Subtype-specific 3D genome alteration in acute myeloid leukaemia

Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases 1 – 5 . The extent to which mutations in AML drive alterations in chromatin 3D structure and contribute to myeloid transfor...

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Published in:	Nature (London) Vol. 611; no. 7935; pp. 387 - 398
Main Authors:	Xu, Jie, Song, Fan, Lyu, Huijue, Kobayashi, Mikoto, Zhang, Baozhen, Zhao, Ziyu, Hou, Ye, Wang, Xiaotao, Luan, Yu, Jia, Bei, Stasiak, Lena, Wong, Josiah Hiu-yuen, Wang, Qixuan, Jin, Qi, Jin, Qiushi, Fu, Yihao, Yang, Hongbo, Hardison, Ross C., Dovat, Sinisa, Platanias, Leonidas C., Diao, Yarui, Yang, Yue, Yamada, Tomoko, Viny, Aaron D., Levine, Ross L., Claxton, David, Broach, James. R., Zheng, Hong, Yue, Feng
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 10-11-2022 Nature Publishing Group
Subjects:	38 45/15 45/23 631/67/1990/283/1897 631/67/69 Acute myeloid leukemia Bisulfite Chromatin Chromatin - genetics CRISPR CRISPR-Cas Systems Deoxyribonucleic acid DNA DNA (Cytosine-5-)-Methyltransferases DNA Methylation DNMT1 protein Enhancer Elements, Genetic Enhancers Epigenetics Gene expression Gene Expression Regulation, Leukemic Gene sequencing Gene Silencing Genetic engineering Genome, Human - genetics Genomes Humanities and Social Sciences Humans Interference Leukemia Leukemia, Myeloid, Acute - genetics Malignancy multidisciplinary Mutation Promoter Regions, Genetic Regulatory sequences Reproducibility of Results Science Science (multidisciplinary) Sequence Analysis Silencers Transcription factors Whole genome sequencing
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Abstract	Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases 1 – 5 . The extent to which mutations in AML drive alterations in chromatin 3D structure and contribute to myeloid transformation is unclear. Here we use Hi-C and whole-genome sequencing to analyse 25 samples from patients with AML and 7 samples from healthy donors. Recurrent and subtype-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing, ATAC with sequencing and CUT&Tag for CTCF, H3K27ac and H3K27me3 in the same AML samples also revealed extensive and recurrent AML-specific promoter–enhancer and promoter–silencer loops. We validated the role of repressive loops on their target genes by CRISPR deletion and interference. Structural variation-induced enhancer-hijacking and silencer-hijacking events were further identified in AML samples. Hijacked enhancers play a part in AML cell growth, as demonstrated by CRISPR screening, whereas hijacked silencers have a downregulating role, as evidenced by CRISPR-interference-mediated de-repression. Finally, whole-genome bisulfite sequencing of 20 AML and normal samples revealed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Treatment of AML cells with a DNA hypomethylating agent and triple knockdown of DNMT1 , DNMT3A and DNMT3B enabled the manipulation of DNA methylation to revert 3D genome organization and gene expression. Overall, this study provides a resource for leukaemia studies and highlights the role of repressive loops and hijacked cis elements in human diseases. Extensive genomic analyses of the chromatin architecture in acute myeloid leukaemia reveals several characteristics, including subtype-specific distal enhancers and silencers, that may represent new anticancer therapeutic targets.
AbstractList	Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases 1 – 5 . The extent to which mutations in AML drive alterations in chromatin 3D structure and contribute to myeloid transformation is unclear. Here we use Hi-C and whole-genome sequencing to analyse 25 samples from patients with AML and 7 samples from healthy donors. Recurrent and subtype-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing, ATAC with sequencing and CUT&Tag for CTCF, H3K27ac and H3K27me3 in the same AML samples also revealed extensive and recurrent AML-specific promoter–enhancer and promoter–silencer loops. We validated the role of repressive loops on their target genes by CRISPR deletion and interference. Structural variation-induced enhancer-hijacking and silencer-hijacking events were further identified in AML samples. Hijacked enhancers play a part in AML cell growth, as demonstrated by CRISPR screening, whereas hijacked silencers have a downregulating role, as evidenced by CRISPR-interference-mediated de-repression. Finally, whole-genome bisulfite sequencing of 20 AML and normal samples revealed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Treatment of AML cells with a DNA hypomethylating agent and triple knockdown of DNMT1 , DNMT3A and DNMT3B enabled the manipulation of DNA methylation to revert 3D genome organization and gene expression. Overall, this study provides a resource for leukaemia studies and highlights the role of repressive loops and hijacked cis elements in human diseases. Extensive genomic analyses of the chromatin architecture in acute myeloid leukaemia reveals several characteristics, including subtype-specific distal enhancers and silencers, that may represent new anticancer therapeutic targets. Acute myeloid leukemia (AML) represents a set of heterogeneous myeloid malignancies hallmarked by mutations in epigenetic modifiers, transcription factors, and kinases 1 - 5 . It is unclear to what extent AML mutations drive chromatin 3D structure alteration and contribute to myeloid transformation. Here, we first performed Hi-C and whole-genome sequencing in 25 AML patient samples and seven healthy donor samples, and identified recurrent and subtype-specific alterations of A/B compartments, TADs, and chromatin loops. We then performed RNA-Seq, ATAC-Seq and CUT&Tag for CTCF, H3K27ac, and H3K27me3 in the same AML cohort, and identified extensive and recurrent AML-specific promoter-enhancer and promoter-silencer loops. We validated the role of repressive loops on their target genes by CRISPR deletion and interference experiments. Furthermore, we identified structural variation-induced enhancer-hijacking and silencer-hijacking events in AML samples. We demonstrated the role of hijacked enhancers in AML cell growth by CRISPR screening, and the downregulating role of hijacked silencers by CRISPRi de-repression. Finally, we performed whole-genome bisulfite sequencing in 20 AML and normal samples, and showed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. By treating the AML cells with the DNA hypomethylating agent and performing triple knockdown of DNMT1/3A/3B, we demonstrated the impact of manipulating DNA methylation on reverting 3D genome organization and gene expression. Overall, this study provides an invaluable resource for leukemia studies and highlighted the role of repressive-loops and hijacked cis-elements in human diseases. Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases1-5. The extent to which mutations in AML drive alterations in chromatin 3D structure and contribute to myeloid transformation is unclear. Here we use Hi-C and whole-genome sequencing to analyse 25 samples from patients with AML and 7 samples from healthy donors. Recurrent and subtype-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing, ATAC with sequencing and CUT&Tag for CTCF, H3K27ac and H3K27me3 in the same AML samples also revealed extensive and recurrent AML-specific promoter-enhancer and promoter-silencer loops. We validated the role of repressive loops on their target genes by CRISPR deletion and interference. Structural variation-induced enhancer-hijacking and silencer-hijacking events were further identified in AML samples. Hijacked enhancers play a part in AML cell growth, as demonstrated by CRISPR screening, whereas hijacked silencers have a downregulating role, as evidenced by CRISPR-interference-mediated de-repression. Finally, whole-genome bisulfite sequencing of 20 AML and normal samples revealed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Treatment of AML cells with a DNA hypomethylating agent and triple knockdown of DNMT1, DNMT3A and DNMT3B enabled the manipulation ofDNA methylation to revert 3D genome organization and gene expression. Overall, this study provides a resource for leukaemia studies and highlights the role of repressive loops and hijacked cis elements in human diseases. Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases . The extent to which mutations in AML drive alterations in chromatin 3D structure and contribute to myeloid transformation is unclear. Here we use Hi-C and whole-genome sequencing to analyse 25 samples from patients with AML and 7 samples from healthy donors. Recurrent and subtype-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing, ATAC with sequencing and CUT&Tag for CTCF, H3K27ac and H3K27me3 in the same AML samples also revealed extensive and recurrent AML-specific promoter-enhancer and promoter-silencer loops. We validated the role of repressive loops on their target genes by CRISPR deletion and interference. Structural variation-induced enhancer-hijacking and silencer-hijacking events were further identified in AML samples. Hijacked enhancers play a part in AML cell growth, as demonstrated by CRISPR screening, whereas hijacked silencers have a downregulating role, as evidenced by CRISPR-interference-mediated de-repression. Finally, whole-genome bisulfite sequencing of 20 AML and normal samples revealed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Treatment of AML cells with a DNA hypomethylating agent and triple knockdown of DNMT1, DNMT3A and DNMT3B enabled the manipulation of DNA methylation to revert 3D genome organization and gene expression. Overall, this study provides a resource for leukaemia studies and highlights the role of repressive loops and hijacked cis elements in human diseases.
Author	Wong, Josiah Hiu-yuen Yamada, Tomoko Jin, Qi Fu, Yihao Hardison, Ross C. Diao, Yarui Claxton, David Platanias, Leonidas C. Broach, James. R. Song, Fan Jia, Bei Zhao, Ziyu Kobayashi, Mikoto Hou, Ye Wang, Xiaotao Lyu, Huijue Wang, Qixuan Yang, Hongbo Jin, Qiushi Viny, Aaron D. Levine, Ross L. Xu, Jie Zhang, Baozhen Yue, Feng Stasiak, Lena Dovat, Sinisa Luan, Yu Yang, Yue Zheng, Hong
AuthorAffiliation	2 Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Penn State University, Hershey, Pennsylvania, 17033, USA 3 Bioinformatics and Genomics graduate program, Huck Institutes of Life Sciences, Penn State University, State College, Pennsylvania, 16802, USA 5 Department of Neurobiology, Northwestern University, Evanston, 60208, IL, USA 8 Robert H. Lurie Comprehensive Cancer Center. Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611, USA 9 Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, IL 60612, USA 10 Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA 6 Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, Pennsylvania, 17033, USA 1 Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611, USA 4 Current address: Key Laboratory of Carci
AuthorAffiliation_xml	– name: 6 Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, Pennsylvania, 17033, USA – name: 11 Division of Hematology/Oncology and Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA – name: 4 Current address: Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China – name: 7 Department of Biochemistry and Molecular Biology, Huck Institutes of Life Sciences, Penn State University, State College, Pennsylvania, 16802, USA – name: 12 Memorial Sloan Kettering Cancer Center, New York City, New York, 10065, USA – name: 2 Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Penn State University, Hershey, Pennsylvania, 17033, USA – name: 5 Department of Neurobiology, Northwestern University, Evanston, 60208, IL, USA – name: 9 Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, IL 60612, USA – name: 10 Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA – name: 1 Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611, USA – name: 3 Bioinformatics and Genomics graduate program, Huck Institutes of Life Sciences, Penn State University, State College, Pennsylvania, 16802, USA – name: 8 Robert H. Lurie Comprehensive Cancer Center. Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611, USA
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R. orcidid: 0000-0003-1197-0312 surname: Broach fullname: Broach, James. R. organization: Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Penn State University – sequence: 28 givenname: Hong orcidid: 0000-0002-5024-5538 surname: Zheng fullname: Zheng, Hong email: hzheng@pennstatehealth.psu.edu organization: Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University – sequence: 29 givenname: Feng orcidid: 0000-0002-7954-5462 surname: Yue fullname: Yue, Feng email: yue@northwestern.edu organization: Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/36289338$$D View this record in MEDLINE/PubMed
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Cites_doi	10.1038/s41588-019-0564-y 10.1038/s41586-019-1668-3 10.1126/science.aav1898 10.1038/nature14222 10.1038/s41568-018-0060-1 10.1038/s41467-018-06961-0 10.1186/s13059-014-0554-4 10.1016/j.cell.2018.03.072 10.1634/stemcells.2005-0185 10.1038/s41588-020-0581-x 10.1016/j.cels.2015.07.012 10.1093/bioinformatics/btv098 10.1038/nmeth.4264 10.1016/j.ccr.2009.11.020 10.1186/s13059-018-1519-9 10.1182/blood-2016-08-733196 10.1126/science.1181369 10.1038/s41467-019-09982-5 10.1016/j.ccr.2012.03.014 10.1158/2159-8290.CD-17-0399 10.1093/bioinformatics/btz540 10.1101/gr.220640.117 10.4161/fly.19695 10.1038/nature13379 10.1186/s13059-018-1486-1 10.1038/s41587-020-0546-8 10.1038/s41588-018-0270-1 10.1093/bioinformatics/btu268 10.1186/1471-2105-12-323 10.1128/MCB.00712-15 10.1016/j.cell.2017.09.026 10.1038/s41375-020-0856-3 10.1038/s41467-019-09469-3 10.1038/nature11049 10.1038/nmeth.3505 10.1056/NEJMoa1516192 10.1056/NEJMra1406184 10.1371/journal.pgen.1002781 10.1038/s41592-021-01164-w 10.1182/blood-2016-01-693879 10.1038/nature11082 10.1038/s41467-019-14098-x 10.1038/s41588-020-0602-9 10.1038/nprot.2017.016 10.1002/0471142727.mb2129s109 10.1038/ng.3415 10.1016/j.celrep.2017.05.005 10.1038/s41591-021-01389-4 10.1016/j.cell.2014.11.021 10.1016/j.cell.2014.02.019 10.1016/j.stem.2019.08.003 10.1038/nature16490 10.1016/j.molcel.2020.04.018 10.1093/imanum/drs019 10.1179/102453311X12902908411913 10.1093/bioinformatics/bts635 10.1182/blood-2016-03-643544 10.1016/j.stem.2020.06.018 10.1093/bioinformatics/bts378 10.1038/s41588-018-0195-8 10.1038/nature14465 10.1038/sj.leu.2404549 10.1038/nature21373 10.1038/cr.2018.1 10.1038/nprot.2006.238 10.1038/35013100 10.1093/bioinformatics/btr167 10.1182/blood-2017-11-814319 10.1016/j.molcel.2017.08.006 10.1073/pnas.1518552112 10.1038/nmeth.1923 10.1371/journal.pcbi.1006982 10.1038/s41467-020-17239-9 10.3791/50587 10.1038/s41588-021-00993-x 10.1038/s41467-021-20940-y 10.1101/2021.08.05.455340
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Notes	F.Y. conceived and supervised the project. J.X. and F.S. led the investigation. J.X., H.L., B.Z., and M.K. performed Hi-C, ATAC-seq, CUT&Tag, ChIP-seq, RNA-seq, and 5-AZA related experiments, and prepared DNA for WGS and WGBS. J.X. and H.L. performed CRISPR screening. J.X. performed 4C. H.L and J.X. performed CRISPRi. M.K. and L.S. performed CRIPSR deletion. Z.Z. performed DNA FISH. Y.Y. and T.Y. supervised DNA FISH analyses. Qi.J. helped with FACS sorting. J.H.W. performed reporter assay. Y.H. and Qiushi.J. performed DNMT TKD and HiChIP. F.S., J.X., Y.L., Y.F. and Q.W. conducted data analysis. X.W. developed the algorithm for stripe detection. Y.D., S.D., R.C.H. and J.R.B. contributed biological insights. H.Z., B.J., D.C., J.R.B., R.L.L., A.D.V. and L.C.P. provided the samples and clinical insights. J.X., F.S., and F.Y. wrote the manuscript with input from all authors. Contributed equally to this project Author contributions
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References	Achinger-Kawecka (CR39) 2020; 11 Li (CR56) 2014; 15 Akdemir (CR26) 2020; 52 Dobin (CR73) 2013; 29 Groschel (CR21) 2014; 157 Lieberman-Aiden (CR10) 2009; 326 CR31 Dohner (CR1) 2017; 129 Ghasemi, Struthers, Wilson, Spencer (CR9) 2020; 35 Varoquaux, Ay, Noble, Vert (CR68) 2014; 30 Vian (CR34) 2018; 173 Dohner, Weisdorf, Bloomfield (CR2) 2015; 373 Wang (CR66) 2018; 19 Dixon (CR20) 2018; 50 Krueger, Andrews (CR70) 2011; 27 Northcott (CR22) 2014; 511 Bell, Felsenfeld (CR40) 2000; 405 Metzeler (CR25) 2016; 128 Loke (CR52) 2017; 19 Phanstiel (CR37) 2017; 67 Nora (CR12) 2012; 485 Jaatinen (CR28) 2006; 24 Rao (CR76) 2014; 159 Cesana (CR51) 2021; 27 Corces (CR72) 2018; 362 Figueroa (CR41) 2010; 17 Wang (CR36) 2021; 18 Yang (CR16) 2019; 10 Tarasov, Vilella, Cuppen, Nijman, Prins (CR59) 2015; 31 Arber (CR3) 2016; 127 Buenrostro, Wu, Chang, Greenleaf (CR54) 2015; 109 Luo (CR8) 2018; 132 Kloetgen (CR18) 2020; 52 Dixon (CR67) 2015; 518 Durand (CR65) 2016; 3 Langmead, Salzberg (CR69) 2012; 9 Diaz-Blanco (CR29) 2007; 21 Riccardi, Nicoletti (CR58) 2006; 1 Akalin (CR46) 2012; 8 CR19 Chiang (CR62) 2015; 12 McKeown (CR6) 2017; 7 Abdennur, Mirny (CR63) 2020; 36 Harris (CR7) 2012; 21 CR57 Juric (CR75) 2019; 15 Viny (CR15) 2019; 25 Schultz (CR71) 2015; 523 Dixon (CR11) 2012; 485 Joung (CR38) 2017; 12 CR50 Kaya-Okur (CR53) 2019; 10 Morris, Cummings, Korb, Boaglio, Oehler (CR35) 2016; 36 Rao (CR14) 2017; 171 Papaemmanuil (CR4) 2016; 374 Spassov (CR23) 2011; 16 Diao (CR55) 2017; 14 Neri (CR47) 2017; 543 Kataoka (CR32) 2015; 47 Zhang (CR45) 2020; 78 Sanborn (CR48) 2015; 112 Diaz (CR17) 2018; 9 Rausch (CR61) 2012; 28 CR27 Tovy (CR44) 2020; 27 Li, Dewey (CR74) 2011; 12 Flavahan (CR43) 2016; 529 Assi (CR5) 2019; 51 Ngan (CR30) 2020; 52 Flavahan (CR42) 2019; 575 Yang (CR49) 2017; 27 Sondka (CR24) 2018; 18 Knight, Ruiz (CR77) 2012; 33 Yan (CR13) 2018; 28 Goldman (CR33) 2020; 38 Cingolani (CR60) 2012; 6 Kerpedjiev (CR64) 2018; 19 Y Wang (5365_CR66) 2018; 19 Z Sondka (5365_CR24) 2018; 18 E Diaz-Blanco (5365_CR29) 2007; 21 CY Ngan (5365_CR30) 2020; 52 B Langmead (5365_CR69) 2012; 9 F Neri (5365_CR47) 2017; 543 A Kloetgen (5365_CR18) 2020; 52 5365_CR50 SSP Rao (5365_CR14) 2017; 171 JR Dixon (5365_CR20) 2018; 50 L Vian (5365_CR34) 2018; 173 5365_CR57 NC Durand (5365_CR65) 2016; 3 P Kerpedjiev (5365_CR64) 2018; 19 N Abdennur (5365_CR63) 2020; 36 B Li (5365_CR74) 2011; 12 T Jaatinen (5365_CR28) 2006; 24 WA Flavahan (5365_CR42) 2019; 575 SA Assi (5365_CR5) 2019; 51 5365_CR19 J Achinger-Kawecka (5365_CR39) 2020; 11 AD Viny (5365_CR15) 2019; 25 K Kataoka (5365_CR32) 2015; 47 PA Northcott (5365_CR22) 2014; 511 ME Figueroa (5365_CR41) 2010; 17 PA Knight (5365_CR77) 2012; 33 R Ghasemi (5365_CR9) 2020; 35 J Yan (5365_CR13) 2018; 28 T Rausch (5365_CR61) 2012; 28 F Krueger (5365_CR70) 2011; 27 W Li (5365_CR56) 2014; 15 AL Sanborn (5365_CR48) 2015; 112 T Yang (5365_CR49) 2017; 27 MR McKeown (5365_CR6) 2017; 7 Y Diao (5365_CR55) 2017; 14 A Tarasov (5365_CR59) 2015; 31 AC Bell (5365_CR40) 2000; 405 JR Dixon (5365_CR67) 2015; 518 N Diaz (5365_CR17) 2018; 9 A Tovy (5365_CR44) 2020; 27 EP Nora (5365_CR12) 2012; 485 I Juric (5365_CR75) 2019; 15 5365_CR31 WA Flavahan (5365_CR43) 2016; 529 HS Kaya-Okur (5365_CR53) 2019; 10 SS Rao (5365_CR76) 2014; 159 H Dohner (5365_CR2) 2015; 373 X Zhang (5365_CR45) 2020; 78 WJ Harris (5365_CR7) 2012; 21 MD Schultz (5365_CR71) 2015; 523 MJ Goldman (5365_CR33) 2020; 38 N Varoquaux (5365_CR68) 2014; 30 P Cingolani (5365_CR60) 2012; 6 A Dobin (5365_CR73) 2013; 29 H Luo (5365_CR8) 2018; 132 J Loke (5365_CR52) 2017; 19 E Lieberman-Aiden (5365_CR10) 2009; 326 DH Phanstiel (5365_CR37) 2017; 67 J Joung (5365_CR38) 2017; 12 KH Metzeler (5365_CR25) 2016; 128 H Dohner (5365_CR1) 2017; 129 DA Arber (5365_CR3) 2016; 127 D Cesana (5365_CR51) 2021; 27 E Papaemmanuil (5365_CR4) 2016; 374 M Yang (5365_CR16) 2019; 10 VA Morris (5365_CR35) 2016; 36 JR Dixon (5365_CR11) 2012; 485 A Akalin (5365_CR46) 2012; 8 5365_CR27 C Riccardi (5365_CR58) 2006; 1 C Chiang (5365_CR62) 2015; 12 BV Spassov (5365_CR23) 2011; 16 X Wang (5365_CR36) 2021; 18 KC Akdemir (5365_CR26) 2020; 52 MR Corces (5365_CR72) 2018; 362 S Groschel (5365_CR21) 2014; 157 JD Buenrostro (5365_CR54) 2015; 109
References_xml	– volume: 52 start-page: 294 year: 2020 end-page: 305 ident: CR26 article-title: Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer publication-title: Nat. Genet. doi: 10.1038/s41588-019-0564-y contributor: fullname: Akdemir – volume: 575 start-page: 229 year: 2019 end-page: 233 ident: CR42 article-title: Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs publication-title: Nature doi: 10.1038/s41586-019-1668-3 contributor: fullname: Flavahan – volume: 362 start-page: eaav1898 year: 2018 ident: CR72 article-title: The chromatin accessibility landscape of primary human cancers publication-title: Science doi: 10.1126/science.aav1898 contributor: fullname: Corces – volume: 518 start-page: 331 year: 2015 end-page: 336 ident: CR67 article-title: Chromatin architecture reorganization during stem cell differentiation publication-title: Nature doi: 10.1038/nature14222 contributor: fullname: Dixon – volume: 18 start-page: 696 year: 2018 end-page: 705 ident: CR24 article-title: The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers publication-title: Nat. Rev. Cancer doi: 10.1038/s41568-018-0060-1 contributor: fullname: Sondka – volume: 9 year: 2018 ident: CR17 article-title: Chromatin conformation analysis of primary patient tissue using a low input Hi-C method publication-title: Nat. Commun. doi: 10.1038/s41467-018-06961-0 contributor: fullname: Diaz – volume: 15 year: 2014 ident: CR56 article-title: MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens publication-title: Genome Biol. doi: 10.1186/s13059-014-0554-4 contributor: fullname: Li – volume: 173 start-page: 1165 year: 2018 end-page: 1178.e20 ident: CR34 article-title: The energetics and physiological impact of cohesin extrusion publication-title: Cell doi: 10.1016/j.cell.2018.03.072 contributor: fullname: Vian – volume: 24 start-page: 631 year: 2006 end-page: 641 ident: CR28 article-title: Global gene expression profile of human cord blood-derived CD133 cells publication-title: Stem Cells doi: 10.1634/stemcells.2005-0185 contributor: fullname: Jaatinen – volume: 52 start-page: 264 year: 2020 end-page: 272 ident: CR30 article-title: Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development publication-title: Nat. Genet. doi: 10.1038/s41588-020-0581-x contributor: fullname: Ngan – volume: 3 start-page: 99 year: 2016 end-page: 101 ident: CR65 article-title: Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom publication-title: Cell Syst. doi: 10.1016/j.cels.2015.07.012 contributor: fullname: Durand – volume: 31 start-page: 2032 year: 2015 end-page: 2034 ident: CR59 article-title: Sambamba: fast processing of NGS alignment formats publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv098 contributor: fullname: Prins – ident: CR19 – volume: 14 start-page: 629 year: 2017 end-page: 635 ident: CR55 article-title: A tiling-deletion-based genetic screen for -regulatory element identification in mammalian cells publication-title: Nat. Methods doi: 10.1038/nmeth.4264 contributor: fullname: Diao – volume: 17 start-page: 13 year: 2010 end-page: 27 ident: CR41 article-title: DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia publication-title: Cancer Cell doi: 10.1016/j.ccr.2009.11.020 contributor: fullname: Figueroa – volume: 19 year: 2018 ident: CR66 article-title: The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions publication-title: Genome Biol. doi: 10.1186/s13059-018-1519-9 contributor: fullname: Wang – ident: CR50 – volume: 129 start-page: 424 year: 2017 end-page: 447 ident: CR1 article-title: Diagnosis and management of AML in adults: 2017 ELN recommendations from an international expert panel publication-title: Blood doi: 10.1182/blood-2016-08-733196 contributor: fullname: Dohner – ident: CR57 – volume: 326 start-page: 289 year: 2009 end-page: 293 ident: CR10 article-title: Comprehensive mapping of long-range interactions reveals folding principles of the human genome publication-title: Science doi: 10.1126/science.1181369 contributor: fullname: Lieberman-Aiden – volume: 10 year: 2019 ident: CR53 article-title: CUT&Tag for efficient epigenomic profiling of small samples and single cells publication-title: Nat. Commun. doi: 10.1038/s41467-019-09982-5 contributor: fullname: Kaya-Okur – volume: 21 start-page: 473 year: 2012 end-page: 487 ident: CR7 article-title: The histone demethylase KDM1A sustains the oncogenic potential of MLL-AF9 leukemia stem cells publication-title: Cancer Cell doi: 10.1016/j.ccr.2012.03.014 contributor: fullname: Harris – volume: 7 start-page: 1136 year: 2017 end-page: 1153 ident: CR6 article-title: Superenhancer analysis defines novel epigenomic subtypes of non-APL AML, including an RARα dependency targetable by SY-1425, a potent and selective RARα agonist publication-title: Cancer Discov. doi: 10.1158/2159-8290.CD-17-0399 contributor: fullname: McKeown – volume: 36 start-page: 311 year: 2020 end-page: 316 ident: CR63 article-title: Cooler: scalable storage for Hi-C data and other genomically labeled arrays publication-title: Bioinformatics doi: 10.1093/bioinformatics/btz540 contributor: fullname: Mirny – volume: 27 start-page: 1939 year: 2017 end-page: 1949 ident: CR49 article-title: HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient publication-title: Genome Res. doi: 10.1101/gr.220640.117 contributor: fullname: Yang – volume: 6 start-page: 80 year: 2012 end-page: 92 ident: CR60 article-title: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of strain w1118; iso-2; iso-3 publication-title: Fly (Austin) doi: 10.4161/fly.19695 contributor: fullname: Cingolani – volume: 511 start-page: 428 year: 2014 end-page: 434 ident: CR22 article-title: Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma publication-title: Nature doi: 10.1038/nature13379 contributor: fullname: Northcott – volume: 19 year: 2018 ident: CR64 article-title: HiGlass: web-based visual exploration and analysis of genome interaction maps publication-title: Genome Biol. doi: 10.1186/s13059-018-1486-1 contributor: fullname: Kerpedjiev – volume: 38 start-page: 675 year: 2020 end-page: 678 ident: CR33 article-title: Visualizing and interpreting cancer genomics data via the Xena platform publication-title: Nat. Biotechnol. doi: 10.1038/s41587-020-0546-8 contributor: fullname: Goldman – volume: 51 start-page: 151 year: 2019 end-page: 162 ident: CR5 article-title: Subtype-specific regulatory network rewiring in acute myeloid leukemia publication-title: Nat. Genet. doi: 10.1038/s41588-018-0270-1 contributor: fullname: Assi – volume: 30 start-page: i26 year: 2014 end-page: i33 ident: CR68 article-title: A statistical approach for inferring the 3D structure of the genome publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu268 contributor: fullname: Vert – volume: 12 start-page: 323 year: 2011 ident: CR74 article-title: RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-12-323 contributor: fullname: Dewey – volume: 36 start-page: 559 year: 2016 end-page: 573 ident: CR35 article-title: Deregulated KLF4 expression in myeloid leukemias alters cell proliferation and differentiation through microRNA and gene targets publication-title: Mol. Cell. Biol. doi: 10.1128/MCB.00712-15 contributor: fullname: Oehler – volume: 171 start-page: 305 year: 2017 end-page: 320.e24 ident: CR14 article-title: Cohesin loss eliminates all loop domains publication-title: Cell doi: 10.1016/j.cell.2017.09.026 contributor: fullname: Rao – volume: 35 start-page: 404 year: 2020 end-page: 416 ident: CR9 article-title: Contribution of CTCF binding to transcriptional activity at the locus in NPM1-mutant AML cells publication-title: Leukemia doi: 10.1038/s41375-020-0856-3 contributor: fullname: Spencer – volume: 10 year: 2019 ident: CR16 article-title: Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia publication-title: Nat. Commun. doi: 10.1038/s41467-019-09469-3 contributor: fullname: Yang – volume: 485 start-page: 381 year: 2012 end-page: 385 ident: CR12 article-title: Spatial partitioning of the regulatory landscape of the X-inactivation centre publication-title: Nature doi: 10.1038/nature11049 contributor: fullname: Nora – volume: 12 start-page: 966 year: 2015 end-page: 968 ident: CR62 article-title: SpeedSeq: ultra-fast personal genome analysis and interpretation publication-title: Nat. Methods doi: 10.1038/nmeth.3505 contributor: fullname: Chiang – volume: 374 start-page: 2209 year: 2016 end-page: 2221 ident: CR4 article-title: Genomic classification and prognosis in acute myeloid leukemia publication-title: N. Engl. J. Med. doi: 10.1056/NEJMoa1516192 contributor: fullname: Papaemmanuil – volume: 373 start-page: 1136 year: 2015 end-page: 1152 ident: CR2 article-title: Acute myeloid leukemia publication-title: N. Engl. J. Med. doi: 10.1056/NEJMra1406184 contributor: fullname: Bloomfield – volume: 8 start-page: e1002781 year: 2012 ident: CR46 article-title: Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1002781 contributor: fullname: Akalin – volume: 18 start-page: 661 year: 2021 end-page: 668 ident: CR36 article-title: Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes publication-title: Nat. Methods doi: 10.1038/s41592-021-01164-w contributor: fullname: Wang – volume: 128 start-page: 686 year: 2016 end-page: 698 ident: CR25 article-title: Spectrum and prognostic relevance of driver gene mutations in acute myeloid leukemia publication-title: Blood doi: 10.1182/blood-2016-01-693879 contributor: fullname: Metzeler – volume: 485 start-page: 376 year: 2012 end-page: 380 ident: CR11 article-title: Topological domains in mammalian genomes identified by analysis of chromatin interactions publication-title: Nature doi: 10.1038/nature11082 contributor: fullname: Dixon – volume: 11 year: 2020 ident: CR39 article-title: Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer publication-title: Nat. Commun. doi: 10.1038/s41467-019-14098-x contributor: fullname: Achinger-Kawecka – volume: 52 start-page: 388 year: 2020 end-page: 400 ident: CR18 article-title: Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia publication-title: Nat. Genet. doi: 10.1038/s41588-020-0602-9 contributor: fullname: Kloetgen – volume: 12 start-page: 828 year: 2017 end-page: 863 ident: CR38 article-title: Genome-scale CRISPR–Cas9 knockout and transcriptional activation screening publication-title: Nat. Protoc. doi: 10.1038/nprot.2017.016 contributor: fullname: Joung – volume: 109 start-page: 21.29.1 year: 2015 end-page: 21.29.9 ident: CR54 article-title: ATAC-seq: a method for assaying chromatin accessibility genome-wide publication-title: Curr. Protoc. Mol. Biol. doi: 10.1002/0471142727.mb2129s109 contributor: fullname: Greenleaf – ident: CR27 – volume: 47 start-page: 1304 year: 2015 end-page: 1315 ident: CR32 article-title: Integrated molecular analysis of adult T cell leukemia/lymphoma publication-title: Nat. Genet. doi: 10.1038/ng.3415 contributor: fullname: Kataoka – volume: 19 start-page: 1654 year: 2017 end-page: 1668 ident: CR52 article-title: RUNX1-ETO and RUNX1-EVI1 differentially reprogram the chromatin landscape in t(8;21) and t(3;21) AML publication-title: Cell Rep. doi: 10.1016/j.celrep.2017.05.005 contributor: fullname: Loke – volume: 27 start-page: 1458 year: 2021 end-page: 1470 ident: CR51 article-title: Retrieval of vector integration sites from cell-free DNA publication-title: Nat. Med. doi: 10.1038/s41591-021-01389-4 contributor: fullname: Cesana – volume: 159 start-page: 1665 year: 2014 end-page: 1680 ident: CR76 article-title: A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping publication-title: Cell doi: 10.1016/j.cell.2014.11.021 contributor: fullname: Rao – volume: 157 start-page: 369 year: 2014 end-page: 381 ident: CR21 article-title: A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia publication-title: Cell doi: 10.1016/j.cell.2014.02.019 contributor: fullname: Groschel – volume: 25 start-page: 682 year: 2019 end-page: 696.e8 ident: CR15 article-title: Cohesin members Stag1 and Stag2 display distinct roles in chromatin accessibility and topological control of HSC self-Renewal and differentiation publication-title: Cell Stem Cell doi: 10.1016/j.stem.2019.08.003 contributor: fullname: Viny – volume: 529 start-page: 110 year: 2016 end-page: 114 ident: CR43 article-title: Insulator dysfunction and oncogene activation in IDH mutant gliomas publication-title: Nature doi: 10.1038/nature16490 contributor: fullname: Flavahan – volume: 78 start-page: 506 year: 2020 end-page: 521.e6 ident: CR45 article-title: Large DNA methylation nadirs anchor chromatin loops maintaining hematopoietic stem cell identity publication-title: Mol. Cell doi: 10.1016/j.molcel.2020.04.018 contributor: fullname: Zhang – volume: 33 start-page: 1029 year: 2012 end-page: 1047 ident: CR77 article-title: A fast algorithm for matrix balancing publication-title: IMA J. Numer. Anal. doi: 10.1093/imanum/drs019 contributor: fullname: Ruiz – volume: 16 start-page: 37 year: 2011 end-page: 42 ident: CR23 article-title: Wilms’ tumor protein and FLT3-internal tandem duplication expression in patients with de novo acute myeloid leukemia publication-title: Hematology doi: 10.1179/102453311X12902908411913 contributor: fullname: Spassov – volume: 29 start-page: 15 year: 2013 end-page: 21 ident: CR73 article-title: STAR: ultrafast universal RNA-seq aligner publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts635 contributor: fullname: Dobin – volume: 127 start-page: 2391 year: 2016 end-page: 2405 ident: CR3 article-title: The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia publication-title: Blood doi: 10.1182/blood-2016-03-643544 contributor: fullname: Arber – volume: 27 start-page: 326 year: 2020 end-page: 335.e4 ident: CR44 article-title: Tissue-biased expansion of DNMT3A-mutant clones in a mosaic individual is associated with conserved epigenetic erosion publication-title: Cell Stem Cell doi: 10.1016/j.stem.2020.06.018 contributor: fullname: Tovy – ident: CR31 – volume: 28 start-page: i333 year: 2012 end-page: i339 ident: CR61 article-title: DELLY: structural variant discovery by integrated paired-end and split-read analysis publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts378 contributor: fullname: Rausch – volume: 50 start-page: 1388 year: 2018 end-page: 1398 ident: CR20 article-title: Integrative detection and analysis of structural variation in cancer genomes publication-title: Nat. Genet. doi: 10.1038/s41588-018-0195-8 contributor: fullname: Dixon – volume: 523 start-page: 212 year: 2015 end-page: 216 ident: CR71 article-title: Human body epigenome maps reveal noncanonical DNA methylation variation publication-title: Nature doi: 10.1038/nature14465 contributor: fullname: Schultz – volume: 21 start-page: 494 year: 2007 end-page: 504 ident: CR29 article-title: Molecular signature of CD34 hematopoietic stem and progenitor cells of patients with CML in chronic phase publication-title: Leukemia doi: 10.1038/sj.leu.2404549 contributor: fullname: Diaz-Blanco – volume: 543 start-page: 72 year: 2017 end-page: 77 ident: CR47 article-title: Intragenic DNA methylation prevents spurious transcription initiation publication-title: Nature doi: 10.1038/nature21373 contributor: fullname: Neri – volume: 28 start-page: 204 year: 2018 end-page: 220 ident: CR13 article-title: Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers publication-title: Cell Res. doi: 10.1038/cr.2018.1 contributor: fullname: Yan – volume: 1 start-page: 1458 year: 2006 end-page: 1461 ident: CR58 article-title: Analysis of apoptosis by propidium iodide staining and flow cytometry publication-title: Nat. Protoc. doi: 10.1038/nprot.2006.238 contributor: fullname: Nicoletti – volume: 405 start-page: 482 year: 2000 end-page: 485 ident: CR40 article-title: Methylation of a CTCF-dependent boundary controls imprinted expression of the gene publication-title: Nature doi: 10.1038/35013100 contributor: fullname: Felsenfeld – volume: 27 start-page: 1571 year: 2011 end-page: 1572 ident: CR70 article-title: Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr167 contributor: fullname: Andrews – volume: 132 start-page: 837 year: 2018 end-page: 848 ident: CR8 article-title: CTCF boundary remodels chromatin domain and drives aberrant gene transcription in acute myeloid leukemia publication-title: Blood doi: 10.1182/blood-2017-11-814319 contributor: fullname: Luo – volume: 67 start-page: 1037 year: 2017 end-page: 1048.e6 ident: CR37 article-title: Static and dynamic DNA loops form AP-1-bound activation hubs during macrophage development publication-title: Mol. Cell doi: 10.1016/j.molcel.2017.08.006 contributor: fullname: Phanstiel – volume: 112 start-page: E6456 year: 2015 end-page: E6465 ident: CR48 article-title: Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes publication-title: Proc. Natl Acad. Sci. USA doi: 10.1073/pnas.1518552112 contributor: fullname: Sanborn – volume: 9 start-page: 357 year: 2012 end-page: 359 ident: CR69 article-title: Fast gapped-read alignment with Bowtie 2 publication-title: Nat. Methods doi: 10.1038/nmeth.1923 contributor: fullname: Salzberg – volume: 15 start-page: e1006982 year: 2019 ident: CR75 article-title: MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments publication-title: PLoS Comput. Biol. doi: 10.1371/journal.pcbi.1006982 contributor: fullname: Juric – ident: 5365_CR27 doi: 10.1038/s41467-020-17239-9 – volume: 18 start-page: 661 year: 2021 ident: 5365_CR36 publication-title: Nat. Methods doi: 10.1038/s41592-021-01164-w contributor: fullname: X Wang – volume: 19 year: 2018 ident: 5365_CR66 publication-title: Genome Biol. doi: 10.1186/s13059-018-1519-9 contributor: fullname: Y Wang – volume: 485 start-page: 381 year: 2012 ident: 5365_CR12 publication-title: Nature doi: 10.1038/nature11049 contributor: fullname: EP Nora – ident: 5365_CR57 doi: 10.3791/50587 – volume: 52 start-page: 388 year: 2020 ident: 5365_CR18 publication-title: Nat. Genet. doi: 10.1038/s41588-020-0602-9 contributor: fullname: A Kloetgen – volume: 27 start-page: 326 year: 2020 ident: 5365_CR44 publication-title: Cell Stem Cell doi: 10.1016/j.stem.2020.06.018 contributor: fullname: A Tovy – volume: 373 start-page: 1136 year: 2015 ident: 5365_CR2 publication-title: N. Engl. J. Med. doi: 10.1056/NEJMra1406184 contributor: fullname: H Dohner – volume: 159 start-page: 1665 year: 2014 ident: 5365_CR76 publication-title: Cell doi: 10.1016/j.cell.2014.11.021 contributor: fullname: SS Rao – volume: 12 start-page: 828 year: 2017 ident: 5365_CR38 publication-title: Nat. Protoc. doi: 10.1038/nprot.2017.016 contributor: fullname: J Joung – volume: 15 year: 2014 ident: 5365_CR56 publication-title: Genome Biol. doi: 10.1186/s13059-014-0554-4 contributor: fullname: W Li – ident: 5365_CR19 doi: 10.1038/s41588-021-00993-x – volume: 14 start-page: 629 year: 2017 ident: 5365_CR55 publication-title: Nat. Methods doi: 10.1038/nmeth.4264 contributor: fullname: Y Diao – volume: 9 start-page: 357 year: 2012 ident: 5365_CR69 publication-title: Nat. Methods doi: 10.1038/nmeth.1923 contributor: fullname: B Langmead – volume: 511 start-page: 428 year: 2014 ident: 5365_CR22 publication-title: Nature doi: 10.1038/nature13379 contributor: fullname: PA Northcott – volume: 36 start-page: 311 year: 2020 ident: 5365_CR63 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btz540 contributor: fullname: N Abdennur – volume: 52 start-page: 264 year: 2020 ident: 5365_CR30 publication-title: Nat. Genet. doi: 10.1038/s41588-020-0581-x contributor: fullname: CY Ngan – volume: 21 start-page: 473 year: 2012 ident: 5365_CR7 publication-title: Cancer Cell doi: 10.1016/j.ccr.2012.03.014 contributor: fullname: WJ Harris – volume: 171 start-page: 305 year: 2017 ident: 5365_CR14 publication-title: Cell doi: 10.1016/j.cell.2017.09.026 contributor: fullname: SSP Rao – volume: 1 start-page: 1458 year: 2006 ident: 5365_CR58 publication-title: Nat. Protoc. doi: 10.1038/nprot.2006.238 contributor: fullname: C Riccardi – volume: 132 start-page: 837 year: 2018 ident: 5365_CR8 publication-title: Blood doi: 10.1182/blood-2017-11-814319 contributor: fullname: H Luo – volume: 78 start-page: 506 year: 2020 ident: 5365_CR45 publication-title: Mol. Cell doi: 10.1016/j.molcel.2020.04.018 contributor: fullname: X Zhang – volume: 27 start-page: 1458 year: 2021 ident: 5365_CR51 publication-title: Nat. Med. doi: 10.1038/s41591-021-01389-4 contributor: fullname: D Cesana – volume: 47 start-page: 1304 year: 2015 ident: 5365_CR32 publication-title: Nat. Genet. doi: 10.1038/ng.3415 contributor: fullname: K Kataoka – volume: 12 start-page: 966 year: 2015 ident: 5365_CR62 publication-title: Nat. Methods doi: 10.1038/nmeth.3505 contributor: fullname: C Chiang – volume: 27 start-page: 1571 year: 2011 ident: 5365_CR70 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr167 contributor: fullname: F Krueger – volume: 35 start-page: 404 year: 2020 ident: 5365_CR9 publication-title: Leukemia doi: 10.1038/s41375-020-0856-3 contributor: fullname: R Ghasemi – volume: 19 year: 2018 ident: 5365_CR64 publication-title: Genome Biol. doi: 10.1186/s13059-018-1486-1 contributor: fullname: P Kerpedjiev – volume: 9 year: 2018 ident: 5365_CR17 publication-title: Nat. Commun. doi: 10.1038/s41467-018-06961-0 contributor: fullname: N Diaz – volume: 16 start-page: 37 year: 2011 ident: 5365_CR23 publication-title: Hematology doi: 10.1179/102453311X12902908411913 contributor: fullname: BV Spassov – volume: 50 start-page: 1388 year: 2018 ident: 5365_CR20 publication-title: Nat. Genet. doi: 10.1038/s41588-018-0195-8 contributor: fullname: JR Dixon – volume: 128 start-page: 686 year: 2016 ident: 5365_CR25 publication-title: Blood doi: 10.1182/blood-2016-01-693879 contributor: fullname: KH Metzeler – volume: 326 start-page: 289 year: 2009 ident: 5365_CR10 publication-title: Science doi: 10.1126/science.1181369 contributor: fullname: E Lieberman-Aiden – volume: 28 start-page: i333 year: 2012 ident: 5365_CR61 publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts378 contributor: fullname: T Rausch – volume: 485 start-page: 376 year: 2012 ident: 5365_CR11 publication-title: Nature doi: 10.1038/nature11082 contributor: fullname: JR Dixon – volume: 28 start-page: 204 year: 2018 ident: 5365_CR13 publication-title: Cell Res. doi: 10.1038/cr.2018.1 contributor: fullname: J Yan – volume: 523 start-page: 212 year: 2015 ident: 5365_CR71 publication-title: Nature doi: 10.1038/nature14465 contributor: fullname: MD Schultz – volume: 21 start-page: 494 year: 2007 ident: 5365_CR29 publication-title: Leukemia doi: 10.1038/sj.leu.2404549 contributor: fullname: E Diaz-Blanco – volume: 6 start-page: 80 year: 2012 ident: 5365_CR60 publication-title: Fly (Austin) doi: 10.4161/fly.19695 contributor: fullname: P Cingolani – volume: 11 year: 2020 ident: 5365_CR39 publication-title: Nat. Commun. doi: 10.1038/s41467-019-14098-x contributor: fullname: J Achinger-Kawecka – volume: 12 start-page: 323 year: 2011 ident: 5365_CR74 publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-12-323 contributor: fullname: B Li – volume: 17 start-page: 13 year: 2010 ident: 5365_CR41 publication-title: Cancer Cell doi: 10.1016/j.ccr.2009.11.020 contributor: fullname: ME Figueroa – ident: 5365_CR31 doi: 10.1038/s41467-021-20940-y – volume: 575 start-page: 229 year: 2019 ident: 5365_CR42 publication-title: Nature doi: 10.1038/s41586-019-1668-3 contributor: fullname: WA Flavahan – volume: 19 start-page: 1654 year: 2017 ident: 5365_CR52 publication-title: Cell Rep. doi: 10.1016/j.celrep.2017.05.005 contributor: fullname: J Loke – volume: 18 start-page: 696 year: 2018 ident: 5365_CR24 publication-title: Nat. Rev. Cancer doi: 10.1038/s41568-018-0060-1 contributor: fullname: Z Sondka – volume: 3 start-page: 99 year: 2016 ident: 5365_CR65 publication-title: Cell Syst. doi: 10.1016/j.cels.2015.07.012 contributor: fullname: NC Durand – volume: 127 start-page: 2391 year: 2016 ident: 5365_CR3 publication-title: Blood doi: 10.1182/blood-2016-03-643544 contributor: fullname: DA Arber – volume: 7 start-page: 1136 year: 2017 ident: 5365_CR6 publication-title: Cancer Discov. doi: 10.1158/2159-8290.CD-17-0399 contributor: fullname: MR McKeown – ident: 5365_CR50 doi: 10.1101/2021.08.05.455340 – volume: 67 start-page: 1037 year: 2017 ident: 5365_CR37 publication-title: Mol. Cell doi: 10.1016/j.molcel.2017.08.006 contributor: fullname: DH Phanstiel – volume: 543 start-page: 72 year: 2017 ident: 5365_CR47 publication-title: Nature doi: 10.1038/nature21373 contributor: fullname: F Neri – volume: 51 start-page: 151 year: 2019 ident: 5365_CR5 publication-title: Nat. Genet. doi: 10.1038/s41588-018-0270-1 contributor: fullname: SA Assi – volume: 24 start-page: 631 year: 2006 ident: 5365_CR28 publication-title: Stem Cells doi: 10.1634/stemcells.2005-0185 contributor: fullname: T Jaatinen – volume: 362 start-page: eaav1898 year: 2018 ident: 5365_CR72 publication-title: Science doi: 10.1126/science.aav1898 contributor: fullname: MR Corces – volume: 10 year: 2019 ident: 5365_CR16 publication-title: Nat. Commun. doi: 10.1038/s41467-019-09469-3 contributor: fullname: M Yang – volume: 518 start-page: 331 year: 2015 ident: 5365_CR67 publication-title: Nature doi: 10.1038/nature14222 contributor: fullname: JR Dixon – volume: 129 start-page: 424 year: 2017 ident: 5365_CR1 publication-title: Blood doi: 10.1182/blood-2016-08-733196 contributor: fullname: H Dohner – volume: 27 start-page: 1939 year: 2017 ident: 5365_CR49 publication-title: Genome Res. doi: 10.1101/gr.220640.117 contributor: fullname: T Yang – volume: 25 start-page: 682 year: 2019 ident: 5365_CR15 publication-title: Cell Stem Cell doi: 10.1016/j.stem.2019.08.003 contributor: fullname: AD Viny – volume: 30 start-page: i26 year: 2014 ident: 5365_CR68 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu268 contributor: fullname: N Varoquaux – volume: 15 start-page: e1006982 year: 2019 ident: 5365_CR75 publication-title: PLoS Comput. Biol. doi: 10.1371/journal.pcbi.1006982 contributor: fullname: I Juric – volume: 374 start-page: 2209 year: 2016 ident: 5365_CR4 publication-title: N. Engl. J. Med. doi: 10.1056/NEJMoa1516192 contributor: fullname: E Papaemmanuil – volume: 8 start-page: e1002781 year: 2012 ident: 5365_CR46 publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1002781 contributor: fullname: A Akalin – volume: 29 start-page: 15 year: 2013 ident: 5365_CR73 publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts635 contributor: fullname: A Dobin – volume: 38 start-page: 675 year: 2020 ident: 5365_CR33 publication-title: Nat. Biotechnol. doi: 10.1038/s41587-020-0546-8 contributor: fullname: MJ Goldman – volume: 31 start-page: 2032 year: 2015 ident: 5365_CR59 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv098 contributor: fullname: A Tarasov – volume: 173 start-page: 1165 year: 2018 ident: 5365_CR34 publication-title: Cell doi: 10.1016/j.cell.2018.03.072 contributor: fullname: L Vian – volume: 112 start-page: E6456 year: 2015 ident: 5365_CR48 publication-title: Proc. Natl Acad. Sci. USA doi: 10.1073/pnas.1518552112 contributor: fullname: AL Sanborn – volume: 10 year: 2019 ident: 5365_CR53 publication-title: Nat. Commun. doi: 10.1038/s41467-019-09982-5 contributor: fullname: HS Kaya-Okur – volume: 33 start-page: 1029 year: 2012 ident: 5365_CR77 publication-title: IMA J. Numer. Anal. doi: 10.1093/imanum/drs019 contributor: fullname: PA Knight – volume: 405 start-page: 482 year: 2000 ident: 5365_CR40 publication-title: Nature doi: 10.1038/35013100 contributor: fullname: AC Bell – volume: 52 start-page: 294 year: 2020 ident: 5365_CR26 publication-title: Nat. Genet. doi: 10.1038/s41588-019-0564-y contributor: fullname: KC Akdemir – volume: 529 start-page: 110 year: 2016 ident: 5365_CR43 publication-title: Nature doi: 10.1038/nature16490 contributor: fullname: WA Flavahan – volume: 109 start-page: 21.29.1 year: 2015 ident: 5365_CR54 publication-title: Curr. Protoc. Mol. Biol. doi: 10.1002/0471142727.mb2129s109 contributor: fullname: JD Buenrostro – volume: 157 start-page: 369 year: 2014 ident: 5365_CR21 publication-title: Cell doi: 10.1016/j.cell.2014.02.019 contributor: fullname: S Groschel – volume: 36 start-page: 559 year: 2016 ident: 5365_CR35 publication-title: Mol. Cell. Biol. doi: 10.1128/MCB.00712-15 contributor: fullname: VA Morris
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Snippet	Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription... Acute myeloid leukemia (AML) represents a set of heterogeneous myeloid malignancies hallmarked by mutations in epigenetic modifiers, transcription factors, and...
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SubjectTerms	38 45/15 45/23 631/67/1990/283/1897 631/67/69 Acute myeloid leukemia Bisulfite Chromatin Chromatin - genetics CRISPR CRISPR-Cas Systems Deoxyribonucleic acid DNA DNA (Cytosine-5-)-Methyltransferases DNA Methylation DNMT1 protein Enhancer Elements, Genetic Enhancers Epigenetics Gene expression Gene Expression Regulation, Leukemic Gene sequencing Gene Silencing Genetic engineering Genome, Human - genetics Genomes Humanities and Social Sciences Humans Interference Leukemia Leukemia, Myeloid, Acute - genetics Malignancy multidisciplinary Mutation Promoter Regions, Genetic Regulatory sequences Reproducibility of Results Science Science (multidisciplinary) Sequence Analysis Silencers Transcription factors Whole genome sequencing
Title	Subtype-specific 3D genome alteration in acute myeloid leukaemia
URI	https://link.springer.com/article/10.1038/s41586-022-05365-x https://www.ncbi.nlm.nih.gov/pubmed/36289338 https://www.proquest.com/docview/2735565128 https://pubmed.ncbi.nlm.nih.gov/PMC10060167
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