of dissected spinal column from Taf9b KO mice confirmed that TAF9B also regulates neuronal gene transcription in vivo. Our findings suggest that alternative core promoter complexes may provide a key mechanism to lock in and maintain specific transcriptional programs in terminally differentiated cell types. DOI:http://dx.doi.org/10.7554/eLife.02559.001 Almost all the cells in an organism contain the same genetic information, but they develop into many different types of cells that perform a variety of specialized functions in the body. Brain cells, for example, have a very different shape and function from red blood cells. A small group of proteins act inside cells to switch on the expression of genes it needs to carry out the specific functions of a given cell-type, and switch off the genes that are only needed in other cell types. Some of these regulatory proteins called ‘core promoter factors’ bind to the DNA near the start of genes. These core factors are known to work in combination with various other proteins to switch genes on or off in specific cell types. However, the specific core promoter factors and partner proteins that guide a cell into becoming a neuron have not been well characterized. Now, Herrera et al. have identified a core promoter factor called TAF9B that is produced at higher levels when mouse stem cells are coaxed into becoming the motor neurons that carry nerve impulses to muscles. The TAF9B protein works together with an enzyme (called PCAF) to help to switch on the genes that control the development of these cells. Without this regulatory protein, mouse stem cells grown in the lab fail to properly switch on the genes that are necessary to become motor neurons. These mutant stem cells also fail to efficiently switch off genes that stop stem cells from becoming more specialized. High levels of TAF9B were also found in the spinal cord of newborn mice and when Herrera et al. engineered mice that lack TAF9B, these mice did not properly regulate the expression of neuronal genes in their spines. These new findings might, in the future, improve our ability to guide stem cells into forming neurons, or to reprogram other types of specialized cells into becoming motor neurons. This new information could also prove useful for researchers interested in better understanding neuronal development and might aid in the design of therapies to treat neuronal injuries or diseases, such as motor neuron disease. DOI:http://dx.doi.org/10.7554/eLife.02559.002
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Affiliation(s)
- Francisco J Herrera
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States CIRM Center of Excellence, Li Ka Shing Center For Biomedical and Health Sciences, University of California, Berkeley, Berkeley, United States
| | - Teppei Yamaguchi
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States CIRM Center of Excellence, Li Ka Shing Center For Biomedical and Health Sciences, University of California, Berkeley, Berkeley, United States
| | - Henk Roelink
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States CIRM Center of Excellence, Li Ka Shing Center For Biomedical and Health Sciences, University of California, Berkeley, Berkeley, United States
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Wang YL, Duttke SHC, Chen K, Johnston J, Kassavetis GA, Zeitlinger J, Kadonaga JT. TRF2, but not TBP, mediates the transcription of ribosomal protein genes. Genes Dev 2014; 28:1550-5. [PMID: 24958592 PMCID: PMC4102762 DOI: 10.1101/gad.245662.114] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The TCT core promoter element is present in most ribosomal protein (RP) genes in Drosophila and humans. Here we show that TBP (TATA box-binding protein)-related factor TRF2, but not TBP, is required for transcription of the TCT-dependent RP genes. In cells, TCT-dependent transcription, but not TATA-dependent transcription, increases or decreases upon overexpression or depletion of TRF2. In vitro, purified TRF2 activates TCT but not TATA promoters. ChIP-seq (chromatin immunoprecipitation [ChIP] combined with deep sequencing) experiments revealed the preferential localization of TRF2 at TCT versus TATA promoters. Hence, a specialized TRF2-based RNA polymerase II system functions in the synthesis of RPs and complements the RNA polymerase I and III systems.
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Affiliation(s)
- Yuan-Liang Wang
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Sascha H C Duttke
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Kai Chen
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jeff Johnston
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA; Department of Pathology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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50
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Zhou H, Wan B, Grubisic I, Kaplan T, Tjian R. TAF7L modulates brown adipose tissue formation. eLife 2014; 3. [PMID: 24876128 PMCID: PMC4066819 DOI: 10.7554/elife.02811] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 05/25/2014] [Indexed: 01/18/2023] Open
Abstract
Brown adipose tissue (BAT) plays an essential role in metabolic homeostasis by dissipating energy via thermogenesis through uncoupling protein 1 (UCP1). Previously, we reported that the TATA-binding protein associated factor 7L (TAF7L) is an important regulator of white adipose tissue (WAT) differentiation. In this study, we show that TAF7L also serves as a molecular switch between brown fat and muscle lineages in vivo and in vitro. In adipose tissue, TAF7L-containing TFIID complexes associate with PPARγ to mediate DNA looping between distal enhancers and core promoter elements. Our findings suggest that the presence of the tissue-specific TAF7L subunit in TFIID functions to promote long-range chromatin interactions during BAT lineage specification. DOI:http://dx.doi.org/10.7554/eLife.02811.001 Mammals produce two distinct types of adipose tissue: white adipose tissue (white fat) is the more common type and is used to store energy; brown adipose tissue (brown fat) is mostly found in young animals and infants, and it plays an important role in dissipating energy as heat rather than storing it in fat for future use. In adults, higher levels of brown fat are associated with lower levels of fat overall, so there is considerable interest in learning more about this form of fat to help address rising levels of obesity in the world. Building on previous work in which they showed that a gene control protein called TAF7L has a central role in the development of the cells that make up white adipose tissue, Zhou et al. now show that this protein also helps to regulate the development of brown adipose tissue. Mice lacking the gene for this protein developed embryos with 40% less brown fat than wild-type mice with the gene. Moreover, these mice developed muscle-like cells in the regions that should have contained brown fat. Gene expression analysis revealed that ‘knocking out’ the gene for TAF7L changed the expression of more than a thousand genes in these mice. Zhou et al. suggest that TAF7L works as a ‘molecular switch’ that determines whether certain precursor cells (called mesenchymal stem cells) go on to become brown fat cells or muscle cells. A future challenge will be to devise interventions to regulate the activity or levels of TAF7L as a potential means of modulating brown fat depots in animals and humans. DOI:http://dx.doi.org/10.7554/eLife.02811.002
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Affiliation(s)
- Haiying Zhou
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Bo Wan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Ivan Grubisic
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Robert Tjian
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
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