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Dolfini D, Imbriano C, Mantovani R. The role(s) of NF-Y in development and differentiation. Cell Death Differ 2024:10.1038/s41418-024-01388-1. [PMID: 39327506 DOI: 10.1038/s41418-024-01388-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 09/18/2024] [Accepted: 09/19/2024] [Indexed: 09/28/2024] Open
Abstract
NF-Y is a conserved sequence-specific trimeric Transcription Factor -TF- binding to the CCAAT element. We review here the role(s) in development, from pre-implantation embryo to terminally differentiated tissues, by rationalizing and commenting on genetic, genomic, epigenetic and biochemical studies. This effort brings to light the impact of NF-YA isoforms on stemness and differentiation, as well as binding to distal vs promoter proximal sites and connections with selected TFs.
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Affiliation(s)
- Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Carol Imbriano
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
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2
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Miyazaki H, Nishioka S, Yamanaka T, Abe M, Imamura Y, Miyasaka T, Kakuda N, Oohashi T, Shimogori T, Yamakawa K, Ikawa M, Nukina N. Generation and characterization of cerebellar granule neurons specific knockout mice of Golli-MBP. Transgenic Res 2024; 33:99-117. [PMID: 38684589 PMCID: PMC11176102 DOI: 10.1007/s11248-024-00382-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/02/2024] [Indexed: 05/02/2024]
Abstract
Golli-myelin basic proteins, encoded by the myelin basic protein gene, are widely expressed in neurons and oligodendrocytes in the central nervous system. Further, prior research has shown that Golli-myelin basic protein is necessary for myelination and neuronal maturation during central nervous system development. In this study, we established Golli-myelin basic protein-floxed mice to elucidate the cell-type-specific effects of Golli-myelin basic protein knockout through the generation of conditional knockout mice (Golli-myelin basic proteinsfl/fl; E3CreN), in which Golli-myelin basic proteins were specifically deleted in cerebellar granule neurons, where Golli-myelin basic proteins are expressed abundantly in wild-type mice. To investigate the role of Golli-myelin basic proteins in cerebellar granule neurons, we further performed histopathological analyses of these mice, with results indicating no morphological changes or degeneration of the major cellular components of the cerebellum. Furthermore, behavioral analysis showed that Golli-myelin basic proteinsfl/fl; E3CreN mice were healthy and did not display any abnormal behavior. These results suggest that the loss of Golli-myelin basic proteins in cerebellar granule neurons does not lead to cerebellar perturbations or behavioral abnormalities. This mouse model could therefore be employed to analyze the effect of Golli-myelin basic protein deletion in specific cell types of the central nervous system, such as other neuronal cells and oligodendrocytes, or in lymphocytes of the immune system.
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Grants
- 16K07005 Grants-in-Aid from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan
- 16H06276 Grants-in-Aid from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan
- 17H01564 Grants-in-Aid from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan
- 20ek0109310h0003 AMED
- The Center for Baby Science, Doshisha University
- Takeda Science Foundation
- Ichiro Kanehara Foundation for the Promotion of Medical Sciences and Medical Care
- Okayama University
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Affiliation(s)
- Haruko Miyazaki
- Laboratory of Structural Neuropathology, Graduate School of Brain Science, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe-shi, Kyoto, 610-0394, Japan.
- Department of Molecular Biology and Biochemistry, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan.
| | - Saki Nishioka
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomoyuki Yamanaka
- Laboratory of Structural Neuropathology, Graduate School of Brain Science, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe-shi, Kyoto, 610-0394, Japan
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, 951-8585, Japan
| | - Manabu Abe
- Department of Animal Model Development, Brain Research Institute, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, 951-8585, Japan
| | - Yukio Imamura
- Laboratory of Structural Neuropathology, Graduate School of Brain Science, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe-shi, Kyoto, 610-0394, Japan
| | - Tomohiro Miyasaka
- Faculty of Life and Medical Sciences, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe-shi, Kyoto, 610-0394, Japan
| | - Nobuto Kakuda
- Faculty of Life and Medical Sciences, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe-shi, Kyoto, 610-0394, Japan
| | - Toshitaka Oohashi
- Department of Molecular Biology and Biochemistry, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Tomomi Shimogori
- Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Kazuhiro Yamakawa
- Laboratory for Neurogenetics, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
- Department of Neurodevelopmental Disorder Genetics, Institute of Brain Sciences, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Nobuyuki Nukina
- Laboratory of Structural Neuropathology, Graduate School of Brain Science, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe-shi, Kyoto, 610-0394, Japan.
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3
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Olechnowicz A, Blatkiewicz M, Jopek K, Isalan M, Mielcarek M, Rucinski M. Deregulated Transcriptome as a Platform for Adrenal Huntington's Disease-Related Pathology. Int J Mol Sci 2024; 25:2176. [PMID: 38396853 PMCID: PMC10888552 DOI: 10.3390/ijms25042176] [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: 01/05/2024] [Revised: 01/31/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder that affects mainly the central nervous system (CNS) by inducing progressive deterioration in both its structure and function. In recent years, there has been growing interest in the impact of HD on peripheral tissue function. Herein, we used the R6/2 mouse model of HD to investigate the influence of the disease on adrenal gland functioning. A transcriptomic analysis conducted using a well-established quantitative method, an Affymetrix array, revealed changes in gene expression in the R6/2 model compared to genetic background controls. For the first time, we identified disruptions in cholesterol and sterol metabolism, blood coagulation, and xenobiotic metabolism in HD adrenal glands. This study showed that the disrupted expression of these genes may contribute to the underlying mechanisms of Huntington's disease. Our findings may contribute to developing a better understanding of Huntington's disease progression and aid in the development of novel diagnostic or therapeutic approaches.
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Affiliation(s)
- Anna Olechnowicz
- Department of Histology and Embryology, Poznan University of Medical Sciences, 61-701 Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Małgorzata Blatkiewicz
- Department of Histology and Embryology, Poznan University of Medical Sciences, 61-701 Poznan, Poland
| | - Karol Jopek
- Department of Histology and Embryology, Poznan University of Medical Sciences, 61-701 Poznan, Poland
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Michal Mielcarek
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Marcin Rucinski
- Department of Histology and Embryology, Poznan University of Medical Sciences, 61-701 Poznan, Poland
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Saito-Diaz K, James C, Patel AJ, Zeltner N. Isolation of human pluripotent stem cell-derived sensory neuron subtypes by immunopanning. Front Cell Dev Biol 2023; 11:1101423. [PMID: 37206924 PMCID: PMC10189519 DOI: 10.3389/fcell.2023.1101423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/12/2023] [Indexed: 05/21/2023] Open
Abstract
Sensory neurons (SNs) detect a wide range of information from the body and the environment that is critical for homeostasis. There are three main subtypes of SNs: nociceptors, mechanoreceptors, and proprioceptors, which express different membrane proteins, such as TRKA, TRKB, or TRKC, respectively. Human pluripotent stem cell technology provides an ideal platform to study development and diseases of SNs, however there is not a viable method to isolate individual SN subtype for downstream analysis available. Here, we employ the method immunopanning to isolate each SN subtype. This method is very gentle and allows proper survival after the isolation. We use antibodies against TRKA, TRKB, and TRKC to isolate nociceptors, mechanoreceptors, and proprioceptors, respectively. We show that our cultures are enriched for each subtype and express their respective subtype markers. Furthermore, we show that the immunopanned SNs are electrically active and respond to specific stimuli. Thus, our method can be used to purify viable neuronal subtypes using respective membrane proteins for downstream studies.
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Affiliation(s)
- Kenyi Saito-Diaz
- Center for Molecular Medicine, University of Georgia, Athens, GA, United States
| | - Christina James
- Center for Molecular Medicine, University of Georgia, Athens, GA, United States
| | - Archie Jayesh Patel
- Center for Molecular Medicine, University of Georgia, Athens, GA, United States
| | - Nadja Zeltner
- Center for Molecular Medicine, University of Georgia, Athens, GA, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Department of Cellular Biology, University of Georgia, Athens, GA, United States
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Troshev D, Blokhin V, Ukrainskaya V, Kolacheva A, Ugrumov M. Isolation of living dopaminergic neurons labeled with a fluorescent ligand of the dopamine transporter from mouse substantia nigra as a new tool for basic and applied research. Front Mol Neurosci 2022; 15:1020070. [PMID: 36568278 PMCID: PMC9780273 DOI: 10.3389/fnmol.2022.1020070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Dopaminergic neurons (DNs) of the nigrostriatal system control the motor function, and their degeneration leads to the development of Parkinson's disease (PD). A stumbling block in the study of DNs in the whole substantia nigra (SN) is the lack of tools to analyze the expression of most of the genes involved in neurotransmission, neurodegeneration, and neuroplasticity, since they are also expressed in other cells of the SN. Therefore, this study aimed to develop a fluorescence-activated cell sorting method for isolating living DNs from the SN of wild-type mice using two fluorescent dyes, DRAQ5 (nuclear stain) and a dopamine uptake inhibitor GBR 12909 coupled to a fluorophore (DN stain). We have developed a method for selecting a population of DNs from the SN of mice, as evidenced by: (i) immunopositivity of 95% of the sorted cells for tyrosine hydroxylase, the first enzyme of dopamine synthesis; (ii) the sorted cells expressing the genes for specific proteins of the dopaminergic phenotype, tyrosine hydroxylase, the dopamine transporter, and vesicular monoamine transporter 2 and non-specific proteins, such as aromatic L-amino acid decarboxylase, non-specific enzyme of dopamine synthesis. We then compared the changes in gene expression found in the sorted DNs and in the SN homogenate in a PD model we developed, reproduced in mice by treatment with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Using quantitative PCR, we obtained evidence of the same changes in the expression of specific genes in the sorted DNs of SN and in the SN homogenate of a MPTP mouse model of PD, compared with the control. The undoubted advantage of our approach is the possibility of obtaining a large amount of readily available and relatively cheap primary material (SN) from wild-type mice, which can be used to solve both research and applied problems. In addition, this method can be easily adapted to the isolation of DNs from the SN in other animal species, including non-human primates.
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Affiliation(s)
- Dmitry Troshev
- Laboratory of Neural and Neuroendocrine Regulations, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Victor Blokhin
- Laboratory of Neural and Neuroendocrine Regulations, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Valeria Ukrainskaya
- Laboratory of Biocatalysis, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anna Kolacheva
- Laboratory of Neural and Neuroendocrine Regulations, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Michael Ugrumov
- Laboratory of Neural and Neuroendocrine Regulations, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia,*Correspondence: Michael Ugrumov,
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Kim C, Yousefian-Jazi A, Choi SH, Chang I, Lee J, Ryu H. Non-Cell Autonomous and Epigenetic Mechanisms of Huntington's Disease. Int J Mol Sci 2021; 22:12499. [PMID: 34830381 PMCID: PMC8617801 DOI: 10.3390/ijms222212499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Huntington's disease (HD) is a rare neurodegenerative disorder caused by an expansion of CAG trinucleotide repeat located in the exon 1 of Huntingtin (HTT) gene in human chromosome 4. The HTT protein is ubiquitously expressed in the brain. Specifically, mutant HTT (mHTT) protein-mediated toxicity leads to a dramatic degeneration of the striatum among many regions of the brain. HD symptoms exhibit a major involuntary movement followed by cognitive and psychiatric dysfunctions. In this review, we address the conventional role of wild type HTT (wtHTT) and how mHTT protein disrupts the function of medium spiny neurons (MSNs). We also discuss how mHTT modulates epigenetic modifications and transcriptional pathways in MSNs. In addition, we define how non-cell autonomous pathways lead to damage and death of MSNs under HD pathological conditions. Lastly, we overview therapeutic approaches for HD. Together, understanding of precise neuropathological mechanisms of HD may improve therapeutic approaches to treat the onset and progression of HD.
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Affiliation(s)
- Chaebin Kim
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (C.K.); (A.Y.-J.); (S.-H.C.)
| | - Ali Yousefian-Jazi
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (C.K.); (A.Y.-J.); (S.-H.C.)
| | - Seung-Hye Choi
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (C.K.); (A.Y.-J.); (S.-H.C.)
| | - Inyoung Chang
- Department of Biology, Boston University, Boston, MA 02215, USA;
| | - Junghee Lee
- Boston University Alzheimer’s Disease Research Center, Boston University, Boston, MA 02118, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
- VA Boston Healthcare System, Boston, MA 02130, USA
| | - Hoon Ryu
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (C.K.); (A.Y.-J.); (S.-H.C.)
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Seefelder M, Kochanek S. A meta-analysis of transcriptomic profiles of Huntington's disease patients. PLoS One 2021; 16:e0253037. [PMID: 34111223 PMCID: PMC8191979 DOI: 10.1371/journal.pone.0253037] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/27/2021] [Indexed: 12/22/2022] Open
Abstract
Description of robust transcriptomic alterations in Huntington’s disease is essential to identify targets for biochemical studies and drug development. We analysed publicly available transcriptome data from the brain and blood of 220 HD patients and 241 healthy controls and identified 737 and 661 genes with robustly altered mRNA levels in the brain and blood of HD patients, respectively. In the brain, a subnetwork of 320 genes strongly correlated with HD and was enriched in transport-related genes. Bioinformatical analysis of this subnetwork highlighted CDC42, PAK1, YWHAH, NFY, DLX1, HMGN3, and PRMT3. Moreover, we found that CREB1 can regulate 78.0% of genes whose mRNA levels correlated with HD in the blood of patients. Alterations in protein transport, metabolism, transcriptional regulation, and CDC42-mediated functions are likely central features of HD. Further our data substantiate the role of transcriptional regulators that have not been reported in the context of HD (e.g. DLX1, HMGN3 and PRMT3) and strongly suggest dysregulation of NFY and its target genes across tissues. A large proportion of the identified genes such as CDC42 were also altered in Parkinson’s (PD) and Alzheimer’s disease (AD). The observed dysregulation of CDC42 and YWHAH in samples from HD, AD and PD patients indicates that those genes and their upstream regulators may be interesting therapeutic targets.
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Affiliation(s)
- Manuel Seefelder
- Department of Gene Therapy, Ulm University, Ulm, Germany
- * E-mail:
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Donaldson J, Powell S, Rickards N, Holmans P, Jones L. What is the Pathogenic CAG Expansion Length in Huntington's Disease? J Huntingtons Dis 2021; 10:175-202. [PMID: 33579866 PMCID: PMC7990448 DOI: 10.3233/jhd-200445] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Huntington's disease (HD) (OMIM 143100) is caused by an expanded CAG repeat tract in the HTT gene. The inherited CAG length is known to expand further in somatic and germline cells in HD subjects. Age at onset of the disease is inversely correlated with the inherited CAG length, but is further modulated by a series of genetic modifiers which are most likely to act on the CAG repeat in HTT that permit it to further expand. Longer repeats are more prone to expansions, and this expansion is age dependent and tissue-specific. Given that the inherited tract expands through life and most subjects develop disease in mid-life, this implies that in cells that degenerate, the CAG length is likely to be longer than the inherited length. These findings suggest two thresholds- the inherited CAG length which permits further expansion, and the intracellular pathogenic threshold, above which cells become dysfunctional and die. This two-step mechanism has been previously proposed and modelled mathematically to give an intracellular pathogenic threshold at a tract length of 115 CAG (95% confidence intervals 70- 165 CAG). Empirically, the intracellular pathogenic threshold is difficult to determine. Clues from studies of people and models of HD, and from other diseases caused by expanded repeat tracts, place this threshold between 60- 100 CAG, most likely towards the upper part of that range. We assess this evidence and discuss how the intracellular pathogenic threshold in manifest disease might be better determined. Knowing the cellular pathogenic threshold would be informative for both understanding the mechanism in HD and deploying treatments.
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Affiliation(s)
- Jasmine Donaldson
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Sophie Powell
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Nadia Rickards
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Lesley Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
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Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y. Sci Rep 2020; 10:21714. [PMID: 33303918 PMCID: PMC7728767 DOI: 10.1038/s41598-020-78682-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/27/2020] [Indexed: 11/09/2022] Open
Abstract
A heterotrimeric transcription factor NF-Y is crucial for cell-cycle progression in various types of cells. In contrast, studies using NF-YA knockout mice have unveiled its essential role in endoplasmic reticulum (ER) homeostasis in neuronal cells. However, whether NF-Y modulates a different transcriptome to mediate distinct cellular functions remains obscure. Here, we knocked down NF-Y in two types of neuronal cells, neuro2a neuroblastoma cells and mouse brain striatal cells, and performed gene expression profiling. We found that down-regulated genes preferentially contained NF-Y-binding motifs in their proximal promoters, and notably enriched genes related to ER functions rather than those for cell cycle. This contrasts with the profiling data of HeLa and embryonic stem cells in which distinct down-regulation of cell cycle-related genes was observed. Clustering analysis further identified several functional clusters where populations of the down-regulated genes were highly distinct. Further analyses using chromatin immunoprecipitation and RNA-seq data revealed that the transcriptomic difference was not correlated with DNA binding of NF-Y but with splicing of NF-YA. These data suggest that neuronal cells have a different type of transcriptome in which ER-related genes are dominantly modulated by NF-Y, and imply that NF-YA splicing alteration could be involved in this cell type-specific gene modulation.
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