1
|
Zhang M, Hyle J, Chen X, Xin Y, Jin Y, Zhang J, Yang X, Chen X, Wright S, Liu Z, Rosikiewicz W, Xu B, He L, Liu H, Ping N, Wu D, Wen F, Li C, Xu P. RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9. Genome Biol 2024; 25:16. [PMID: 38216972 PMCID: PMC10785552 DOI: 10.1186/s13059-023-03149-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 12/20/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND The oncogenic protein HOXA9 plays a critical role in leukemia transformation and maintenance, and its aberrant expression is a hallmark of most aggressive acute leukemia. Although inhibiting the upstream regulators of HOXA9 has been proven as a significant therapeutic intervention, the comprehensive regulation network controlling HOXA9 expression in leukemia has not been systematically investigated. RESULTS Here, we perform genome-wide CRISPR/Cas9 screening in the HOXA9-driven reporter acute leukemia cells. We identify a poorly characterized RNA-binding protein, RBM5, as the top candidate gene required to maintain leukemia cell fitness. RBM5 is highly overexpressed in acute myeloid leukemia (AML) patients compared to healthy individuals. RBM5 loss triggered by CRISPR knockout and shRNA knockdown significantly impairs leukemia maintenance in vitro and in vivo. Through domain CRISPR screening, we reveal that RBM5 functions through a noncanonical transcriptional regulation circuitry rather than RNA splicing, such an effect depending on DNA-binding domains. By integrative analysis and functional assays, we identify HOXA9 as the downstream target of RBM5. Ectopic expression of HOXA9 rescues impaired leukemia cell proliferation upon RBM5 loss. Importantly, acute protein degradation of RBM5 through auxin-inducible degron system immediately reduces HOXA9 transcription. CONCLUSIONS We identify RBM5 as a new upstream regulator of HOXA9 and reveal its essential role in controlling the survival of AML. These functional and molecular mechanisms further support RBM5 as a promising therapeutic target for myeloid leukemia treatment.
Collapse
Affiliation(s)
- Mengli Zhang
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Judith Hyle
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xiaowen Chen
- Division of Hematology and Oncology, Shenzhen Children's Hospital, Shenzhen Institute of Pediatrics, 7019 Yi Tian Road, Shenzhen, 518038, China
| | - Ye Xin
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Yingcai Jin
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Jianxiang Zhang
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Xue Yang
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Xinfeng Chen
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Shaela Wright
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Zhenling Liu
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Liusheng He
- Core Facility of Flow Cytometry, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Hong Liu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215123, Jiangsu, China
| | - Nana Ping
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215123, Jiangsu, China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215123, Jiangsu, China
| | - Feiqiu Wen
- Division of Hematology and Oncology, Shenzhen Children's Hospital, Shenzhen Institute of Pediatrics, 7019 Yi Tian Road, Shenzhen, 518038, China
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Peng Xu
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, Jiangsu, China.
| |
Collapse
|
2
|
Wright S, Zhao X, Rosikiewicz W, Mryncza S, Hyle J, Qi W, Liu Z, Yi S, Cheng Y, Xu B, Li C. Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by noncoding CRISPR screens. Nat Commun 2023; 14:7464. [PMID: 38016946 PMCID: PMC10684515 DOI: 10.1038/s41467-023-43264-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/02/2023] [Indexed: 11/30/2023] Open
Abstract
Accumulating evidence indicates that HOXA9 dysregulation is necessary and sufficient for leukemic transformation and maintenance. However, it remains largely unknown how HOXA9, as a homeobox transcriptional factor, binds to noncoding regulatory sequences and controls the downstream genes. Here, we conduct dropout CRISPR screens against 229 HOXA9-bound peaks identified by ChIP-seq. Integrative data analysis identifies reproducible noncoding hits, including those located in the distal enhancer of FLT3 and intron of CDK6. The Cas9-editing and dCas9-KRAB silencing of the HOXA9-bound sites significantly reduce corresponding gene transcription and impair cell proliferation in vitro, and in vivo by transplantation into NSG female mice. In addition, RNA-seq, Q-PCR analysis, chromatin accessibility change, and chromatin conformation evaluation uncover the noncoding regulation mechanism of HOXA9 and its functional downstream genes. In summary, our work improves our understanding of how HOXA9-associated transcription programs reconstruct the regulatory network specifying MLL-r dependency.
Collapse
Affiliation(s)
- Shaela Wright
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xujie Zhao
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Zhongda Hospital, School of Life Sciences and Technology, Advanced Institute for Life and Health, Southeast University, Nanjing, 210096, China
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shelby Mryncza
- Department of Biology, Rhodes College, 2000 North Pkwy, Memphis, TN, 38112, USA
| | - Judith Hyle
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Wenjie Qi
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Zhenling Liu
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Siqi Yi
- Department of Hematology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yong Cheng
- Department of Hematology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| |
Collapse
|
3
|
Wright S, Hu J, Wang H, Hyle J, Zhang Y, Du G, Konopleva MY, Kornblau SM, Djekidel MN, Rosikiewicz W, Xu B, Lu R, Yang JJ, Li C. Interrogating bromodomain inhibitor resistance in KMT2A-rearranged leukemia through combinatorial CRISPR screens. Proc Natl Acad Sci U S A 2023; 120:e2220134120. [PMID: 37036970 PMCID: PMC10120025 DOI: 10.1073/pnas.2220134120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
Bromo- and extra-terminal domain inhibitors (BETi) have exhibited therapeutic activities in many cancers. However, the mechanisms controlling BETi response and resistance are not well understood. We conducted genome-wide loss-of-function CRISPR screens using BETi-treated KMT2A-rearranged (KMT2A-r) cell lines. We revealed that Speckle-type POZ protein (SPOP) gene (Speckle Type BTB/POZ Protein) deficiency caused significant BETi resistance, which was further validated in cell lines and xenograft models. Proteomics analysis and a kinase-vulnerability CRISPR screen indicated that cells treated with BETi are sensitive to GSK3 perturbation. Pharmaceutical inhibition of GSK3 reversed the BETi-resistance phenotype. Based on this observation, a combination therapy regimen inhibiting both BET and GSK3 was developed to impede KMT2A-r leukemia progression in patient-derived xenografts in vivo. Our results revealed molecular mechanisms underlying BETi resistance and a promising combination treatment regimen of ABBV-744 and CHIR-98014 by utilizing unique ex vivo and in vivo KMT2A-r PDX models.
Collapse
Affiliation(s)
- Shaela Wright
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Jianzhong Hu
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Hong Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Judith Hyle
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Yang Zhang
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Guoqing Du
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Marina Y Konopleva
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | | | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Rui Lu
- Division of Hematology/Oncology, O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| |
Collapse
|
4
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
5
|
Xu B, Wang H, Wright S, Hyle J, Zhang Y, Shao Y, Niu M, Fan Y, Rosikiewicz W, Djekidel MN, Peng J, Lu R, Li C. Acute depletion of CTCF rewires genome-wide chromatin accessibility. Genome Biol 2021; 22:244. [PMID: 34429148 PMCID: PMC8386078 DOI: 10.1186/s13059-021-02466-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 08/12/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The transcription factor CTCF appears indispensable in defining topologically associated domain boundaries and maintaining chromatin loop structures within these domains, supported by numerous functional studies. However, acute depletion of CTCF globally reduces chromatin interactions but does not significantly alter transcription. RESULTS Here, we systematically integrate multi-omics data including ATAC-seq, RNA-seq, WGBS, Hi-C, Cut&Run, and CRISPR-Cas9 survival dropout screens, and time-solved deep proteomic and phosphoproteomic analyses in cells carrying auxin-induced degron at endogenous CTCF locus. Acute CTCF protein degradation markedly rewires genome-wide chromatin accessibility. Increased accessible chromatin regions are frequently located adjacent to CTCF-binding sites at promoter regions and insulator sites associated with enhanced transcription of nearby genes. In addition, we use CTCF-associated multi-omics data to establish a combinatorial data analysis pipeline to discover CTCF co-regulatory partners. We successfully identify 40 candidates, including multiple established partners. Interestingly, many CTCF co-regulators that have alterations of their respective downstream gene expression do not show changes of their own expression levels across the multi-omics measurements upon acute CTCF loss, highlighting the strength of our system to discover hidden co-regulatory partners associated with CTCF-mediated transcription. CONCLUSIONS This study highlights that CTCF loss rewires genome-wide chromatin accessibility, which plays a critical role in transcriptional regulation.
Collapse
Affiliation(s)
- Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Hong Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shaela Wright
- Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Judith Hyle
- Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yang Zhang
- Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ying Shao
- Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Mingming Niu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Mohamed Nadhir Djekidel
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Junmin Peng
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Rui Lu
- Division of Hematology/Oncology, University of Alabama at Birmingham, 1824 6th Ave S WTI 510G, Birmingham, AL, 35294, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, 1824 6th Ave S WTI 510G, Birmingham, AL, 35294, USA
| | - Chunliang Li
- Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| |
Collapse
|
6
|
Zhang H, Zhang Y, Zhou X, Wright S, Hyle J, Zhao L, An J, Zhao X, Shao Y, Xu B, Lee HM, Chen T, Zhou Y, Chen X, Lu R, Li C. Functional interrogation of HOXA9 regulome in MLLr leukemia via reporter-based CRISPR/Cas9 screen. eLife 2020; 9:e57858. [PMID: 33001025 PMCID: PMC7599066 DOI: 10.7554/elife.57858] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 09/30/2020] [Indexed: 12/26/2022] Open
Abstract
Aberrant HOXA9 expression is a hallmark of most aggressive acute leukemias, notably those with KMT2A (MLL) gene rearrangements. HOXA9 overexpression not only predicts poor diagnosis and outcome but also plays a critical role in leukemia transformation and maintenance. However, our current understanding of HOXA9 regulation in leukemia is limited, hindering development of therapeutic strategies. Here, we generated the HOXA9-mCherry knock-in reporter cell lines to dissect HOXA9 regulation. By utilizing the reporter and CRISPR/Cas9 screens, we identified transcription factors controlling HOXA9 expression, including a novel regulator, USF2, whose depletion significantly down-regulated HOXA9 expression and impaired MLLr leukemia cell proliferation. Ectopic expression of Hoxa9 rescued impaired leukemia cell proliferation upon USF2 loss. Cut and Run analysis revealed the direct occupancy of USF2 at HOXA9 promoter in MLLr leukemia cells. Collectively, the HOXA9 reporter facilitated the functional interrogation of the HOXA9 regulome and has advanced our understanding of the molecular regulation network in HOXA9-driven leukemia.
Collapse
Affiliation(s)
- Hao Zhang
- Division of Hematology/Oncology, University of Alabama at BirminghamBirminghamUnited States
- O’Neal Comprehensive Cancer Center, University of Alabama at BirminghamBirminghamUnited States
| | - Yang Zhang
- Department of Tumor Cell Biology, St. Jude Children’s Research HospitalMemphisUnited States
- Cancer Biology Program/Comprehensive Cancer Center, St. Jude Children’s Research HospitalMemphisUnited States
| | - Xinyue Zhou
- Division of Hematology/Oncology, University of Alabama at BirminghamBirminghamUnited States
- O’Neal Comprehensive Cancer Center, University of Alabama at BirminghamBirminghamUnited States
| | - Shaela Wright
- Department of Tumor Cell Biology, St. Jude Children’s Research HospitalMemphisUnited States
- Cancer Biology Program/Comprehensive Cancer Center, St. Jude Children’s Research HospitalMemphisUnited States
| | - Judith Hyle
- Department of Tumor Cell Biology, St. Jude Children’s Research HospitalMemphisUnited States
- Cancer Biology Program/Comprehensive Cancer Center, St. Jude Children’s Research HospitalMemphisUnited States
| | - Lianzhong Zhao
- Division of Hematology/Oncology, University of Alabama at BirminghamBirminghamUnited States
- O’Neal Comprehensive Cancer Center, University of Alabama at BirminghamBirminghamUnited States
| | - Jie An
- Division of Hematology/Oncology, University of Alabama at BirminghamBirminghamUnited States
- O’Neal Comprehensive Cancer Center, University of Alabama at BirminghamBirminghamUnited States
| | - Xujie Zhao
- Department of Pharmaceutical Sciences, St. Jude Children’s Research HospitalMemphisUnited States
| | - Ying Shao
- Department of Computational Biology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Hyeong-Min Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research HospitalMemphisUnited States
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research HospitalMemphisUnited States
| | - Yang Zhou
- Department of Biomedical Engineering School of Engineering, University of Alabama at BirminghamBirminghamUnited States
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Rui Lu
- Division of Hematology/Oncology, University of Alabama at BirminghamBirminghamUnited States
- O’Neal Comprehensive Cancer Center, University of Alabama at BirminghamBirminghamUnited States
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children’s Research HospitalMemphisUnited States
- Cancer Biology Program/Comprehensive Cancer Center, St. Jude Children’s Research HospitalMemphisUnited States
| |
Collapse
|
7
|
Liu Y, Li C, Shen S, Chen X, Szlachta K, Edmonson MN, Shao Y, Ma X, Hyle J, Wright S, Ju B, Rusch MC, Liu Y, Li B, Macias M, Tian L, Easton J, Qian M, Yang JJ, Hu S, Look AT, Zhang J. Discovery of regulatory noncoding variants in individual cancer genomes by using cis-X. Nat Genet 2020; 52:811-818. [PMID: 32632335 PMCID: PMC7679232 DOI: 10.1038/s41588-020-0659-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 06/05/2020] [Indexed: 12/30/2022]
Abstract
We developed cis-X, a computational method for discovering regulatory noncoding variants in cancer by integrating whole-genome and transcriptome sequencing data from a single cancer sample. cis-X first finds aberrantly cis-activated genes that exhibit allele-specific expression accompanied by an elevated outlier expression. It then searches for causal noncoding variants that may introduce aberrant transcription factor binding motifs or enhancer hijacking by structural variations. Analysis of 13 T-lineage acute lymphoblastic leukemias identified a recurrent intronic variant predicted to cis-activate the TAL1 oncogene, a finding validated in vivo by chromatin immunoprecipitation sequencing of a patient-derived xenograft. Candidate oncogenes include the prolactin receptor PRLR activated by a focal deletion that removes a CTCF-insulated neighborhood boundary. cis-X may be applied to pediatric and adult solid tumors that are aneuploid and heterogeneous. In contrast to existing approaches, which require large sample cohorts, cis-X enables the discovery of regulatory noncoding variants in individual cancer genomes.
Collapse
Affiliation(s)
- Yu Liu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shuhong Shen
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Karol Szlachta
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael N Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ying Shao
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Judith Hyle
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shaela Wright
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bensheng Ju
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael C Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Benshang Li
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Michael Macias
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Maoxiang Qian
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.,Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shaoyan Hu
- Children's Hospital of Soochow University, Suzhou, China
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| |
Collapse
|
8
|
Zhang Y, Hyle J, Wright S, Shao Y, Zhao X, Zhang H, Li C. A cis-element within the ARF locus mediates repression of p16INK4A expression via long-range chromatin interactions. Proc Natl Acad Sci U S A 2019; 116:26644-26652. [PMID: 31818950 PMCID: PMC6936709 DOI: 10.1073/pnas.1909720116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Loss of function of CDKN2A/B, also known as INK4/ARF [encoding p16INK4A, p15INK4B, and p14ARF (mouse p19Arf)], confers susceptibility to cancers, whereas its up-regulation during organismal aging provokes cellular senescence and tissue degenerative disorders. To better understand the transcriptional regulation of p16INK4A, a CRISPR screen targeting open, noncoding chromatin regions adjacent to p16INK4A was performed in a human p16INK4A-P2A-mCherry reporter cell line. We identified a repressive element located in the 3' region adjacent to the ARF promoter that controls p16INK4A expression via long-distance chromatin interactions. Coinfection of lentiviral dCas9-KRAB with selected single-guide RNAs against the repressive element abrogated the ARF/p16INK4A chromatin contacts, thus reactivating p16INK4A expression. Genetic CRISPR screening identified candidate transcription factors inhibiting p16INK4A regulation, including ZNF217, which was confirmed to bind the ARF/p16INK4A interaction loop. In summary, direct physical interactions between p16INK4A and ARF genes provide mechanistic insights into their cross-regulation.
Collapse
Affiliation(s)
- Yang Zhang
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Judith Hyle
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Shaela Wright
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Ying Shao
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Xujie Zhao
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Hui Zhang
- Department of Hematology and Oncology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 Guangdong, People’s Republic of China
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| |
Collapse
|
9
|
Hyle J, Zhang Y, Wright S, Xu B, Shao Y, Easton J, Tian L, Feng R, Xu P, Li C. Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping. Nucleic Acids Res 2019; 47:6699-6713. [PMID: 31127282 PMCID: PMC6648894 DOI: 10.1093/nar/gkz462] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/12/2019] [Accepted: 05/14/2019] [Indexed: 12/11/2022] Open
Abstract
Numerous pieces of evidence support the complex, 3D spatial organization of the genome dictates gene expression. CTCF is essential to define topologically associated domain boundaries and to facilitate the formation of insulated chromatin loop structures. To understand CTCF's direct role in global transcriptional regulation, we integrated the miniAID-mClover3 cassette to the endogenous CTCF locus in a human pediatric B-ALL cell line, SEM, and an immortal erythroid precursor cell line, HUDEP-2, to allow for acute depletion of CTCF protein by the auxin-inducible degron system. In SEM cells, CTCF loss notably disrupted intra-TAD loops and TAD integrity in concurrence with a reduction in CTCF-binding affinity, while showing no perturbation to nuclear compartment integrity. Strikingly, the overall effect of CTCF's loss on transcription was minimal. Whole transcriptome analysis showed hundreds of genes differentially expressed in CTCF-depleted cells, among which MYC and a number of MYC target genes were specifically downregulated. Mechanically, acute depletion of CTCF disrupted the direct interaction between the MYC promoter and its distal enhancer cluster residing ∼1.8 Mb downstream. Notably, MYC expression was not profoundly affected upon CTCF loss in HUDEP-2 cells suggesting that CTCF could play a B-ALL cell line specific role in maintaining MYC expression.
Collapse
Affiliation(s)
- Judith Hyle
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Yang Zhang
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Shaela Wright
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ying Shao
- Department of Computational Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ruopeng Feng
- Department of Hematology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Peng Xu
- Department of Hematology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| |
Collapse
|
10
|
Choi HH, Choi HK, Jung SY, Hyle J, Kim BJ, Yoon K, Cho EJ, Youn HD, Lahti JM, Qin J, Kim ST. CHK2 kinase promotes pre-mRNA splicing via phosphorylating CDK11(p110). Oncogene 2012. [PMID: 23178491 DOI: 10.1038/onc.2012.535] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Checkpoint kinase 2 (CHK2) kinase is a key mediator in many cellular responses to genotoxic stresses, including ionizing radiation (IR) and topoisomerase inhibitors. Upon IR, CHK2 is activated by ataxia telangiectasia mutated kinase and regulates the S-phase and G1-S checkpoints, apoptosis and DNA repair by phosphorylating downstream target proteins, such as p53 and Brca1. In addition, CHK2 is thought to be a multi-organ cancer susceptibility gene. In this study, we used a tandem affinity purification strategy to identify proteins that interact with CHK2 kinase. Cyclin-dependent kinase 11 (CDK11)(p110) kinase, implicated in pre-mRNA splicing and transcription, was identified as a CHK2-interacting protein. CHK2 kinase phosphorylated CDK11(p110) on serine 737 in vitro. Unexpectedly, CHK2 kinase constitutively phosphorylated CDK11(p110) in a DNA damage-independent manner. At a molecular level, CDK11(p110) phosphorylation was required for homodimerization without affecting its kinase activity. Overexpression of CHK2 promoted pre-mRNA splicing. Conversely, CHK2 depletion decreased endogenous splicing activity. Mutation of the phosphorylation site in CDK11(p110) to alanine abrogated its splicing-activating activity. These results provide the first evidence that CHK2 kinase promotes pre-mRNA splicing via phosphorylating CDK11(p110).
Collapse
Affiliation(s)
- H-H Choi
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon, Republic of Korea
| | - H-K Choi
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon, Republic of Korea
| | - S Y Jung
- Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, USA
| | - J Hyle
- Department of Genetics and Tumor Cell Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - B-J Kim
- Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, USA
| | - K Yoon
- School of Life Science and Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - E-J Cho
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - H-D Youn
- National Research Laboratory for Metabolic Checkpoint, Departments of Biomedical Sciences and Biochemistry and Molecular Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - J M Lahti
- Department of Genetics and Tumor Cell Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - J Qin
- Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, USA
| | - S-T Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon, Republic of Korea
| |
Collapse
|
11
|
Inoue A, Hyle J, Lechner MS, Lahti JM. Mammalian ChlR1 has a role in heterochromatin organization. Exp Cell Res 2011; 317:2522-35. [PMID: 21854770 DOI: 10.1016/j.yexcr.2011.08.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 07/18/2011] [Accepted: 08/03/2011] [Indexed: 11/16/2022]
Abstract
The ChlR1 DNA helicase, encoded by DDX11 gene, which is responsible for Warsaw breakage syndrome (WABS), has a role in sister-chromatid cohesion. In this study, we show that human ChlR1 deficient cells exhibit abnormal heterochromatin organization. While constitutive heterochromatin is discretely localized at perinuclear and perinucleolar regions in control HeLa cells, ChlR1-depleted cells showed dispersed localization of constitutive heterochromatin accompanied by disrupted centromere clustering. Cells isolated from Ddx11(-/-) embryos also exhibited diffuse localization of centromeres and heterochromatin foci. Similar abnormalities were found in HeLa cells depleted of combinations of HP1α and HP1β. Immunofluorescence and chromatin immunoprecipitation showed a decreased level of HP1α at pericentric regions in ChlR1-depleted cells. Trimethyl-histone H3 at lysine 9 (H3K9-me3) was also modestly decreased at pericentric sequences. The abnormality in pericentric heterochromatin was further supported by decreased DNA methylation within major satellite repeats of Ddx11(-/-) embryos. Furthermore, micrococcal nuclease (MNase) assay revealed a decreased chromatin density at the telomeres. These data suggest that in addition to a role in sister-chromatid cohesion, ChlR1 is also involved in the proper formation of heterochromatin, which in turn contributes to global nuclear organization and pleiotropic effects.
Collapse
Affiliation(s)
- Akira Inoue
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | | | | |
Collapse
|
12
|
Loyer P, Busson A, Trembley JH, Hyle J, Grenet J, Zhao W, Ribault C, Montier T, Kidd VJ, Lahti JM. The RNA binding motif protein 15B (RBM15B/OTT3) is a functional competitor of serine-arginine (SR) proteins and antagonizes the positive effect of the CDK11p110-cyclin L2α complex on splicing. J Biol Chem 2010; 286:147-59. [PMID: 21044963 DOI: 10.1074/jbc.m110.192518] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Here, we report the identification of the RNA binding motif protein RBM15B/OTT3 as a new CDK11(p110) binding partner that alters the effects of CDK11 on splicing. RBM15B was initially identified as a binding partner of the Epstein-Barr virus mRNA export factor and, more recently, as a cofactor of the nuclear export receptor NXF1. In this study, we found that RBM15B co-elutes with CDK11(p110), cyclin L2α, and serine-arginine (SR) proteins, including SF2/ASF, in a large nuclear complex of ∼1-MDa molecular mass following size exclusion chromatography. Using co-immunoprecipitation experiments and in vitro pulldown assays, we mapped two distinct domains of RBM15B that are essential for its direct interaction with the N-terminal extension of CDK11(p110), cyclin L2α, and SR proteins such as 9G8 and SF2/ASF. Finally, we established that RBM15B is a functional competitor of the SR proteins SF2/ASF and 9G8, inhibits formation of the functional spliceosomal E complex, and antagonizes the positive effect of the CDK11(p110)-cyclin L2α complex on splicing both in vitro and in vivo.
Collapse
Affiliation(s)
- Pascal Loyer
- INSERM UMR 991 Foie, Métabolismes et Cancer, IFR140, Université de Rennes 1, Hôpital Pontchaillou, 35033 Rennes, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Lagisetti C, Pourpak A, Goronga T, Jiang Q, Cui X, Hyle J, Lahti JM, Morris SW, Webb TR. Synthetic mRNA splicing modulator compounds with in vivo antitumor activity. J Med Chem 2009; 52:6979-90. [PMID: 19877647 DOI: 10.1021/jm901215m] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report our progress on the development of new synthetic anticancer lead compounds that modulate the splicing of mRNA. We also report the synthesis and evaluation of new biologically active ester and carbamate analogues. Further, we describe initial animal studies demonstrating the antitumor efficacy of compound 5 in vivo. Additionally, we report the enantioselective and diastereospecific synthesis of a new 1,3-dioxane series of active analogues. We confirm that compound 5 inhibits the splicing of mRNA in cell-free nuclear extracts and in a cell-based dual-reporter mRNA splicing assay. In summary, we have developed totally synthetic novel spliceosome modulators as therapeutic lead compounds for a number of highly aggressive cancers. Future efforts will be directed toward the more complete optimization of these compounds as potential human therapeutics.
Collapse
Affiliation(s)
- Chandraiah Lagisetti
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, MS 1000, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Inoue A, Hyle J, Lechner MS, Lahti JM. Perturbation of HP1 localization and chromatin binding ability causes defects in sister-chromatid cohesion. Mutat Res 2008; 657:48-55. [PMID: 18790078 DOI: 10.1016/j.mrgentox.2008.08.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Accepted: 08/11/2008] [Indexed: 01/06/2023]
Abstract
Sister-chromatid cohesion, the machinery used in eukaryote organisms to prevent aneuploidy, tethers sister chromatids together after their replication in S phase until mitosis. Previous studies in fission yeast, Drosophila and mammals have demonstrated the requirement for the heterochromatin formation pathway for proper centromeric cohesion. However, the exact role of heterochromatin protein 1 (HP1) in sister-chromatid cohesion in mammals is still unknown. In this study, we disrupted endogenous HP1 expression in HeLa cells using a dominant-negative mutant of HP1beta and wild-type or mutant forms of HP1alpha. We then examined their effects on chromosome alignment, segregation and cohesion. Enforced expression of these constructs leads to frequent chromosome misalignment and missegregation. Mitotic chromosomes from these cells also exhibit a loosened primary constriction and separated sister chromatids. We further demonstrate that alignment of the cohesin proteins around kinetochores was also aberrant and that cohesin complexes bound less tightly in these cells. Unexpectedly, we observed a "wavy" chromosome morphology resembling that seen upon depletion of condensin proteins in cells with over-expression of HP1alpha, but not in cells expressing the HP1beta mutant. These results indicate that proper HP1 status is required for sister-chromatid cohesion in mammalian cells, and suggest that HP1alpha might be required for chromosome condensation.
Collapse
Affiliation(s)
- Akira Inoue
- Department of Genetics and Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | | | | | | |
Collapse
|