1
|
Wang M, He B, Hao Y, Srinivasan D, Shrinet J, Fraser P. Cellular reprogramming is driven by widespread rewiring of promoter-enhancer interactions. BMC Biol 2023; 21:264. [PMID: 37981682 PMCID: PMC10658794 DOI: 10.1186/s12915-023-01766-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Long-range interactions between promoters and cis-regulatory elements, such as enhancers, play critical roles in gene regulation. However, the role of three-dimensional (3D) chromatin structure in orchestrating changes in transcriptional regulation during direct cell reprogramming is not fully understood. RESULTS Here, we performed integrated analyses of chromosomal architecture, epigenetics, and gene expression using Hi-C, promoter Capture Hi-C (PCHi-C), ChIP-seq, and RNA-seq during trans-differentiation of Pre-B cells into macrophages with a β-estradiol inducible C/EBPαER transgene. Within 1h of β-estradiol induction, C/EBPα translocated from the cytoplasm to the nucleus, binding to thousands of promoters and putative regulatory elements, resulting in the downregulation of Pre-B cell-specific genes and induction of macrophage-specific genes. Hi-C results were remarkably consistent throughout trans-differentiation, revealing only a small number of TAD boundary location changes, and A/B compartment switches despite significant changes in the expression of thousands of genes. PCHi-C revealed widespread changes in promoter-anchored loops with decreased interactions in parallel with decreased gene expression, and new and increased promoter-anchored interactions in parallel with increased expression of macrophage-specific genes. CONCLUSIONS Overall, our data demonstrate that C/EBPα-induced trans-differentiation involves few changes in genome architecture at the level of TADs and A/B compartments, in contrast with widespread reorganization of thousands of promoter-anchored loops in association with changes in gene expression and cell identity.
Collapse
Affiliation(s)
- Miao Wang
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Bing He
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Yueling Hao
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Divyaa Srinivasan
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Jatin Shrinet
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Peter Fraser
- Department of Biological Science, Florida State University, Tallahassee, FL, USA.
| |
Collapse
|
2
|
Llinàs-Arias P, Ensenyat-Méndez M, Orozco JIJ, Íñiguez-Muñoz S, Valdez B, Wang C, Mezger A, Choi E, Tran YZ, Yao L, Bonath F, Olsen RA, Ormestad M, Esteller M, Lupien M, Marzese DM. 3-D chromatin conformation, accessibility, and gene expression profiling of triple-negative breast cancer. BMC Genom Data 2023; 24:61. [PMID: 37919672 PMCID: PMC10621134 DOI: 10.1186/s12863-023-01166-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023] Open
Abstract
OBJECTIVES Triple-negative breast cancer (TNBC) is a highly aggressive breast cancer subtype with limited treatment options. Unlike other breast cancer subtypes, the scarcity of specific therapies and greater frequencies of distant metastases contribute to its aggressiveness. We aimed to find epigenetic changes that aid in the understanding of the dissemination process of these cancers. DATA DESCRIPTION Using CRISPR/Cas9, our experimental approach led us to identify and disrupt an insulator element, IE8, whose activity seemed relevant for cell invasion. The experiments were performed in two well-established TNBC cellular models, the MDA-MB-231 and the MDA-MB-436. To gain insights into the underlying molecular mechanisms of TNBC invasion ability, we generated and characterized high-resolution chromatin interaction (Hi-C) and chromatin accessibility (ATAC-seq) maps in both cell models and complemented these datasets with gene expression profiling (RNA-seq) in MDA-MB-231, the cell line that showed more significant changes in chromatin accessibility. Altogether, our data provide a comprehensive resource for understanding the spatial organization of the genome in TNBC cells, which may contribute to accelerating the discovery of TNBC-specific alterations triggering advances for this devastating disease.
Collapse
Affiliation(s)
- Pere Llinàs-Arias
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Health Research Institute of the Balearic Islands (IdISBa), 07120, Palma, Spain
| | - Miquel Ensenyat-Méndez
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Health Research Institute of the Balearic Islands (IdISBa), 07120, Palma, Spain
| | - Javier I J Orozco
- Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Sandra Íñiguez-Muñoz
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Health Research Institute of the Balearic Islands (IdISBa), 07120, Palma, Spain
| | - Betsy Valdez
- Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Chuan Wang
- Department of Biosciences and Nutrition, Science for Life Laboratory,, Karolinska Institutet, Stockholm, Sweden
| | - Anja Mezger
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Eunkyoung Choi
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Yan Zhou Tran
- Department of Biosciences and Nutrition, Science for Life Laboratory,, Karolinska Institutet, Stockholm, Sweden
| | - Liqun Yao
- Department of Biosciences and Nutrition, Science for Life Laboratory,, Karolinska Institutet, Stockholm, Sweden
| | - Franziska Bonath
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Remi-André Olsen
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Mattias Ormestad
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red Cancer (CIBERONC), 28029, Madrid, Spain
- Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, Toronto, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Ontario Institute for Cancer Research, Toronto, ON, M5G 0A3, Canada
| | - Diego M Marzese
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Health Research Institute of the Balearic Islands (IdISBa), 07120, Palma, Spain.
| |
Collapse
|
3
|
Abstract
The accumulated knowledge about the structure of protein-DNA complexes allowed us to understand the mechanisms of protein-DNA recognition and searching for a specific site on DNA. Obviously, the mechanism of specific DNA recognition by a protein must satisfy two requirements. First, the probability of incorrect binding should be very small. Second, the time to find the "correct" binding site should not be too long. If we assume that protein recognition of a precise site on DNA occurs at some distance from DNA and calculate global minima, we can avoid local minima at short distances. The only long-range interaction is the interaction of charges. The location of charges on DNA in three-dimensional space depends on the local conformation of DNA and thus reflects the DNA sequence and sets the spatial pattern for recognition. Various factors such as counter ion concentration, ionic strength, and pH can affect protein recognition of DNA. Nowadays, the theory of long-range interactions makes it possible to calculate the best mutual spatial arrangement of protein and DNA molecules by charged groups and avoid misplaced binding.
Collapse
Affiliation(s)
- Anastasia A. Anashkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| |
Collapse
|
4
|
Antosiewicz JM. On the possibility of the existence of orienting hydrodynamic steering effects in the kinetics of receptor-ligand association. Eur Biophys J 2023; 52:559-568. [PMID: 37173574 PMCID: PMC10618320 DOI: 10.1007/s00249-023-01653-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/10/2023] [Accepted: 04/11/2023] [Indexed: 05/15/2023]
Abstract
In the vast majority of biologically relevant cases of receptor-ligand complex formation, the binding site of the receptor is a small part of its surface, and moreover, formation of a biologically active complex often requires a specific orientation of the ligand relative to the binding site. Before the formation of the initial form of the complex, only long-range, electrostatic and hydrodynamic interactions can act between the ligand approaching the binding site and the receptor. In this context, the question arises whether as a result of these interactions, there is a pre-orientation of the ligand towards the binding site, which to some extent would accelerate the formation of the complex. The role of electrostatic interactions in the orientation of the ligand relative to the binding site of the receptor is well documented. The analogous role of hydrodynamic interactions, although assessed as very significant by Brune and Kim (PNAS 91, 2930-2934, (1994)), is still debatable. In this article, I present the current state of knowledge on this subject and consider the possibilities of demonstrating the orienting effect of hydrodynamic interactions in the processes of receptor-ligand association, in an experimental way supported by computer simulations.
Collapse
Affiliation(s)
- Jan M Antosiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland.
| |
Collapse
|
5
|
Yang Z, Ge X, Li W, Jin Y, Liu L, Hu W, Liu F, Chen Y, Peng S, Li F. Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance divergence. BMC Biol 2021; 19:115. [PMID: 34082735 PMCID: PMC8176745 DOI: 10.1186/s12915-021-01041-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many of genome features which could help unravel the often complex post-speciation evolution of closely related species are obscured because of their location in chromosomal regions difficult to accurately characterize using standard genome analysis methods, including centromeres and repeat regions. RESULTS Here, we analyze the genome evolution and diversification of two recently diverged sister cotton species based on nanopore long-read sequence assemblies and Hi-C 3D genome data. Although D genomes are conserved in gene content, they have diversified in gene order, gene structure, gene family diversification, 3D chromatin structure, long-range regulation, and stress-related traits. Inversions predominate among D genome rearrangements. Our results support roles for 5mC and 6mA in gene activation, and 3D chromatin analysis showed that diversification in proximal-vs-distal regulatory-region interactions shape the regulation of defense-related-gene expression. Using a newly developed method, we accurately positioned cotton centromeres and found that these regions have undergone obviously more rapid evolution relative to chromosome arms. We also discovered a cotton-specific LTR class that clarifies evolutionary trajectories among diverse cotton species and identified genetic networks underlying the Verticillium tolerance of Gossypium thurberi (e.g., SA signaling) and salt-stress tolerance of Gossypium davidsonii (e.g., ethylene biosynthesis). Finally, overexpression of G. thurberi genes in upland cotton demonstrated how wild cottons can be exploited for crop improvement. CONCLUSIONS Our study substantially deepens understanding about how centromeres have developed and evolutionarily impacted the divergence among closely related cotton species and reveals genes and 3D genome structures which can guide basic investigations and applied efforts to improve crops.
Collapse
Affiliation(s)
- Zhaoen Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaoyang Ge
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Weinan Li
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
| | - Yuying Jin
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lisen Liu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wei Hu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fuyan Liu
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Yanli Chen
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Shaoliang Peng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China. .,School of Computer Science, National University of Defense Technology, Changsha, 410073, China. .,Peng Cheng Lab, Shenzhen, 518000, China.
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China. .,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| |
Collapse
|
6
|
Li H, Zeng J, Zhao Y, Xu X. MZF1 regulates α-globin gene transcription via long-range interactions in erythroid differentiation. Blood Cells Mol Dis 2020; 87:102533. [PMID: 33352376 DOI: 10.1016/j.bcmd.2020.102533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 11/16/2022]
Abstract
Precise spatiotemporal gene expression regulation is crucial for human erythropoiesis. However, dramatic changes in the chromatin structure and transcriptome involved in α-globin gene expression during erythropoiesis still not fully understand. To identify candidate regulators for α-globin gene regulation, we carried out an integrated approach by integrating publicly available transcriptomic and epigenomic data. We computed active enhancers by overlapping enriched regions marked with H3K4me1 and H3K27ac and correlated their activity with mRNA expression. Next, we cataloged potential transcription factors via de novo motif analysis. We highlighted the discovery of potential novel transcription factor MZF1 of the α-globin gene in erythroid differentiation. To validate the role of MZF1, we quantified the expression level of MZF1 and α-globin gene in HSPCs, early erythroid progenitors and late erythroid precursors cells. Both the mRNA and protein expression patterns of MZF1 were consistent with the α-globin gene. Also, the qPCR result showed that the expression of the α-globin gene was significantly increased by the MZF1 overexpression. To further investigate the role of MZF1 regulating α-globin gene transcriptional activity during erythroid differentiation, we performed ChIP-qPCR at the α-globin locus. Our results showed that MZF1 recruitment both at 4 upstream HS sites and α-globin gene promoter in erythroid precursor cells. To determine the importance of the MZF1 to enhancer-promoter interaction at the α-globin locus, we compared interaction frequency before and after knockdown of MZF1 by chromosome conformation capture (3C) assay. Upon MZF1 depletion, both the expression of the α-globin gene and all 3C signals were significantly decreased. Taken together, MZF1 plays an important role in regulating α-globin gene expression by binding to long-region enhancers and α-globin gene promoter and facilitates the organization of specific 3D chromatin architecture in erythroid differentiation.
Collapse
Affiliation(s)
- Haoli Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Jingjing Zeng
- The Central Laboratory, The Second People's Hospital of Shenzhen, Shenzhen 518035, People's Republic of China
| | - Yongzhong Zhao
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Xiangmin Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China.
| |
Collapse
|
7
|
Abstract
Class switch recombination (CSR) plays an important role in humoral immunity by generating antibodies with different effector functions. CSR to a particular antibody isotype is induced by external stimuli, and occurs between highly repetitive switch (S) sequences. CSR requires transcription across S regions, which generates long non-coding RNAs and secondary structures that promote accessibility of S sequences to activation-induced cytidine deaminase (AID). AID initiates DNA double-strand breaks (DSBs) intermediates that are repaired by general DNA repair pathways. Switch transcription is controlled by various regulatory elements, including enhancers and insulators. The current paradigm posits that transcriptional control of CSR involves long-range chromatin interactions between regulatory elements and chromatin loops-stabilizing factors, which promote alignment of partner S regions in a CSR centre (CSRC) and initiation of CSR. In this review, we focus on the role of IgH transcriptional control elements in CSR and the chromatin-based mechanisms underlying this control.
Collapse
Affiliation(s)
- Chloé Oudinet
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, Toulouse, France; Institut de Pharmacologie et de Biologie Structurale, CNRS, Université Paul Sabatier, Toulouse, France
| | - Fatima-Zohra Braikia
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, Toulouse, France; Institut de Pharmacologie et de Biologie Structurale, CNRS, Université Paul Sabatier, Toulouse, France
| | - Audrey Dauba
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, Toulouse, France; Institut de Pharmacologie et de Biologie Structurale, CNRS, Université Paul Sabatier, Toulouse, France
| | - Ahmed Amine Khamlichi
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, Toulouse, France; Institut de Pharmacologie et de Biologie Structurale, CNRS, Université Paul Sabatier, Toulouse, France.
| |
Collapse
|
8
|
Abstract
Chromosome conformation capture (3C) allows for the determination of the proximity in nuclei of DNA sequences that are linearly distant from one another in the genome. Proximity that is above that expected from random interaction provides evidence for potential long-range functional interactions such as between enhancers and their target genes. Many controls are required to convincingly demonstrate increased frequency of interaction between sequences and stringent functional tests must also be applied. Here, we present methodology suitable for 3C experiments that can also be applied as the basis for related 4C, 5C, and Hi-C approaches. These procedures are widely applicable to erythroid cell lines, progenitor cells, and tissues.
Collapse
|
9
|
Li P, Shi ML, Shen WL, Zhang Z, Xie DJ, Zhang XY, He C, Zhang Y, Zhao ZH. Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions. Biochim Biophys Acta Gene Regul Mech 2017; 1860:885-893. [PMID: 28511927 PMCID: PMC7102783 DOI: 10.1016/j.bbagrm.2017.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/21/2017] [Accepted: 05/08/2017] [Indexed: 11/26/2022]
Abstract
Interferon-induced transmembrane protein (IFITM) 1, 2 and 3 genes encode a family of interferon (IFN)-induced transmembrane proteins that block entry of a broad spectrum of pathogens. However, the transcriptional regulation of these genes, especially whether there exist any enhancers and their roles during the IFN induction process remain elusive. Here, through public data mining, episomal luciferase reporter assay and in vivo CRISPR-Cas9 genome editing, we identified an IFN-responsive enhancer located 35kb upstream of IFITM3 gene promoter upregulating the IFN-induced expression of IFITM1, 2 and 3 genes. Chromatin immunoprecipitation (ChIP), electrophoretic mobility shift assay (EMSA) and luciferase reporter assay demonstrated that signal transducers and activators of transcription (STAT) 1 bound to the enhancer with the treatment of IFN and was indispensable for the enhancer activity. Furthermore, using chromosome conformation capture technique, we revealed that the IFITM1, 2 and 3 genes physically clustered together and constitutively looped to the distal enhancer through long-range interactions in both HEK293 and A549 cells, providing structural basis for coordinated regulation of IFITM1, 2 and 3 by the enhancer. Finally, we showed that in vivo truncation of the enhancer impaired IFN-induced resistance to influenza A virus (IAV) infection. These findings expand our understanding of the mechanisms underlying the transcriptional regulation of IFITM1, 2 and 3 expression and its ability to mediate IFN signaling.
Collapse
Affiliation(s)
- Ping Li
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Ming-Lei Shi
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Wen-Long Shen
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Zhang Zhang
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China
| | - De-Jian Xie
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Xiang-Yuan Zhang
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Chao He
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Yan Zhang
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China.
| | - Zhi-Hu Zhao
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China.
| |
Collapse
|
10
|
Bewick S, Staniczenko PPA, Li B, Karig DK, Fagan WF. Invasion speeds in microbial systems with toxin production and quorum sensing. J Theor Biol 2017; 420:290-303. [PMID: 28126526 DOI: 10.1016/j.jtbi.2017.01.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 01/13/2017] [Accepted: 01/19/2017] [Indexed: 11/20/2022]
Abstract
The theory of invasions and invasion speeds has traditionally been studied in macroscopic systems. Surprisingly, microbial invasions have received less attention. Although microbes share many of the features associated with competition between larger-bodied organisms, they also exhibit distinctive behaviors that require new mathematical treatments to fully understand invasions in microbial systems. Most notable is the possibility for long-distance interactions, including competition between populations mediated by diffusible toxins and cooperation among individuals of a single population using quorum sensing. In this paper, we model bacterial invasion using a system of coupled partial differential equations based on Fisher's equation. Our model considers a competitive system with diffusible toxins that, in some cases, are expressed in response to quorum sensing. First, we derive analytical approximations for invasion speeds in the limits of fast and slow toxin diffusion. We then test the validity of our analytical approximations and explore intermediate rates of toxin diffusion using numerical simulations. Interestingly, we find that toxins should diffuse quickly when used offensively, but that there are two optimal strategies when toxins are used as a defense mechanism. Specifically, toxins should diffuse quickly when their killing efficacy is high, but should diffuse slowly when their killing efficacy is low. Our approach permits an explicit investigation of the properties and characteristics of diffusible compounds used in non-local competition, and is relevant for microbial systems and select macroscopic taxa, such as plants and corals, that can interact through biochemicals.
Collapse
|
11
|
Abstract
Glucocorticoids and their receptor (GR) have been an important area of research because of their pleiotropic physiological functions and extensive use in the clinic. In addition, the association between GR and glucocorticoids, which is highly specific, leads to rapid nuclear translocation where GR associates with chromatin to regulate gene transcription. This simplified model system has been instrumental for studying the complexity of transcription regulation processes occurring at chromatin. In this review we discuss our current understanding of GR action that has been enhanced by recent developments in genome wide measurements of chromatin accessibility, histone marks, chromatin remodeling and 3D chromatin structure in various cell types responding to glucocorticoids.
Collapse
Affiliation(s)
- Ivana Grbesa
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, 5290002, Ramat-Gan, Israel
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, 5290002, Ramat-Gan, Israel.
| |
Collapse
|
12
|
Wang J, Zhou Y, Li X, Meng X, Fan M, Chen H, Xue J, Chen M. Genome-Wide Analysis of the Distinct Types of Chromatin Interactions in Arabidopsis thaliana. Plant Cell Physiol 2017; 58:57-70. [PMID: 28064247 DOI: 10.1093/pcp/pcw194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 06/15/2016] [Indexed: 06/06/2023]
Abstract
The three-dimensional shapes of chromosomes regulate gene expression and genome function. Our knowledge of the role of chromatin interaction is evolving rapidly. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. High-throughput experimental techniques have been developed to map long-range interactions within chromatin. We have integrated data from multiple experimental sources including Hi-C, BS-seq, ChIP-chip and ChIP-seq data for 17 epigenetic marks and 35 transcription factors. We identified seven groups of interacting loci, which can be distinguished by their epigenetic profiles. Furthermore, the seven groups of interacting loci can be divided into three types of chromatin linkages based on expression status. We observed that two interacting loci sometimes share common epigenetic and transcription factor-binding profiles. Different groups of loci display very different relationships between epigenetic marks and the binding of transcription factors. Distinctive types of chromatin linkages exhibit different gene expression profiles. Our study unveils an entirely unexplored regulatory interaction, linking epigenetic profiles, transcription factor binding and the three-dimensional spatial organization of the Arabidopsis nuclear genome.
Collapse
Affiliation(s)
- Jingjing Wang
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Yincong Zhou
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Xue Li
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Xianwen Meng
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Miao Fan
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Hongjun Chen
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Jitong Xue
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Ming Chen
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| |
Collapse
|
13
|
Montavon T, Soshnikova N. Hox gene regulation and timing in embryogenesis. Semin Cell Dev Biol 2014; 34:76-84. [PMID: 24930771 DOI: 10.1016/j.semcdb.2014.06.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/15/2014] [Accepted: 06/05/2014] [Indexed: 11/22/2022]
Abstract
Hox genes are critical regulators of embryonic development in bilaterian animals. They exhibit a unique mode of transcriptional regulation where the position of the genes along the chromosome corresponds to the time and place of their expression during development. The sequential temporal activation of these genes in the primitive streak helps determining their subsequent pattern of expression along the anterior-posterior axis of the embryo, yet the precise correspondence between these two collinear processes is not fully understood. In addition, vertebrate Hox genes evolved similar modes of regulation along secondary body axes, such as the developing limbs. We review the current understanding of the mechanisms operating during activation, maintenance and silencing of Hox gene expression in these various contexts, and discuss the evolutionary significance of their genomic organization.
Collapse
|