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Chang LH, Noordermeer D. Permeable TAD boundaries and their impact on genome-associated functions. Bioessays 2024:e2400137. [PMID: 39093600 DOI: 10.1002/bies.202400137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024]
Abstract
TAD boundaries are genomic elements that separate biological processes in neighboring domains by blocking DNA loops that are formed through Cohesin-mediated loop extrusion. Most TAD boundaries consist of arrays of binding sites for the CTCF protein, whose interaction with the Cohesin complex blocks loop extrusion. TAD boundaries are not fully impermeable though and allow a limited amount of inter-TAD loop formation. Based on the reanalysis of Nano-C data, a multicontact Chromosome Conformation Capture assay, we propose a model whereby clustered CTCF binding sites promote the successive stalling of Cohesin and subsequent dissociation from the chromatin. A fraction of Cohesin nonetheless achieves boundary read-through. Due to a constant rate of Cohesin dissociation elsewhere in the genome, the maximum length of inter-TAD loops is restricted though. We speculate that the DNA-encoded organization of stalling sites regulates TAD boundary permeability and discuss implications for enhancer-promoter loop formation and other genomic processes.
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Affiliation(s)
- Li-Hsin Chang
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Blood and Transplant Research Unit in Precision Cellular Therapeutics, National Institute of Health Research, Oxford, UK
| | - Daan Noordermeer
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
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2
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Schwaiger M, Mohn F, Bühler M, Kaaij LJT. guidedNOMe-seq quantifies chromatin states at single allele resolution for hundreds of custom regions in parallel. BMC Genomics 2024; 25:732. [PMID: 39075377 PMCID: PMC11288131 DOI: 10.1186/s12864-024-10625-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 07/15/2024] [Indexed: 07/31/2024] Open
Abstract
Since the introduction of next generation sequencing technologies, the field of epigenomics has evolved rapidly. However, most commonly used assays are enrichment-based methods and thus only semi-quantitative. Nucleosome occupancy and methylome sequencing (NOMe-seq) allows for quantitative inference of chromatin states with single locus resolution, but this requires high sequencing depth and is therefore prohibitively expensive to routinely apply to organisms with large genomes. To overcome this limitation, we introduce guidedNOMe-seq, where we combine NOMe profiling with large scale sgRNA synthesis and Cas9-mediated region-of-interest (ROI) liberation. To facilitate quantitative comparisons between multiple samples, we additionally develop an R package to standardize differential analysis of any type of NOMe-seq data. We extensively benchmark guidedNOMe-seq in a proof-of-concept study, dissecting the interplay of ChAHP and CTCF on chromatin. In summary we present a cost-effective, scalable, and customizable target enrichment extension to the existing NOMe-seq protocol allowing genome-scale quantification of nucleosome occupancy and transcription factor binding at single allele resolution.
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Affiliation(s)
- Michaela Schwaiger
- Friedrich Miescher Institute for Biomedical Research, Basel, 4056, Switzerland
- Swiss Institute of Bioinformatics, Basel, 4056, Switzerland
| | - Fabio Mohn
- Friedrich Miescher Institute for Biomedical Research, Basel, 4056, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, 4056, Switzerland
- University of Basel, Basel, 4003, Switzerland
| | - Lucas J T Kaaij
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands.
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3
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Wang H, Ma B, Stevens T, Knapp J, Lu J, Prochownik EV. MYC Binding Near Transcriptional End Sites Regulates Basal Gene Expression, Read-Through Transcription and Intragenic Contacts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603118. [PMID: 39071289 PMCID: PMC11275772 DOI: 10.1101/2024.07.11.603118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The MYC oncoprotein regulates numerous genes involved in cellular processes such as cell cycle and mitochondrial and ribosomal structure and function. This requires heterodimerization with its partner, MAX, and binding to specific promoter and enhancer elements. Here, we show that MYC and MAX also bind near transcriptional end sites (TESs) of over one-sixth of all annotated genes. These interactions are dose-dependent, evolutionarily conserved, stabilize the normally short-lived MYC protein and regulate expression both in concert with and independent of MYC's binding elsewhere. MYC's TES binding occurs in association with other transcription factors, alters the chromatin landscape, increases nuclease susceptibility and can alter transcriptional read-through, particularly in response to certain stresses. MYC-bound TESs can directly contact promoters and may fine-tune gene expression in response to both physiologic and pathologic stimuli. Collectively, these findings support a previously unrecognized role for MYC in regulating transcription and its read-through via direct intragenic contacts between TESs and promoters.
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4
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Galanopoulou O, Tachmatzidi EC, Deligianni E, Botskaris D, Nikolaou KC, Gargani S, Dalezios Y, Chalepakis G, Talianidis I. Endonucleosis mediates internalization of cytoplasm into the nucleus. Nat Commun 2024; 15:5843. [PMID: 38992049 PMCID: PMC11239883 DOI: 10.1038/s41467-024-50259-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 07/03/2024] [Indexed: 07/13/2024] Open
Abstract
Setd8 regulates transcription elongation, mitotic DNA condensation, DNA damage response and replication licensing. Here we show that, in mitogen-stimulated liver-specific Setd8-KO mice, most of the hepatocytes are eliminated by necrosis but a significant number of them survive via entering a stage exhibiting several senescence-related features. Setd8-deficient hepatocytes had enlarged nuclei, chromosomal hyperploidy and nuclear engulfments progressing to the formation of intranuclear vesicles surrounded by nuclear lamina. These vesicles contain glycogen, cytoplasmic proteins and even entire organelles. We term this process "endonucleosis". Intranuclear vesicles are absent in hepatocytes of Setd8/Atg5 knockout mice, suggesting that the process requires the function of the canonical autophagy machinery. Endonucleosis and hyperploidization are temporary, early events in the surviving Setd8-deficient cells. Larger vesicles break down into microvesicles over time and are eventually eliminated. The results reveal sequential events in cells with extensive DNA damage, which function as part of survival mechanisms to prevent necrotic death.
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Affiliation(s)
- Ourania Galanopoulou
- Institute of Molecular Biology & Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Dept. of Biology University of Crete, Heraklion, Crete, Greece
| | - Evangelia C Tachmatzidi
- Institute of Molecular Biology & Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Dept. of Biology University of Crete, Heraklion, Crete, Greece
| | - Elena Deligianni
- Institute of Molecular Biology & Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Dimitris Botskaris
- Institute of Molecular Biology & Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Dept. of Biology University of Crete, Heraklion, Crete, Greece
| | | | - Sofia Gargani
- Biomedical Sciences Research Center Alexander Fleming, Vari, Greece
| | - Yannis Dalezios
- School of Medicine University of Crete, Heraklion, Crete, Greece
| | | | - Iannis Talianidis
- Institute of Molecular Biology & Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete, Greece.
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5
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Wulfridge P, Sarma K. Intertwining roles of R-loops and G-quadruplexes in DNA repair, transcription and genome organization. Nat Cell Biol 2024; 26:1025-1036. [PMID: 38914786 DOI: 10.1038/s41556-024-01437-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/10/2024] [Indexed: 06/26/2024]
Abstract
R-loops are three-stranded nucleic acid structures that are abundant and widespread across the genome and that have important physiological roles in many nuclear processes. Their accumulation is observed in cancers and neurodegenerative disorders. Recent studies have implicated a function for R-loops and G-quadruplex (G4) structures, which can form on the displaced single strand of R-loops, in three-dimensional genome organization in both physiological and pathological contexts. Here we discuss the interconnected functions of DNA:RNA hybrids and G4s within R-loops, their impact on DNA repair and gene regulatory networks, and their emerging roles in genome organization during development and disease.
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Affiliation(s)
- Phillip Wulfridge
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Kavitha Sarma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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6
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Huber J, Tanasie NL, Zernia S, Stigler J. Single-molecule imaging reveals a direct role of CTCF's zinc fingers in SA interaction and cluster-dependent RNA recruitment. Nucleic Acids Res 2024; 52:6490-6506. [PMID: 38742641 PMCID: PMC11194110 DOI: 10.1093/nar/gkae391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/21/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
CTCF is a zinc finger protein associated with transcription regulation that also acts as a barrier factor for topologically associated domains (TADs) generated by cohesin via loop extrusion. These processes require different properties of CTCF-DNA interaction, and it is still unclear how CTCF's structural features may modulate its diverse roles. Here, we employ single-molecule imaging to study both full-length CTCF and truncation mutants. We show that CTCF enriches at CTCF binding sites (CBSs), displaying a longer lifetime than observed previously. We demonstrate that the zinc finger domains mediate CTCF clustering and that clustering enables RNA recruitment, possibly creating a scaffold for interaction with RNA-binding proteins like cohesin's subunit SA. We further reveal a direct recruitment and an increase of SA residence time by CTCF bound at CBSs, suggesting that CTCF-SA interactions are crucial for cohesin stability on chromatin at TAD borders. Furthermore, we establish a single-molecule T7 transcription assay and show that although a transcribing polymerase can remove CTCF from CBSs, transcription is impaired. Our study shows that context-dependent nucleic acid binding determines the multifaceted CTCF roles in genome organization and transcription regulation.
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Affiliation(s)
- Jonas Huber
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Sarah Zernia
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Johannes Stigler
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
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7
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Lee YH, Hass EP, Campodonico W, Lee YK, Lasda E, Shah J, Rinn J, Hwang T. Massively parallel dissection of RNA in RNA-protein interactions in vivo. Nucleic Acids Res 2024; 52:e48. [PMID: 38726866 PMCID: PMC11162807 DOI: 10.1093/nar/gkae334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 06/11/2024] Open
Abstract
Many of the biological functions performed by RNA are mediated by RNA-binding proteins (RBPs), and understanding the molecular basis of these interactions is fundamental to biology. Here, we present massively parallel RNA assay combined with immunoprecipitation (MPRNA-IP) for in vivo high-throughput dissection of RNA-protein interactions and describe statistical models for identifying RNA domains and parsing the structural contributions of RNA. By using custom pools of tens of thousands of RNA sequences containing systematically designed truncations and mutations, MPRNA-IP is able to identify RNA domains, sequences, and secondary structures necessary and sufficient for protein binding in a single experiment. We show that this approach is successful for multiple RNAs of interest, including the long noncoding RNA NORAD, bacteriophage MS2 RNA, and human telomerase RNA, and we use it to interrogate the hitherto unknown sequence or structural RNA-binding preferences of the DNA-looping factor CTCF. By integrating systematic mutation analysis with crosslinking immunoprecipitation, MPRNA-IP provides a novel high-throughput way to elucidate RNA-based mechanisms behind RNA-protein interactions in vivo.
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Affiliation(s)
- Yu Hsuan Lee
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Evan P Hass
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Will Campodonico
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Yong Kyu Lee
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Erika Lasda
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Jaynish S Shah
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - John L Rinn
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Taeyoung Hwang
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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8
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Crewe M, Segev A, Rueda R, Madabhushi R. Atypical Modes of CTCF Binding Facilitate Tissue-Specific and Neuronal Activity-Dependent Gene Expression States. Mol Neurobiol 2024; 61:3240-3257. [PMID: 37979036 DOI: 10.1007/s12035-023-03762-5] [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: 07/27/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
Multivalent binding of CTCF to variable DNA sequences is thought to underlie its ability to mediate diverse cellular functions. CTCF typically binds a 20 base-pair consensus DNA sequence, but the full diversity of CTCF binding sites (CBS) within the genome has not been interrogated. We assessed CTCF occupancy in cultured cortical neurons and observed surprisingly that ~ 22% of CBS lack the consensus CTCF motif. We report here that sequence diversity at most of these atypical CBS involves degeneracy at specific nucleotide positions within the consensus CTCF motif, which likely affect the binding of CTCF zinc fingers 6 and 7. This mode of atypical CTCF binding defines most CBS at gene promoters, as well as CBS that are dynamically altered during neural differentiation and following neuronal stimulation, revealing how atypical CTCF binding could influence gene activity. Dynamic CBS are distributed both within and outside loop anchors and TAD boundaries, suggesting both looping-dependent and independent roles for CTCF. Finally, we describe a second mode of atypical CTCF binding to DNA sequences that are completely unrelated to the consensus CTCF motif, which are enriched within the bodies of tissue-specific genes. These tissue-specific atypical CBS are also enriched in H3K27ac, which marks cis-regulatory elements within chromatin, including enhancers. Overall, these results indicate how atypical CBS could dynamically regulate gene activity patterns during differentiation, development, and in response to environmental cues.
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Affiliation(s)
- Morgan Crewe
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Amir Segev
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Richard Rueda
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ram Madabhushi
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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9
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Li Y, Tan M, Akkari-Henić A, Zhang L, Kip M, Sun S, Sepers JJ, Xu N, Ariyurek Y, Kloet SL, Davis RP, Mikkers H, Gruber JJ, Snyder MP, Li X, Pang B. Genome-wide Cas9-mediated screening of essential non-coding regulatory elements via libraries of paired single-guide RNAs. Nat Biomed Eng 2024:10.1038/s41551-024-01204-8. [PMID: 38778183 DOI: 10.1038/s41551-024-01204-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/27/2024] [Indexed: 05/25/2024]
Abstract
The functions of non-coding regulatory elements (NCREs), which constitute a major fraction of the human genome, have not been systematically studied. Here we report a method involving libraries of paired single-guide RNAs targeting both ends of an NCRE as a screening system for the Cas9-mediated deletion of thousands of NCREs genome-wide to study their functions in distinct biological contexts. By using K562 and 293T cell lines and human embryonic stem cells, we show that NCREs can have redundant functions, and that many ultra-conserved elements have silencer activity and play essential roles in cell growth and in cellular responses to drugs (notably, the ultra-conserved element PAX6_Tarzan may be critical for heart development, as removing it from human embryonic stem cells led to defects in cardiomyocyte differentiation). The high-throughput screen, which is compatible with single-cell sequencing, may allow for the identification of druggable NCREs.
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Affiliation(s)
- Yufeng Li
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Minkang Tan
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Almira Akkari-Henić
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Limin Zhang
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Maarten Kip
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Shengnan Sun
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Jorian J Sepers
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ningning Xu
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Yavuz Ariyurek
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Susan L Kloet
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Richard P Davis
- Department of Anatomy and Embryology, The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, the Netherlands
| | - Harald Mikkers
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Joshua J Gruber
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Xiao Li
- Department of Biochemistry, The Center for RNA Science and Therapeutics, Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA.
| | - Baoxu Pang
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.
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10
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Kaur S, Arpna, Jha D, Khosla R, Kaur M, Parkash J, Sharma A, Changotra H. Autophagy related gene 5 polymorphism rs17587319 (C/G) in asthmatic patients in North Indian population. J Asthma 2024; 61:472-478. [PMID: 38009708 DOI: 10.1080/02770903.2023.2289156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/25/2023] [Indexed: 11/29/2023]
Abstract
Objective: Genetic background and environmental stimuli play an important role in asthma, which is an individual's hyper-responsiveness to these stimuli leading to airway inflammation. Autophagy Related Gene 5 (ATG5) plays a critical role in the autophagy pathway and has been shown to be involved in asthma. The genetic polymorphisms in the ATG5 have been reported to predispose individuals to asthma. The role of single nucleotide polymorphism rs17587319 (C/G) of ATG5 in asthma has not been studied so far. Materials and methods: In this study, we in silico analysed rs17587319 (C/G) using web-based tools Human Splice Finder (HSF) and RegulomeDB and further a case-control study was conducted that included 187 blood samples (94 asthmatic and 93 healthy controls). Results: In silico analysis suggested alteration of splicing signals by this intronic variant. The samples were genotyped by applying the PCR-RFLP method. The MAF obtained was 0.022 and 0.043 in healthy controls and asthmatic individuals, respectively. The statistical analysis revealed no association (allelic model, OR = 2.02, 95%CI = 0.59-6.83, p = 0.25; co-dominant model, OR = 2.06, 95%CI = 0.6-7.12, p = 0.24) of rs17587319 (C/G) with the susceptibility to asthma in the north Indian population. Conclusions: In conclusion, rs17587319 (C/G) of ATG5 does not predispose individuals to asthma in our part of the world. Further studies are needed including more number of samples to ascertain the role of this polymorphism in asthma.
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Affiliation(s)
- Sargeet Kaur
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - Arpna
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Durga Jha
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - Rajiv Khosla
- Department of Biotechnology, Doaba College Jalandhar, Punjab, India
| | - Manpreet Kaur
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Jyoti Parkash
- Centre for Animal Sciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India
| | - Arti Sharma
- Department of Computational Biology, School of Biological Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Harish Changotra
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
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11
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Tang X, Zeng P, Liu K, Qing L, Sun Y, Liu X, Lu L, Wei C, Wang J, Jiang S, Sun J, Chang W, Yu H, Chen H, Zhou J, Xu C, Fan L, Miao YL, Ding J. The PTM profiling of CTCF reveals the regulation of 3D chromatin structure by O-GlcNAcylation. Nat Commun 2024; 15:2813. [PMID: 38561336 PMCID: PMC10985093 DOI: 10.1038/s41467-024-47048-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
CCCTC-binding factor (CTCF), a ubiquitously expressed and highly conserved protein, is known to play a critical role in chromatin structure. Post-translational modifications (PTMs) diversify the functions of protein to regulate numerous cellular processes. However, the effects of PTMs on the genome-wide binding of CTCF and the organization of three-dimensional (3D) chromatin structure have not been fully understood. In this study, we uncovered the PTM profiling of CTCF and demonstrated that CTCF can be O-GlcNAcylated and arginine methylated. Functionally, we demonstrated that O-GlcNAcylation inhibits CTCF binding to chromatin. Meanwhile, deficiency of CTCF O-GlcNAcylation results in the disruption of loop domains and the alteration of chromatin loops associated with cellular development. Furthermore, the deficiency of CTCF O-GlcNAcylation increases the expression of developmental genes and negatively regulates maintenance and establishment of stem cell pluripotency. In conclusion, these results provide key insights into the role of PTMs for the 3D chromatin structure.
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Affiliation(s)
- Xiuxiao Tang
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Pharmacology and Cardiac & Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Pengguihang Zeng
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Kezhi Liu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Li Qing
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yifei Sun
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Xinyi Liu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Lizi Lu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Chao Wei
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Jia Wang
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Shaoshuai Jiang
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Jun Sun
- West China Biomedical Big Data Center, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Wakam Chang
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Haopeng Yu
- West China Biomedical Big Data Center, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Jiaguo Zhou
- Department of Pharmacology and Cardiac & Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Chengfang Xu
- The obstetric and gynecology Department of The third affiliated hospital of Sun Yat-Sen University, Guangzhou, China.
| | - Lili Fan
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong, China.
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.
| | - Junjun Ding
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China.
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China.
- West China Biomedical Big Data Center, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China.
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12
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Kim M, Wang P, Clow PA, Chien I(E, Wang X, Peng J, Chai H, Liu X, Lee B, Ngan CY, Yue F, Milenkovic O, Chuang JH, Wei CL, Casellas R, Cheng AW, Ruan Y. Multifaceted roles of cohesin in regulating transcriptional loops. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586715. [PMID: 38585764 PMCID: PMC10996690 DOI: 10.1101/2024.03.25.586715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cohesin is required for chromatin loop formation. However, its precise role in regulating gene transcription remains largely unknown. We investigated the relationship between cohesin and RNA Polymerase II (RNAPII) using single-molecule mapping and live-cell imaging methods in human cells. Cohesin-mediated transcriptional loops were highly correlated with those of RNAPII and followed the direction of gene transcription. Depleting RAD21, a subunit of cohesin, resulted in the loss of long-range (>100 kb) loops between distal (super-)enhancers and promoters of cell-type-specific genes. By contrast, the short-range (<50 kb) loops were insensitive to RAD21 depletion and connected genes that are mostly housekeeping. This result explains why only a small fraction of genes are affected by the loss of long-range chromatin interactions due to cohesin depletion. Remarkably, RAD21 depletion appeared to up-regulate genes located in early initiation zones (EIZ) of DNA replication, and the EIZ signals were amplified drastically without RAD21. Our results revealed new mechanistic insights of cohesin's multifaceted roles in establishing transcriptional loops, preserving long-range chromatin interactions for cell-specific genes, and maintaining timely order of DNA replication.
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Affiliation(s)
- Minji Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Present address: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
- Equal contributions
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Evanston, IL, 60201, USA
- Equal contributions
| | - Patricia A. Clow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Equal contributions
| | - I (Eli) Chien
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA
| | - Xiaotao Wang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Reproduction and Development, Shanghai, China
| | - Jianhao Peng
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA
| | - Haoxi Chai
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Xiyuan Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, P.R. China
| | - Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Evanston, IL, 60201, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Olgica Milenkovic
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA
| | - Jeffrey H. Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, 06030, USA
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Rafael Casellas
- Hematopoietic Biology and Malignancy, MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Albert W. Cheng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, 85281, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang Province, 310058, P.R. China
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Chea S, Kreger J, Lopez-Burks ME, MacLean AL, Lander AD, Calof AL. Gastrulation-stage gene expression in Nipbl+/- mouse embryos foreshadows the development of syndromic birth defects. SCIENCE ADVANCES 2024; 10:eadl4239. [PMID: 38507484 PMCID: PMC10954218 DOI: 10.1126/sciadv.adl4239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
In animal models, Nipbl deficiency phenocopies gene expression changes and birth defects seen in Cornelia de Lange syndrome, the most common cause of which is Nipbl haploinsufficiency. Previous studies in Nipbl+/- mice suggested that heart development is abnormal as soon as cardiogenic tissue is formed. To investigate this, we performed single-cell RNA sequencing on wild-type and Nipbl+/- mouse embryos at gastrulation and early cardiac crescent stages. Nipbl+/- embryos had fewer mesoderm cells than wild-type and altered proportions of mesodermal cell subpopulations. These findings were associated with underexpression of genes implicated in driving specific mesodermal lineages. In addition, Nanog was found to be overexpressed in all germ layers, and many gene expression changes observed in Nipbl+/- embryos could be attributed to Nanog overexpression. These findings establish a link between Nipbl deficiency, Nanog overexpression, and gene expression dysregulation/lineage misallocation, which ultimately manifest as birth defects in Nipbl+/- animals and Cornelia de Lange syndrome.
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Affiliation(s)
- Stephenson Chea
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Jesse Kreger
- Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Martha E. Lopez-Burks
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Adam L. MacLean
- Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Arthur D. Lander
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Anne L. Calof
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
- Department of Anatomy and Neurobiology, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
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14
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Monteagudo-Sánchez A, Noordermeer D, Greenberg MVC. The impact of DNA methylation on CTCF-mediated 3D genome organization. Nat Struct Mol Biol 2024; 31:404-412. [PMID: 38499830 DOI: 10.1038/s41594-024-01241-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/05/2024] [Indexed: 03/20/2024]
Abstract
Cytosine DNA methylation is a highly conserved epigenetic mark in eukaryotes. Although the role of DNA methylation at gene promoters and repetitive elements has been extensively studied, the function of DNA methylation in other genomic contexts remains less clear. In the nucleus of mammalian cells, the genome is spatially organized at different levels, and strongly influences myriad genomic processes. There are a number of factors that regulate the three-dimensional (3D) organization of the genome, with the CTCF insulator protein being among the most well-characterized. Pertinently, CTCF binding has been reported as being DNA methylation-sensitive in certain contexts, perhaps most notably in the process of genomic imprinting. Therefore, it stands to reason that DNA methylation may play a broader role in the regulation of chromatin architecture. Here we summarize the current understanding that is relevant to both the mammalian DNA methylation and chromatin architecture fields and attempt to assess the extent to which DNA methylation impacts the folding of the genome. The focus is in early embryonic development and cellular transitions when the epigenome is in flux, but we also describe insights from pathological contexts, such as cancer, in which the epigenome and 3D genome organization are misregulated.
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Affiliation(s)
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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15
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Company C, Schmitt MJ, Dramaretska Y, Serresi M, Kertalli S, Jiang B, Yin JA, Aguzzi A, Barozzi I, Gargiulo G. Logical design of synthetic cis-regulatory DNA for genetic tracing of cell identities and state changes. Nat Commun 2024; 15:897. [PMID: 38316783 PMCID: PMC10844330 DOI: 10.1038/s41467-024-45069-6] [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: 10/13/2022] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Descriptive data are rapidly expanding in biomedical research. Instead, functional validation methods with sufficient complexity remain underdeveloped. Transcriptional reporters allow experimental characterization and manipulation of developmental and disease cell states, but their design lacks flexibility. Here, we report logical design of synthetic cis-regulatory DNA (LSD), a computational framework leveraging phenotypic biomarkers and trans-regulatory networks as input to design reporters marking the activity of selected cellular states and pathways. LSD uses bulk or single-cell biomarkers and a reference genome or custom cis-regulatory DNA datasets with user-defined boundary regions. By benchmarking validated reporters, we integrate LSD with a computational ranking of phenotypic specificity of putative cis-regulatory DNA. Experimentally, LSD-designed reporters targeting a wide range of cell states are functional without minimal promoters. Applied to broadly expressed genes from human and mouse tissues, LSD generates functional housekeeper-like sLCRs compatible with size constraints of AAV vectors for gene therapy applications. A mesenchymal glioblastoma reporter designed by LSD outperforms previously validated ones and canonical cell surface markers. In genome-scale CRISPRa screens, LSD facilitates the discovery of known and novel bona fide cell-state drivers. Thus, LSD captures core principles of cis-regulation and is broadly applicable to studying complex cell states and mechanisms of transcriptional regulation.
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Affiliation(s)
- Carlos Company
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Matthias Jürgen Schmitt
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Yuliia Dramaretska
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Michela Serresi
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Sonia Kertalli
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Ben Jiang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Jiang-An Yin
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Gaetano Gargiulo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany.
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16
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Verruma CG, Santos RS, Marchesi JAP, Sales SLA, Vila RA, Rios ÁFL, Furtado CLM, Ramos ES. Dynamic methylation pattern of H19DMR and KvDMR1 in bovine oocytes and preimplantation embryos. J Assist Reprod Genet 2024; 41:333-345. [PMID: 38231285 PMCID: PMC10894807 DOI: 10.1007/s10815-023-03011-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024] Open
Abstract
PURPOSE This study aimed to evaluate the epigenetic reprogramming of ICR1 (KvDMR1) and ICR2 (H19DMR) and expression of genes controlled by them as well as those involved in methylation, demethylation, and pluripotency. METHODS We collected germinal vesicle (GV) and metaphase II (MII) oocytes, and preimplantation embryos at five stages [zygote, 4-8 cells, 8-16 cells, morula, and expanded blastocysts (ExB)]. DNA methylation was assessed by BiSeq, and the gene expression was evaluated using qPCR. RESULTS H19DMR showed an increased DNA methylation from GV to MII oocytes (68.04% and 98.05%, respectively), decreasing in zygotes (85.83%) until morula (61.65%), and ExB (63.63%). H19 and IGF2 showed increased expression in zygotes, which decreased in further stages. KvDMR1 was hypermethylated in both GV (71.82%) and MII (69.43%) and in zygotes (73.70%) up to morula (77.84%), with a loss of methylation at the ExB (36.64%). The zygote had higher expression of most genes, except for CDKN1C and PHLDA2, which were highly expressed in MII and GV oocytes, respectively. DNMTs showed increased expression in oocytes, followed by a reduction in the earliest stages of embryo development. TET1 was downregulated until 4-8-cell and upregulated in 8-16-cell embryos. TET2 and TET3 showed higher expression in oocytes, and a downregulation in MII oocytes and 4-8-cell embryo. CONCLUSION We highlighted the heterogeneity in the DNA methylation of H19DMR and KvDMR1 and a dynamic expression pattern of genes controlled by them. The expression of DNMTs and TETs genes was also dynamic owing to epigenetic reprogramming.
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Affiliation(s)
- Carolina G Verruma
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Renan S Santos
- Postgraduate Program in Physiology and Pharmacology, Drug Research and Development Center (NPDM), Federal University of Ceara (UFC), Fortaleza, CE, 60430-275, Brazil
| | - Jorge A P Marchesi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Sarah L A Sales
- Postgraduate Program in Physiology and Pharmacology, Drug Research and Development Center (NPDM), Federal University of Ceara (UFC), Fortaleza, CE, 60430-275, Brazil
| | - Reginaldo A Vila
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Álvaro F L Rios
- Biotechnology Laboratory, Center of Bioscience and Biotechnology, State University of North Fluminense Darcy Ribeiro, Goitacazes Campus, Rio de Janeiro, Brazil
| | - Cristiana L M Furtado
- Experimental Biology Center, Graduate Program in Medical Sciences, University of Fortaleza - UNIFOR, Fortaleza, CE, 60811-905, Brazil
- Drug Research and Development Center (NPDM), Postgraduate Program in Translational Medicine, Federal University of Ceara (UFC), Fortaleza, CE, 60430-275, Brazil
| | - Ester S Ramos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil.
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17
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Montes-de-Oca-Fuentes EV, Jácome-López K, Zarco-Mendoza A, Guerrero G, Ventura-Gallegos JL, Juárez-Méndez S, Cabrera-Quintero AJ, Recillas-Targa F, Zentella-Dehesa A. Differential DNA methylation and CTCF binding between the ESR1 promoter a of MCF-7 and MDA-MB-231 breast cancer cells. Mol Biol Rep 2024; 51:148. [PMID: 38236307 PMCID: PMC10796618 DOI: 10.1007/s11033-023-09171-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND ESR1 is expressed by 60-70% of breast tumours. it's a good prognosis factor and the target of hormone therapy. Optimization of ESR1 reactivation therapy is currently ongoing. Here we probe if the transcription factor CTCF plays a role in the differential expression of ESR1 in the breast cancer cell lines MCF-7 (ESR1+) and MDA-MB-231 (ESR1-). METHODS AND RESULTS Knockdown of CTCF in MCF-7 resulted in decreased ESR1 gene expression. CTCF binds to the promoter of ESR1 in MCF-7 but not in MDA-MB-231 cells. CTCF ESR1 binding sites are unmethylated in MCF7 but methylated in MDA-MB-231 cells. CONCLUSION ESR1 expression in MCF7 cells is dependent on CTCF expression. CTCF can bind to specific regions of the promotor of ESR1 gene in MCF-7 cells but not in MDA-MB-231 cells, this correlates with the methylation status of these regions and could be involved in the transcriptional regulation of ESR1.
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Affiliation(s)
- Edén Víctor Montes-de-Oca-Fuentes
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
- Programa de Investigación en Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
- Unidad de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, 14080, México
| | - Karina Jácome-López
- Unidad de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, 14080, México
| | - Anaís Zarco-Mendoza
- División de Investigación Básica, Laboratorio de Virus y Cancer, Secretaría de Salud, Instituto Nacional de Cancerología, Ciudad de México, 14080, México
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Georgina Guerrero
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - José Luis Ventura-Gallegos
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
- Programa de Investigación en Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
- Unidad de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, 14080, México
| | - Sergio Juárez-Méndez
- Laboratorio de Oncología Experimental, Secretaría de Salud, Instituto Nacional de Pediatría, Ciudad de México, 04530, México
| | - Alberto Jose Cabrera-Quintero
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
- Unidad de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, 14080, México
| | - Félix Recillas-Targa
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Alejandro Zentella-Dehesa
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México.
- Programa de Investigación en Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico.
- Unidad de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, 14080, México.
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México‑Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, 14080, México.
- Cancer Center, American British Cowdray Medical Center, Ciudad de México, 01120, Mexico.
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18
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Schoen JR, Chen J, Rankin S. The intrinsically disordered tail of ESCO1 binds DNA in a charge-dependent manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570177. [PMID: 38106185 PMCID: PMC10723360 DOI: 10.1101/2023.12.05.570177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
ESCO1 is an acetyltransferase enzyme that regulates chromosome organization and gene expression. It does this by modifying the Smc3 subunit of the Cohesin complex. Although ESCO1 is enriched at the base of chromatin loops in a Cohesin-dependent manner, precisely how it interacts with chromatin is unknown. Here we show that the basic and intrinsically disordered tail of ESCO1 binds DNA with very high affinity, likely through electrostatic interaction. We show that neutralization of positive residues in the N-tail reduces both DNA binding in vitro and association of the enzyme with chromatin in cells. Additionally, disruption of the chromatin state and charge distribution reduces chromatin bound ESCO1. Strikingly, defects in DNA binding do not affect total SMC3 acetylation or sister chromatid cohesion, suggesting that ESCO1-dependent acetylation can occur independently of direct chromatin association. We conclude that the intrinsically disordered tail of ESCO1 binds DNA with both high affinity and turnover, but surprisingly, ESCO1 catalytic activity occurs independently of direct DNA binding by the enzyme.
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Affiliation(s)
- Jeffrey R. Schoen
- Cell Cycle and Cancer Biology program, Oklahoma Medical Research Foundation, 825 NE 13 St, Oklahoma City, OK 73104
- Cell Biology Department, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Oklahoma City, OK 73104
| | - Jingrong Chen
- Cell Cycle and Cancer Biology program, Oklahoma Medical Research Foundation, 825 NE 13 St, Oklahoma City, OK 73104
| | - Susannah Rankin
- Cell Cycle and Cancer Biology program, Oklahoma Medical Research Foundation, 825 NE 13 St, Oklahoma City, OK 73104
- Cell Biology Department, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Oklahoma City, OK 73104
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19
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Bose S, Saha S, Goswami H, Shanmugam G, Sarkar K. Involvement of CCCTC-binding factor in epigenetic regulation of cancer. Mol Biol Rep 2023; 50:10383-10398. [PMID: 37840067 DOI: 10.1007/s11033-023-08879-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023]
Abstract
A major global health burden continues to be borne by the complex and multifaceted disease of cancer. Epigenetic changes, which are essential for the emergence and spread of cancer, have drawn a huge amount of attention recently. The CCCTC-binding factor (CTCF), which takes part in a wide range of cellular processes including genomic imprinting, X chromosome inactivation, 3D chromatin architecture, local modifications of histone, and RNA polymerase II-mediated gene transcription, stands out among the diverse array of epigenetic regulators. CTCF not only functions as an architectural protein but also modulates DNA methylation and histone modifications. Epigenetic regulation of cancer has already been the focus of plenty of studies. Understanding the role of CTCF in the cancer epigenetic landscape may lead to the development of novel targeted therapeutic strategies for cancer. CTCF has already earned its status as a tumor suppressor gene by acting like a homeostatic regulator of genome integrity and function. Moreover, CTCF has a direct effect on many important transcriptional regulators that control the cell cycle, apoptosis, senescence, and differentiation. As we learn more about CTCF-mediated epigenetic modifications and transcriptional regulations, the possibility of utilizing CTCF as a diagnostic marker and therapeutic target for cancer will also increase. Thus, the current review intends to promote personalized and precision-based therapeutics for cancer patients by shedding light on the complex interplay between CTCF and epigenetic processes.
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Affiliation(s)
- Sayani Bose
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Srawsta Saha
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Harsita Goswami
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Geetha Shanmugam
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Koustav Sarkar
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India.
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20
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Puri D, Maaßen C, Varona Baranda M, Zeevaert K, Hahnfeld L, Hauser A, Fornero G, Elsafi Mabrouk MH, Wagner W. CTCF deletion alters the pluripotency and DNA methylation profile of human iPSCs. Front Cell Dev Biol 2023; 11:1302448. [PMID: 38099298 PMCID: PMC10720430 DOI: 10.3389/fcell.2023.1302448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
Pluripotent stem cells are characterized by their differentiation potential toward endoderm, mesoderm, and ectoderm. However, it is still largely unclear how these cell-fate decisions are mediated by epigenetic mechanisms. In this study, we explored the relevance of CCCTC-binding factor (CTCF), a zinc finger-containing DNA-binding protein, which mediates long-range chromatin organization, for directed cell-fate determination. We generated human induced pluripotent stem cell (iPSC) lines with deletions in the protein-coding region in exon 3 of CTCF, resulting in shorter transcripts and overall reduced protein expression. Chromatin immunoprecipitation showed a considerable loss of CTCF binding to target sites. The CTCF deletions resulted in slower growth and modest global changes in gene expression, with downregulation of a subset of pluripotency-associated genes and neuroectodermal genes. CTCF deletion also evoked DNA methylation changes, which were moderately associated with differential gene expression. Notably, CTCF-deletions lead to upregulation of endo-mesodermal associated marker genes and epigenetic signatures, whereas ectodermal differentiation was defective. These results indicate that CTCF plays an important role in the maintenance of pluripotency and differentiation, especially towards ectodermal lineages.
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Affiliation(s)
- Deepika Puri
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Catharina Maaßen
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Monica Varona Baranda
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Kira Zeevaert
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Lena Hahnfeld
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Annika Hauser
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Giulia Fornero
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Mohamed H. Elsafi Mabrouk
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Wolfgang Wagner
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
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21
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Lee GE, Byun J, Lee CJ, Cho YY. Molecular Mechanisms for the Regulation of Nuclear Membrane Integrity. Int J Mol Sci 2023; 24:15497. [PMID: 37895175 PMCID: PMC10607757 DOI: 10.3390/ijms242015497] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/19/2023] [Accepted: 10/22/2023] [Indexed: 10/29/2023] Open
Abstract
The nuclear membrane serves a critical role in protecting the contents of the nucleus and facilitating material and signal exchange between the nucleus and cytoplasm. While extensive research has been dedicated to topics such as nuclear membrane assembly and disassembly during cell division, as well as interactions between nuclear transmembrane proteins and both nucleoskeletal and cytoskeletal components, there has been comparatively less emphasis on exploring the regulation of nuclear morphology through nuclear membrane integrity. In particular, the role of type II integral proteins, which also function as transcription factors, within the nuclear membrane remains an area of research that is yet to be fully explored. The integrity of the nuclear membrane is pivotal not only during cell division but also in the regulation of gene expression and the communication between the nucleus and cytoplasm. Importantly, it plays a significant role in the development of various diseases. This review paper seeks to illuminate the biomolecules responsible for maintaining the integrity of the nuclear membrane. It will delve into the mechanisms that influence nuclear membrane integrity and provide insights into the role of type II membrane protein transcription factors in this context. Understanding these aspects is of utmost importance, as it can offer valuable insights into the intricate processes governing nuclear membrane integrity. Such insights have broad-reaching implications for cellular function and our understanding of disease pathogenesis.
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Affiliation(s)
- Ga-Eun Lee
- BK21-4th, and BRL, College of Pharmacy, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea; (G.-E.L.); (J.B.)
| | - Jiin Byun
- BK21-4th, and BRL, College of Pharmacy, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea; (G.-E.L.); (J.B.)
| | - Cheol-Jung Lee
- Research Center for Materials Analysis, Korea Basic Science Institute, 169-148, Gwahak-ro, Yuseong-gu, Daejeon 34133, Chungcheongnam-do, Republic of Korea
| | - Yong-Yeon Cho
- BK21-4th, and BRL, College of Pharmacy, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea; (G.-E.L.); (J.B.)
- RCD Control and Material Research Institute, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea
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22
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Gunsalus LM, Keiser MJ, Pollard KS. In silico discovery of repetitive elements as key sequence determinants of 3D genome folding. CELL GENOMICS 2023; 3:100410. [PMID: 37868032 PMCID: PMC10589630 DOI: 10.1016/j.xgen.2023.100410] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/08/2022] [Accepted: 08/31/2023] [Indexed: 10/24/2023]
Abstract
Natural and experimental genetic variants can modify DNA loops and insulating boundaries to tune transcription, but it is unknown how sequence perturbations affect chromatin organization genome wide. We developed a deep-learning strategy to quantify the effect of any insertion, deletion, or substitution on chromatin contacts and systematically scored millions of synthetic variants. While most genetic manipulations have little impact, regions with CTCF motifs and active transcription are highly sensitive, as expected. Our unbiased screen and subsequent targeted experiments also point to noncoding RNA genes and several families of repetitive elements as CTCF-motif-free DNA sequences with particularly large effects on nearby chromatin interactions, sometimes exceeding the effects of CTCF sites and explaining interactions that lack CTCF. We anticipate that our disruption tracks may be of broad interest and utility as a measure of 3D genome sensitivity, and our computational strategies may serve as a template for biological inquiry with deep learning.
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Affiliation(s)
- Laura M. Gunsalus
- Gladstone Institutes, San Francisco, CA, USA
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Michael J. Keiser
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA, USA
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23
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Lyu X, Rowley MJ, Kulik MJ, Dalton S, Corces VG. Regulation of CTCF loop formation during pancreatic cell differentiation. Nat Commun 2023; 14:6314. [PMID: 37813869 PMCID: PMC10562423 DOI: 10.1038/s41467-023-41964-6] [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: 04/13/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023] Open
Abstract
Transcription reprogramming during cell differentiation involves targeting enhancers to genes responsible for establishment of cell fates. To understand the contribution of CTCF-mediated chromatin organization to cell lineage commitment, we analyzed 3D chromatin architecture during the differentiation of human embryonic stem cells into pancreatic islet organoids. We find that CTCF loops are formed and disassembled at different stages of the differentiation process by either recruitment of CTCF to new anchor sites or use of pre-existing sites not previously involved in loop formation. Recruitment of CTCF to new sites in the genome involves demethylation of H3K9me3 to H3K9me2, demethylation of DNA, recruitment of pioneer factors, and positioning of nucleosomes flanking the new CTCF sites. Existing CTCF sites not involved in loop formation become functional loop anchors via the establishment of new cohesin loading sites containing NIPBL and YY1 at sites between the new anchors. In both cases, formation of new CTCF loops leads to strengthening of enhancer promoter interactions and increased transcription of genes adjacent to loop anchors. These results suggest an important role for CTCF and cohesin in controlling gene expression during cell differentiation.
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Affiliation(s)
- Xiaowen Lyu
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China.
- Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China.
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Michael J Kulik
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA, 30602, USA
- Center for Molecular Medicine, The University of Georgia, Athens, GA, 30602, USA
| | - Stephen Dalton
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA, 30602, USA
- Center for Molecular Medicine, The University of Georgia, Athens, GA, 30602, USA
- School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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24
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Kassouf M, Ford S, Blayney J, Higgs D. Understanding fundamental principles of enhancer biology at a model locus: Analysing the structure and function of an enhancer cluster at the α-globin locus. Bioessays 2023; 45:e2300047. [PMID: 37404089 DOI: 10.1002/bies.202300047] [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: 03/08/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 07/06/2023]
Abstract
Despite ever-increasing accumulation of genomic data, the fundamental question of how individual genes are switched on during development, lineage-specification and differentiation is not fully answered. It is widely accepted that this involves the interaction between at least three fundamental regulatory elements: enhancers, promoters and insulators. Enhancers contain transcription factor binding sites which are bound by transcription factors (TFs) and co-factors expressed during cell fate decisions and maintain imposed patterns of activation, at least in part, via their epigenetic modification. This information is transferred from enhancers to their cognate promoters often by coming into close physical proximity to form a 'transcriptional hub' containing a high concentration of TFs and co-factors. The mechanisms underlying these stages of transcriptional activation are not fully explained. This review focuses on how enhancers and promoters are activated during differentiation and how multiple enhancers work together to regulate gene expression. We illustrate the currently understood principles of how mammalian enhancers work and how they may be perturbed in enhanceropathies using expression of the α-globin gene cluster during erythropoiesis, as a model.
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Affiliation(s)
- Mira Kassouf
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Seren Ford
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Joseph Blayney
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Doug Higgs
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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25
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Li Y, Fan H, Qin W, Wang Y, Chen S, Bao W, Sun MA. Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen. Comput Struct Biotechnol J 2023; 21:4580-4588. [PMID: 37790243 PMCID: PMC10542605 DOI: 10.1016/j.csbj.2023.09.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/23/2023] [Accepted: 09/23/2023] [Indexed: 10/05/2023] Open
Abstract
Like other mammalian species, the pig genome is abundant with transposable elements (TEs). The importance of TEs for three-dimensional (3D) chromatin organization has been observed in species like human and mouse, yet current understanding about pig TEs is absent. Here, we investigated the contribution of TEs for the 3D chromatin organization in three pig tissues, focusing on spleen which is crucial for both adaptive and innate immunity. We identified dozens of TE families overrepresented with CTCF binding sites, including LTR22_SS, LTR15_SS and LTR16_SSc which are pig-specific families of endogenous retroviruses (ERVs). Interestingly, LTR22_SS elements harbor a CTCF motif and create hundreds of CTCF binding sites that are associated with adaptive immunity. We further applied Hi-C to profile the 3D chromatin structure in spleen and found that TE-derived CTCF binding sites correlate with chromatin insulation and frequently overlap TAD borders and loop anchors. Notably, one LTR22_SS-derived CTCF binding site demarcate a TAD boundary upstream of XCL1, which is a spleen-enriched chemokine gene important for lymphocyte trafficking and inflammation. Overall, this study represents a first step toward understanding the function of TEs on 3D chromatin organization regulation in pigs and expands our understanding about the functional importance of TEs in mammals.
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Affiliation(s)
- Yuzhuo Li
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Hairui Fan
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, Jiangsu, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Weiyun Qin
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, Jiangsu, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Yejun Wang
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Shuai Chen
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Wenbin Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Ming-an Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, Jiangsu, China
- Joint International Research Laboratory of Important Animal Infectious Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, Jiangsu, China
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26
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Wulfridge P, Yan Q, Rell N, Doherty J, Jacobson S, Offley S, Deliard S, Feng K, Phillips-Cremins JE, Gardini A, Sarma K. G-quadruplexes associated with R-loops promote CTCF binding. Mol Cell 2023; 83:3064-3079.e5. [PMID: 37552993 PMCID: PMC10529333 DOI: 10.1016/j.molcel.2023.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/24/2023] [Accepted: 07/07/2023] [Indexed: 08/10/2023]
Abstract
CTCF is a critical regulator of genome architecture and gene expression that binds thousands of sites on chromatin. CTCF genomic localization is controlled by the recognition of a DNA sequence motif and regulated by DNA modifications. However, CTCF does not bind to all its potential sites in all cell types, raising the question of whether the underlying chromatin structure can regulate CTCF occupancy. Here, we report that R-loops facilitate CTCF binding through the formation of associated G-quadruplex (G4) structures. R-loops and G4s co-localize with CTCF at many genomic regions in mouse embryonic stem cells and promote CTCF binding to its cognate DNA motif in vitro. R-loop attenuation reduces CTCF binding in vivo. Deletion of a specific G4-forming motif in a gene reduces CTCF binding and alters gene expression. Conversely, chemical stabilization of G4s results in CTCF gains and accompanying alterations in chromatin organization, suggesting a pivotal role for G4 structures in reinforcing long-range genome interactions through CTCF.
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Affiliation(s)
- Phillip Wulfridge
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qingqing Yan
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathaniel Rell
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John Doherty
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Skye Jacobson
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah Offley
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sandra Deliard
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Kelly Feng
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer E Phillips-Cremins
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessandro Gardini
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Kavitha Sarma
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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27
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Watanabe K, Fujita M, Okamoto K, Yoshioka H, Moriwaki M, Tagashira H, Awazu A, Yamamoto T, Sakamoto N. The crucial role of CTCF in mitotic progression during early development of sea urchin. Dev Growth Differ 2023; 65:395-407. [PMID: 37421304 DOI: 10.1111/dgd.12875] [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: 05/25/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/10/2023]
Abstract
CCCTC-binding factor (CTCF), an insulator protein with 11 zinc fingers, is enriched at the boundaries of topologically associated domains (TADs) in eukaryotic genomes. In this study, we isolated and analyzed the cDNAs encoding HpCTCF, the CTCF homolog in the sea urchin Hemicentrotus pulcherrimus, to investigate its expression patterns and functions during the early development of sea urchin. HpCTCF contains nine zinc fingers corresponding to fingers 2-10 of the vertebrate CTCF. Expression pattern analysis revealed that HpCTCF mRNA was detected at all developmental stages and in the entire embryo. Upon expressing the HpCTCF-GFP fusion protein in early embryos, we observed its uniform distribution within interphase nuclei. However, during mitosis, it disappeared from the chromosomes and subsequently reassembled on the chromosome during telophase. Moreover, the morpholino-mediated knockdown of HpCTCF resulted in mitotic arrest during the morula to blastula stage. Most of the arrested chromosomes were not phospholylated at serine 10 of histone H3, indicating that mitosis was arrested at the telophase by HpCTCF depletion. Furthermore, impaired sister chromatid segregation was observed using time-lapse imaging of HpCTCF-knockdown embryos. Thus, HpCTCF is essential for mitotic progression during the early development of sea urchins, especially during the telophase-to-interphase transition. However, the normal development of pluteus larvae in CRISPR-mediated HpCTCF-knockout embryos suggests that disruption of zygotic HpCTCF expression has little effect on embryonic and larval development.
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Affiliation(s)
- Kaichi Watanabe
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Megumi Fujita
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kazuko Okamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hajime Yoshioka
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Miki Moriwaki
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hideki Tagashira
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Akinori Awazu
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashi-Hiroshima, Japan
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashi-Hiroshima, Japan
| | - Naoaki Sakamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashi-Hiroshima, Japan
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28
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Ochoa S, Hernández-Lemus E. Molecular mechanisms of multi-omic regulation in breast cancer. Front Oncol 2023; 13:1148861. [PMID: 37564937 PMCID: PMC10411627 DOI: 10.3389/fonc.2023.1148861] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
Breast cancer is a complex disease that is influenced by the concurrent influence of multiple genetic and environmental factors. Recent advances in genomics and other high throughput biomolecular techniques (-omics) have provided numerous insights into the molecular mechanisms underlying breast cancer development and progression. A number of these mechanisms involve multiple layers of regulation. In this review, we summarize the current knowledge on the role of multiple omics in the regulation of breast cancer, including the effects of DNA methylation, non-coding RNA, and other epigenomic changes. We comment on how integrating such diverse mechanisms is envisioned as key to a more comprehensive understanding of breast carcinogenesis and cancer biology with relevance to prognostics, diagnostics and therapeutics. We also discuss the potential clinical implications of these findings and highlight areas for future research. Overall, our understanding of the molecular mechanisms of multi-omic regulation in breast cancer is rapidly increasing and has the potential to inform the development of novel therapeutic approaches for this disease.
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Affiliation(s)
- Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
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29
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Pandupuspitasari NS, Khan FA, Huang C, Ali A, Yousaf MR, Shakeel F, Putri EM, Negara W, Muktiani A, Prasetiyono BWHE, Kustiawan L, Wahyuni DS. Recent advances in chromosome capture techniques unraveling 3D genome architecture in germ cells, health, and disease. Funct Integr Genomics 2023; 23:214. [PMID: 37386239 DOI: 10.1007/s10142-023-01146-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
In eukaryotes, the genome does not emerge in a specific shape but rather as a hierarchial bundle within the nucleus. This multifaceted genome organization consists of multiresolution cellular structures, such as chromosome territories, compartments, and topologically associating domains, which are frequently defined by architecture, design proteins including CTCF and cohesin, and chromatin loops. This review briefly discusses the advances in understanding the basic rules of control, chromatin folding, and functional areas in early embryogenesis. With the use of chromosome capture techniques, the latest advancements in technologies for visualizing chromatin interactions come close to revealing 3D genome formation frameworks with incredible detail throughout all genomic levels, including at single-cell resolution. The possibility of detecting variations in chromatin architecture might open up new opportunities for disease diagnosis and prevention, infertility treatments, therapeutic approaches, desired exploration, and many other application scenarios.
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Affiliation(s)
- Nuruliarizki Shinta Pandupuspitasari
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia.
| | - Faheem Ahmed Khan
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Chunjie Huang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Azhar Ali
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Rizwan Yousaf
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Farwa Shakeel
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Ezi Masdia Putri
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Windu Negara
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Anis Muktiani
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Bambang Waluyo Hadi Eko Prasetiyono
- Laboratory of Feed Technology, Animal Science Department, Faculty of Animal and Agricultural Sciences Universitas Diponegoro, Semarang, Indonesia
| | - Limbang Kustiawan
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Dimar Sari Wahyuni
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
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Bobbitt JR, Seachrist DD, Keri RA. Chromatin Organization and Transcriptional Programming of Breast Cancer Cell Identity. Endocrinology 2023; 164:bqad100. [PMID: 37394919 PMCID: PMC10370366 DOI: 10.1210/endocr/bqad100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/04/2023]
Abstract
The advent of sequencing technologies for assessing chromosome conformations has provided a wealth of information on the organization of the 3-dimensional genome and its role in cancer progression. It is now known that changes in chromatin folding and accessibility can promote aberrant activation or repression of transcriptional programs that can drive tumorigenesis and progression in diverse cancers. This includes breast cancer, which comprises several distinct subtypes defined by their unique transcriptomes that dictate treatment response and patient outcomes. Of these, basal-like breast cancer is an aggressive subtype controlled by a pluripotency-enforcing transcriptome. Meanwhile, the more differentiated luminal subtype of breast cancer is driven by an estrogen receptor-dominated transcriptome that underlies its responsiveness to antihormone therapies and conveys improved patient outcomes. Despite the clear differences in molecular signatures, the genesis of each subtype from normal mammary epithelial cells remains unclear. Recent technical advances have revealed key distinctions in chromatin folding and organization between subtypes that could underlie their transcriptomic and, hence, phenotypic differences. These studies also suggest that proteins controlling particular chromatin states may be useful targets for treating aggressive disease. In this review, we explore the current state of understanding of chromatin architecture in breast cancer subtypes and its potential role in defining their phenotypic characteristics.
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Affiliation(s)
- Jessica R Bobbitt
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Darcie D Seachrist
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Ruth A Keri
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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Zuo Z, Billings T, Walker M, Petkov PM, Fordyce P, Stormo GD. On the dependent recognition of some long zinc finger proteins. Nucleic Acids Res 2023; 51:5364-5376. [PMID: 36951113 PMCID: PMC10287918 DOI: 10.1093/nar/gkad207] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 03/24/2023] Open
Abstract
The human genome contains about 800 C2H2 zinc finger proteins (ZFPs), and most of them are composed of long arrays of zinc fingers. Standard ZFP recognition model asserts longer finger arrays should recognize longer DNA-binding sites. However, recent experimental efforts to identify in vivo ZFP binding sites contradict this assumption, with many exhibiting short motifs. Here we use ZFY, CTCF, ZIM3, and ZNF343 as examples to address three closely related questions: What are the reasons that impede current motif discovery methods? What are the functions of those seemingly unused fingers and how can we improve the motif discovery algorithms based on long ZFPs' biophysical properties? Using ZFY, we employed a variety of methods and find evidence for 'dependent recognition' where downstream fingers can recognize some previously undiscovered motifs only in the presence of an intact core site. For CTCF, high-throughput measurements revealed its upstream specificity profile depends on the strength of its core. Moreover, the binding strength of the upstream site modulates CTCF's sensitivity to different epigenetic modifications within the core, providing new insight into how the previously identified intellectual disability-causing and cancer-related mutant R567W disrupts upstream recognition and deregulates the epigenetic control by CTCF. Our results establish that, because of irregular motif structures, variable spacing and dependent recognition between sub-motifs, the specificities of long ZFPs are significantly underestimated, so we developed an algorithm, ModeMap, to infer the motifs and recognition models of ZIM3 and ZNF343, which facilitates high-confidence identification of specific binding sites, including repeats-derived elements. With revised concept, technique, and algorithm, we can discover the overlooked specificities and functions of those 'extra' fingers, and therefore decipher their broader roles in human biology and diseases.
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Affiliation(s)
- Zheng Zuo
- Department of Genetics, Stanford University, CA, USA
- Department of Genetics, Washington University in St. Louis, MO, USA
| | | | | | | | - Polly M Fordyce
- Department of Genetics, Stanford University, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Bioengineering, Stanford University, CA, USA
- Stanford ChEM-H Institute, Stanford University, CA, USA
| | - Gary D Stormo
- Department of Genetics, Washington University in St. Louis, MO, USA
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Price E, Fedida LM, Pugacheva EM, Ji YJ, Loukinov D, Lobanenkov VV. An updated catalog of CTCF variants associated with neurodevelopmental disorder phenotypes. Front Mol Neurosci 2023; 16:1185796. [PMID: 37324587 PMCID: PMC10264798 DOI: 10.3389/fnmol.2023.1185796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction CTCF-related disorder (CRD) is a neurodevelopmental disorder (NDD) caused by monoallelic pathogenic variants in CTCF. The first CTCF variants in CRD cases were documented in 2013. To date, 76 CTCF variants have been further described in the literature. In recent years, due to the increased application of next-generation sequencing (NGS), growing numbers of CTCF variants are being identified, and multiple genotype-phenotype databases cataloging such variants are emerging. Methods In this study, we aimed to expand the genotypic spectrum of CRD, by cataloging NDD phenotypes associated with reported CTCF variants. Here, we systematically reviewed all known CTCF variants reported in case studies and large-scale exome sequencing cohorts. We also conducted a meta-analysis using public variant data from genotype-phenotype databases to identify additional CTCF variants, which we then curated and annotated. Results From this combined approach, we report an additional 86 CTCF variants associated with NDD phenotypes that have not yet been described in the literature. Furthermore, we describe and explain inconsistencies in the quality of reported variants, which impairs the reuse of data for research of NDDs and other pathologies. Discussion From this integrated analysis, we provide a comprehensive and annotated catalog of all currently known CTCF mutations associated with NDD phenotypes, to aid diagnostic applications, as well as translational and basic research.
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Villaman C, Pollastri G, Saez M, Martin AJ. Benefiting from the intrinsic role of epigenetics to predict patterns of CTCF binding. Comput Struct Biotechnol J 2023; 21:3024-3031. [PMID: 37266407 PMCID: PMC10229758 DOI: 10.1016/j.csbj.2023.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/03/2023] Open
Abstract
Motivation One of the most relevant mechanisms involved in the determination of chromatin structure is the formation of structural loops that are also related with the conservation of chromatin states. Many of these loops are stabilized by CCCTC-binding factor (CTCF) proteins at their base. Despite the relevance of chromatin structure and the key role of CTCF, the role of the epigenetic factors that are involved in the regulation of CTCF binding, and thus, in the formation of structural loops in the chromatin, is not thoroughly understood. Results Here we describe a CTCF binding predictor based on Random Forest that employs different epigenetic data and genomic features. Importantly, given the ability of Random Forests to determine the relevance of features for the prediction, our approach also shows how the different types of descriptors impact the binding of CTCF, confirming previous knowledge on the relevance of chromatin accessibility and DNA methylation, but demonstrating the effect of epigenetic modifications on the activity of CTCF. We compared our approach against other predictors and found improved performance in terms of areas under PR and ROC curves (PRAUC-ROCAUC), outperforming current state-of-the-art methods.
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Affiliation(s)
- Camilo Villaman
- Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Escuela de Ingeniería, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | | | - Mauricio Saez
- Centro de Oncología de Precisión, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
- Laboratorio de Investigación en Salud de Precisión, Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Chile
| | - Alberto J.M. Martin
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Escuela de Ingeniería, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
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Del Moral-Morales A, Salgado-Albarrán M, Sánchez-Pérez Y, Wenke NK, Baumbach J, Soto-Reyes E. CTCF and Its Multi-Partner Network for Chromatin Regulation. Cells 2023; 12:1357. [PMID: 37408191 DOI: 10.3390/cells12101357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 07/07/2023] Open
Abstract
Architectural proteins are essential epigenetic regulators that play a critical role in organizing chromatin and controlling gene expression. CTCF (CCCTC-binding factor) is a key architectural protein responsible for maintaining the intricate 3D structure of chromatin. Because of its multivalent properties and plasticity to bind various sequences, CTCF is similar to a Swiss knife for genome organization. Despite the importance of this protein, its mechanisms of action are not fully elucidated. It has been hypothesized that its versatility is achieved through interaction with multiple partners, forming a complex network that regulates chromatin folding within the nucleus. In this review, we delve into CTCF's interactions with other molecules involved in epigenetic processes, particularly histone and DNA demethylases, as well as several long non-coding RNAs (lncRNAs) that are able to recruit CTCF. Our review highlights the importance of CTCF partners to shed light on chromatin regulation and pave the way for future exploration of the mechanisms that enable the finely-tuned role of CTCF as a master regulator of chromatin.
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Affiliation(s)
- Aylin Del Moral-Morales
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Marisol Salgado-Albarrán
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Yesennia Sánchez-Pérez
- Subdirección de Investigación, Instituto Nacional de Cancerología, Mexico City 14080, Mexico
| | - Nina Kerstin Wenke
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
- Computational BioMedicine Lab., University of Southern Denmark, DK-5230 Odense, Denmark
| | - Ernesto Soto-Reyes
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
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Smits WK, Vermeulen C, Hagelaar R, Kimura S, Vroegindeweij EM, Buijs-Gladdines JGCAM, van de Geer E, Verstegen MJAM, Splinter E, van Reijmersdal SV, Buijs A, Galjart N, van Eyndhoven W, van Min M, Kuiper R, Kemmeren P, Mullighan CG, de Laat W, Meijerink JPP. Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia. Cell Rep 2023; 42:112373. [PMID: 37060567 PMCID: PMC10750298 DOI: 10.1016/j.celrep.2023.112373] [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: 10/25/2022] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 04/16/2023] Open
Abstract
Monoallelic inactivation of CCCTC-binding factor (CTCF) in human cancer drives altered methylated genomic states, altered CTCF occupancy at promoter and enhancer regions, and deregulated global gene expression. In patients with T cell acute lymphoblastic leukemia (T-ALL), we find that acquired monoallelic CTCF-inactivating events drive subtle and local genomic effects in nearly half of t(5; 14) (q35; q32.2) rearranged patients, especially when CTCF-binding sites are preserved in between the BCL11B enhancer and the TLX3 oncogene. These solitary intervening sites insulate TLX3 from the enhancer by inducing competitive looping to multiple binding sites near the TLX3 promoter. Reduced CTCF levels or deletion of the intervening CTCF site abrogates enhancer insulation by weakening competitive looping while favoring TLX3 promoter to BCL11B enhancer looping, which elevates oncogene expression levels and leukemia burden.
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Affiliation(s)
- Willem K Smits
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Carlo Vermeulen
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands; Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rico Hagelaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Shunsuke Kimura
- Laboratory of Pathology, St. Jude's Children's Research Hospital, Memphis TN, USA
| | | | | | - Ellen van de Geer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Marjon J A M Verstegen
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands
| | | | | | - Arjan Buijs
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Niels Galjart
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | | | - Roland Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Charles G Mullighan
- Laboratory of Pathology, St. Jude's Children's Research Hospital, Memphis TN, USA
| | - Wouter de Laat
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands
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Kabirova E, Nurislamov A, Shadskiy A, Smirnov A, Popov A, Salnikov P, Battulin N, Fishman V. Function and Evolution of the Loop Extrusion Machinery in Animals. Int J Mol Sci 2023; 24:ijms24055017. [PMID: 36902449 PMCID: PMC10003631 DOI: 10.3390/ijms24055017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/25/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Structural maintenance of chromosomes (SMC) complexes are essential proteins found in genomes of all cellular organisms. Essential functions of these proteins, such as mitotic chromosome formation and sister chromatid cohesion, were discovered a long time ago. Recent advances in chromatin biology showed that SMC proteins are involved in many other genomic processes, acting as active motors extruding DNA, which leads to the formation of chromatin loops. Some loops formed by SMC proteins are highly cell type and developmental stage specific, such as SMC-mediated DNA loops required for VDJ recombination in B-cell progenitors, or dosage compensation in Caenorhabditis elegans and X-chromosome inactivation in mice. In this review, we focus on the extrusion-based mechanisms that are common for multiple cell types and species. We will first describe an anatomy of SMC complexes and their accessory proteins. Next, we provide biochemical details of the extrusion process. We follow this by the sections describing the role of SMC complexes in gene regulation, DNA repair, and chromatin topology.
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Affiliation(s)
- Evelyn Kabirova
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Artem Nurislamov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Artem Shadskiy
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexander Smirnov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Andrey Popov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Pavel Salnikov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nariman Battulin
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Veniamin Fishman
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Artificial Intelligence Research Institute (AIRI), 121108 Moscow, Russia
- Correspondence:
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Low-affinity CTCF binding drives transcriptional regulation whereas high-affinity binding encompasses architectural functions. iScience 2023; 26:106106. [PMID: 36852270 PMCID: PMC9958374 DOI: 10.1016/j.isci.2023.106106] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/14/2022] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
CTCF is a DNA-binding protein which plays critical roles in chromatin structure organization and transcriptional regulation; however, little is known about the functional determinants of different CTCF-binding sites (CBS). Using a conditional mouse model, we have identified one set of CBSs that are lost upon CTCF depletion (lost CBSs) and another set that persists (retained CBSs). Retained CBSs are more similar to the consensus CTCF-binding sequence and usually span tandem CTCF peaks. Lost CBSs are enriched at enhancers and promoters and associate with active chromatin marks and higher transcriptional activity. In contrast, retained CBSs are enriched at TAD and loop boundaries. Integration of ChIP-seq and RNA-seq data has revealed that retained CBSs are located at the boundaries between distinct chromatin states, acting as chromatin barriers. Our results provide evidence that transient, lost CBSs are involved in transcriptional regulation, whereas retained CBSs are critical for establishing higher-order chromatin architecture.
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Hyle J, Djekidel MN, Williams J, Wright S, Shao Y, Xu B, Li C. Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation. Genome Biol 2023; 24:14. [PMID: 36698211 PMCID: PMC9878928 DOI: 10.1186/s13059-022-02843-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/29/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND CTCF is a well-established chromatin architectural protein that also plays various roles in transcriptional regulation. While CTCF biology has been extensively studied, how the domains of CTCF function to regulate transcription remains unknown. Additionally, the original auxin-inducible degron 1 (AID1) system has limitations in investigating the function of CTCF. RESULTS We employ an improved auxin-inducible degron technology, AID2, to facilitate the study of acute depletion of CTCF while overcoming the limitations of the previous AID system. As previously observed through the AID1 system and steady-state RNA analysis, the new AID2 system combined with SLAM-seq confirms that CTCF depletion leads to modest nascent and steady-state transcript changes. A CTCF domain sgRNA library screening identifies the zinc finger (ZF) domain as the region within CTCF with the most functional relevance, including ZFs 1 and 10. Removal of ZFs 1 and 10 reveals genomic regions that independently require these ZFs for DNA binding and transcriptional regulation. Notably, loci regulated by either ZF1 or ZF10 exhibit unique CTCF binding motifs specific to each ZF. CONCLUSIONS By extensively comparing the AID1 and AID2 systems for CTCF degradation in SEM cells, we confirm that AID2 degradation is superior for achieving miniAID-tagged protein degradation without the limitations of the AID1 system. The model we create that combines AID2 depletion of CTCF with exogenous overexpression of CTCF mutants allows us to demonstrate how peripheral ZFs intricately orchestrate transcriptional regulation in a cellular context for the first time.
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Affiliation(s)
- Judith Hyle
- grid.240871.80000 0001 0224 711XDepartment of Tumor Cell Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 USA
| | - Mohamed Nadhir Djekidel
- grid.240871.80000 0001 0224 711XCenter for Applied Bioinformatics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 USA
| | - Justin Williams
- grid.240871.80000 0001 0224 711XDepartment of Tumor Cell Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 USA
| | - Shaela Wright
- grid.240871.80000 0001 0224 711XDepartment of Tumor Cell Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 USA
| | - Ying Shao
- grid.240871.80000 0001 0224 711XDepartment of Computational Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 USA
| | - Beisi Xu
- grid.240871.80000 0001 0224 711XCenter for Applied Bioinformatics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 USA
| | - Chunliang Li
- grid.240871.80000 0001 0224 711XDepartment of Tumor Cell Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 USA
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Zagelbaum J, Schooley A, Zhao J, Schrank BR, Callen E, Zha S, Gottesman ME, Nussenzweig A, Rabadan R, Dekker J, Gautier J. Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization. Nat Struct Mol Biol 2023; 30:99-106. [PMID: 36564591 PMCID: PMC10104780 DOI: 10.1038/s41594-022-00893-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022]
Abstract
Nuclear actin-based movements have been shown to orchestrate clustering of DNA double-strand breaks (DSBs) into homology-directed repair domains. Here we describe multiscale three-dimensional genome reorganization following DNA damage and analyze the contribution of the nuclear WASP-ARP2/3-actin pathway toward chromatin topology alterations and pathologic repair. Hi-C analysis reveals genome-wide, DNA damage-induced chromatin compartment flips facilitated by ARP2/3 that enrich for open, A compartments. Damage promotes interactions between DSBs, which in turn facilitate aberrant, actin-dependent intra- and inter-chromosomal rearrangements. Our work establishes that clustering of resected DSBs into repair domains by nuclear actin assembly is coordinated with multiscale alterations in genome architecture that enable homology-directed repair while also increasing nonhomologous end-joining-dependent translocation frequency.
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Affiliation(s)
- Jennifer Zagelbaum
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Allana Schooley
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Junfei Zhao
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Benjamin R Schrank
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elsa Callen
- Laboratory of Genome Integrity, National Institutes of Health, Bethesda, MD, USA
| | - Shan Zha
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Pathology and Cell Biology and Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Max E Gottesman
- Department of Biochemistry and Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Institutes of Health, Bethesda, MD, USA
| | - Raul Rabadan
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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40
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Dozmorov MG, Mu W, Davis ES, Lee S, Triche TJ, Phanstiel DH, Love MI. CTCF: an R/bioconductor data package of human and mouse CTCF binding sites. BIOINFORMATICS ADVANCES 2022; 2:vbac097. [PMID: 36699364 PMCID: PMC9793704 DOI: 10.1093/bioadv/vbac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
Summary CTCF (CCCTC-binding factor) is an 11-zinc-finger DNA binding protein which regulates much of the eukaryotic genome's 3D structure and function. The diversity of CTCF binding motifs has led to a fragmented landscape of CTCF binding data. We collected position weight matrices of CTCF binding motifs and defined strand-oriented CTCF binding sites in the human and mouse genomes, including the recent Telomere to Telomere and mm39 assemblies. We included selected experimentally determined and predicted CTCF binding sites, such as CTCF-bound cis-regulatory elements from SCREEN ENCODE. We recommend filtering strategies for CTCF binding motifs and demonstrate that liftOver is a viable alternative to convert CTCF coordinates between assemblies. Our comprehensive data resource and usage recommendations can serve to harmonize and strengthen the reproducibility of genomic studies utilizing CTCF binding data. Availability and implementation https://bioconductor.org/packages/CTCF. Companion website: https://dozmorovlab.github.io/CTCF/; Code to reproduce the analyses: https://github.com/dozmorovlab/CTCF.dev. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | - Wancen Mu
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Eric S Davis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stuart Lee
- Department of Econometrics and Business Statistics, Monash University, Clayton, NC 3168, Australia,Molecular Medicine Division, Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia
| | - Timothy J Triche
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA,Department of Pediatrics, College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA,Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Douglas H Phanstiel
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael I Love
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
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41
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Jiang L, Liu Y, Wen Z, Yang Y, Singer SD, Bennett D, Xu W, Su Z, Yu Z, Cohn J, Luo X, Liu Z, Chae H, Que Q, Liu Z. CW198 acts as a genetic insulator to block enhancer-promoter interaction in plants. Transgenic Res 2022; 31:647-660. [PMID: 36053433 DOI: 10.1007/s11248-022-00326-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 08/15/2022] [Indexed: 01/20/2023]
Abstract
Insulators in vertebrates play a role in genome architecture and orchestrate temporo-spatial enhancer-promoter interactions. In plants, insulators and their associated binding factors have not been documented as of yet, largely as a result of a lack of characterized insulators. In this study, we took a comprehensive strategy to identify and validate the enhancer-blocking insulator CW198. We show that a 1.08-kb CW198 fragment from Arabidopsis can, when interposed between an enhancer and a promoter, efficiently abrogate the activation function of both constitutive and floral organ-specific enhancers in transgenic Arabidopsis and tobacco plants. In plants, both transcriptional crosstalk and spreading of histone modifications were rarely detectable across CW198, which resembles the insulation property observed across the CTCF insulator in the mammalian genome. Taken together, our findings support that CW198 acts as an enhancer-blocking insulator in both Arabidopsis and tobacco. The significance of the present findings and their relevance to the mitigation of mutual interference between enhancers and promoters, as well as multiple promoters in transgenes, is discussed.
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Affiliation(s)
- Li Jiang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,USDA-ARS, -Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA
| | - Yue Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhifeng Wen
- USDA-ARS, -Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA.,College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yingjun Yang
- USDA-ARS, -Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA.,Forestry College, Henan University of Science and Technology, Luoyang, 471023, China
| | - Stacy D Singer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, T1J 4B1, Canada
| | - Dennis Bennett
- USDA-ARS, -Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhifang Yu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Josh Cohn
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - Xi Luo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Hyunsook Chae
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - Qiudeng Que
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - Zongrang Liu
- USDA-ARS, -Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA.
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42
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Hirayama T, Kadooka Y, Tarusawa E, Saitoh S, Nakayama H, Hoshino N, Nakama S, Fukuishi T, Kawanishi Y, Umeshima H, Tomita K, Yoshimura Y, Galjart N, Hashimoto K, Ohno N, Yagi T. CTCF loss induces giant lamellar bodies in Purkinje cell dendrites. Acta Neuropathol Commun 2022; 10:172. [PMID: 36447271 PMCID: PMC9706876 DOI: 10.1186/s40478-022-01478-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
CCCTC-binding factor (CTCF) has a key role in higher-order chromatin architecture that is important for establishing and maintaining cell identity by controlling gene expression. In the mature cerebellum, CTCF is highly expressed in Purkinje cells (PCs) as compared with other cerebellar neurons. The cerebellum plays an important role in motor function by regulating PCs, which are the sole output neurons, and defects in PCs cause motor dysfunction. However, the role of CTCF in PCs has not yet been explored. Here we found that the absence of CTCF in mouse PCs led to progressive motor dysfunction and abnormal dendritic morphology in those cells, which included dendritic self-avoidance defects and a proximal shift in the climbing fibre innervation territory on PC dendrites. Furthermore, we found the peculiar lamellar structures known as "giant lamellar bodies" (GLBs), which have been reported in PCs of patients with Werdnig-Hoffman disease, 13q deletion syndrome, and Krabbe disease. GLBs are localized to PC dendrites and are assumed to be associated with neurodegeneration. They have been noted, however, only in case reports following autopsy, and reports of their existence have been very limited. Here we show that GLBs were reproducibly formed in PC dendrites of a mouse model in which CTCF was deleted. GLBs were not noted in PC dendrites at infancy but instead developed over time. In conjunction with GLB development in PC dendrites, the endoplasmic reticulum was almost absent around the nuclei, the mitochondria were markedly swollen and their cristae had decreased drastically, and almost all PCs eventually disappeared as severe motor deficits manifested. Our results revealed the important role of CTCF during normal development and in maintaining PCs and provide new insights into the molecular mechanism of GLB formation during neurodegenerative disease.
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Affiliation(s)
- Teruyoshi Hirayama
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan ,grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Yuuki Kadooka
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan
| | - Etsuko Tarusawa
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan
| | - Sei Saitoh
- grid.467811.d0000 0001 2272 1771Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, 444-8787 Japan ,grid.256115.40000 0004 1761 798XDepartment of Anatomy II and Cell Biology, Fujita Health University School of Medicine, 1-98 Dengakubo, Kutsukake-cho, Toyoake, 470-1192 Japan
| | - Hisako Nakayama
- grid.410818.40000 0001 0720 6587Department of Physiology, Division of Neurophysiology, School of Medicine, Tokyo Women’s Medical University, Tokyo, 162-8666 Japan ,grid.257022.00000 0000 8711 3200Department of Neurophysiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551 Japan
| | - Natsumi Hoshino
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan
| | - Soichiro Nakama
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Takahiro Fukuishi
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Yudai Kawanishi
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Hiroki Umeshima
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Koichi Tomita
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Yumiko Yoshimura
- grid.467811.d0000 0001 2272 1771Section of Visual Information Processing, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585 Japan ,grid.275033.00000 0004 1763 208XDepartment of Physiological Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585 Japan
| | - Niels Galjart
- grid.5645.2000000040459992XDepartment of Cell Biology, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Kouichi Hashimoto
- grid.257022.00000 0000 8711 3200Department of Neurophysiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551 Japan
| | - Nobuhiko Ohno
- grid.467811.d0000 0001 2272 1771Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, 444-8585 Japan ,grid.410804.90000000123090000Department of Anatomy, Division of Histology and Cell Biology, Jichi Medical University, Shimotsuke, 329-0498 Japan
| | - Takeshi Yagi
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan
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CLIMB: High-dimensional association detection in large scale genomic data. Nat Commun 2022; 13:6874. [PMID: 36371401 PMCID: PMC9653391 DOI: 10.1038/s41467-022-34360-z] [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: 12/05/2020] [Accepted: 10/21/2022] [Indexed: 11/14/2022] Open
Abstract
Joint analyses of genomic datasets obtained in multiple different conditions are essential for understanding the biological mechanism that drives tissue-specificity and cell differentiation, but they still remain computationally challenging. To address this we introduce CLIMB (Composite LIkelihood eMpirical Bayes), a statistical methodology that learns patterns of condition-specificity present in genomic data. CLIMB provides a generic framework facilitating a host of analyses, such as clustering genomic features sharing similar condition-specific patterns and identifying which of these features are involved in cell fate commitment. We apply CLIMB to three sets of hematopoietic data, which examine CTCF ChIP-seq measured in 17 different cell populations, RNA-seq measured across constituent cell populations in three committed lineages, and DNase-seq in 38 cell populations. Our results show that CLIMB improves upon existing alternatives in statistical precision, while capturing interpretable and biologically relevant clusters in the data.
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44
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Munk M, Villalobo E, Villalobo A, Berchtold MW. Differential expression of the three independent CaM genes coding for an identical protein: Potential relevance of distinct mRNA stability by different codon usage. Cell Calcium 2022; 107:102656. [DOI: 10.1016/j.ceca.2022.102656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/01/2022] [Accepted: 09/25/2022] [Indexed: 11/24/2022]
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45
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Ni P, Wilson D, Su Z. A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome. BMC Genomics 2022; 23:714. [PMID: 36261804 PMCID: PMC9583556 DOI: 10.1186/s12864-022-08933-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mouse is probably the most important model organism to study mammal biology and human diseases. A better understanding of the mouse genome will help understand the human genome, biology and diseases. However, despite the recent progress, the characterization of the regulatory sequences in the mouse genome is still far from complete, limiting its use to understand the regulatory sequences in the human genome. RESULTS Here, by integrating binding peaks in ~ 9,000 transcription factor (TF) ChIP-seq datasets that cover 79.9% of the mouse mappable genome using an efficient pipeline, we were able to partition these binding peak-covered genome regions into a cis-regulatory module (CRM) candidate (CRMC) set and a non-CRMC set. The CRMCs contain 912,197 putative CRMs and 38,554,729 TF binding sites (TFBSs) islands, covering 55.5% and 24.4% of the mappable genome, respectively. The CRMCs tend to be under strong evolutionary constraints, indicating that they are likely cis-regulatory; while the non-CRMCs are largely selectively neutral, indicating that they are unlikely cis-regulatory. Based on evolutionary profiles of the genome positions, we further estimated that 63.8% and 27.4% of the mouse genome might code for CRMs and TFBSs, respectively. CONCLUSIONS Validation using experimental data suggests that at least most of the CRMCs are authentic. Thus, this unprecedentedly comprehensive map of CRMs and TFBSs can be a good resource to guide experimental studies of regulatory genomes in mice and humans.
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Affiliation(s)
- Pengyu Ni
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - David Wilson
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
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46
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The Epstein-Barr Virus Enhancer Interaction Landscapes in Virus-Associated Cancer Cell Lines. J Virol 2022; 96:e0073922. [PMID: 36094314 PMCID: PMC9517713 DOI: 10.1128/jvi.00739-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Epstein-Barr virus (EBV) persists in human cells as episomes. EBV episomes are chromatinized and their 3D conformation varies greatly in cells expressing different latency genes. We used HiChIP, an assay which combines genome-wide chromatin conformation capture followed by deep sequencing (Hi-C) and chromatin immunoprecipitation (ChIP), to interrogate the EBV episome 3D conformation in different cancer cell lines. In an EBV-transformed lymphoblastoid cell line (LCL) GM12878 expressing type III EBV latency genes, abundant genomic interactions were identified by H3K27ac HiChIP. A strong enhancer was located near the BILF2 gene and looped to multiple genes around BALFs loci. Perturbation of the BILF2 enhancer by CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) altered the expression of BILF2 enhancer-linked genes, including BARF0 and BALF2, suggesting that this enhancer regulates the expression of linked genes. H3K27ac ChIP followed by deep sequencing (ChIP-seq) identified several strong EBV enhancers in T/NK (natural killer) lymphoma cells that express type II EBV latency genes. Extensive intragenomic interactions were also found which linked enhancers to target genes. A strong enhancer at BILF2 also looped to the BALF loci. CRISPRi also validated the functional connection between BILF2 enhancer and BARF1 gene. In contrast, H3K27ac HiChIP found significantly fewer intragenomic interactions in type I EBV latency gene-expressing primary effusion lymphoma (PEL) cell lines. These data provided new insight into the regulation of EBV latency gene expression in different EBV-associated tumors. IMPORTANCE EBV is the first human DNA tumor virus identified, discovered over 50 years ago. EBV causes ~200,000 cases of various cancers each year. EBV-encoded oncogenes, noncoding RNAs, and microRNAs (miRNAs) can promote cell growth and survival and suppress senescence. Regulation of EBV gene expression is very complex. The viral C promoter regulates the expression of all EBV nuclear antigens (EBNAs), some of which are very far away from the C promoter. Another way by which the virus activates remote gene expression is through DNA looping. In this study, we describe the viral genome looping patterns in various EBV-associated cancer cell lines and identify important EBV enhancers in these cells. This study also identified novel opportunities to perturb and eventually control EBV gene expression in these cancer cells.
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47
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Downes DJ, Hughes JR. Natural and Experimental Rewiring of Gene Regulatory Regions. Annu Rev Genomics Hum Genet 2022; 23:73-97. [PMID: 35472292 DOI: 10.1146/annurev-genom-112921-010715] [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] [Indexed: 11/09/2022]
Abstract
The successful development and ongoing functioning of complex organisms depend on the faithful execution of the genetic code. A critical step in this process is the correct spatial and temporal expression of genes. The highly orchestrated transcription of genes is controlled primarily by cis-regulatory elements: promoters, enhancers, and insulators. The medical importance of this key biological process can be seen by the frequency with which mutations and inherited variants that alter cis-regulatory elements lead to monogenic and complex diseases and cancer. Here, we provide an overview of the methods available to characterize and perturb gene regulatory circuits. We then highlight mechanisms through which regulatory rewiring contributes to disease, and conclude with a perspective on how our understanding of gene regulation can be used to improve human health.
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Affiliation(s)
- Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
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48
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Yang MG, Ling E, Cowley CJ, Greenberg ME, Vierbuchen T. Characterization of sequence determinants of enhancer function using natural genetic variation. eLife 2022; 11:76500. [PMID: 36043696 PMCID: PMC9662815 DOI: 10.7554/elife.76500] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 08/30/2022] [Indexed: 02/04/2023] Open
Abstract
Sequence variation in enhancers that control cell-type-specific gene transcription contributes significantly to phenotypic variation within human populations. However, it remains difficult to predict precisely the effect of any given sequence variant on enhancer function due to the complexity of DNA sequence motifs that determine transcription factor (TF) binding to enhancers in their native genomic context. Using F1-hybrid cells derived from crosses between distantly related inbred strains of mice, we identified thousands of enhancers with allele-specific TF binding and/or activity. We find that genetic variants located within the central region of enhancers are most likely to alter TF binding and enhancer activity. We observe that the AP-1 family of TFs (Fos/Jun) are frequently required for binding of TEAD TFs and for enhancer function. However, many sequence variants outside of core motifs for AP-1 and TEAD also impact enhancer function, including sequences flanking core TF motifs and AP-1 half sites. Taken together, these data represent one of the most comprehensive assessments of allele-specific TF binding and enhancer function to date and reveal how sequence changes at enhancers alter their function across evolutionary timescales.
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Affiliation(s)
- Marty G Yang
- Department of Neurobiology, Harvard Medical School, Boston, United States.,Program in Neuroscience, Harvard Medical School, Boston, United States
| | - Emi Ling
- Department of Neurobiology, Harvard Medical School, Boston, United States
| | | | | | - Thomas Vierbuchen
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, United States.,Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, United States
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49
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Boschiero C, Gao Y, Baldwin RL, Ma L, Li CJ, Liu GE. Butyrate Induces Modifications of the CTCF-Binding Landscape in Cattle Cells. Biomolecules 2022; 12:biom12091177. [PMID: 36139015 PMCID: PMC9496099 DOI: 10.3390/biom12091177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/24/2022] Open
Abstract
Butyrate is produced in the rumen from microbial fermentation and is related to several functions, including cell differentiation and proliferation. Butyrate supplementation in calves can accelerate rumen development. DNA-protein interactions, such as the CCCTC-binding factor (CTCF), play essential roles in chromatin organization and gene expression regulation. Although CTCF-binding sites have been identified recently in cattle, a deeper characterization, including differentially CTCF-binding sites (DCBS), is vital for a better understanding of butyrate’s role in the chromatin landscape. This study aimed to identify CTCF-binding regions and DCBS under a butyrate-induced condition using ChIP-seq in bovine cells; 61,915 CTCF peaks were identified in the butyrate and 51,347 in the control. From these regions, 2265 DCBS were obtained for the butyrate vs. control comparison, comprising ~90% of induced sites. Most of the butyrate DCBS were in distal intergenic regions, showing a potential role as insulators. Gene ontology enrichment showed crucial terms for the induced DCBS, mainly related to cellular proliferation, cell adhesion, and growth regulation. Interestingly, the ECM-receptor interaction pathway was observed for the induced DCBS. Motif enrichment analysis further identified transcription factors, including CTCF, BORIS, TGIF2, and ZIC3. When DCBS was integrated with RNA-seq data, putative genes were identified for the repressed DCBS, including GATA4. Our study revealed promising candidate genes in bovine cells by a butyrate-induced condition that might be related to the regulation of rumen development, such as integrins, keratins, and collagens. These results provide a better understanding of the function of butyrate in cattle rumen development and chromatin landscape regulation.
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Affiliation(s)
- Clarissa Boschiero
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Ransom L. Baldwin
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Cong-jun Li
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
- Correspondence: (C.-j.L.); (G.E.L.); Tel.: +1-301-504-7216 (C.-j.L.); +1-301-504-9843 (G.E.L.); Fax: +1-301-504-8414 (C.-j.L. & G.E.L.)
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
- Correspondence: (C.-j.L.); (G.E.L.); Tel.: +1-301-504-7216 (C.-j.L.); +1-301-504-9843 (G.E.L.); Fax: +1-301-504-8414 (C.-j.L. & G.E.L.)
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50
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Boschiero C, Gao Y, Baldwin RL, Ma L, Li CJ, Liu GE. Differentially CTCF-Binding Sites in Cattle Rumen Tissue during Weaning. Int J Mol Sci 2022; 23:ijms23169070. [PMID: 36012336 PMCID: PMC9408924 DOI: 10.3390/ijms23169070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022] Open
Abstract
The weaning transition in calves is characterized by major structural changes such as an increase in the rumen capacity and surface area due to diet changes. Studies evaluating rumen development in calves are vital to identify genetic mechanisms affected by weaning. This study aimed to provide a genome-wide characterization of CTCF-binding sites and differentially CTCF-binding sites (DCBS) in rumen tissue during the weaning transition of four Holstein calves to uncover regulatory elements in rumen epithelial tissue using ChIP-seq. Our study generated 67,280 CTCF peaks for the before weaning (BW) and 39,891 for after weaning (AW). Then, 7401 DCBS were identified for the AW vs. BW comparison representing 0.15% of the cattle genome, comprising ~54% of induced DCBS and ~46% of repressed DCBS. Most of the induced and repressed DCBS were in distal intergenic regions, showing a potential role as insulators. Gene ontology enrichment revealed many shared GO terms for the induced and the repressed DCBS, mainly related to cellular migration, proliferation, growth, differentiation, cellular adhesion, digestive tract morphogenesis, and response to TGFβ. In addition, shared KEGG pathways were obtained for adherens junction and focal adhesion. Interestingly, other relevant KEGG pathways were observed for the induced DCBS like gastric acid secretion, salivary secretion, bacterial invasion of epithelial cells, apelin signaling, and mucin-type O-glycan biosynthesis. IPA analysis further revealed pathways with potential roles in rumen development during weaning, including TGFβ, Integrin-linked kinase, and Integrin signaling. When DCBS were further integrated with RNA-seq data, 36 putative target genes were identified for the repressed DCBS, including KRT84, COL9A2, MATN3, TSPAN1, and AJM1. This study successfully identified DCBS in cattle rumen tissue after weaning on a genome-wide scale and revealed several candidate target genes that may have a role in rumen development, such as TGFβ, integrins, keratins, and SMADs. The information generated in this preliminary study provides new insights into bovine genome regulation and chromatin landscape.
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Affiliation(s)
- Clarissa Boschiero
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Ransom L. Baldwin
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Cong-jun Li
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
- Correspondence: (C.-j.L.); (G.E.L.); Tel.: +1-301-504-7216 (C.-j.L.); +1-301-504-9843 (G.E.L.); Fax: +1-301-504-8414 (C.-j.L. & G.E.L.)
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
- Correspondence: (C.-j.L.); (G.E.L.); Tel.: +1-301-504-7216 (C.-j.L.); +1-301-504-9843 (G.E.L.); Fax: +1-301-504-8414 (C.-j.L. & G.E.L.)
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