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Bose A, Schuster K, Kodali C, Sonam S, Smith-Bolton R. The pioneer transcription factor Zelda facilitates the exit from regeneration and restoration of patterning in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596672. [PMID: 38854062 PMCID: PMC11160785 DOI: 10.1101/2024.05.30.596672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
For a damaged tissue to regenerate, the injured site must repair the wound, proliferate, and restore the correct patterning and cell types. We found that Zelda, a pioneer transcription factor largely known for its role in embryonic zygotic genome activation, is dispensable for normal wing development but crucial for wing disc patterning during regeneration. Impairing Zelda function during disc regeneration resulted in adult wings with a plethora of cell fate errors, affecting the veins, margins, and posterior compartment identity. Using CUT&RUN, we identified and validated targets of Zelda including the cell fate genes cut, Delta and achaete, which failed to return to their normal expression patterns upon loss of Zelda. In addition, Zelda controls expression of factors previously established to preserve cell fate during regeneration like taranis and osa, which stabilizes engrailed expression during regeneration, thereby preserving posterior identity. Finally, Zelda ensures proper expression of the integrins encoded by multiple edematous wings and myospheroid during regeneration to prevent blisters in the resuting adult wing. Thus, Zelda is crucial for maintaining cell fate and structural architecture of the regenerating tissue.
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Affiliation(s)
- Anish Bose
- Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Keaton Schuster
- Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chandril Kodali
- Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Surabhi Sonam
- Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rachel Smith-Bolton
- Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Akpoghiran O, Afonso DJS, Zhang Y, Koh K. TARANIS Interacts with VRILLE and PDP1 to Modulate the Circadian Transcriptional Feedback Mechanism in Drosophila. J Neurosci 2024; 44:e0922232023. [PMID: 38296648 PMCID: PMC10860567 DOI: 10.1523/jneurosci.0922-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 11/18/2023] [Accepted: 11/22/2023] [Indexed: 02/02/2024] Open
Abstract
The molecular clock that generates daily rhythms of behavior and physiology consists of interlocked transcription-translation feedback loops. In Drosophila, the primary feedback loop involving the CLOCK-CYCLE transcriptional activators and the PERIOD-TIMELESS transcriptional repressors is interlocked with a secondary loop involving VRILLE (VRI) and PAR DOMAIN PROTEIN 1 (PDP1), a repressor and activator of Clock transcription, respectively. Whereas extensive studies have found numerous transcriptional, translational, and posttranslational modulators of the primary loop, relatively little is known about the secondary loop. In this study, using male and female flies as well as cultured cells, we demonstrate that TARANIS (TARA), a Drosophila homolog of the TRIP-Br/SERTAD family of transcriptional coregulators, functions with VRI and PDP1 to modulate the circadian period and rhythm strength. Knocking down tara reduces rhythm amplitude and can shorten the period length, while overexpressing TARA lengthens the circadian period. Additionally, tara mutants exhibit reduced rhythmicity and lower expression of the PDF neuropeptide. We find that TARA can form a physical complex with VRI and PDP1, enhancing their repressor and activator functions, respectively. The conserved SERTA domain of TARA is required to regulate the transcriptional activity of VRI and PDP1, and its deletion leads to reduced locomotor rhythmicity. Consistent with TARA's role in enhancing VRI and PDP1 activity, overexpressing tara has a similar effect on the circadian period and rhythm strength as simultaneously overexpressing vri and Pdp1 Together, our results suggest that TARA modulates circadian behavior by enhancing the transcriptional activity of VRI and PDP1.
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Affiliation(s)
- Oghenerukevwe Akpoghiran
- Department of Neuroscience, the Farber Institute for Neurosciences, and Synaptic Biology Center, Thomas Jefferson University, Philadelphia 19107, Pennsylvania
| | - Dinis J S Afonso
- Department of Neuroscience, the Farber Institute for Neurosciences, and Synaptic Biology Center, Thomas Jefferson University, Philadelphia 19107, Pennsylvania
| | - Yanan Zhang
- Department of Neuroscience, the Farber Institute for Neurosciences, and Synaptic Biology Center, Thomas Jefferson University, Philadelphia 19107, Pennsylvania
| | - Kyunghee Koh
- Department of Neuroscience, the Farber Institute for Neurosciences, and Synaptic Biology Center, Thomas Jefferson University, Philadelphia 19107, Pennsylvania
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Akpoghiran O, Afonso DJ, Zhang Y, Koh K. TARANIS interacts with VRILLE and PDP1 to modulate the circadian transcriptional feedback mechanism in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541420. [PMID: 38076905 PMCID: PMC10705542 DOI: 10.1101/2023.05.19.541420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
The molecular clock that generates daily rhythms of behavior and physiology consists of interlocked transcription-translation feedback loops. In Drosophila, the primary feedback loop involving the CLOCK-CYCLE transcriptional activators and the PERIOD-TIMELESS transcriptional repressors is interlocked with a secondary loop involving VRILLE (VRI) and PAR DOMAIN PROTEIN 1 (PDP1), a repressor and activator of Clock transcription, respectively. Whereas extensive studies have found numerous transcriptional, translational, and post-translational modulators of the primary loop, relatively little is known about the secondary loop. In this study, using male and female flies as well as cultured cells, we demonstrate that TARANIS (TARA), a Drosophila homolog of the TRIP-Br/SERTAD family of transcriptional coregulators, functions with VRI and PDP1 to modulate the circadian period and rhythm strength. Knocking down tara reduces rhythm amplitude and can shorten the period length, while overexpressing TARA lengthens the circadian period. Additionally, tara mutants exhibit reduced rhythmicity and lower expression of the PDF neuropeptide. We find that TARA can form a physical complex with VRI and PDP1, enhancing their repressor and activator functions, respectively. The conserved SERTA domain of TARA is required to regulate the transcriptional activity of VRI and PDP1, and its deletion leads to reduced locomotor rhythmicity. Consistent with TARA's role in enhancing VRI and PDP1 activity, overexpressing tara has a similar effect on the circadian period and rhythm strength as simultaneously overexpressing vri and Pdp1. Together, our results suggest that TARA modulates circadian behavior by enhancing the transcriptional activity of VRI and PDP1.
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Affiliation(s)
- Oghenerukevwe Akpoghiran
- Department of Neuroscience, the Farber Institute for Neurosciences, and Synaptic Biology Center, Thomas Jefferson University, Philadelphia, USA. 19107
| | - Dinis J.S. Afonso
- Department of Neuroscience, the Farber Institute for Neurosciences, and Synaptic Biology Center, Thomas Jefferson University, Philadelphia, USA. 19107
| | - Yanan Zhang
- Department of Neuroscience, the Farber Institute for Neurosciences, and Synaptic Biology Center, Thomas Jefferson University, Philadelphia, USA. 19107
| | - Kyunghee Koh
- Department of Neuroscience, the Farber Institute for Neurosciences, and Synaptic Biology Center, Thomas Jefferson University, Philadelphia, USA. 19107
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Tian Y, Smith-Bolton RK. Regulation of growth and cell fate during tissue regeneration by the two SWI/SNF chromatin-remodeling complexes of Drosophila. Genetics 2021; 217:1-16. [PMID: 33683366 DOI: 10.1093/genetics/iyaa028] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 11/10/2020] [Indexed: 11/12/2022] Open
Abstract
To regenerate, damaged tissue must heal the wound, regrow to the proper size, replace the correct cell types, and return to the normal gene-expression program. However, the mechanisms that temporally and spatially control the activation or repression of important genes during regeneration are not fully understood. To determine the role that chromatin modifiers play in regulating gene expression after tissue damage, we induced ablation in Drosophila melanogaster imaginal wing discs, and screened for chromatin regulators that are required for epithelial tissue regeneration. Here, we show that many of these genes are indeed important for promoting or constraining regeneration. Specifically, the two SWI/SNF chromatin-remodeling complexes play distinct roles in regulating different aspects of regeneration. The PBAP complex regulates regenerative growth and developmental timing, and is required for the expression of JNK signaling targets and the growth promoter Myc. By contrast, the BAP complex ensures correct patterning and cell fate by stabilizing the expression of the posterior gene engrailed. Thus, both SWI/SNF complexes are essential for proper gene expression during tissue regeneration, but they play distinct roles in regulating growth and cell fate.
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Affiliation(s)
- Yuan Tian
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rachel K Smith-Bolton
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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5
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Dutta P, Nath S, Li J, Li WX. Drosophila SERTAD domain protein Taranis is required in somatic cells for maintenance of male germline stem cells. Dev Dyn 2020; 250:237-248. [PMID: 32969117 DOI: 10.1002/dvdy.255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Polycomb proteins are essential for maintaining stem cell identity across different stem cell niches. However, how they function to maintain stem cell niches is not fully understood. RESULTS Here we show that the SERTAD protein Taranis (Tara), which is a Polycomb-trithorax group protein, is expressed in the adult testis niche and plays a role in its maintenance in Drosophila. We found that tara is expressed in early cyst cells, likely including somatic cyst stem cells (CySCs) of Drosophila male testis tip region, which houses both germline and somatic cyst stem cells along with the hub cells, forming the stem cell niche. Consistent with its expression, we found that, while loss of tara in germline cells only had minimal effects, tara knockdown in all cells or only in somatic cells of the niche reduced the number of not only somatic cells, but also germline stem cells (GSCs). We further found that Tara might antagonize Notch signaling in CySCs to maintain the stem cell niche. CONCLUSIONS Our studies suggest that Tara might function in somatic CySCs for GSC maintenance in the Drosophila testis.
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Affiliation(s)
- Pranabananda Dutta
- Department of Medicine, University of California San Diego, La Jolla, California, USA.,Division of Cancer Research and Training, Department of Medicine, Charles R. Drew University of Medicine and Science, Los Angeles, California, USA
| | - Soma Nath
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Jinghong Li
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Willis X Li
- Department of Medicine, University of California San Diego, La Jolla, California, USA
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Zhang CU, Cadigan KM. The matrix protein Tiggrin regulates plasmatocyte maturation in Drosophila larva. Development 2017; 144:2415-2427. [PMID: 28526755 DOI: 10.1242/dev.149641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/11/2017] [Indexed: 01/24/2023]
Abstract
The lymph gland (LG) is a major source of hematopoiesis during Drosophila development. In this tissue, prohemocytes differentiate into multiple lineages, including macrophage-like plasmatocytes, which comprise the vast majority of mature hemocytes. Previous studies have uncovered genetic pathways that regulate prohemocyte maintenance and some cell fate choices between hemocyte lineages. However, less is known about how the plasmatocyte pool of the LG is established and matures. Here, we report that Tiggrin, a matrix protein expressed in the LG, is a specific regulator of plasmatocyte maturation. Tiggrin mutants exhibit precocious maturation of plasmatocytes, whereas Tiggrin overexpression blocks this process, resulting in a buildup of intermediate progenitors (IPs) expressing prohemocyte and hemocyte markers. These IPs likely represent a transitory state in prohemocyte to plasmatocyte differentiation. We also found that overexpression of Wee1 kinase, which slows G2/M progression, results in a phenotype similar to Tiggrin overexpression, whereas String/Cdc25 expression phenocopies Tiggrin mutants. Further analysis revealed that Wee1 inhibits plasmatocyte maturation through upregulation of Tiggrin transcription. Our results elucidate connections between the extracellular matrix and cell cycle regulators in the regulation of hematopoiesis.
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Affiliation(s)
- Chen U Zhang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ken M Cadigan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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7
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Abstract
Sleep is essential for health and cognition, but the molecular and neural mechanisms of sleep regulation are not well understood. We recently reported the identification of TARANIS (TARA) as a sleep-promoting factor that acts in a previously unknown arousal center in Drosophila. tara mutants exhibit a dose-dependent reduction in sleep amount of up to ∼60%. TARA and its mammalian homologs, the Trip-Br (Transcriptional Regulators Interacting with PHD zinc fingers and/or Bromodomains) family of proteins, are primarily known as transcriptional coregulators involved in cell cycle progression, and contain a conserved Cyclin-A (CycA) binding homology domain. We found that tara and CycA synergistically promote sleep, and CycA levels are reduced in tara mutants. Additional data demonstrated that Cyclin-dependent kinase 1 (Cdk1) antagonizes tara and CycA to promote wakefulness. Moreover, we identified a subset of CycA expressing neurons in the pars lateralis, a brain region proposed to be analogous to the mammalian hypothalamus, as an arousal center. In this Extra View article, we report further characterization of tara mutants and provide an extended discussion of our findings and future directions within the framework of a working model, in which a network of cell cycle genes, tara, CycA, and Cdk1, interact in an arousal center to regulate sleep.
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Affiliation(s)
- Dinis J S Afonso
- a Department of Neuroscience ; the Farber Institute for Neurosciences; and Kimmel Cancer Center; Thomas Jefferson University ; Philadelphia , PA USA.,b Life and Health Sciences Research Institute (ICVS); School of Health Sciences; University of Minho ; 4710-057 Braga , Portugal.,c ICVS/3B's; PT Government Associate Laboratory ; 4710-057 Braga/Guimarães ; Portugal
| | - Daniel R Machado
- a Department of Neuroscience ; the Farber Institute for Neurosciences; and Kimmel Cancer Center; Thomas Jefferson University ; Philadelphia , PA USA.,b Life and Health Sciences Research Institute (ICVS); School of Health Sciences; University of Minho ; 4710-057 Braga , Portugal.,c ICVS/3B's; PT Government Associate Laboratory ; 4710-057 Braga/Guimarães ; Portugal
| | - Kyunghee Koh
- a Department of Neuroscience ; the Farber Institute for Neurosciences; and Kimmel Cancer Center; Thomas Jefferson University ; Philadelphia , PA USA
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Wang GZ, Hickey SL, Shi L, Huang HC, Nakashe P, Koike N, Tu BP, Takahashi JS, Konopka G. Cycling Transcriptional Networks Optimize Energy Utilization on a Genome Scale. Cell Rep 2015; 13:1868-80. [PMID: 26655902 DOI: 10.1016/j.celrep.2015.10.043] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 09/08/2015] [Accepted: 10/14/2015] [Indexed: 12/22/2022] Open
Abstract
Genes expressing circadian RNA rhythms are enriched for metabolic pathways, but the adaptive significance of cyclic gene expression remains unclear. We estimated the genome-wide synthetic and degradative cost of transcription and translation in three organisms and found that the cost of cycling genes is strikingly higher compared to non-cycling genes. Cycling genes are expressed at high levels and constitute the most costly proteins to synthesize in the genome. We demonstrate that metabolic cycling is accelerated in yeast grown under higher nutrient flux and the number of cycling genes increases ∼40%, which are achieved by increasing the amplitude and not the mean level of gene expression. These results suggest that rhythmic gene expression optimizes the metabolic cost of global gene expression and that highly expressed genes have been selected to be downregulated in a cyclic manner for energy conservation.
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Affiliation(s)
- Guang-Zhong Wang
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Stephanie L Hickey
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lei Shi
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hung-Chung Huang
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prachi Nakashe
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nobuya Koike
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benjamin P Tu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joseph S Takahashi
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Genevieve Konopka
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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9
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Taranis Protects Regenerating Tissue from Fate Changes Induced by the Wound Response in Drosophila. Dev Cell 2015; 34:119-28. [DOI: 10.1016/j.devcel.2015.04.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/25/2015] [Accepted: 04/23/2015] [Indexed: 12/15/2022]
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10
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Afonso DJS, Liu D, Machado DR, Pan H, Jepson JEC, Rogulja D, Koh K. TARANIS Functions with Cyclin A and Cdk1 in a Novel Arousal Center to Control Sleep in Drosophila. Curr Biol 2015; 25:1717-26. [PMID: 26096977 DOI: 10.1016/j.cub.2015.05.037] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 04/20/2015] [Accepted: 05/19/2015] [Indexed: 12/22/2022]
Abstract
Sleep is an essential and conserved behavior whose regulation at the molecular and anatomical level remains to be elucidated. Here, we identify TARANIS (TARA), a Drosophila homolog of the Trip-Br (SERTAD) family of transcriptional coregulators, as a molecule that is required for normal sleep patterns. Through a forward-genetic screen, we isolated tara as a novel sleep gene associated with a marked reduction in sleep amount. Targeted knockdown of tara suggests that it functions in cholinergic neurons to promote sleep. tara encodes a conserved cell-cycle protein that contains a Cyclin A (CycA)-binding homology domain. TARA regulates CycA protein levels and genetically and physically interacts with CycA to promote sleep. Furthermore, decreased levels of Cyclin-dependent kinase 1 (Cdk1), a kinase partner of CycA, rescue the short-sleeping phenotype of tara and CycA mutants, while increased Cdk1 activity mimics the tara and CycA phenotypes, suggesting that Cdk1 mediates the role of TARA and CycA in sleep regulation. Finally, we describe a novel wake-promoting role for a cluster of ∼14 CycA-expressing neurons in the pars lateralis (PL), previously proposed to be analogous to the mammalian hypothalamus. We propose that TARANIS controls sleep amount by regulating CycA protein levels and inhibiting Cdk1 activity in a novel arousal center.
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Affiliation(s)
- Dinis J S Afonso
- Department of Neuroscience, Farber Institute for Neurosciences and Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's, PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Die Liu
- Department of Neuroscience, Farber Institute for Neurosciences and Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Daniel R Machado
- Department of Neuroscience, Farber Institute for Neurosciences and Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's, PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Huihui Pan
- Department of Neuroscience, Farber Institute for Neurosciences and Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - James E C Jepson
- Department of Neuroscience, Farber Institute for Neurosciences and Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Dragana Rogulja
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Kyunghee Koh
- Department of Neuroscience, Farber Institute for Neurosciences and Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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Burow DA, Umeh-Garcia MC, True MB, Bakhaj CD, Ardell DH, Cleary MD. Dynamic regulation of mRNA decay during neural development. Neural Dev 2015; 10:11. [PMID: 25896902 PMCID: PMC4413985 DOI: 10.1186/s13064-015-0038-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/07/2015] [Indexed: 01/06/2023] Open
Abstract
Background Gene expression patterns are determined by rates of mRNA transcription and decay. While transcription is known to regulate many developmental processes, the role of mRNA decay is less extensively defined. A critical step toward defining the role of mRNA decay in neural development is to measure genome-wide mRNA decay rates in neural tissue. Such information should reveal the degree to which mRNA decay contributes to differential gene expression and provide a foundation for identifying regulatory mechanisms that affect neural mRNA decay. Results We developed a technique that allows genome-wide mRNA decay measurements in intact Drosophila embryos, across all tissues and specifically in the nervous system. Our approach revealed neural-specific decay kinetics, including stabilization of transcripts encoding regulators of axonogenesis and destabilization of transcripts encoding ribosomal proteins and histones. We also identified correlations between mRNA stability and physiologic properties of mRNAs; mRNAs that are predicted to be translated within axon growth cones or dendrites have long half-lives while mRNAs encoding transcription factors that regulate neurogenesis have short half-lives. A search for candidate cis-regulatory elements identified enrichment of the Pumilio recognition element (PRE) in mRNAs encoding regulators of neurogenesis. We found that decreased expression of the RNA-binding protein Pumilio stabilized predicted neural mRNA targets and that a PRE is necessary to trigger reporter-transcript decay in the nervous system. Conclusions We found that differential mRNA decay contributes to the relative abundance of transcripts involved in cell-fate decisions, axonogenesis, and other critical events during Drosophila neural development. Neural-specific decay kinetics and the functional specificity of mRNA decay suggest the existence of a dynamic neurodevelopmental mRNA decay network. We found that Pumilio is one component of this network, revealing a novel function for this RNA-binding protein. Electronic supplementary material The online version of this article (doi:10.1186/s13064-015-0038-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dana A Burow
- Quantitative and Systems Biology Graduate Program, University of California, 5200 N. Lake Rd, Merced, CA, USA.
| | - Maxine C Umeh-Garcia
- Quantitative and Systems Biology Graduate Program, University of California, 5200 N. Lake Rd, Merced, CA, USA.
| | - Marie B True
- Quantitative and Systems Biology Graduate Program, University of California, 5200 N. Lake Rd, Merced, CA, USA.
| | - Crystal D Bakhaj
- Quantitative and Systems Biology Graduate Program, University of California, 5200 N. Lake Rd, Merced, CA, USA.
| | - David H Ardell
- Quantitative and Systems Biology Graduate Program, University of California, 5200 N. Lake Rd, Merced, CA, USA.
| | - Michael D Cleary
- Quantitative and Systems Biology Graduate Program, University of California, 5200 N. Lake Rd, Merced, CA, USA.
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12
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Ma Y, Kanakousaki K, Buttitta L. How the cell cycle impacts chromatin architecture and influences cell fate. Front Genet 2015; 6:19. [PMID: 25691891 PMCID: PMC4315090 DOI: 10.3389/fgene.2015.00019] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/14/2015] [Indexed: 01/17/2023] Open
Abstract
Since the earliest observations of cells undergoing mitosis, it has been clear that there is an intimate relationship between the cell cycle and nuclear chromatin architecture. The nuclear envelope and chromatin undergo robust assembly and disassembly during the cell cycle, and transcriptional and post-transcriptional regulation of histone biogenesis and chromatin modification is controlled in a cell cycle-dependent manner. Chromatin binding proteins and chromatin modifications in turn influence the expression of critical cell cycle regulators, the accessibility of origins for DNA replication, DNA repair, and cell fate. In this review we aim to provide an integrated discussion of how the cell cycle machinery impacts nuclear architecture and vice-versa. We highlight recent advances in understanding cell cycle-dependent histone biogenesis and histone modification deposition, how cell cycle regulators control histone modifier activities, the contribution of chromatin modifications to origin firing for DNA replication, and newly identified roles for nucleoporins in regulating cell cycle gene expression, gene expression memory and differentiation. We close with a discussion of how cell cycle status may impact chromatin to influence cell fate decisions, under normal contexts of differentiation as well as in instances of cell fate reprogramming.
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Affiliation(s)
- Yiqin Ma
- Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor, MI, USA
| | - Kiriaki Kanakousaki
- Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor, MI, USA
| | - Laura Buttitta
- Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor, MI, USA
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