1
|
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.
Collapse
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
| |
Collapse
|
2
|
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 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.
Collapse
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
| |
Collapse
|
3
|
Wang X, Liu J, Wang T, Ma B, Wu P, Xu X, Xiong J. The downstream PPARγ target LRRC1 participates in early stage adipocytic differentiation. Mol Cell Biochem 2023; 478:1465-1473. [PMID: 36370237 PMCID: PMC10209303 DOI: 10.1007/s11010-022-04609-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
LRRC1 is a regulator of cellular polarity that is expressed at high levels in a range of tumor tissue types. Here, we conducted an analysis of the previously unexplored role of LRRC1 as a component of the adipogenic differentiation network. During the early stage (days 3-7) adipocytic differentiation of human mesenchymal stem cells (MSCs), LRRC1 was found to be upregulated at both the mRNA and protein levels. Moreover, the expression of LRRC1 was found to be controlled by PPARγ, which is a key transcriptional regulator of adipogenesis. Inhibiting LRRC1 expression reduced the adipogenic potential of hMSCs, with a concomitant reduction in the expression of three adipogenesis-associated proteins (SCD, LIPE, FASN). Together, these data offer new insight into the functional importance of LRRC1 both in general and in the context of adipocytic differentiation.
Collapse
Affiliation(s)
- Xinping Wang
- College of Basic Medical Science, Jiujiang University, 551 Qianjindong Road, Jiujiang, 332005, China
| | - Jianyun Liu
- College of Basic Medical Science, Jiujiang University, 551 Qianjindong Road, Jiujiang, 332005, China
| | - Ting Wang
- College of Basic Medical Science, Jiujiang University, 551 Qianjindong Road, Jiujiang, 332005, China
| | - Baicheng Ma
- College of Basic Medical Science, Jiujiang University, 551 Qianjindong Road, Jiujiang, 332005, China
| | - Ping Wu
- College of Basic Medical Science, Jiujiang University, 551 Qianjindong Road, Jiujiang, 332005, China
| | - Xiaoyuan Xu
- College of Basic Medical Science, Jiujiang University, 551 Qianjindong Road, Jiujiang, 332005, China
| | - Jianjun Xiong
- College of Basic Medical Science, Jiujiang University, 551 Qianjindong Road, Jiujiang, 332005, China.
| |
Collapse
|
4
|
Chen L, Xu Y. Low temperature upregulating HSP70 expression to mitigate the paclitaxel-induced damages in NHEK cell. PeerJ 2023; 11:e14630. [PMID: 36684674 PMCID: PMC9854382 DOI: 10.7717/peerj.14630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/02/2022] [Indexed: 01/18/2023] Open
Abstract
Scalp cooling is the most approved treatment for preventing chemotherapy-induced alopecia (CIA). However, the protective mechanism of scalp cooling has rarely been reported. The goal of the present study was to study the relationship between paclitaxel concentration and temperature and the inhibitory effect of low temperature on paclitaxel-induced alopecia. The results showed that the dose of paclitaxel should not exceed 60-70 mg/mL during scalp cooling treatment, and the optimal cooling temperature under different paclitaxel concentrations was determined. Normal human epidermal keratinocytes (NHEK) cells were analyzed by global transcriptome analysis, functional annotation and pathway analysis of differentially expressed genes (DEGs) and ELISA kit to analyze the mechanism of low temperature therapy. The expression of HSPA8, HSPA1A and HSPA1B, which belongs to HSP70, was up-regulated by low temperature. These genes are important target genes of low temperature treatment, which were confirmed by ELISA. The up-regulation of PLK2 and the down-regulation of TXNIP expression are the upstream of mitochondrial dysfunction and ROS, inhibiting the accumulation of ROS and up-regulating the mitochondrial membrane potential. Our research partially elucidates the therapeutic mechanism of scalp cooling, which provides a new idea on the drug research and development in CIA.
Collapse
Affiliation(s)
- Liang Chen
- Institute of Biothermal Science & Technology, University of Shanghai for Science and Technology, Shanghai, China,Shanghai Co-innovation Center for Energy Therapy of Tumors, Shanghai, China,Shanghai Technical Service Platform for Cryopreservation of Biological Resources, Shanghai, China
| | - Yi Xu
- Institute of Biothermal Science & Technology, University of Shanghai for Science and Technology, Shanghai, China,Shanghai Co-innovation Center for Energy Therapy of Tumors, Shanghai, China,Shanghai Technical Service Platform for Cryopreservation of Biological Resources, Shanghai, China
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Roberts AGK, Catchpoole DR, Kennedy PJ. Identification of differentially distributed gene expression and distinct sets of cancer-related genes identified by changes in mean and variability. NAR Genom Bioinform 2022; 4:lqab124. [PMID: 35047816 PMCID: PMC8759562 DOI: 10.1093/nargab/lqab124] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 11/19/2021] [Accepted: 12/16/2021] [Indexed: 12/13/2022] Open
Abstract
There is increasing evidence that changes in the variability or overall distribution of gene expression are important both in normal biology and in diseases, particularly cancer. Genes whose expression differs in variability or distribution without a difference in mean are ignored by traditional differential expression-based analyses. Using a Bayesian hierarchical model that provides tests for both differential variability and differential distribution for bulk RNA-seq data, we report here an investigation into differential variability and distribution in cancer. Analysis of eight paired tumour-normal datasets from The Cancer Genome Atlas confirms that differential variability and distribution analyses are able to identify cancer-related genes. We further demonstrate that differential variability identifies cancer-related genes that are missed by differential expression analysis, and that differential expression and differential variability identify functionally distinct sets of potentially cancer-related genes. These results suggest that differential variability analysis may provide insights into genetic aspects of cancer that would not be revealed by differential expression, and that differential distribution analysis may allow for more comprehensive identification of cancer-related genes than analyses based on changes in mean or variability alone.
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Role of Distinct Fat Depots in Metabolic Regulation and Pathological Implications. Rev Physiol Biochem Pharmacol 2022; 186:135-176. [PMID: 35915363 DOI: 10.1007/112_2022_73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
People suffering from obesity and associated metabolic disorders including diabetes are increasing exponentially around the world. Adipose tissue (AT) distribution and alteration in their biochemical properties play a major role in the pathogenesis of these diseases. Emerging evidence suggests that AT heterogeneity and depot-specific physiological changes are vital in the development of insulin resistance in peripheral tissues like muscle and liver. Classically, AT depots are classified into white adipose tissue (WAT) and brown adipose tissue (BAT); WAT is the site of fatty acid storage, while BAT is a dedicated organ of metabolic heat production. The discovery of beige adipocyte clusters in WAT depots indicates AT heterogeneity has a more central role than hither to ascribed. Therefore, we have discussed in detail the current state of understanding on cellular and molecular origin of different AT depots and their relevance toward physiological metabolic homeostasis. A major focus is to highlight the correlation between altered WAT distribution in the body and metabolic pathogenesis in animal models and humans. We have also underscored the disparity in the molecular (including signaling) changes in various WAT tissues during diabetic pathogenesis. Exercise-mediated beneficial alteration in WAT physiology/distribution that protects against metabolic disorders is evolving. Here we have discussed the depot-specific biochemical adjustments induced by different forms of exercise. A detailed understanding of the molecular details of inter-organ crosstalk via substrate utilization/storage and signaling through chemokines provide strategies to target selected WAT depots to pharmacologically mimic the benefits of exercise countering metabolic diseases including diabetes.
Collapse
|
9
|
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.
Collapse
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:
| |
Collapse
|
10
|
Zhang T, Chen L, Ding H, Wu P, Zhang G, Pan PZ, Xie PK, Dai G, Wang J. Construction of miRNA-mRNA network in the differentiation of chicken preadipocytes. Br Poult Sci 2021; 63:298-306. [PMID: 34738495 DOI: 10.1080/00071668.2021.2000585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. MicroRNAs (miRNAs) play key roles in regulating lipid metabolism, adipogenesis and fat deposition in chicken. To date, there are only a few miRNAs that had been confirmed to be involved in chicken adipogenesis. The detailed mechanisms by which miRNAs regulate chicken adipogenesis remain largely unknown. 2. To identify candidate miRNAs involved in chicken preadipocyte differentiation and explore potential mechanisms behind their functions, the following study analysed and identified miRNA and mRNA expression levels in undifferentiated and differentiated preadipocytes. Hub miRNA-mRNA interactions were identified, and the degree of connectivity of DE miRNAs in the network was established. 3. A total of 145 DE miRNAs and 660 DE mRNAs were identified between undifferentiated and differentiated preadipocytes. An miRNA-mRNA network was constructed, including 29 DE miRNAs and 155 DE mRNAs, forming 470 miRNA-mRNA interactions. Functional enrichment analysis showed that DE mRNAs in the network were significantly enriched in 712 biological processes and 13 KEGG pathways. Based on the connectivity degree, five DE miRNAs with higher degrees miR-195-x, gga-miR-200a-3p, gga-miR-135a-5p, novel-m0067-5p and novel-m0270-5p were identified as hub miRNAs. Fifty-eight DE mRNAs interacted with these five hub miRNAs and formed 70 miRNA-mRNA interactions. 4. This study constructed a miRNA-mRNA network associated with chicken preadipocyte differentiation and identified five hub miRNAs in the network. The findings identified the number of chicken adipogenic miRNAs and laid the foundation for elucidating the miRNA-mediated regulatory mechanism in chicken adipogenesis.
Collapse
Affiliation(s)
- Tao Zhang
- Yangzhou University, College of Animal Science and Technology, Yangzhou, 225009 China.,Yangzhou University, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009 China
| | - Lan Chen
- Yangzhou University, College of Veterinary Medicine, Yangzhou, China
| | - Hao Ding
- Yangzhou University, College of Animal Science and Technology, Yangzhou, 225009 China
| | - Pengfei Wu
- Yangzhou University, College of Animal Science and Technology, Yangzhou, 225009 China
| | - Genxi Zhang
- 88 Daxue South Road, Yangzhou City, Jiangsu Province, Yangzhou, 225009 China
| | - Professor Zhiming Pan
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA, Yangzhou University, Yangzhou, 225009 China
| | - Professor Kaizhou Xie
- Yangzhou University, College of Animal Science and Technology, Yangzhou, 225009 China
| | - Guojun Dai
- Yangzhou University, College of Animal Science and Technology, Yangzhou, 225009 China
| | - Jinyu Wang
- College of animal Science & Technology, Department of Animal Genetics, Breeding & Reproduction, Yangzhou, China
| |
Collapse
|
11
|
Srivastava D, Mahony S. Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194443. [PMID: 31639474 PMCID: PMC7166147 DOI: 10.1016/j.bbagrm.2019.194443] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/21/2019] [Accepted: 10/06/2019] [Indexed: 12/14/2022]
Abstract
Transcription factors (TFs) selectively bind distinct sets of sites in different cell types. Such cell type-specific binding specificity is expected to result from interplay between the TF's intrinsic sequence preferences, cooperative interactions with other regulatory proteins, and cell type-specific chromatin landscapes. Cell type-specific TF binding events are highly correlated with patterns of chromatin accessibility and active histone modifications in the same cell type. However, since concurrent chromatin may itself be a consequence of TF binding, chromatin landscapes measured prior to TF activation provide more useful insights into how cell type-specific TF binding events became established in the first place. Here, we review the various sequence and chromatin determinants of cell type-specific TF binding specificity. We identify the current challenges and opportunities associated with computational approaches to characterizing, imputing, and predicting cell type-specific TF binding patterns. We further focus on studies that characterize TF binding in dynamic regulatory settings, and we discuss how these studies are leading to a more complex and nuanced understanding of dynamic protein-DNA binding activities. We propose that TF binding activities at individual sites can be viewed along a two-dimensional continuum of local sequence and chromatin context. Under this view, cell type-specific TF binding activities may result from either strongly favorable sequence features or strongly favorable chromatin context.
Collapse
Affiliation(s)
- Divyanshi Srivastava
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America.
| |
Collapse
|
12
|
Nteeba J, Varberg KM, Scott RL, Simon ME, Iqbal K, Soares MJ. Poorly controlled diabetes mellitus alters placental structure, efficiency, and plasticity. BMJ Open Diabetes Res Care 2020; 8:8/1/e001243. [PMID: 32595139 PMCID: PMC7322553 DOI: 10.1136/bmjdrc-2020-001243] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/11/2020] [Accepted: 05/21/2020] [Indexed: 12/19/2022] Open
Abstract
INTRODUCTION The hemochorial placenta provides a critical barrier at the maternal-fetal interface to modulate maternal immune tolerance and enable gas and nutrient exchange between mother and conceptus. Pregnancy outcomes are adversely affected by diabetes mellitus; however, the effects of poorly controlled diabetes on placental formation, and subsequently fetal development, are not fully understood. RESEARCH DESIGN AND METHODS Streptozotocin was used to induce hyperglycemia in pregnant rats for the purpose of investigating the impact of poorly controlled diabetes on placental formation and fetal development. The experimental paradigm of hypoxia exposure in the pregnant rat was also used to assess properties of placental plasticity. Euglycemic and hyperglycemic rats were exposed to ambient conditions (~21% oxygen) or hypoxia (10.5% oxygen) beginning on gestation day (gd) 6.5 and sacrificed on gd 13.5. To determine whether the interaction of hyperglycemia and hypoxia was directly altering trophoblast lineage development, rat trophoblast stem (TS) cells were cultured in high glucose (25 mM) and/or exposed to low oxygen (0.5% to 1.5%). RESULTS Diabetes caused placentomegaly and placental malformation, decreasing placental efficiency and fetal size. Elevated glucose disrupted rat TS cell differentiation in vitro. Evidence of altered trophoblast differentiation was also observed in vivo, as hyperglycemia affected the junctional zone transcriptome and interfered with intrauterine trophoblast invasion and uterine spiral artery remodeling. When exposed to hypoxia, hyperglycemic rats showed decreased proliferation and ectoplacental cone development on gd 9.5 and complete pregnancy loss by gd 13.5. Furthermore, elevated glucose concentrations inhibited TS cell responses to hypoxia in vitro. CONCLUSIONS Overall, these results indicate that alterations in placental development, efficiency, and plasticity could contribute to the suboptimal fetal outcomes in offspring from pregnancies complicated by poorly controlled diabetes.
Collapse
Affiliation(s)
- Jackson Nteeba
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
- Institute for Reproduction and Perinatal Research, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Kaela M Varberg
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
- Institute for Reproduction and Perinatal Research, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Regan L Scott
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
- Institute for Reproduction and Perinatal Research, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Mikaela E Simon
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
- Institute for Reproduction and Perinatal Research, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Khursheed Iqbal
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
- Institute for Reproduction and Perinatal Research, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Michael J Soares
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
- Institute for Reproduction and Perinatal Research, 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
- Department of Pediatrics, University of Kansas Medical Center, Kansas City, Kansas, USA
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, Kansas, USA
| |
Collapse
|
13
|
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.
Collapse
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:
| |
Collapse
|
14
|
Rennie S, Dalby M, Lloret-Llinares M, Bakoulis S, Dalager Vaagensø C, Heick Jensen T, Andersson R. Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities. Nucleic Acids Res 2019; 46:5455-5469. [PMID: 29659982 PMCID: PMC6009668 DOI: 10.1093/nar/gky244] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/22/2018] [Indexed: 12/19/2022] Open
Abstract
Mammalian gene promoters and enhancers share many properties. They are composed of a unified promoter architecture of divergent transcripton initiation and gene promoters may exhibit enhancer function. However, it is currently unclear how expression strength of a regulatory element relates to its enhancer strength and if the unifying architecture is conserved across Metazoa. Here we investigate the transcription initiation landscape and its associated RNA decay in Drosophila melanogaster. We find that the majority of active gene-distal enhancers and a considerable fraction of gene promoters are divergently transcribed. We observe quantitative relationships between enhancer potential, expression level and core promoter strength, providing an explanation for indirectly related histone modifications that are reflecting expression levels. Lowly abundant unstable RNAs initiated from weak core promoters are key characteristics of gene-distal developmental enhancers, while the housekeeping enhancer strengths of gene promoters reflect their expression strengths. The seemingly separable layer of regulation by gene promoters with housekeeping enhancer potential is also indicated by chromatin interaction data. Our results suggest a unified promoter architecture of many D. melanogaster regulatory elements, that is universal across Metazoa, whose regulatory functions seem to be related to their core promoter elements.
Collapse
Affiliation(s)
- Sarah Rennie
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Maria Dalby
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Marta Lloret-Llinares
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Stylianos Bakoulis
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Christian Dalager Vaagensø
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| |
Collapse
|
15
|
Portuguez AS, Schwartz M, Siersbaek R, Nielsen R, Sung MH, Mandrup S, Kaplan T, Hakim O. Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis. FEBS J 2017; 284:3230-3244. [PMID: 28755519 PMCID: PMC5626622 DOI: 10.1111/febs.14183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/24/2017] [Accepted: 07/25/2017] [Indexed: 12/24/2022]
Abstract
The three dimensional folding of mammalian genomes is cell type specific and difficult to alter suggesting that it is an important component of gene regulation. However, given the multitude of chromatin-associating factors, the mechanisms driving the colocalization of active chromosomal domains and the role of this organization in regulating the transcription program in adipocytes are not clear. Analysis of genome-wide chromosomal associations revealed cell type-specific spatial clustering of adipogenic genes in 3T3-L1 cells. Time course analysis demonstrated that the adipogenic 'hub', sampled by PPARγ and Lpin1, undergoes orchestrated reorganization during adipogenesis. Coupling the dynamics of genome architecture with multiple chromatin datasets indicated that among all the transcription factors (TFs) tested, RXR is central to genome reorganization at the beginning of adipogenesis. Interestingly, at the end of differentiation, the adipogenic hub was shifted to an H3K27me3-repressive environment in conjunction with attenuation of gene transcription. We propose a stage-specific hierarchy for the activity of TFs contributing to the establishment of an adipogenic genome architecture that brings together the adipogenic genetic program. In addition, the repositioning of this network in a H3K27me3-rich environment at the end of differentiation may contribute to the stabilization of gene transcription levels and reduce the developmental plasticity of these specialized cells. DATABASE All sequence data reported in this paper have been deposited at GEO (http://www.ncbi.nlm.nih.gov/geo/) (GSE92475).
Collapse
Affiliation(s)
- Avital Sarusi Portuguez
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Michal Schwartz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Rasmus Siersbaek
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Ronni Nielsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, NIA, National Institutes of Health, Baltimore, MD 21224, USA
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 5290002, Israel
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Johnson SA, Lin JJ, Walkey CJ, Leathers MP, Coarfa C, Johnson DL. Elevated TATA-binding protein expression drives vascular endothelial growth factor expression in colon cancer. Oncotarget 2017; 8:48832-48845. [PMID: 28415573 PMCID: PMC5564728 DOI: 10.18632/oncotarget.16384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/13/2017] [Indexed: 11/26/2022] Open
Abstract
The TATA-binding protein (TBP) plays a central role in eukaryotic gene transcription. Given its key function in transcription initiation, TBP was initially thought to be an invariant protein. However, studies showed that TBP expression is upregulated by oncogenic signaling pathways. Furthermore, depending on the cell type, small increases in cellular TBP amounts can induce changes in cellular growth properties towards a transformed phenotype. Here we sought to identify the specific TBP-regulated gene targets that drive its ability to induce tumorigenesis. Using microarray analysis, our results reveal that increases in cellular TBP concentrations produce selective alterations in gene expression that include an enrichment for genes involved in angiogenesis. Accordingly, we find that TBP levels modulate VEGFA expression, the master regulator of angiogenesis. Increases in cellular TBP amounts induce VEGFA expression and secretion to enhance cell migration and tumor vascularization. TBP mediates changes in VEGFA transcription requiring its recruitment at a hypoxia-insensitive proximal TSS, revealing a mechanism for VEGF regulation under non-stress conditions. The results are clinically relevant as TBP expression is significantly increased in both colon adenocarcinomas as well as adenomas relative to normal tissue. Furthermore, TBP expression is positively correlated with VEGFA expression. Collectively, these studies support the idea that increases in TBP expression contribute to enhanced VEGFA transcription early in colorectal cancer development to drive tumorigenesis.
Collapse
Affiliation(s)
- Sandra A.S. Johnson
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Justin J. Lin
- Zymo Research, Irvine, California, United States of America
| | - Christopher J. Walkey
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael P. Leathers
- Department of Orthopedic Surgery, University of California Los Angeles, David Geffen School of Medicine, Los Angeles, California, United States of America
| | - Cristian Coarfa
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Deborah L. Johnson
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas, United States of America
| |
Collapse
|
18
|
Drosophila TRF2 and TAF9 regulate lipid droplet size and phospholipid fatty acid composition. PLoS Genet 2017; 13:e1006664. [PMID: 28273089 PMCID: PMC5362240 DOI: 10.1371/journal.pgen.1006664] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/22/2017] [Accepted: 02/28/2017] [Indexed: 11/19/2022] Open
Abstract
The general transcription factor TBP (TATA-box binding protein) and its associated factors (TAFs) together form the TFIID complex, which directs transcription initiation. Through RNAi and mutant analysis, we identified a specific TBP family protein, TRF2, and a set of TAFs that regulate lipid droplet (LD) size in the Drosophila larval fat body. Among the three Drosophila TBP genes, trf2, tbp and trf1, only loss of function of trf2 results in increased LD size. Moreover, TRF2 and TAF9 regulate fatty acid composition of several classes of phospholipids. Through RNA profiling, we found that TRF2 and TAF9 affects the transcription of a common set of genes, including peroxisomal fatty acid β-oxidation-related genes that affect phospholipid fatty acid composition. We also found that knockdown of several TRF2 and TAF9 target genes results in large LDs, a phenotype which is similar to that of trf2 mutants. Together, these findings provide new insights into the specific role of the general transcription machinery in lipid homeostasis. Lipid droplets (LD) are main lipid storage structures in most cells. The size of LDs varies greatly in different cell types or different metabolic states to accommodate cellular functions and metabolism demands. How cells regulate the lipid storage and LD dynamics is not fully understood. Here, we identified that general transcription factors, including a specific TBP (TATA-box binding protein) family protein TRF2 (TBP-related factor 2) and several TAFs (TBP-associated factors), regulate LD size in the fruitfly larval fat body. Moreover, quantitated lipid analysis reveals that TRF2 and TAF9 affect the fatty acid composition of several classes of phospholipids. We showed that TRF2 and TAF9 regulate transcription of several target genes, including peroxisomal fatty acid β-oxidation-related genes which likely mediate the effect of TRF2 and TAF9 on phospholipid fatty acid composition. We also found that overexpression of some target genes restores the LD phenotype in trf2 mutants. Our findings therefore reveal specific roles of general transcription factors in lipid homeostasis.
Collapse
|
19
|
Abstract
Obesity is a worldwide epidemic that predisposes individuals to cardiometabolic complications, such as type 2 diabetes mellitus (T2DM) and nonalcoholic fatty liver disease (NAFLD), which are all related to inappropriate ectopic lipid deposition. Identification of the pathogenic molecular mechanisms and effective therapeutic approaches are highly needed. The peroxisome proliferator-activated receptors (PPARs) modulate several biological processes that are perturbed in obesity, including inflammation, lipid and glucose metabolism and overall energy homeostasis. Here, we review how PPARs regulate the functions of adipose tissues, such as adipogenesis, lipid storage and adaptive thermogenesis, under healthy and pathological conditions. We also discuss the clinical use and mechanism of PPAR agonists in the treatment of obesity comorbidities such as dyslipidaemia, T2DM and NAFLD. First generation PPAR agonists, primarily those acting on PPARγ, are associated with adverse effects that outweigh their clinical benefits, which led to the discontinuation of their development. An improved understanding of the physiological roles of PPARs might, therefore, enable the development of safe, new PPAR agonists with improved therapeutic potential.
Collapse
Affiliation(s)
- Barbara Gross
- Université de Lille, INSERM, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Michal Pawlak
- International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
| | - Philippe Lefebvre
- Université de Lille, INSERM, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Bart Staels
- Université de Lille, INSERM, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| |
Collapse
|
20
|
Kikani CK, Wu X, Paul L, Sabic H, Shen Z, Shakya A, Keefe A, Villanueva C, Kardon G, Graves B, Tantin D, Rutter J. Pask integrates hormonal signaling with histone modification via Wdr5 phosphorylation to drive myogenesis. eLife 2016; 5. [PMID: 27661449 PMCID: PMC5035144 DOI: 10.7554/elife.17985] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/08/2016] [Indexed: 01/08/2023] Open
Abstract
PAS domain containing protein kinase (Pask) is an evolutionarily conserved protein kinase implicated in energy homeostasis and metabolic regulation across eukaryotic species. We now describe an unexpected role of Pask in promoting the differentiation of myogenic progenitor cells, embryonic stem cells and adipogenic progenitor cells. This function of Pask is dependent upon its ability to phosphorylate Wdr5, a member of several protein complexes including those that catalyze histone H3 Lysine 4 trimethylation (H3K4me3) during transcriptional activation. Our findings suggest that, during myoblast differentiation, Pask stimulates the conversion of repressive H3K4me1 to activating H3K4me3 marks on the promoter of the differentiation gene myogenin (Myog) via Wdr5 phosphorylation. This enhances accessibility of the MyoD transcription factor and enables transcriptional activation of the Myog promoter to initiate muscle differentiation. Thus, as an upstream kinase of Wdr5, Pask integrates signaling cues with the transcriptional network to regulate the differentiation of progenitor cells. DOI:http://dx.doi.org/10.7554/eLife.17985.001
Collapse
Affiliation(s)
- Chintan K Kikani
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Xiaoying Wu
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Litty Paul
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, United States.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Hana Sabic
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Zuolian Shen
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Arvind Shakya
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Alexandra Keefe
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Claudio Villanueva
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Gabrielle Kardon
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Barbara Graves
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, United States.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States.,Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States.,Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, United States
| |
Collapse
|
21
|
Langer D, Martianov I, Alpern D, Rhinn M, Keime C, Dollé P, Mengus G, Davidson I. Essential role of the TFIID subunit TAF4 in murine embryogenesis and embryonic stem cell differentiation. Nat Commun 2016; 7:11063. [PMID: 27026076 PMCID: PMC4820908 DOI: 10.1038/ncomms11063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 02/17/2016] [Indexed: 12/15/2022] Open
Abstract
TAF4 (TATA-binding protein-associated factor 4) and its paralogue TAF4b are components of the TFIID core module. We inactivated the murine Taf4a gene to address Taf4 function during embryogenesis. Here we show that Taf4a−/− embryos survive until E9.5 where primary germ layers and many embryonic structures are identified showing Taf4 is dispensable for their specification. In contrast, Taf4 is required for correct patterning of the trunk and anterior structures, ventral morphogenesis and proper heart positioning. Overlapping expression of Taf4a and Taf4b during embryogenesis suggests their redundancy at early stages. In agreement with this, Taf4a−/− embryonic stem cells (ESCs) are viable and comprise Taf4b-containing TFIID. Nevertheless, Taf4a−/− ESCs do not complete differentiation into glutamatergic neurons and cardiomyocytes in vitro due to impaired preinitiation complex formation at the promoters of critical differentiation genes. We define an essential role of a core TFIID TAF in differentiation events during mammalian embryogenesis. The role of TFIID core module TAFs (TATA-binding protein-associated factors) in embryogenesis is unknown. Here, the authors show that Taf4 is essential at mid-gestation and for complete neuronal differentiation of embryonic stem cells, but that Taf4a and Taf4b are redundant at early embryonic stages.
Collapse
Affiliation(s)
- Diana Langer
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Igor Martianov
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Daniel Alpern
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France.,L'École polytechnique fédérale de Lausanne, Route Cantonale, 1015 Lausanne, Switzerland
| | - Muriel Rhinn
- Department of Development and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Céline Keime
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Pascal Dollé
- Department of Development and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Gabrielle Mengus
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| |
Collapse
|
22
|
Malecova B, Dall'Agnese A, Madaro L, Gatto S, Coutinho Toto P, Albini S, Ryan T, Tora L, Puri PL. TBP/TFIID-dependent activation of MyoD target genes in skeletal muscle cells. eLife 2016; 5. [PMID: 26880551 PMCID: PMC4775216 DOI: 10.7554/elife.12534] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/21/2016] [Indexed: 02/07/2023] Open
Abstract
Change in the identity of the components of the transcription pre-initiation complex is proposed to control cell type-specific gene expression. Replacement of the canonical TFIID-TBP complex with TRF3/TBP2 was reported to be required for activation of muscle-gene expression. The lack of a developmental phenotype in TBP2 null mice prompted further analysis to determine whether TBP2 deficiency can compromise adult myogenesis. We show here that TBP2 null mice have an intact regeneration potential upon injury and that TBP2 is not expressed in established C2C12 muscle cell or in primary mouse MuSCs. While TFIID subunits and TBP are downregulated during myoblast differentiation, reduced amounts of these proteins form a complex that is detectable on promoters of muscle genes and is essential for their expression. This evidence demonstrates that TBP2 does not replace TBP during muscle differentiation, as previously proposed, with limiting amounts of TFIID-TBP being required to promote muscle-specific gene expression. DOI:http://dx.doi.org/10.7554/eLife.12534.001 The muscles that allow animal’s to move are built predominantly of cells called myofibers. Like other specialized cell types, these myofibers develop via a regulated set of events called differentiation. In adults, this phenomenon occurs when muscles regenerate after an injury, and new myofibers differentiate from so-called satellite cells that already reside within the muscles. Differentiation is regulated at the genetic level, and the development of myofibers relies on the activation of muscle-specific genes. A gene’s expression is typically controlled via a nearby regulatory region of DNA called a promoter that can be recognized by various molecular machines made from protein complexes. In most adult tissues, such regulatory machineries contain a complex called TFIID. Previously it was reported that the TFIID complex was eliminated from cells during muscle differentiation, and that an alternative protein complex called TBP2/TAF3 recognizes and regulates the promoters of muscle-specific genes. However, Malecova et al. have now discovered that TFIID is actually present, albeit at reduced amounts, in differentiated muscles and that it drives the activation of muscle-specific genes during differentiation. Further experiments also showed that the TBP2 protein is not required for differentiation of muscle cells or for the regeneration of injured muscles, and is actually absent in muscle cells. Further studies are now needed to explore how the TFIID-containing complex works with other regulatory protein complexes that are known to help make muscle-specific genes accessible to TFIID. It will also be important to study the relationship between the down-regulation of TFIID components and the activation of muscle-specific genes that typically occurs in mature myofbers. Together these efforts will allow the various aspects of gene regulation to be integrated, which will help provide a more complete understanding of the process of muscle differentiation. DOI:http://dx.doi.org/10.7554/eLife.12534.002
Collapse
Affiliation(s)
- Barbora Malecova
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Alessandra Dall'Agnese
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Luca Madaro
- Fondazione Santa Lucia - Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Sole Gatto
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Paula Coutinho Toto
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Sonia Albini
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Tammy Ryan
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Làszlò Tora
- Cellular Signaling and Nuclear Dynamics Program, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CU de Strasbourg, France
| | - Pier Lorenzo Puri
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States.,Fondazione Santa Lucia - Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| |
Collapse
|
23
|
Li L, Martinez SS, Hu W, Liu Z, Tjian R. A specific E3 ligase/deubiquitinase pair modulates TBP protein levels during muscle differentiation. eLife 2015; 4:e08536. [PMID: 26393420 PMCID: PMC4576175 DOI: 10.7554/elife.08536] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/24/2015] [Indexed: 01/23/2023] Open
Abstract
TFIID—a complex of TATA-binding protein (TBP) and TBP-associated factors (TAFs)—is a central component of the Pol II promoter recognition apparatus. Recent studies have revealed significant downregulation of TFIID subunits in terminally differentiated myocytes, hepatocytes and adipocytes. Here, we report that TBP protein levels are tightly regulated by the ubiquitin-proteasome system. Using an in vitro ubiquitination assay coupled with biochemical fractionation, we identified Huwe1 as an E3 ligase targeting TBP for K48-linked ubiquitination and proteasome-mediated degradation. Upregulation of Huwe1 expression during myogenesis induces TBP degradation and myotube differentiation. We found that Huwe1 activity on TBP is antagonized by the deubiquitinase USP10, which protects TBP from degradation. Thus, modulating the levels of both Huwe1 and USP10 appears to fine-tune the requisite degradation of TBP during myogenesis. Together, our study unmasks a previously unknown interplay between an E3 ligase and a deubiquitinating enzyme regulating TBP levels during cellular differentiation. DOI:http://dx.doi.org/10.7554/eLife.08536.001 Most animal cells specialize to perform particular roles that contribute to the survival of the animal in different ways. For example, the cells that form our muscles are able to contract, while other cells in the body are efficient at storing fat. The different types of cells develop from unspecialized cells, but it is not clear what controls this process to form a particular type of cell in the right place at the right time. The TATA-box binding protein (TBP) is one of a group of proteins that helps to activate the expression of genes in animal cells. Recent studies have revealed that TBP is deliberately destroyed by a group of proteins called the proteasome in muscle cells, in a type of liver cell, and in fat cells. Here, Li et al. used biochemical techniques to study the regulation of TBP during the formation of muscle cells from less specialist mouse cells called myoblasts. The experiments show that an enzyme called Huwe1 selectively adds a tag to TBP that marks TBP for destruction by the proteasome. Another protein called USP10 acts to remove the tags to prevent TBP from being destroyed. Therefore, it appears that changes in the levels of Huwe1 and USP10 fine-tune the amount of TBP that is degraded during the formation of muscle cells. Li et al.'s findings suggest that other proteins that are also involved in activating gene expression may also be destroyed as muscle cells form. The next step is to understand how important the degradation of these proteins is to the formation of other types of specialist cells. DOI:http://dx.doi.org/10.7554/eLife.08536.002
Collapse
Affiliation(s)
- Li Li
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | | | - Wenxin Hu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Zhe Liu
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Robert Tjian
- Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| |
Collapse
|
24
|
Andersson R, Sandelin A, Danko CG. A unified architecture of transcriptional regulatory elements. Trends Genet 2015; 31:426-33. [PMID: 26073855 DOI: 10.1016/j.tig.2015.05.007] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 11/19/2022]
Abstract
Gene expression is precisely controlled in time and space through the integration of signals that act at gene promoters and gene-distal enhancers. Classically, promoters and enhancers are considered separate classes of regulatory elements, often distinguished by histone modifications. However, recent studies have revealed broad similarities between enhancers and promoters, blurring the distinction: active enhancers often initiate transcription, and some gene promoters have the potential to enhance transcriptional output of other promoters. Here, we propose a model in which promoters and enhancers are considered a single class of functional element, with a unified architecture for transcription initiation. The context of interacting regulatory elements and the surrounding sequences determine local transcriptional output as well as the enhancer and promoter activities of individual elements.
Collapse
Affiliation(s)
- Robin Andersson
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA; Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
25
|
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.
Collapse
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.
| |
Collapse
|
26
|
Diversity in TAF proteomics: consequences for cellular differentiation and migration. Int J Mol Sci 2014; 15:16680-97. [PMID: 25244017 PMCID: PMC4200853 DOI: 10.3390/ijms150916680] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/25/2014] [Accepted: 08/27/2014] [Indexed: 12/31/2022] Open
Abstract
Development is a highly controlled process of cell proliferation and differentiation driven by mechanisms of dynamic gene regulation. Specific DNA binding factors for establishing cell- and tissue-specific transcriptional programs have been characterised in different cell and animal models. However, much less is known about the role of “core transcription machinery” during cell differentiation, given that general transcription factors and their spatiotemporally patterned activity govern different aspects of cell function. In this review, we focus on the role of TATA-box associated factor 4 (TAF4) and its functional isoforms generated by alternative splicing in controlling lineage-specific differentiation of normal mesenchymal stem cells and cancer stem cells. In the light of our recent findings, induction, control and maintenance of cell differentiation status implies diversification of the transcription initiation apparatus orchestrated by alternative splicing.
Collapse
|
27
|
Alpern D, Langer D, Ballester B, Le Gras S, Romier C, Mengus G, Davidson I. TAF4, a subunit of transcription factor II D, directs promoter occupancy of nuclear receptor HNF4A during post-natal hepatocyte differentiation. eLife 2014; 3:e03613. [PMID: 25209997 PMCID: PMC4359380 DOI: 10.7554/elife.03613] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 09/09/2014] [Indexed: 12/25/2022] Open
Abstract
The functions of the TAF subunits of mammalian TFIID in physiological processes remain poorly characterised. In this study, we describe a novel function of TAFs in directing genomic occupancy of a transcriptional activator. Using liver-specific inactivation in mice, we show that the TAF4 subunit of TFIID is required for post-natal hepatocyte maturation. TAF4 promotes pre-initiation complex (PIC) formation at post-natal expressed liver function genes and down-regulates a subset of embryonic expressed genes by increased RNA polymerase II pausing. The TAF4–TAF12 heterodimer interacts directly with HNF4A and in vivo TAF4 is necessary to maintain HNF4A-directed embryonic gene expression at post-natal stages and promotes HNF4A occupancy of functional cis-regulatory elements adjacent to the transcription start sites of post-natal expressed genes. Stable HNF4A occupancy of these regulatory elements requires TAF4-dependent PIC formation highlighting that these are mutually dependent events. Local promoter-proximal HNF4A–TFIID interactions therefore act as instructive signals for post-natal hepatocyte differentiation. DOI:http://dx.doi.org/10.7554/eLife.03613.001 To decode the information contained within a gene, a number of processes need to occur. For example, the DNA sequence that makes up the gene needs to be copied to make a molecule of RNA, which is then translated to build the corresponding protein. The first steps in the manufacture of RNA involve a structure called a ‘pre-initiation complex’ moving an enzyme called RNA polymerase II to the start of the gene that needs to be copied. The pre-initiation complex is made up of many types of protein, including a set of proteins called TAFs. However, the way that these proteins work in mammals is not well understood. There are good reasons for this: proteins are often studied by seeing what happens when the protein is removed, but many TAFs are so important that removing them is lethal. Alpern et al. have now studied the function of TAF4 by removing this protein from mouse liver cells. This causes severe hypoglycemia (that is, a drop in sugar levels in the blood). Moreover, it seems as if these cells start dying before they become fully mature. In liver cells lacking TAF4, some 1408 genes that are normally turned on just after birth are not properly switched on; these genes are necessary for the metabolic functions of the liver. Furthermore, 776 genes that are normally turned off after birth continue to be expressed. It seems that the absence of TAF4 sometimes disrupts the formation of the pre-initiation complex, which would slow down the production of RNA. However, it can also have the opposite effect by increasing the activity of RNA polymerase II, hence making too many copies of RNA from some genes. Alpern et al. also find that TAF4 is needed to allow a protein called HNF4A, which is important in the development of the liver and in controlling metabolism, to interact with over 7000 important DNA sequences. Mutations in HNF4A are responsible for a syndrome known as Maturity Onset of Diabetes in the Young. The next stage in this work will be to explore if these mutations influence the interaction between HNF4A and TAF4, and if they do, whether these changes contribute to this form of diabetes. DOI:http://dx.doi.org/10.7554/eLife.03613.002
Collapse
Affiliation(s)
- Daniil Alpern
- Department of Functional Genomics and Cancer, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/UDS, Illkirch, France
| | - Diana Langer
- Department of Functional Genomics and Cancer, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/UDS, Illkirch, France
| | - Benoit Ballester
- Laboratoire TAGC, Aix-Marseille Université, UMR1090, Marseille, France
| | - Stephanie Le Gras
- Department of Functional Genomics and Cancer, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/UDS, Illkirch, France
| | - Christophe Romier
- Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/UDS, Illkirch, France
| | - Gabrielle Mengus
- Department of Functional Genomics and Cancer, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/UDS, Illkirch, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/UDS, Illkirch, France
| |
Collapse
|
28
|
Gubelmann C, Schwalie PC, Raghav SK, Röder E, Delessa T, Kiehlmann E, Waszak SM, Corsinotti A, Udin G, Holcombe W, Rudofsky G, Trono D, Wolfrum C, Deplancke B. Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network. eLife 2014; 3:e03346. [PMID: 25163748 PMCID: PMC4359378 DOI: 10.7554/elife.03346] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/24/2014] [Indexed: 12/12/2022] Open
Abstract
Adipose tissue is a key determinant of whole body metabolism and energy homeostasis. Unraveling the regulatory mechanisms underlying adipogenesis is therefore highly relevant from a biomedical perspective. Our current understanding of fat cell differentiation is centered on the transcriptional cascades driven by the C/EBP protein family and the master regulator PPARγ. To elucidate further components of the adipogenic gene regulatory network, we performed a large-scale transcription factor (TF) screen overexpressing 734 TFs in mouse pre-adipocytes and probed their effect on differentiation. We identified 22 novel pro-adipogenic TFs and characterized the top ranking TF, ZEB1, as being essential for adipogenesis both in vitro and in vivo. Moreover, its expression levels correlate with fat cell differentiation potential in humans. Genomic profiling further revealed that this TF directly targets and controls the expression of most early and late adipogenic regulators, identifying ZEB1 as a central transcriptional component of fat cell differentiation. DOI:http://dx.doi.org/10.7554/eLife.03346.001 The growing rates of obesity and related metabolic diseases are a major public health concern worldwide. People who are overweight or obese are at increased risk for a range of diseases including diabetes and heart disease, which may reduce their quality of life and shorten their lifespans. Obese people have more, larger fat cells than individuals of healthy weight, and so understanding how the body creates fat cells may provide new insights into ways to prevent or treat obesity. Fat cells arise from a population of stem cells that can also give rise to bone cells and cartilage. Some of the proteins—called transcription factors—that work together to turn on the expression of genes needed for a stem cell to become a fat cell have been identified. However, the exact regulatory processes that cause an unspecialized cell to develop into a fat cell remain unclear. Gubelmann et al. set out to identify more of the transcription factors that cause stem cells to become fat cells. A high-throughput, automated process was used to test the effect of over-expressing each of 734 transcription factors in mouse cells that are primed to become fat cells. Twenty-six transcription factors were found to increase the number of these primed cells that became mature fat cells—most of which had not previously been shown to affect how fat cells develop. The most powerful driver of fat cell development was ZEB1: a transcription factor that has previously been implicated in many other biological processes. Most notably, ZEB1 was linked to a transition during development that allows cells to migrate to the correct location in the embryo, but also to a mechanism that allows cancerous cells to spread to new tissues. Using studies of mouse cells and live mice, computational analyses, and biopsies from obese patients, Gubelmann et al. show that ZEB1 regulates numerous other transcription factors that promote the development of fat cells. These include factors that initially set an unspecialized cell on the path to becoming a fat cell and those that guide the changes that occur as the fat cell matures. Further studies will be required to show whether the ZEB1 protein itself is needed to prime stem cells to start becoming fat cells. DOI:http://dx.doi.org/10.7554/eLife.03346.002
Collapse
Affiliation(s)
- Carine Gubelmann
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Petra C Schwalie
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sunil K Raghav
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Eva Röder
- Institute of Food Nutrition and Health, Eidgenössische Technische Hochschule Zürich, Schwerzenbach, Switzerland
| | - Tenagne Delessa
- Institute of Food Nutrition and Health, Eidgenössische Technische Hochschule Zürich, Schwerzenbach, Switzerland
| | - Elke Kiehlmann
- Institute of Food Nutrition and Health, Eidgenössische Technische Hochschule Zürich, Schwerzenbach, Switzerland
| | - Sebastian M Waszak
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andrea Corsinotti
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gilles Udin
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Wiebke Holcombe
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gottfried Rudofsky
- Ärztlicher Leiter Endokrinologie, Diabetologie und Klinische Ernährung Kantonsspital Olten, Olten, Switzerland
| | - Didier Trono
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Christian Wolfrum
- Institute of Food Nutrition and Health, Eidgenössische Technische Hochschule Zürich, Schwerzenbach, Switzerland
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| |
Collapse
|
29
|
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
Collapse
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
| |
Collapse
|
30
|
Abstract
Different members of the TAF family of proteins work in differentiated cells, such as motor neurons or brown fat cells, to control the expression of genes that are specific to each cell type.
Collapse
Affiliation(s)
- Katherine A Jones
- Katherine A Jones is in the Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
| |
Collapse
|
31
|
Abstract
Comparative genome analyses reveal that organismal complexity scales not with gene number but with gene regulation. Recent efforts indicate that the human genome likely contains hundreds of thousands of enhancers, with a typical gene embedded in a milieu of tens of enhancers. Proliferation of cis-regulatory DNAs is accompanied by increased complexity and functional diversification of transcriptional machineries recognizing distal enhancers and core promoters and by the high-order spatial organization of genetic elements. We review progress in unraveling one of the outstanding mysteries of modern biology: the dynamic communication of remote enhancers with target promoters in the specification of cellular identity.
Collapse
|
32
|
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
Collapse
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
| |
Collapse
|
33
|
Oger F, Dubois-Chevalier J, Gheeraert C, Avner S, Durand E, Froguel P, Salbert G, Staels B, Lefebvre P, Eeckhoute J. Peroxisome proliferator-activated receptor γ regulates genes involved in insulin/insulin-like growth factor signaling and lipid metabolism during adipogenesis through functionally distinct enhancer classes. J Biol Chem 2013; 289:708-22. [PMID: 24288131 DOI: 10.1074/jbc.m113.526996] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The nuclear receptor peroxisome proliferator-activated receptor (PPAR) is a transcription factor whose expression is induced during adipogenesis and that is required for the acquisition and control of mature adipocyte functions. Indeed, PPAR induces the expression of genes involved in lipid synthesis and storage through enhancers activated during adipocyte differentiation. Here, we show that PPAR also binds to enhancers already active in preadipocytes as evidenced by an active chromatin state including lower DNA methylation levels despite higher CpG content. These constitutive enhancers are linked to genes involved in the insulin/insulin-like growth factor signaling pathway that are transcriptionally induced during adipogenesis but to a lower extent than lipid metabolism genes, because of stronger basal expression levels in preadipocytes. This is consistent with the sequential involvement of hormonal sensitivity and lipid handling during adipocyte maturation and correlates with the chromatin structure dynamics at constitutive and activated enhancers. Interestingly, constitutive enhancers are evolutionary conserved and can be activated in other tissues, in contrast to enhancers controlling lipid handling genes whose activation is more restricted to adipocytes. Thus, PPAR utilizes both broadly active and cell type-specific enhancers to modulate the dynamic range of activation of genes involved in the adipogenic process.
Collapse
|
34
|
Guglielmi B, La Rochelle N, Tjian R. Gene-specific transcriptional mechanisms at the histone gene cluster revealed by single-cell imaging. Mol Cell 2013; 51:480-92. [PMID: 23973376 DOI: 10.1016/j.molcel.2013.08.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 05/20/2013] [Accepted: 07/31/2013] [Indexed: 10/26/2022]
Abstract
To bridge the gap between in vivo and in vitro molecular mechanisms, we dissected the transcriptional control of the endogenous histone gene cluster (His-C) by single-cell imaging. A combination of quantitative immunofluorescence, RNA FISH, and FRAP measurements revealed atypical promoter recognition complexes and differential transcription kinetics directing histone H1 versus core histone gene expression. While H1 is transcribed throughout S phase, core histones are only transcribed in a short pulse during early S phase. Surprisingly, no TFIIB or TFIID was detectable or functionally required at the initiation complexes of these promoters. Instead, a highly stable, preloaded TBP/TFIIA "pioneer" complex primes the rapid initiation of His-C transcription during early S phase. These results provide mechanistic insights for the role of gene-specific core promoter factors and implications for cell cycle-regulated gene expression.
Collapse
Affiliation(s)
- Benjamin Guglielmi
- Howard Hughes Medical Institute, Department of Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | | |
Collapse
|
35
|
Abstract
TATA-binding protein (TBP)-associated factor 7l (Taf7l; a paralogue of Taf7) and TBP-related factor 2 (Trf2) are components of the core promoter complex required for gene/tissue-specific transcription of protein-coding genes by RNA polymerase II. Previous studies reported that Taf7l knockout (KO) mice exhibit structurally abnormal sperm, reduced sperm count, weakened motility, and compromised fertility. Here we find that continued backcrossing of Taf7l(-/Y) mice from N5 to N9 produced KO males that are essentially sterile. Genome-wide expression profiling by mRNA-sequencing analysis of wild-type (WT) and Taf7l(-/Y) (KO) testes revealed that Taf7l ablation impairs the expression of many postmeiotic spermatogenic-specific as well as metabolic genes. Importantly, histological analysis of testes revealed that Taf7l(-/Y) mice develop postmeiotic arrest at the first stage of spermiogenesis, phenotypically similar to Trf2(-/-) mice, but distinct from Taf4b(-/-) mice. Indeed, we find that Taf7l and Trf2 coregulate postmeiotic genes, but none of Taf4b-regulated germ stem cell genes in testes. Genome-wide ChIP-sequencing studies indicate that TAF7L binds to promoters of activated postmeiotic genes in testis. Moreover, biochemical studies show that TAF7L associates with TRF2 both in vitro and in testis, suggesting that TAF7L likely cooperates directly with TRF2 at promoters of a subset of postmeiotic genes to regulate spermiogenesis. Our findings thus provide a previously undescribed mechanism for cell-type-specific transcriptional control involving an interaction between a "nonprototypic" core promoter recognition factor (Trf2) and an orphan TAF subunit (Taf7l) in mammalian testis-specific gene transcription.
Collapse
|