1
|
Lewin TD, Liao IJY, Luo YJ. Annelid Comparative Genomics and the Evolution of Massive Lineage-Specific Genome Rearrangement in Bilaterians. Mol Biol Evol 2024; 41:msae172. [PMID: 39141777 PMCID: PMC11371463 DOI: 10.1093/molbev/msae172] [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: 05/15/2024] [Revised: 08/05/2024] [Accepted: 08/08/2024] [Indexed: 08/16/2024] Open
Abstract
The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained in others. However, the evolutionary forces driving these differences and the processes by which they emerge have remained largely uncharacterized. Here, we analyze genome organization across the phylum Annelida using 23 chromosome-level annelid genomes. We find that while many annelid lineages have maintained the conserved bilaterian genome structure, the Clitellata, a group containing leeches and earthworms, possesses completely scrambled genomes. We develop a rearrangement index to quantify the extent of genome structure evolution and show that, compared to the last common ancestor of bilaterians, leeches and earthworms have among the most highly rearranged genomes of any currently sampled species. We further show that bilaterian genomes can be classified into two distinct categories-high and low rearrangement-largely influenced by the presence or absence, respectively, of chromosome fission events. Our findings demonstrate that animal genome structure can be highly variable within a phylum and reveal that genome rearrangement can occur both in a gradual, stepwise fashion, or rapid, all-encompassing changes over short evolutionary timescales.
Collapse
Affiliation(s)
- Thomas D Lewin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Yi-Jyun Luo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
2
|
Yu W, Chakravarthi VP, Borosha S, Dilower I, Lee EB, Ratri A, Starks RR, Fields PE, Wolfe MW, Faruque MO, Tuteja G, Rumi MAK. Transcriptional regulation of Satb1 in mouse trophoblast stem cells. Front Cell Dev Biol 2022; 10:918235. [PMID: 36589740 PMCID: PMC9795202 DOI: 10.3389/fcell.2022.918235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Abstract
SATB homeobox proteins are important regulators of developmental gene expression. Among the stem cell lineages that emerge during early embryonic development, trophoblast stem (TS) cells exhibit robust SATB expression. Both SATB1 and SATB2 act to maintain the trophoblast stem-state. However, the molecular mechanisms that regulate TS-specific Satb expression are not yet known. We identified Satb1 variant 2 as the predominant transcript in trophoblasts. Histone marks, and RNA polymerase II occupancy in TS cells indicated an active state of the promoter. A novel cis-regulatory region with active histone marks was identified ∼21 kbp upstream of the variant 2 promoter. CRISPR/Cas9 mediated disruption of this sequence decreased Satb1 expression in TS cells and chromosome conformation capture analysis confirmed looping of this distant regulatory region into the proximal promoter. Scanning position weight matrices across the enhancer predicted two ELF5 binding sites in close proximity to SATB1 sites, which were confirmed by chromatin immunoprecipitation. Knockdown of ELF5 downregulated Satb1 expression in TS cells and overexpression of ELF5 increased the enhancer-reporter activity. Interestingly, ELF5 interacts with SATB1 in TS cells, and the enhancer activity was upregulated following SATB overexpression. Our findings indicate that trophoblast-specific Satb1 expression is regulated by long-range chromatin looping of an enhancer that interacts with ELF5 and SATB proteins.
Collapse
Affiliation(s)
- Wei Yu
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - V. Praveen Chakravarthi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Shaon Borosha
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Iman Dilower
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Eun Bee Lee
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Anamika Ratri
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Rebekah R. Starks
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Patrick E. Fields
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Michael W. Wolfe
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, United States
| | - M. Omar Faruque
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Geetu Tuteja
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - M. A. Karim Rumi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States,*Correspondence: M. A. Karim Rumi,
| |
Collapse
|
3
|
Nguyen NH, Vu NT, Cheong JJ. Transcriptional Stress Memory and Transgenerational Inheritance of Drought Tolerance in Plants. Int J Mol Sci 2022; 23:12918. [PMID: 36361708 PMCID: PMC9654142 DOI: 10.3390/ijms232112918] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 12/03/2023] Open
Abstract
Plants respond to drought stress by producing abscisic acid, a chemical messenger that regulates gene expression and thereby expedites various physiological and cellular processes including the stomatal operation to mitigate stress and promote tolerance. To trigger or suppress gene transcription under drought stress conditions, the surrounding chromatin architecture must be converted between a repressive and active state by epigenetic remodeling, which is achieved by the dynamic interplay among DNA methylation, histone modifications, loop formation, and non-coding RNA generation. Plants can memorize chromatin status under drought conditions to enable them to deal with recurrent stress. Furthermore, drought tolerance acquired during plant growth can be transmitted to the next generation. The epigenetically modified chromatin architectures of memory genes under stressful conditions can be transmitted to newly developed cells by mitotic cell division, and to germline cells of offspring by overcoming the restraints on meiosis. In mammalian cells, the acquired memory state is completely erased and reset during meiosis. The mechanism by which plant cells overcome this resetting during meiosis to transmit memory is unclear. In this article, we review recent findings on the mechanism underlying transcriptional stress memory and the transgenerational inheritance of drought tolerance in plants.
Collapse
Affiliation(s)
- Nguyen Hoai Nguyen
- Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City 700000, Vietnam
| | - Nam Tuan Vu
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
| | - Jong-Joo Cheong
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
| |
Collapse
|
4
|
Abstract
We found the three-dimensional (3D) structure of chromatin at the chromosome level to be highly conserved for more than 50 million y of carnivore evolution. Intrachromosomal contacts were maintained even after chromosome rearrangements within carnivore lineages, demonstrating that the maintenance of 3D chromatin architecture is essential for conserved genome functions. These discoveries enabled the identification of orthologous chromosomal DNA segments among related species, a method we call 3D comparative scaffotyping. The method has application for putative chromosome assignment of chromosome-scale DNA sequence scaffolds produced by de novo genome sequencing. Broadly applied to biodiversity genome sequencing efforts, the approach can reduce costs associated with karyotyping and the physical mapping of DNA segments to chromosomes. High throughput chromatin conformation capture (Hi-C) of leukocyte DNA was used to investigate the evolutionary stability of chromatin conformation at the chromosomal level in 11 species from three carnivore families: Felidae, Canidae, and Ursidae. Chromosome-scale scaffolds (C-scaffolds) of each species were initially used for whole-genome alignment to a reference genome within each family. This approach established putative orthologous relationships between C-scaffolds among the different species. Hi-C contact maps for all C-scaffolds were then visually compared and found to be distinct for a given reference chromosome or C-scaffold within a species and indistinguishable for orthologous C-scaffolds having a 1:1 relationship within a family. The visual patterns within families were strongly supported by eigenvectors from the Hi-C contact maps. Analysis of Hi-C contact maps and eigenvectors across the three carnivore families revealed that most cross-family orthologous subchromosomal fragments have a conserved three-dimensional (3D) chromatin structure and thus have been under strong evolutionary constraint for ∼54 My of carnivore evolution. The most pronounced differences in chromatin conformation were observed for the X chromosome and the red fox genome, whose chromosomes have undergone extensive rearrangements relative to other canids. We also demonstrate that Hi-C contact map pattern analysis can be used to accurately identify orthologous relationships between C-scaffolds and chromosomes, a method we termed “3D comparative scaffotyping.” This method provides a powerful means for estimating karyotypes in de novo sequenced species that have unknown karyotype and no physical mapping information.
Collapse
|
5
|
Yadav VK, Singh S, Yadav A, Agarwal N, Singh B, Jalmi SK, Yadav VK, Tiwari VK, Kumar V, Singh R, Sawant SV. Stress Conditions Modulate the Chromatin Interactions Network in Arabidopsis. Front Genet 2022; 12:799805. [PMID: 35069698 PMCID: PMC8766718 DOI: 10.3389/fgene.2021.799805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/15/2021] [Indexed: 11/26/2022] Open
Abstract
Stresses have been known to cause various responses like cellular physiology, gene regulation, and genome remodeling in the organism to cope and survive. Here, we assessed the impact of stress conditions on the chromatin-interactome network of Arabidopsis thaliana. We identified thousands of chromatin interactions in native as well as in salicylic acid treatment and high temperature conditions in a genome-wide fashion. Our analysis revealed the definite pattern of chromatin interactions and stress conditions could modulate the dynamics of chromatin interactions. We found the heterochromatic region of the genome actively involved in the chromatin interactions. We further observed that the establishment or loss of interactions in response to stress does not result in the global change in the expression profile of interacting genes; however, interacting regions (genes) containing motifs for known TFs showed either lower expression or no difference than non-interacting genes. The present study also revealed that interactions preferred among the same epigenetic state (ES) suggest interactions clustered the same ES together in the 3D space of the nucleus. Our analysis showed that stress conditions affect the dynamics of chromatin interactions among the chromatin loci and these interaction networks govern the folding principle of chromatin by bringing together similar epigenetic marks.
Collapse
Affiliation(s)
- Vikash Kumar Yadav
- CSIR-National Botanical Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Swadha Singh
- CSIR-National Botanical Research Institute, Lucknow, India.,School of Natural Sciences, University of California, Merced, Merced, CA, United States
| | - Amrita Yadav
- CSIR-National Botanical Research Institute, Lucknow, India
| | - Neha Agarwal
- CSIR-National Botanical Research Institute, Lucknow, India
| | - Babita Singh
- CSIR-National Botanical Research Institute, Lucknow, India
| | | | | | - Vipin Kumar Tiwari
- CSIR-National Botanical Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Verandra Kumar
- Department of Botany, Manyawar Kanshiram Government Degree College, Aligarh, India
| | | | - Samir Vishwanath Sawant
- CSIR-National Botanical Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
6
|
Davis SZ, Hollin T, Lenz T, Le Roch KG. Three-dimensional chromatin in infectious disease-A role for gene regulation and pathogenicity? PLoS Pathog 2021; 17:e1009207. [PMID: 33539484 PMCID: PMC7861443 DOI: 10.1371/journal.ppat.1009207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The recent Coronavirus Disease 2019 pandemic has once again reminded us the importance of understanding infectious diseases. One important but understudied area in infectious disease research is the role of nuclear architecture or the physical arrangement of the genome in the nucleus in controlling gene regulation and pathogenicity. Recent advances in research methods, such as Genome-wide chromosome conformation capture using high-throughput sequencing (Hi-C), have allowed for easier analysis of nuclear architecture and chromosomal reorganization in both the infectious disease agents themselves as well as in their host cells. This review will discuss broadly on what is known about nuclear architecture in infectious disease, with an emphasis on chromosomal reorganization, and briefly discuss what steps are required next in the field.
Collapse
Affiliation(s)
- Sage Z. Davis
- Department of Molecular, Cell and Systems Biology (MCSB), University of California Riverside, California, United States of America
| | - Thomas Hollin
- Department of Molecular, Cell and Systems Biology (MCSB), University of California Riverside, California, United States of America
| | - Todd Lenz
- Department of Molecular, Cell and Systems Biology (MCSB), University of California Riverside, California, United States of America
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology (MCSB), University of California Riverside, California, United States of America
| |
Collapse
|
7
|
Zhang J, Yao W, Pan Z, Liu H. Long-distance chromatin interaction of IGF1 during embryonic and postnatal development in the liver of Sus scrofa. Funct Integr Genomics 2021; 21:59-72. [PMID: 33404915 DOI: 10.1007/s10142-020-00761-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/25/2020] [Accepted: 11/12/2020] [Indexed: 11/25/2022]
Abstract
The dynamics of chromatin have been the focus of studies aimed at characterizing gene regulation. Among various chromosome conformation capture methods, 4C-seq is a powerful technique to identify genome-wide interactions with a single locus of interest. Insulin-like growth factor 1 (IGF1) is a member of the somatotropin axis that plays a significant role in cell proliferation and growth. Determining the IGF1-involved genome-wide chromatin interaction profile at different growth stages not only is important for understanding IGF1 transcriptional regulation but also provides a representation of genome-wide chromatin transformation during development. Using the IGF1 promoter as a "bait", we identified genome-wide interactomes of embryonic (E70) and postnatal (P1 and P70) pig liver cells by 4C-seq. The IGF1 promoter interactomes varied significantly among the three developmental stages. The most active chromatin interaction was observed in the P1 stage, while the highest interaction variability was observed in the P70 stage. The identified 4C sites were enriched around transcription start sites, CpG sites and functional pig QTLs. In addition, the genes located in the interacting regions and the involved pathways were also analysed. Overall, our work reveals a distinct long-distance regulatory pattern in pig liver during development for the first time, and the identified interacting sites and genes may serve as candidate targets in further transcriptional mechanism studies and effective molecular markers for functional traits.
Collapse
Affiliation(s)
- Jinbi Zhang
- College of Animal Science and Technology, Jinling Institute of Technology, Nanjing, 211169, People's Republic of China
- College of Animal Science and Technology, Nanjing Agriculture University, Nanjing, 210095, People's Republic of China
| | - Wang Yao
- College of Animal Science and Technology, Nanjing Agriculture University, Nanjing, 210095, People's Republic of China
| | - Zengxiang Pan
- College of Animal Science and Technology, Nanjing Agriculture University, Nanjing, 210095, People's Republic of China.
| | - Honglin Liu
- College of Animal Science and Technology, Nanjing Agriculture University, Nanjing, 210095, People's Republic of China
| |
Collapse
|
8
|
Rovina D, La Vecchia M, Cortesi A, Fontana L, Pesant M, Maitz S, Tabano S, Bodega B, Miozzo M, Sirchia SM. Profound alterations of the chromatin architecture at chromosome 11p15.5 in cells from Beckwith-Wiedemann and Silver-Russell syndromes patients. Sci Rep 2020; 10:8275. [PMID: 32427849 PMCID: PMC7237657 DOI: 10.1038/s41598-020-65082-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/24/2020] [Indexed: 01/12/2023] Open
Abstract
Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS) are imprinting-related disorders associated with genetic/epigenetic alterations of the 11p15.5 region, which harbours two clusters of imprinted genes (IGs). 11p15.5 IGs are regulated by the methylation status of imprinting control regions ICR1 and ICR2. 3D chromatin structure is thought to play a pivotal role in gene expression control; however, chromatin architecture models are still poorly defined in most cases, particularly for IGs. Our study aimed at elucidating 11p15.5 3D structure, via 3C and 3D FISH analyses of cell lines derived from healthy, BWS or SRS children. We found that, in healthy cells, IGF2/H19 and CDKN1C/KCNQ1OT1 domains fold in complex chromatin conformations, that facilitate the control of IGs mediated by distant enhancers. In patient-derived cell lines, we observed a profound impairment of such a chromatin architecture. Specifically, we identified a cross-talk between IGF2/H19 and CDKN1C/KCNQ1OT1 domains, consisting in in cis, monoallelic interactions, that are present in healthy cells but lost in patient cell lines: an inter-domain association that sees ICR2 move close to IGF2 on one allele, and to H19 on the other. Moreover, an intra-domain association within the CDKN1C/KCNQ1OT1 locus seems to be crucial for maintaining the 3D organization of the region.
Collapse
Affiliation(s)
- Davide Rovina
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142, Milano, Italy
| | - Marta La Vecchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142, Milano, Italy
| | - Alice Cortesi
- Genome Biology Unit, Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), 20122, Milano, Italy
| | - Laura Fontana
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122, Milano, Italy.,Medical Genetics, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, 20122, Milano, Italy
| | - Matthieu Pesant
- Genome Biology Unit, Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), 20122, Milano, Italy
| | - Silvia Maitz
- Clinical Pediatric, Genetics Unit, MBBM Foundation, San Gerardo di Monza, 20900, Monza, Italy
| | - Silvia Tabano
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122, Milano, Italy.,Medical Genetics, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, 20122, Milano, Italy
| | - Beatrice Bodega
- Genome Biology Unit, Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), 20122, Milano, Italy
| | - Monica Miozzo
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122, Milano, Italy.,Medical Genetics, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, 20122, Milano, Italy
| | - Silvia M Sirchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142, Milano, Italy.
| |
Collapse
|
9
|
Zhu Y, Yan Z, Du Z, Zhang S, Fu C, Meng Y, Wen X, Wang Y, Hoffman AR, Hu JF, Cui J, Li W. Osblr8 orchestrates intrachromosomal loop structure required for maintaining stem cell pluripotency. Int J Biol Sci 2020; 16:1861-1875. [PMID: 32398955 PMCID: PMC7211171 DOI: 10.7150/ijbs.45112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 02/22/2020] [Indexed: 12/11/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs), derived from reprogramming of somatic cells by a cocktail of transcription factors, have the capacity for unlimited self-renewal and the ability to differentiate into all of cell types present in the body. iPSCs may have therapeutic potential in regenerative medicine, replacing injured tissues or even whole organs. In this study, we examine epigenetic factors embedded in the specific 3-dimensional intrachromosomal architecture required for the activation of endogenous pluripotency genes. Using chromatin RNA in situ reverse transcription sequencing (CRIST-seq), we identified an Oct4-Sox2 binding long noncoding RNA, referred as to Osblr8, that is present in association with pluripotency status. Osblr8 was highly expressed in iPSCs and E14 embryonic stem cells, but it was silenced in fibroblasts. By using shRNA to knock down Osblr8, we found that this lncRNA was required for the maintenance of pluripotency. Overexpression of Osblr8 activated endogenous stem cell core factor genes. Mechanistically, Osblr8 participated in the formation of an intrachromosomal looping structure that is required to activate stem cell core factors during reprogramming. In summary, we have demonstrated that lncRNA Osblr8 is a chromatin architecture modulator of pluripotency-associated master gene promoters, highlighting its critical epigenetic role in reprogramming.
Collapse
Affiliation(s)
- Yanbo Zhu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Zi Yan
- Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin 130021, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Zhonghua Du
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Shilin Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Changhao Fu
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Ying Meng
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Xue Wen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yizhuo Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Andrew R Hoffman
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| |
Collapse
|
10
|
Yu J, Hu M, Li C. Joint analyses of multi-tissue Hi-C and eQTL data demonstrate close spatial proximity between eQTLs and their target genes. BMC Genet 2019; 20:43. [PMID: 31039743 PMCID: PMC6492392 DOI: 10.1186/s12863-019-0744-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/16/2019] [Indexed: 01/28/2023] Open
Abstract
Background Gene regulation is important for cells and tissues to function. It has been studied from two aspects at the genomic level, the identification of expression quantitative trait loci (eQTLs) and identification of long-range chromatin interactions. It is important to understand their relationship, such as whether eQTLs regulate their target genes through physical chromatin interaction. Although chromatin interactions have been widely believed to be one of the main mechanisms underlying eQTLs, most evidence came from studies of cell lines and yet no direct evidence exists for tissues. Results We performed various joint analyses of eQTL and high-throughput chromatin conformation capture (Hi-C) data from 11 human primary tissue types and 2 human cell lines. We found that chromatin interaction frequency is positively associated with the number of genes that have eQTLs and that eQTLs and their target genes tend to fall into the same topologically associating domain (TAD). These results are consistent across all tissues and cell lines we evaluated. Moreover, in 6 out of 11 tissues (aorta, dorsolateral prefrontal cortex, hippocampus, pancreas, small bowel, and spleen), tissue-specific eQTLs are significantly enriched in tissue-specific frequently interacting regions (FIREs). Conclusions Our data have demonstrated the close spatial proximity between eQTLs and their target genes among multiple human primary tissues. Electronic supplementary material The online version of this article (10.1186/s12863-019-0744-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jingting Yu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
| | - Chun Li
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA. .,Cleveland Institute for Computational Biology, Cleveland, OH, USA.
| |
Collapse
|
11
|
The Role of RNA Polymerase II Contiguity and Long-Range Interactions in the Regulation of Gene Expression in Human Pluripotent Stem Cells. Stem Cells Int 2019; 2019:1375807. [PMID: 30863449 PMCID: PMC6378007 DOI: 10.1155/2019/1375807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 12/05/2018] [Accepted: 12/24/2018] [Indexed: 12/02/2022] Open
Abstract
The eukaryotic nucleus is a highly complex structure that carries out multiple functions primarily needed for gene expression, and among them, transcription seems to be the most fundamental. Diverse approaches have demonstrated that transcription takes place at discrete sites known as transcription factories, wherein RNA polymerase II (RNAP II) is attached to the factory and immobilized while transcribing DNA. It has been proposed that transcription factories promote chromatin loop formation, creating long-range interactions in which relatively distant genes can be transcribed simultaneously. In this study, we examined long-range interactions between the POU5F1 gene and genes previously identified as being POU5F1 enhancer-interacting, namely, CDYL, TLE2, RARG, and MSX1 (all involved in transcriptional regulation), in human pluripotent stem cells (hPSCs) and their early differentiated counterparts. As a control gene, RUNX1 was used, which is expressed during hematopoietic differentiation and not associated with pluripotency. To reveal how these long-range interactions between POU5F1 and the selected genes change with the onset of differentiation and upon RNAP II inhibition, we performed three-dimensional fluorescence in situ hybridization (3D-FISH) followed by computational simulation analysis. Our analysis showed that the numbers of long-range interactions between specific genes decrease during differentiation, suggesting that the transcription of monitored genes is associated with pluripotency. In addition, we showed that upon inhibition of RNAP II, long-range associations do not disintegrate and remain constant. We also analyzed the distance distributions of these genes in the context of their positions in the nucleus and revealed that they tend to have similar patterns resembling normal distribution. Furthermore, we compared data created in vitro and in silico to assess the biological relevance of our results.
Collapse
|
12
|
Li M, Ma Z, Roy S, Patel SK, Lane DC, Duffy CR, Cai HN. Selective interactions between diverse STEs organize the ANT-C Hox cluster. Sci Rep 2018; 8:15158. [PMID: 30310129 PMCID: PMC6181975 DOI: 10.1038/s41598-018-33588-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/01/2018] [Indexed: 11/09/2022] Open
Abstract
The three-dimensional organization of the eukaryotic genome is important for its structure and function. Recent studies indicate that hierarchies of chromatin loops underlie important aspects of both genomic organization and gene regulation. Looping between insulator or boundary elements interferes with enhancer-promoter communications and limits the spread active or repressive organized chromatin. We have used the SF1 insulator in the Drosophila Antennapedia homeotic gene complex (ANT-C) as a model to study the mechanism and regulation of chromatin looping events. We reported previously that SF1 tethers a transient chromatin loop in the early embryo that insulates the Hox gene Sex comb reduce from the neighbor non-Hox gene fushi tarazu for their independent regulation. To further probe the functional range and connectivity of SF1, we used high-resolution chromosomal conformation capture (3C) to search for SF1 looping partners across ANT-C. We report here the identification of three distal SF1 Tether Elements (STEs) located in the labial, Deformed and Antennapedia Hox gene regions, extending the range of SF1 looping network to the entire complex. These novel STEs are bound by four different combinations of insulator proteins and exhibit distinct behaviors in enhancer block, enhancer-bypass and boundary functions. Significantly, the six STEs we identified so far map to all but one of the major boundaries between repressive and active histone domains, underlining the functional relevance of these long-range chromatin loops in organizing the Hox complex. Importantly, SF1 selectively captured with only 5 STEs out of ~20 sites that display similar insulator binding profiles, indicating that presence of insulator proteins alone is not sufficient to determine looping events. These findings suggest that selective interaction among diverse STE insulators organize the Drosophila Hox genes in the 3D nuclear space.
Collapse
Affiliation(s)
- Mo Li
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Zhibo Ma
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Sharmila Roy
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Sapna K Patel
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Derrick C Lane
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Carly R Duffy
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Haini N Cai
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA.
| |
Collapse
|
13
|
Sun Y, Dai H, Chen S, Zhang Y, Wu T, Cao X, Zhao G, Xu A, Wang J, Wu L. Disruption of Chromosomal Architecture of cox2 Locus Sensitizes Lung Cancer Cells to Radiotherapy. Mol Ther 2018; 26:2456-2465. [PMID: 30131302 PMCID: PMC6171098 DOI: 10.1016/j.ymthe.2018.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/27/2018] [Accepted: 08/01/2018] [Indexed: 11/15/2022] Open
Abstract
Despite treatment of lung cancer with radiotherapy and chemotherapy, the survival rate of lung cancer patients remains poor. Previous studies demonstrated the importance of upregulation of inflammatory factors, such as cyclooxygenase 2 (cox2), in tumor tolerance. In the present study, we investigated the role of cox2 in radiosensitivity of lung cancer. Our results showed that the combination treatment of radiation with aspirin, an anti-inflammatory drug, induced a synergistic reduction of cell survival in A549 and H1299 lung cancer cells. In comparison with normal human lung fibroblasts (NHLFs), the cell viability was significantly decreased and the level of apoptosis was remarkably enhanced in A549 cells. Mechanistic studies revealed that the reduction of cox2 by aspirin in A549 and H1299 was caused by disruption of the chromosomal architecture of the cox2 locus. Moreover, the disruption of chromatin looping was mediated by the inhibition of nuclear translocation of p65 and decreased enrichment of p65 at cox2-regulatory elements. Importantly, disorganization of the chromosomal architecture of cox2 triggered A549 cells sensitive to γ-radiation by the induction of apoptosis. In conclusion, we present evidence of an effective therapeutic treatment targeting the epigenetic regulation of lung cancer and a potential strategy to overcome radiation resistance in cancer cells.
Collapse
Affiliation(s)
- Yuxiang Sun
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - Hui Dai
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - Shaopeng Chen
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China.
| | - Yajun Zhang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - Tao Wu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - Xianbin Cao
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - Guoping Zhao
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - An Xu
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - Jun Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - Lijun Wu
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China.
| |
Collapse
|
14
|
Batugedara G, Le Roch KG. Unraveling the 3D genome of human malaria parasites. Semin Cell Dev Biol 2018; 90:144-153. [PMID: 30009946 DOI: 10.1016/j.semcdb.2018.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/03/2018] [Indexed: 01/31/2023]
Abstract
The chromosomes within the eukaryotic cell nucleus are highly dynamic and adopt complex hierarchical structures. Understanding how this three-dimensional (3D) nuclear architectureaffects gene regulation, cell cycle progression and disease pathogenesis are important biological questions in development and disease. Recently, many genome-wide technologies including chromosome conformation capture (3C) and 3C-based methodologies (4C, 5C, and Hi-C) have been developed to investigate 3D chromatin structure. In this review, we introduce 3D genome methodologies, with a focus on their application for understanding the nuclear architecture of the human malaria parasite, Plasmodium falciparum. An increasing amount of evidence now suggests that gene regulation in the parasite is largely regulated by epigenetic mechanisms and nuclear reorganization. Here, we explore the 3D genome architecture of P. falciparum, including local and global chromatin structure. In addition, molecular components important for maintaining 3D chromatin organization including architectural proteins and long non-coding RNAs are discussed. Collectively, these studies contribute to our understanding of how the plasticity of 3D genome architecture regulates gene expression and cell cycle progression in this deadly parasite.
Collapse
Affiliation(s)
- Gayani Batugedara
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA.
| |
Collapse
|
15
|
Heritable, Allele-Specific Chromosomal Looping between Tandem Promoters Specifies Promoter Usage of SHC1. Mol Cell Biol 2018; 38:MCB.00658-17. [PMID: 29440311 DOI: 10.1128/mcb.00658-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/08/2018] [Indexed: 11/20/2022] Open
Abstract
One-half of the genes in the human genome contain alternative promoters, some of which generate products with opposing functions. Aberrant silencing or activation of such alternative promoters is associated with multiple diseases, including cancer, but little is known regarding the molecular mechanisms that control alternative promoter choice. The SHC1 gene encodes p46Shc/p52Shc and p66Shc, proteins oppositely regulating anchorage-independent growth that are produced by transcription initiated from the upstream and downstream tandem promoters of SHC1, respectively. Here we demonstrate that activation of these promoters is mutually exclusive on separate alleles in single primary endothelial cells in a heritable fashion, ensuring expression of both transcripts by the cell. Peripheral blood lymphocytes that do not transcribe p66Shc transcribed p52Shc biallelically. This distinct monoallelic transcription pattern is established by allele-specific chromosomal looping between tandem promoters, which silences the upstream promoter. Our results reveal a new mechanism to control alternative promoter usage through higher-order chromatin structure.
Collapse
|
16
|
Erdel F. How Communication Between Nucleosomes Enables Spreading and Epigenetic Memory of Histone Modifications. Bioessays 2017; 39. [PMID: 29034500 DOI: 10.1002/bies.201700053] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 09/04/2017] [Indexed: 11/08/2022]
Abstract
Nucleosomes "talk" to each other about their modification state to form extended domains of modified histones independently of the underlying DNA sequence. At the same time, DNA elements promote modification of nucleosomes in their vicinity. How do these site-specific and histone-based activities act together to regulate spreading of histone modifications along the genome? How do they enable epigenetic memory to preserve cell identity? Many models for the dynamics of repressive histone modifications emphasize the role of strong positive feedback loops, which reinforce histone modifications by recruiting histone modifiers to preexisting modifications. Recent experiments question that repressive histone modifications are self-sustained independently of their genomic context, thereby indicating that histone-based feedback is relatively weak. In the present review, current models for the dynamics of histone modifications are compared and it is suggested that limitation of histone-based feedback is key to intrinsic confinement of spreading and coexistence of short- and long-term memory at different genomic loci. See also the video abstract here: https://youtu.be/3bxr_xDEZfQ.
Collapse
Affiliation(s)
- Fabian Erdel
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| |
Collapse
|
17
|
Genome organization: connecting the developmental origins of disease and genetic variation. J Dev Orig Health Dis 2017; 9:260-265. [PMID: 28847340 DOI: 10.1017/s2040174417000678] [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: 11/07/2022]
Abstract
An adverse early life environment can increase the risk of metabolic and other disorders later in life. Genetic variation can modify an individual's susceptibility to these environmental challenges. These gene by environment interactions are important, but difficult, to dissect. The nucleus is the primary organelle where environmental responses impact directly on the genetic variants within the genome, resulting in changes to the biology of the genome and ultimately the phenotype. Understanding genome biology requires the integration of the linear DNA sequence, epigenetic modifications and nuclear proteins that are present within the nucleus. The interactions between these layers of information may be captured in the emergent spatial genome organization. As such genome organization represents a key research area for decoding the role of genetic variation in the Developmental Origins of Health and Disease.
Collapse
|
18
|
Batugedara G, Lu XM, Bunnik EM, Le Roch KG. The Role of Chromatin Structure in Gene Regulation of the Human Malaria Parasite. Trends Parasitol 2017; 33:364-377. [PMID: 28065669 PMCID: PMC5410391 DOI: 10.1016/j.pt.2016.12.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/28/2016] [Accepted: 12/07/2016] [Indexed: 12/11/2022]
Abstract
The human malaria parasite, Plasmodium falciparum, depends on a coordinated regulation of gene expression for development and propagation within the human host. Recent developments suggest that gene regulation in the parasite is largely controlled by epigenetic mechanisms. Here, we discuss recent advancements contributing to our understanding of the mechanisms controlling gene regulation in the parasite, including nucleosome landscape, histone modifications, and nuclear architecture. In addition, various processes involved in regulation of parasite-specific genes and gene families are examined. Finally, we address the use of epigenetic processes as targets for novel antimalarial therapies. Collectively, these topics highlight the unique biology of P. falciparum, and contribute to our understanding of mechanisms regulating gene expression in this deadly parasite.
Collapse
Affiliation(s)
- Gayani Batugedara
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA
| | - Xueqing M Lu
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA
| | - Evelien M Bunnik
- Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Karine G Le Roch
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA.
| |
Collapse
|
19
|
Zhan J, Johnson IM, Wielgosz M, Nienhuis AW. The identification of hematopoietic-specific regulatory elements for WASp gene expression. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2016; 3:16077. [PMID: 28035317 PMCID: PMC5155633 DOI: 10.1038/mtm.2016.77] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/17/2016] [Accepted: 10/18/2016] [Indexed: 12/26/2022]
Abstract
Chromosome Conformation Capture (3C) technology was used to identify physical interactions between the proximal Wiskott-Aldrich Syndrome protein (WASp) promoter and its distant DNA segments in Jurkat-T cells. We found that two hematopoietic specific DNase I hypersensitive (DHS) sites (proximal DHS-A, and distal DHS-B) which had high interaction frequencies with the proximal WASp promoter indicating potential regulatory activity for these DHS sites. Subsequently, we cloned several DNA fragments around the proximal DHS-A site into a luciferase reporter vector. Interestingly, no fragments showed enhancer activity, but two fragments exhibited strong silencing activity in Jurkat-T cells. After aligning the chromatin state profiling for hematopoietic and nonhematopoietic cells using the human genome browser (UCSC), we found a 5 kb putative hematopoietic specific enhancer region located 250 kb downstream of the WAS gene. This putative enhancer region contains two hematopoietic cell specific DHS sites. Subsequently, the hematopoietic specific DHS sites enhanced luciferase expression from the proximal WASp promoter in all hematopoietic cells we tested. Finally, using a lentiviral vector stable expression system, the hematopoietic specific-enhancer(s) increased GFP reporter gene expression in hematopoietic cells, and increased WASp gene expression in WASp deficient cells. This enhancer may have the potential to be used in gene therapy for hematological diseases.
Collapse
Affiliation(s)
- Jun Zhan
- Department of Hematology, Division of Experimental Hematology , St. Jude Children's Research Hospital , Memphis, Tennessee, USA
| | - Irudayam Maria Johnson
- Department of Hematology, Division of Experimental Hematology , St. Jude Children's Research Hospital , Memphis, Tennessee, USA
| | - Matthew Wielgosz
- Department of Hematology, Division of Experimental Hematology , St. Jude Children's Research Hospital , Memphis, Tennessee, USA
| | - Arthur W Nienhuis
- Department of Hematology, Division of Experimental Hematology , St. Jude Children's Research Hospital , Memphis, Tennessee, USA
| |
Collapse
|
20
|
Hossain MA, Barrow JJ, Shen Y, Haq MI, Bungert J. Artificial zinc finger DNA binding domains: versatile tools for genome engineering and modulation of gene expression. J Cell Biochem 2016; 116:2435-44. [PMID: 25989233 DOI: 10.1002/jcb.25226] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 05/11/2015] [Indexed: 02/01/2023]
Abstract
Genome editing and alteration of gene expression by synthetic DNA binding activities gained a lot of momentum over the last decade. This is due to the development of new DNA binding molecules with enhanced binding specificity. The most commonly used DNA binding modules are zinc fingers (ZFs), TALE-domains, and the RNA component of the CRISPR/Cas9 system. These binding modules are fused or linked to either nucleases that cut the DNA and induce DNA repair processes, or to protein domains that activate or repress transcription of genes close to the targeted site in the genome. This review focuses on the structure, design, and applications of ZF DNA binding domains (ZFDBDs). ZFDBDs are relatively small and have been shown to penetrate the cell membrane without additional tags suggesting that they could be delivered to cells without a DNA or RNA intermediate. Advanced algorithms that are based on extensive knowledge of the mode of ZF/DNA interactions are used to design the amino acid composition of ZFDBDs so that they bind to unique sites in the genome. Off-target binding has been a concern for all synthetic DNA binding molecules. Thus, increasing the specificity and affinity of ZFDBDs will have a significant impact on their use in analytical or therapeutic settings.
Collapse
Affiliation(s)
- Mir A Hossain
- Department of Biochemistry and Molecular Biology, College of Medicine, Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, 32610
| | - Joeva J Barrow
- Department of Biochemistry and Molecular Biology, College of Medicine, Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, 32610
| | - Yong Shen
- Department of Biochemistry and Molecular Biology, College of Medicine, Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, 32610
| | - Md Imdadul Haq
- Department of Biochemistry and Molecular Biology, College of Medicine, Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, 32610
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, College of Medicine, Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, 32610
| |
Collapse
|
21
|
Abstract
InDrosophila, homologous chromosome pairing leads to "transvection," in which the enhancer of a gene can regulate the allelic transcription intrans.Interallelic interactions were also observed in vegetative diploid budding yeast, but their functional significance is unknown. Here, we show that aGAL1reporter can interact with its homologous allele and affect its expression. By ectopically inserting two allelic reporters, one driven by wild-typeGAL1promoter (WTGAL1pr) and the other by a mutant promoter with delayed response to galactose induction, we found that the two reporters physically associate, and the WTGAL1prtriggers synchronized firing of the defective promoter and accelerates its activation without affecting its steady-state expression level. This interaction and the transregulatory effect disappear when the same reporters are located at nonallelic sites. We further demonstrated that the activator Gal4 is essential for the interallelic interaction, and the transregulation requires fully activated WTGAL1prtranscription. The mechanism of this phenomenon was further discussed. Taken together, our data revealed the existence of interallelic gene regulation in yeast, which serves as a starting point for understanding long-distance gene regulation in this genetically tractable system.
Collapse
|
22
|
Saha N, Liu M, Gajan A, Pile LA. Genome-wide studies reveal novel and distinct biological pathways regulated by SIN3 isoforms. BMC Genomics 2016; 17:111. [PMID: 26872827 PMCID: PMC4752761 DOI: 10.1186/s12864-016-2428-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/01/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The multisubunit SIN3 complex is a global transcriptional regulator. In Drosophila, a single Sin3A gene encodes different isoforms of SIN3, of which SIN3 187 and SIN3 220 are the major isoforms. Previous studies have demonstrated functional non-redundancy of SIN3 isoforms. The role of SIN3 isoforms in regulating distinct biological processes, however, is not well characterized. RESULTS We established a Drosophila S2 cell culture model system in which cells predominantly express either SIN3 187 or SIN3 220. To identify genomic targets of SIN3 isoforms, we performed chromatin immunoprecipitation followed by deep sequencing. Our data demonstrate that upon overexpression of SIN3 187, the level of SIN3 220 decreased and the large majority of genomic sites bound by SIN3 220 were instead bound by SIN3 187. We used RNA-seq to identify genes regulated by the expression of one isoform or the other. In S2 cells, which predominantly express SIN3 220, we found that SIN3 220 directly regulates genes involved in metabolism and cell proliferation. We also determined that SIN3 187 regulates a unique set of genes and likely modulates expression of many genes also regulated by SIN3 220. Interestingly, biological pathways enriched for genes specifically regulated by SIN3 187 strongly suggest that this isoform plays an important role during the transition from the embryonic to the larval stage of development. CONCLUSION These data establish the role of SIN3 isoforms in regulating distinct biological processes. This study substantially contributes to our understanding of the complexity of gene regulation by SIN3.
Collapse
Affiliation(s)
- Nirmalya Saha
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA.
| | - Mengying Liu
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA.
| | - Ambikai Gajan
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA.
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA.
| |
Collapse
|
23
|
Abstract
To accommodate genomes in the limited space of the cell nucleus and ensure the correct execution of gene expression programs, genomes are packaged in complex fashion in the three-dimensional cell nucleus. As a consequence of the extensive higher-order organization of chromosomes, distantly located genomic regions on the same or distinct chromosomes undergo long-range interactions. This article discusses the nature of long interactions, mechanisms of their formation, and their emerging functional roles in gene regulation and genome maintenance.
Collapse
Affiliation(s)
- Job Dekker
- University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| |
Collapse
|
24
|
An Organizational Hub of Developmentally Regulated Chromatin Loops in the Drosophila Antennapedia Complex. Mol Cell Biol 2015; 35:4018-29. [PMID: 26391952 DOI: 10.1128/mcb.00663-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/14/2015] [Indexed: 12/17/2022] Open
Abstract
Chromatin boundary elements (CBEs) are widely distributed in the genome and mediate formation of chromatin loops, but their roles in gene regulation remain poorly understood. The complex expression pattern of the Drosophila homeotic gene Sex combs reduced (Scr) is directed by an unusually long regulatory sequence harboring diverse cis elements and an intervening neighbor gene fushi tarazu (ftz). Here we report the presence of a multitude of CBEs in the Scr regulatory region. Selective and dynamic pairing among these CBEs mediates developmentally regulated chromatin loops. In particular, the SF1 boundary plays a central role in organizing two subsets of chromatin loops: one subset encloses ftz, limiting its access by the surrounding Scr enhancers and compartmentalizing distinct histone modifications, and the other subset subdivides the Scr regulatory sequences into independent enhancer access domains. We show that these CBEs exhibit diverse enhancer-blocking activities that vary in strength and tissue distribution. Tandem pairing of SF1 and SF2, two strong CBEs that flank the ftz domain, allows the distal enhancers to bypass their block in transgenic Drosophila, providing a mechanism for the endogenous Scr enhancer to circumvent the ftz domain. Our study demonstrates how an endogenous CBE network, centrally orchestrated by SF1, could remodel the genomic environment to facilitate gene regulation during development.
Collapse
|
25
|
Harraghy N, Calabrese D, Fisch I, Girod PA, LeFourn V, Regamey A, Mermod N. Epigenetic regulatory elements: Recent advances in understanding their mode of action and use for recombinant protein production in mammalian cells. Biotechnol J 2015; 10:967-78. [DOI: 10.1002/biot.201400649] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/20/2015] [Accepted: 05/20/2015] [Indexed: 12/18/2022]
|
26
|
Functional validation of a constitutive autonomous silencer element. PLoS One 2015; 10:e0124588. [PMID: 25910277 PMCID: PMC4409358 DOI: 10.1371/journal.pone.0124588] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 03/14/2015] [Indexed: 11/19/2022] Open
Abstract
Sequences of the genome that are capable of silencing gene expression are thought to play a key role in gene regulation. However, very few silencer elements capable of functioning in mammalian cells have been described, and only a fraction of these have been tested for the ability to function in an autonomous fashion. We report here the characterization and functional validation of a constitutive autonomous silencer element from the human genome called T39, and the comparison of T39 to three other putative silencer elements previously described by others. Functional analysis included one assay for enhancer-blocking insulator activity and two independent assays for silencer activity, all based on stable transfection and comparison to a neutral spacer control. In erythroid K562 cells, T39 exhibited potent silencer activity, the previously described element PRE2-S5 exhibited modest silencer activity, and the two other previously described elements exhibited no silencer activity. T39 was further found to be capable of silencing three disparate promoters, of silencing gene expression in three disparate cell lines, and of functioning as a single copy in a topology-independent manner. Of the four elements analyzed, only T39 exhibits a constitutive pattern of DNase hypersensitivity and binding by CTCF. In its native location the T39 element also exhibits a unique interaction profile with a subset of distal putative regulatory elements. Taken together, these studies validate T39 as a constitutive autonomous silencer, identify T39 as a defined control for future studies of other regulatory elements such as insulators, and provide a basic chromatin profile for one highly potent silencer element.
Collapse
|
27
|
Razin SV, Gavrilov AA, Ulyanov SV. Transcription-controlling regulatory elements of the eukaryotic genome. Mol Biol 2015. [DOI: 10.1134/s0026893315020119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
28
|
Le Gall A, Valeri A, Nollmann M. Roles of chromatin insulators in the formation of long-range contacts. Nucleus 2015; 6:118-22. [PMID: 25781057 DOI: 10.1080/19491034.2015.1010962] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Chromatin insulators are factors involved in higher-order, genome-wide organization of chromatin, and play key roles in regulating transcriptional programs. In this review, we discuss recent studies on the diverse composition of insulator complexes, and on the mechanism by which they establish long-range DNA interactions. Particularly, we describe new biophysical methods that allow for the study of the composition of large molecular complexes, and for defining the factors potentially required to establish long-range DNA contacts.
Collapse
Affiliation(s)
- Antoine Le Gall
- a Centre de Biochimie Structurale ; CNRS UMR5048; INSERM U1054; Université de Montpellier ; Montpellier , France
| | | | | |
Collapse
|
29
|
Hegyi H. Enhancer-promoter interaction facilitated by transiently forming G-quadruplexes. Sci Rep 2015; 5:9165. [PMID: 25772493 PMCID: PMC4360481 DOI: 10.1038/srep09165] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/16/2015] [Indexed: 12/03/2022] Open
Abstract
G-quadruplexes are guanine-rich nucleic acid sequences capable of forming a four-stranded structure through Hoogsteen hydrogen bonding. G-quadruplexes are highly concentrated near promoters and transcription start sites suggesting a role in gene regulation. They are less often found on the template than non-template strand where they either inhibit or enhance transcription, respectively. However, their potential role in enhancers and other distal regulatory elements has not been assessed yet. Here we show that DNAse hypersensitive (DHS) cis-regulatory elements are also enriched in Gs and their G-content correlate with that of their respective promoters. Besides local G4s, the distal cis regions may form G-quadruplexes together with the promoters, each contributing half a G4. This model is supported more for the non-template strand and we hypothesised that the G4 forming capability of the promoter and the enhancer non-template strand could facilitate their binding together and making the DHS regions accessible for the transcription factory.
Collapse
Affiliation(s)
- Hedi Hegyi
- CEITEC-Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
| |
Collapse
|
30
|
Cao J, Luo Z, Cheng Q, Xu Q, Zhang Y, Wang F, Wu Y, Song X. Three-dimensional regulation of transcription. Protein Cell 2015; 6:241-53. [PMID: 25670626 PMCID: PMC4383755 DOI: 10.1007/s13238-015-0135-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 01/09/2015] [Indexed: 12/20/2022] Open
Abstract
Cells can adapt to environment and development by reconstructing their transcriptional networks to regulate diverse cellular processes without altering the underlying DNA sequences. These alterations, namely epigenetic changes, occur during cell division, differentiation and cell death. Numerous evidences demonstrate that epigenetic changes are governed by various types of determinants, including DNA methylation patterns, histone posttranslational modification signatures, histone variants, chromatin remodeling, and recently discovered chromosome conformation characteristics and non-coding RNAs (ncRNAs). Here, we highlight recent efforts on how the two latter epigenetic factors participate in the sophisticated transcriptional process and describe emerging techniques which permit us to uncover and gain insights into the fascinating genomic regulation.
Collapse
Affiliation(s)
- Jun Cao
- CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Zhengyu Luo
- CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Qingyu Cheng
- CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Qianlan Xu
- CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Yan Zhang
- CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Fei Wang
- CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Yan Wu
- CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Xiaoyuan Song
- CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| |
Collapse
|
31
|
Paulsen J, Rødland EA, Holden L, Holden M, Hovig E. A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions. Nucleic Acids Res 2014; 42:e143. [PMID: 25114054 PMCID: PMC4191384 DOI: 10.1093/nar/gku738] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/10/2014] [Accepted: 08/01/2014] [Indexed: 12/23/2022] Open
Abstract
Identification of three-dimensional (3D) interactions between regulatory elements across the genome is crucial to unravel the complex regulatory machinery that orchestrates proliferation and differentiation of cells. ChIA-PET is a novel method to identify such interactions, where physical contacts between regions bound by a specific protein are quantified using next-generation sequencing. However, determining the significance of the observed interaction frequencies in such datasets is challenging, and few methods have been proposed. Despite the fact that regions that are close in linear genomic distance have a much higher tendency to interact by chance, no methods to date are capable of taking such dependency into account. Here, we propose a statistical model taking into account the genomic distance relationship, as well as the general propensity of anchors to be involved in contacts overall. Using both real and simulated data, we show that the previously proposed statistical test, based on Fisher's exact test, leads to invalid results when data are dependent on genomic distance. We also evaluate our method on previously validated cell-line specific and constitutive 3D interactions, and show that relevant interactions are significant, while avoiding over-estimating the significance of short nearby interactions.
Collapse
Affiliation(s)
- Jonas Paulsen
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway
| | - Einar A Rødland
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway
| | - Lars Holden
- Statistics for Innovation, Norwegian Computing Center, N-0314 Oslo, Norway
| | - Marit Holden
- Statistics for Innovation, Norwegian Computing Center, N-0314 Oslo, Norway
| | - Eivind Hovig
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway
| |
Collapse
|
32
|
Vogelmann J, Le Gall A, Dejardin S, Allemand F, Gamot A, Labesse G, Cuvier O, Nègre N, Cohen-Gonsaud M, Margeat E, Nöllmann M. Chromatin insulator factors involved in long-range DNA interactions and their role in the folding of the Drosophila genome. PLoS Genet 2014; 10:e1004544. [PMID: 25165871 PMCID: PMC4148193 DOI: 10.1371/journal.pgen.1004544] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 06/17/2014] [Indexed: 11/18/2022] Open
Abstract
Chromatin insulators are genetic elements implicated in the organization of chromatin and the regulation of transcription. In Drosophila, different insulator types were characterized by their locus-specific composition of insulator proteins and co-factors. Insulators mediate specific long-range DNA contacts required for the three dimensional organization of the interphase nucleus and for transcription regulation, but the mechanisms underlying the formation of these contacts is currently unknown. Here, we investigate the molecular associations between different components of insulator complexes (BEAF32, CP190 and Chromator) by biochemical and biophysical means, and develop a novel single-molecule assay to determine what factors are necessary and essential for the formation of long-range DNA interactions. We show that BEAF32 is able to bind DNA specifically and with high affinity, but not to bridge long-range interactions (LRI). In contrast, we show that CP190 and Chromator are able to mediate LRI between specifically-bound BEAF32 nucleoprotein complexes in vitro. This ability of CP190 and Chromator to establish LRI requires specific contacts between BEAF32 and their C-terminal domains, and dimerization through their N-terminal domains. In particular, the BTB/POZ domains of CP190 form a strict homodimer, and its C-terminal domain interacts with several insulator binding proteins. We propose a general model for insulator function in which BEAF32/dCTCF/Su(HW) provide DNA specificity (first layer proteins) whereas CP190/Chromator are responsible for the physical interactions required for long-range contacts (second layer). This network of organized, multi-layer interactions could explain the different activities of insulators as chromatin barriers, enhancer blockers, and transcriptional regulators, and suggest a general mechanism for how insulators may shape the organization of higher-order chromatin during cell division.
Collapse
Affiliation(s)
- Jutta Vogelmann
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Antoine Le Gall
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Stephanie Dejardin
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Frederic Allemand
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Adrien Gamot
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS and Université de Toulouse, Toulouse; France
| | - Gilles Labesse
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Olivier Cuvier
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS and Université de Toulouse, Toulouse; France
| | - Nicolas Nègre
- Laboratoire Diversité, Génomes & Interactions Microorganismes-Insectes, INRA UMR1333, Université de Montpellier 2, Montpellier, France
| | - Martin Cohen-Gonsaud
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Emmanuel Margeat
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Marcelo Nöllmann
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
- * E-mail:
| |
Collapse
|
33
|
Lambrot R, Xu C, Saint-Phar S, Chountalos G, Cohen T, Paquet M, Suderman M, Hallett M, Kimmins S. Low paternal dietary folate alters the mouse sperm epigenome and is associated with negative pregnancy outcomes. Nat Commun 2014; 4:2889. [PMID: 24326934 PMCID: PMC3863903 DOI: 10.1038/ncomms3889] [Citation(s) in RCA: 288] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 11/07/2013] [Indexed: 01/20/2023] Open
Abstract
Epidemiological studies suggest that a father's diet can influence offspring health. A proposed mechanism for paternal transmission of environmental information is via the sperm epigenome. The epigenome includes heritable information such as DNA methylation. We hypothesize that the dietary supply of methyl donors will alter epigenetic reprogramming in sperm. Here we feed male mice either a folate-deficient or folate-sufficient diet throughout life. Paternal folate deficiency is associated with increased birth defects in the offspring, which include craniofacial and musculoskeletal malformations. Genome-wide DNA methylation analysis and the subsequent functional analysis identify differential methylation in sperm of genes implicated in development, chronic diseases such as cancer, diabetes, autism and schizophrenia. While >300 genes are differentially expressed in offspring placenta, only two correspond to genes with differential methylation in sperm. This model suggests epigenetic transmission may involve sperm histone H3 methylation or DNA methylation and that adequate paternal dietary folate is essential for offspring health.
Collapse
Affiliation(s)
- R Lambrot
- 1] Department of Animal Science, McGill University, Ste Anne-de-Bellevue, Québec H9X3V9, Canada [2]
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Transcriptional regulation and spatial interactions of head-to-head genes. BMC Genomics 2014; 15:519. [PMID: 24962804 PMCID: PMC4089025 DOI: 10.1186/1471-2164-15-519] [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: 03/27/2014] [Accepted: 06/19/2014] [Indexed: 11/10/2022] Open
Abstract
Background In eukaryotic genomes, about 10% of genes are arranged in a head-to-head (H2H) orientation, and the distance between the transcription start sites of each gene pair is closer than 1 kb. Two genes in an H2H pair are prone to co-express and co-function. There have been many studies on bidirectional promoters. However, the mechanism by which H2H genes are regulated at the transcriptional level still needs further clarification, especially with regard to the co-regulation of H2H pairs. In this study, we first used the Hi-C data of chromatin linkages to identify spatially interacting H2H pairs, and then integrated ChIP-seq data to compare H2H gene pairs with and without evidence of spatial interactions in terms of their binding transcription factors (TFs). Using ChIP-seq and DNase-seq data, histones and DNase associated with H2H pairs were identified. Furthermore, we looked into the connections between H2H genes in a human co-expression network. Results We found that i) Similar to the behaviour of two genes within an H2H pair (intra-H2H pair), a gene pair involving two distinct H2H pairs (inter-H2H pair) which interact with each other spatially, share common transcription factors (TFs); ii) TFs of intra- and inter-H2H pairs are distributed differently. Factors such as HEY1, GABP, Sin3Ak-20, POL2, E2F6, and c-MYC are essential for the bidirectional transcription of intra-H2H pairs; while factors like CTCF, BDP1, GATA2, RAD21, and POL3 play important roles in coherently regulating inter-H2H pairs; iii) H2H gene blocks are enriched with hypersensitive DNase and modified histones, which participate in active transcriptions; and iv) H2H genes tend to be highly connected compared with non-H2H genes in the human co-expression network. Conclusions Our findings shed new light on the mechanism of the transcriptional regulation of H2H genes through their linear and spatial interactions. For intra-H2H gene pairs, transcription factors regulate their transcriptions through bidirectional promoters, whereas for inter-H2H gene pairs, transcription factors are likely to regulate their activities depending on the spatial interaction of H2H gene pairs. In this way, two distinctive groups of transcription factors mediate intra- and inter-H2H gene transcriptions respectively, resulting in a highly compact gene regulatory network. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-519) contains supplementary material, which is available to authorized users.
Collapse
|
35
|
He C, Wang X, Zhang MQ. Nucleosome eviction and multiple co-factor binding predict estrogen-receptor-alpha-associated long-range interactions. Nucleic Acids Res 2014; 42:6935-44. [PMID: 24782518 PMCID: PMC4066761 DOI: 10.1093/nar/gku327] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 03/17/2014] [Accepted: 04/04/2014] [Indexed: 12/20/2022] Open
Abstract
Many enhancers regulate their target genes via long-distance interactions. High-throughput experiments like ChIA-PET have been developed to map such largely cell-type-specific interactions between cis-regulatory elements genome-widely. In this study, we integrated multiple types of data in order to reveal the general hidden patterns embedded in the ChIA-PET data. We found characteristic distance features related to promoter-promoter, enhancer-enhancer and insulator-insulator interactions. Although a protein may have many binding sites along the genome, our hypothesis is that those sites that share certain open chromatin structure can accommodate relatively larger protein complex consisting of specific regulatory and 'bridging' factors, and may be more likely to form robust long-range deoxyribonucleic acid (DNA) loops. This hypothesis was validated in the estrogen receptor alpha (ERα) ChIA-PET data. An efficient classifier was built to predict ERα-associated long-range interactions solely from the related ChIP-seq data, hence linking distal ERα-dependent enhancers to their target genes. We further applied the classifier to generate additional novel interactions, which were undetected in the original ChIA-PET paper but were validated by other independent experiments. Our work provides a new insight into the long-range chromatin interactions through deeper and integrative ChIA-PET data analysis and demonstrates DNA looping predictability from ordinary ChIP-seq data.
Collapse
Affiliation(s)
- Chao He
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xiaowo Wang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas, Dallas 800 West Campbell Road, RL11 Richardson, TX 75080-3021, USA
| |
Collapse
|
36
|
Schambach A, Moritz T. Toward position-independent retroviral vector expression in pluripotent stem cells. Mol Ther 2014; 21:1474-7. [PMID: 23903574 DOI: 10.1038/mt.2013.161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.
| | | |
Collapse
|
37
|
Antoniou MN, Skipper KA, Anakok O. Optimizing retroviral gene expression for effective therapies. Hum Gene Ther 2014; 24:363-74. [PMID: 23517535 DOI: 10.1089/hum.2013.062] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
With their ability to integrate their genetic material into the target cell genome, retroviral vectors (RV) of both the gamma-retroviral (γ-RV) and lentiviral vector (LV) classes currently remain the most efficient and thus the system of choice for achieving transgene retention and therefore potentially long-term expression and therapeutic benefit. However, γ-RV and LV integration comes at a cost in that transcription units will be present within a native chromatin environment and thus be subject to epigenetic effects (DNA methylation, histone modifications) that can negatively impact on their function. Indeed, highly variable expression and silencing of γ-RV and LV transgenes especially resulting from promoter DNA methylation is well documented and was the cause of the failure of gene therapy in a clinical trial for X-linked chronic granulomatous disease. This review will critically explore the use of different classes of genetic control elements that can in principle reduce vector insertion site position effects and epigenetic-mediated silencing. These transcriptional regulatory elements broadly divide themselves into either those with a chromatin boundary or border function (scaffold/matrix attachment regions, insulators) or those with a dominant chromatin remodeling and transcriptional activating capability (locus control regions,, ubiquitous chromatin opening elements). All these types of elements have their strengths and weaknesses within the constraints of a γ-RV and LV backbone, showing varying degrees of efficacy in improving reproducibility and stability of transgene function. Combinations of boundary and chromatin remodeling; transcriptional activating elements, which do not impede vector production; transduction efficiency; and stability are most likely to meet the requirements within a gene therapy context especially when targeting a stem cell population.
Collapse
Affiliation(s)
- Michael N Antoniou
- Gene Expression and Therapy Group, King's College London School of Medicine, Department of Medical and Molecular Genetics, Guy's Hospital, London, SE1 9RT, United Kingdom.
| | | | | |
Collapse
|
38
|
Nattrass GS, Cafe LM, McIntyre BL, Gardner GE, McGilchrist P, Robinson DL, Wang YH, Pethick DW, Greenwood PL. A post-transcriptional mechanism regulates calpastatin expression in bovine skeletal muscle. J Anim Sci 2014; 92:443-55. [PMID: 24664555 DOI: 10.2527/jas.2013-6978] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The objective of this study was to investigate whether single nucleotide polymorphisms (SNP) in the calpain 1 (CAPN1), calpain 3 (CAPN3) and calpastatin (CAST) genes, which have been shown to be associated with shear force and tenderness differences in the skeletal muscle of cattle, contribute to phenotypic variation in muscle tenderness by modulating the transcriptional activity of their respective gene. The mRNA expression of the calpain and CAST genes was assessed in the longissimus lumborum muscle (LLM) of cattle from two herds located in distinct production zones on the east (New South Wales, NSW) and west (Western Australia, WA) of Australia. The cattle in the herds were mainly Brahman cattle (Bos indicus) with smaller populations of Angus cattle (Bos taurus). There were 191 steers in the WA herd and 107 steers and 106 heifers in the NSW herd. These herds were established by choosing cattle from the diverse population which had different single nucleotide polymorphism (SNP) genotypes at the CAPN1, CAPN3 and CAST loci. Using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), the transcriptional activities of the CAPN1 and the CAST genes, but not the CAPN3 gene, were found to differ between favorable, positively associated with tenderness, and unfavorable, negatively associated with tenderness, allelic variants of these genes. These findings suggest that the muscle shear force and consumer taste panel differences in tenderness explained by the CAPN1 and CAST gene markers are a consequence of alterations in their mRNA levels, which may ultimately influence the protein activity of these genes, thereby altering the rate and(or) the extent of postmortem proteolysis in skeletal muscle. Of particular importance were the significantly lower type II and type III CAST 5' splice variant mRNA levels that were detected in the LLM muscle of Brahman and Angus cattle with 2 favourable alleles of the CAST:c.2832A > G polymorphism. Moreover, a reduction in the abundance of an alternative polyadenylated variant of the CAST transcript, terminated at the proximal polyadenylation site, provides a unique insight into the potential involvement of a post-transcriptional regulatory mechanism which may influence protein expression levels in bovine skeletal muscle.
Collapse
Affiliation(s)
- G S Nattrass
- Australian Cooperative Research Centre for Beef Genetic Technologies, University of New England, Armidale, NSW 2351, Australia
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Cui F, Zhurkin VB. Rotational positioning of nucleosomes facilitates selective binding of p53 to response elements associated with cell cycle arrest. Nucleic Acids Res 2013; 42:836-47. [PMID: 24153113 PMCID: PMC3902933 DOI: 10.1093/nar/gkt943] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The tumor suppressor protein p53 exhibits high affinity to the response elements regulating cell cycle arrest genes (CCA-sites), but relatively low affinity to the sites associated with apoptosis (Apo-sites). This in vivo tendency cannot be explained solely by the p53-DNA binding constants measured in vitro. Since p53 can bind nucleosomal DNA, we sought to understand if the two groups of p53 sites differ in their accessibility when embedded in nucleosomes. To this aim, we analyzed the sequence-dependent bending anisotropy of human genomic DNA containing p53 sites. For the 20 CCA-sites, we calculated rotational positioning patterns predicting that most of the sites are exposed on the nucleosomal surface. This is consistent with experimentally observed positioning of human nucleosomes. Remarkably, the sequence-dependent DNA anisotropy of both the p53 sites and flanking DNA work in concert producing strong positioning signals. By contrast, both the predicted and observed rotational settings of the 38 Apo-sites in nucleosomes suggest that many of these sites are buried inside, thus preventing immediate p53 recognition and delaying gene induction. The distinct chromatin organization of the CCA response elements appears to be one of the key factors facilitating p53-DNA binding and subsequent activation of genes associated with cell cycle arrest.
Collapse
Affiliation(s)
- Feng Cui
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive Rochester, NY 14623, USA and Laboratory of Cell Biology, National Cancer Institute, NIH Bg. 37, Room 3035A, Convent Dr., Bethesda, MD 20892, USA
| | | |
Collapse
|
40
|
Chen J, Haverty J, Deng L, Li G, Qiu P, Liu Z, Shi S. Identification of a novel endogenous regulatory element in Chinese hamster ovary cells by promoter trap. J Biotechnol 2013; 167:255-61. [DOI: 10.1016/j.jbiotec.2013.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 06/12/2013] [Accepted: 07/01/2013] [Indexed: 02/01/2023]
|
41
|
Ilsley GR, Fisher J, Apweiler R, DePace AH, Luscombe NM. Cellular resolution models for even skipped regulation in the entire Drosophila embryo. eLife 2013; 2:e00522. [PMID: 23930223 PMCID: PMC3736529 DOI: 10.7554/elife.00522] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 06/17/2013] [Indexed: 12/14/2022] Open
Abstract
Transcriptional control ensures genes are expressed in the right amounts at the correct times and locations. Understanding quantitatively how regulatory systems convert input signals to appropriate outputs remains a challenge. For the first time, we successfully model even skipped (eve) stripes 2 and 3+7 across the entire fly embryo at cellular resolution. A straightforward statistical relationship explains how transcription factor (TF) concentrations define eve's complex spatial expression, without the need for pairwise interactions or cross-regulatory dynamics. Simulating thousands of TF combinations, we recover known regulators and suggest new candidates. Finally, we accurately predict the intricate effects of perturbations including TF mutations and misexpression. Our approach imposes minimal assumptions about regulatory function; instead we infer underlying mechanisms from models that best fit the data, like the lack of TF-specific thresholds and the positional value of homotypic interactions. Our study provides a general and quantitative method for elucidating the regulation of diverse biological systems. DOI:http://dx.doi.org/10.7554/eLife.00522.001.
Collapse
Affiliation(s)
- Garth R Ilsley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Jasmin Fisher
- Microsoft Research Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Rolf Apweiler
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Angela H DePace
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Nicholas M Luscombe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- UCL Genetics Institute, Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
- London Research Institute, Cancer Research UK, London, United Kingdom
| |
Collapse
|
42
|
Khan MAF, Soto-Jimenez LM, Howe T, Streit A, Sosinsky A, Stern CD. Computational tools and resources for prediction and analysis of gene regulatory regions in the chick genome. Genesis 2013; 51:311-24. [PMID: 23355428 PMCID: PMC3664090 DOI: 10.1002/dvg.22375] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 01/16/2013] [Accepted: 01/17/2013] [Indexed: 11/07/2022]
Abstract
The discovery of cis-regulatory elements is a challenging problem in bioinformatics, owing to distal locations and context-specific roles of these elements in controlling gene regulation. Here we review the current bioinformatics methodologies and resources available for systematic discovery of cis-acting regulatory elements and conserved transcription factor binding sites in the chick genome. In addition, we propose and make available, a novel workflow using computational tools that integrate CTCF analysis to predict putative insulator elements, enhancer prediction, and TFBS analysis. To demonstrate the usefulness of this computational workflow, we then use it to analyze the locus of the gene Sox2 whose developmental expression is known to be controlled by a complex array of cis-acting regulatory elements. The workflow accurately predicts most of the experimentally verified elements along with some that have not yet been discovered. A web version of the CTCF tool, together with instructions for using the workflow can be accessed from http://toolshed.g2.bx.psu.edu/view/mkhan1980/ctcf_analysis. For local installation of the tool, relevant Perl scripts and instructions are provided in the directory named "code" in the supplementary materials.
Collapse
Affiliation(s)
- Mohsin A F Khan
- Department of Cell & Developmental Biology, University College London, London, United Kingdom
| | | | | | | | | | | |
Collapse
|
43
|
Kyrchanova O, Leman D, Parshikov A, Fedotova A, Studitsky V, Maksimenko O, Georgiev P. New properties of Drosophila scs and scs' insulators. PLoS One 2013; 8:e62690. [PMID: 23638134 PMCID: PMC3634774 DOI: 10.1371/journal.pone.0062690] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 03/25/2013] [Indexed: 11/18/2022] Open
Abstract
Insulators are defined as a class of regulatory elements that delimit independent transcriptional domains within eukaryotic genomes. The first insulators to be identified were scs and scs', which flank the domain including two heat shock 70 genes. Zw5 and BEAF bind to scs and scs', respectively, and are responsible for the interaction between these insulators. Using the regulatory regions of yellow and white reporter genes, we have found that the interaction between scs and scs' improves the enhancer-blocking activity of the weak scs' insulator. The sequences of scs and scs' insulators include the promoters of genes that are strongly active in S2 cells but not in the eyes, in which the enhancer-blocking activity of these insulators has been extensively examined. Only the promoter of the Cad87A gene located at the end of the scs insulator drives white expression in the eyes, and the white enhancer can slightly stimulate this promoter. The scs insulator contains polyadenylation signals that may be important for preventing transcription through the insulator. As shown previously, scs and scs' can insulate transcription of the white transgene from the enhancing effects of the surrounding genome, a phenomenon known as the chromosomal position effect (CPE). After analyzing many independent transgenic lines, we have concluded that transgenes carrying the scs insulator are rarely inserted into genomic regions that stimulate the white reporter expression in the eyes.
Collapse
Affiliation(s)
- Olga Kyrchanova
- Group of Transcriptional Regulation, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry Leman
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Parshikov
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Fedotova
- Group of Transcriptional Regulation, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vasily Studitsky
- School of Biology, Moscow State University, Moscow, Russia
- Department of Pharmacology, UMDNJ–Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Oksana Maksimenko
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail:
| |
Collapse
|
44
|
Kim YW, Kim A. Histone acetylation contributes to chromatin looping between the locus control region and globin gene by influencing hypersensitive site formation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:963-9. [PMID: 23607989 DOI: 10.1016/j.bbagrm.2013.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 03/27/2013] [Accepted: 04/11/2013] [Indexed: 01/19/2023]
Abstract
Chromatin loops are formed between enhancers and promoters and between insulators to regulate gene transcription in the eukaryotic genome. These transcription regulatory elements forming loops have highly acetylated histones. To understand the correlation between histone acetylation and chromatin loop formation, we inhibited the expression of histone acetyltransferase CBP and p300 in erythroid K562 cells and analyzed the chromatin structure of the β-globin locus. The proximity between the locus control region (LCR) and the active (G)γ-globin gene was decreased in the β-globin locus when histones were hypoacetylated by the double knockdown of CBP and p300. Sensitivity to DNase I and binding of erythroid specific activators were reduced in the hypoacetylated LCR hypersensitive sites (HSs) and gene promoter. Interestingly, the chromatin loop between HS5 and 3'HS1 was formed regardless of the hypoacetylation of the β-globin locus. CTCF binding was maintained at HS5 and 3'HS1 in the hypoacetylated locus. Thus, these results indicate that histone acetylation contributes to chromatin looping through the formation of HSs in the LCR and gene promoter. However, looping between insulators appears to be independent from histone acetylation.
Collapse
Affiliation(s)
- Yea Woon Kim
- Department of Molecular Biology, Pusan National University, Busan, South Korea
| | | |
Collapse
|
45
|
Abstract
Long noncoding RNAs (lncRNAs) have gained widespread attention in recent years as a potentially new and crucial layer of biological regulation. lncRNAs of all kinds have been implicated in a range of developmental processes and diseases, but knowledge of the mechanisms by which they act is still surprisingly limited, and claims that almost the entirety of the mammalian genome is transcribed into functional noncoding transcripts remain controversial. At the same time, a small number of well-studied lncRNAs have given us important clues about the biology of these molecules, and a few key functional and mechanistic themes have begun to emerge, although the robustness of these models and classification schemes remains to be seen. Here, we review the current state of knowledge of the lncRNA field, discussing what is known about the genomic contexts, biological functions, and mechanisms of action of lncRNAs. We also reflect on how the recent interest in lncRNAs is deeply rooted in biology's longstanding concern with the evolution and function of genomes.
Collapse
Affiliation(s)
- Johnny T Y Kung
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02114, USA
| | | | | |
Collapse
|
46
|
A model for the 3D chromatin architecture of pro and eukaryotes. Methods 2012; 58:307-14. [DOI: 10.1016/j.ymeth.2012.04.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 04/05/2012] [Accepted: 04/17/2012] [Indexed: 12/14/2022] Open
|
47
|
Marsman J, Horsfield JA. Long distance relationships: enhancer-promoter communication and dynamic gene transcription. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:1217-27. [PMID: 23124110 DOI: 10.1016/j.bbagrm.2012.10.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/18/2012] [Accepted: 10/22/2012] [Indexed: 11/27/2022]
Abstract
The three-dimensional regulation of gene transcription involves loop formation between enhancer and promoter elements, controlling spatiotemporal gene expression in multicellular organisms. Enhancers are usually located in non-coding DNA and can activate gene transcription by recruiting transcription factors, chromatin remodeling factors and RNA Polymerase II. Research over the last few years has revealed that enhancers have tell-tale characteristics that facilitate their detection by several approaches, although the hallmarks of enhancers are not always uniform. Enhancers likely play an important role in the activation of genes by functioning as a primary point of contact for transcriptional activators, and by making physical contact with gene promoters often by means of a chromatin loop. Although numerous transcriptional regulators participate in the formation of chromatin loops that bring enhancers into proximity with promoters, the mechanism(s) of enhancer-promoter connectivity remain enigmatic. Here we discuss enhancer function, review some of the many proteins shown to be involved in establishing enhancer-promoter loops, and describe the dynamics of enhancer-promoter contacts during development, differentiation and in specific cell types.
Collapse
Affiliation(s)
- Judith Marsman
- Department of Pathology, The University of Otago, Dunedin, New Zealand
| | | |
Collapse
|
48
|
Naumova N, Smith EM, Zhan Y, Dekker J. Analysis of long-range chromatin interactions using Chromosome Conformation Capture. Methods 2012; 58:192-203. [PMID: 22903059 DOI: 10.1016/j.ymeth.2012.07.022] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 07/18/2012] [Indexed: 10/28/2022] Open
Abstract
Chromosome Conformation Capture, or 3C, is a pioneering method for investigating the three-dimensional structure of chromatin. 3C is used to analyze long-range looping interactions between any pair of selected genomic loci. Most 3C studies focus on defined genomic regions of interest that can be up to several hundred Kb in size. The method has become widely adopted and has been modified to increase throughput to allow unbiased genome-wide analysis. These large-scale adaptations are presented in other articles in this issue of Methods. Here we describe the 3C procedure in detail, including the appropriate use of the technology, the experimental set-up, an optimized protocol and troubleshooting guide, and considerations for data analysis. The protocol described here contains previously unpublished improvements, which save time and reduce labor. We pay special attention to primer design, appropriate controls and data analysis. We include notes and discussion based on our extensive experience to help researchers understand the principles of 3C-based techniques and to avoid common pitfalls and mistakes. This paper represents a complete resource and detailed guide for anyone who desires to perform 3C.
Collapse
Affiliation(s)
- Natalia Naumova
- Programs in Systems Biology and Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-0103, USA
| | | | | | | |
Collapse
|
49
|
Deng W, Lee J, Wang H, Miller J, Reik A, Gregory PD, Dean A, Blobel GA. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell 2012; 149:1233-44. [PMID: 22682246 DOI: 10.1016/j.cell.2012.03.051] [Citation(s) in RCA: 511] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 03/05/2012] [Accepted: 03/30/2012] [Indexed: 11/19/2022]
Abstract
Chromatin loops juxtapose distal enhancers with active promoters, but their molecular architecture and relationship with transcription remain unclear. In erythroid cells, the locus control region (LCR) and β-globin promoter form a chromatin loop that requires transcription factor GATA1 and the associated molecule Ldb1. We employed artificial zinc fingers (ZF) to tether Ldb1 to the β-globin promoter in GATA1 null erythroblasts, in which the β-globin locus is relaxed and inactive. Remarkably, targeting Ldb1 or only its self-association domain to the β-globin promoter substantially activated β-globin transcription in the absence of GATA1. Promoter-tethered Ldb1 interacted with endogenous Ldb1 complexes at the LCR to form a chromatin loop, causing recruitment and phosphorylation of RNA polymerase II. ZF-Ldb1 proteins were inactive at alleles lacking the LCR, demonstrating that their activities depend on long-range interactions. Our findings establish Ldb1 as a critical effector of GATA1-mediated loop formation and indicate that chromatin looping causally underlies gene regulation.
Collapse
Affiliation(s)
- Wulan Deng
- Division of Hematology, The Children's Hospital of Philadelphia, PA 19104, USA
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Mitotic chromosome structure. Exp Cell Res 2012; 318:1381-5. [DOI: 10.1016/j.yexcr.2012.03.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 03/19/2012] [Accepted: 03/24/2012] [Indexed: 11/18/2022]
|